diff --git a/coverage/class_index.html b/coverage/class_index.html
index 86473d95..c3e77595 100644
--- a/coverage/class_index.html
+++ b/coverage/class_index.html
@@ -11,7 +11,7 @@
 <header>
     <div class="content">
         <h1>Coverage report:
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+            <span class="pc_cov">81%</span>
         </h1>
         <aside id="help_panel_wrapper">
             <input id="help_panel_state" type="checkbox">
@@ -54,8 +54,8 @@ <h2>
                 <a class="button current">Classes</a>
         </h2>
         <p class="text">
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.5.4">coverage.py v7.5.4</a>,
-            created at 2024-07-03 19:03 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
+            created at 2024-07-16 13:32 +0000
         </p>
     </div>
 </header>
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             <tr class="region">
                 <td class="name left"><a href="z_8f1e855dacab84e4_acpype_params_ac_py.html">biobb_chemistry/acpype/acpype_params_ac.py</a></td>
                 <td class="name left"><a href="z_8f1e855dacab84e4_acpype_params_ac_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>15</td>
-                <td>1</td>
+                <td>28</td>
+                <td>13</td>
                 <td>0</td>
-                <td class="right" data-ratio="14 15">93%</td>
+                <td class="right" data-ratio="15 28">54%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_8f1e855dacab84e4_acpype_params_cns_py.html#t11">biobb_chemistry/acpype/acpype_params_cns.py</a></td>
@@ -115,10 +115,10 @@ <h2>
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                 <td class="name left"><a href="z_8f1e855dacab84e4_acpype_params_cns_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>15</td>
-                <td>1</td>
+                <td>28</td>
+                <td>13</td>
                 <td>0</td>
-                <td class="right" data-ratio="14 15">93%</td>
+                <td class="right" data-ratio="15 28">54%</td>
             </tr>
             <tr class="region">
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@@ -131,10 +131,10 @@ <h2>
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                 <td class="name left"><a href="z_8f1e855dacab84e4_acpype_params_gmx_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>15</td>
-                <td>1</td>
+                <td>27</td>
+                <td>12</td>
                 <td>0</td>
-                <td class="right" data-ratio="14 15">93%</td>
+                <td class="right" data-ratio="15 27">56%</td>
             </tr>
             <tr class="region">
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@@ -147,18 +147,18 @@ <h2>
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                 <td class="name left"><a href="z_8f1e855dacab84e4_acpype_params_gmx_opls_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
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-                <td>1</td>
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+                <td>11</td>
                 <td>0</td>
-                <td class="right" data-ratio="14 15">93%</td>
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             <tr class="region">
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                 <td class="name left"><a href="z_8f1e855dacab84e4_common_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
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-                <td>0</td>
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+                <td>15</td>
                 <td>0</td>
-                <td class="right" data-ratio="18 18">100%</td>
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             <tr class="region">
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             <tr class="region">
                 <td class="name left"><a href="z_10d4d9cbb07d09e4_common_py.html">biobb_chemistry/ambertools/common.py</a></td>
                 <td class="name left"><a href="z_10d4d9cbb07d09e4_common_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>7</td>
-                <td>0</td>
+                <td>30</td>
+                <td>9</td>
                 <td>0</td>
-                <td class="right" data-ratio="7 7">100%</td>
+                <td class="right" data-ratio="21 30">70%</td>
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             <tr class="region">
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             <tr class="region">
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-                <td>15</td>
-                <td>1</td>
+                <td>25</td>
+                <td>10</td>
                 <td>0</td>
-                <td class="right" data-ratio="14 15">93%</td>
+                <td class="right" data-ratio="15 25">60%</td>
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             <tr class="region">
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                 <td class="name left"><a href="z_10d4d9cbb07d09e4_reduce_remove_hydrogens_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>15</td>
-                <td>1</td>
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+                <td>10</td>
                 <td>0</td>
-                <td class="right" data-ratio="14 15">93%</td>
+                <td class="right" data-ratio="15 25">60%</td>
             </tr>
             <tr class="region">
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                 <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t11"><data value='BabelAddHydrogens'>BabelAddHydrogens</data></a></td>
-                <td>50</td>
-                <td>2</td>
+                <td>61</td>
+                <td>4</td>
                 <td>0</td>
-                <td class="right" data-ratio="48 50">96%</td>
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             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html">biobb_chemistry/babelm/babel_add_hydrogens.py</a></td>
                 <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>15</td>
-                <td>1</td>
+                <td>25</td>
+                <td>10</td>
                 <td>0</td>
-                <td class="right" data-ratio="14 15">93%</td>
+                <td class="right" data-ratio="15 25">60%</td>
             </tr>
             <tr class="region">
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                 <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t11"><data value='BabelConvert'>BabelConvert</data></a></td>
-                <td>53</td>
-                <td>1</td>
+                <td>64</td>
+                <td>6</td>
                 <td>0</td>
-                <td class="right" data-ratio="52 53">98%</td>
+                <td class="right" data-ratio="58 64">91%</td>
             </tr>
             <tr class="region">
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                 <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>15</td>
-                <td>1</td>
+                <td>25</td>
+                <td>10</td>
                 <td>0</td>
-                <td class="right" data-ratio="14 15">93%</td>
+                <td class="right" data-ratio="15 25">60%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_minimize_py.html#t12">biobb_chemistry/babelm/babel_minimize.py</a></td>
@@ -259,34 +259,34 @@ <h2>
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                 <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_minimize_py.html">biobb_chemistry/babelm/babel_minimize.py</a></td>
                 <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_minimize_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>16</td>
-                <td>1</td>
+                <td>26</td>
+                <td>10</td>
                 <td>0</td>
-                <td class="right" data-ratio="15 16">94%</td>
+                <td class="right" data-ratio="16 26">62%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t11">biobb_chemistry/babelm/babel_remove_hydrogens.py</a></td>
                 <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t11"><data value='BabelRemoveHydrogens'>BabelRemoveHydrogens</data></a></td>
-                <td>50</td>
-                <td>1</td>
+                <td>61</td>
+                <td>5</td>
                 <td>0</td>
-                <td class="right" data-ratio="49 50">98%</td>
+                <td class="right" data-ratio="56 61">92%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html">biobb_chemistry/babelm/babel_remove_hydrogens.py</a></td>
                 <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>15</td>
-                <td>1</td>
+                <td>25</td>
+                <td>10</td>
                 <td>0</td>
-                <td class="right" data-ratio="14 15">93%</td>
+                <td class="right" data-ratio="15 25">60%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_8e6f3ef91f4b94fc_common_py.html">biobb_chemistry/babelm/common.py</a></td>
                 <td class="name left"><a href="z_8e6f3ef91f4b94fc_common_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>18</td>
-                <td>0</td>
+                <td>129</td>
+                <td>47</td>
                 <td>0</td>
-                <td class="right" data-ratio="18 18">100%</td>
+                <td class="right" data-ratio="82 129">64%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_6aaa09282563964e___init___py.html">biobb_chemistry/test/__init__.py</a></td>
@@ -461,10 +461,10 @@ <h2>
             <tr class="total">
                 <td class="name left">Total</td>
                 <td class="name left">&nbsp;</td>
-                <td>820</td>
-                <td>45</td>
+                <td>1186</td>
+                <td>226</td>
                 <td>0</td>
-                <td class="right" data-ratio="775 820">95%</td>
+                <td class="right" data-ratio="960 1186">81%</td>
             </tr>
         </tfoot>
     </table>
@@ -475,8 +475,8 @@ <h2>
 <footer>
     <div class="content">
         <p>
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.5.4">coverage.py v7.5.4</a>,
-            created at 2024-07-03 19:03 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
+            created at 2024-07-16 13:32 +0000
         </p>
     </div>
     <aside class="hidden">
diff --git a/coverage/coverage.xml b/coverage/coverage.xml
index c3a2e201..d14cd14b 100644
--- a/coverage/coverage.xml
+++ b/coverage/coverage.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" ?>
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 	<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
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@@ -658,7 +658,7 @@
 				</class>
 			</classes>
 		</package>
-		<package name="biobb_chemistry.babelm" line-rate="0.7919" branch-rate="0" complexity="0">
+		<package name="biobb_chemistry.babelm" line-rate="0.7832" branch-rate="0" complexity="0">
 			<classes>
 				<class name="__init__.py" filename="biobb_chemistry/babelm/__init__.py" complexity="0" line-rate="1" branch-rate="0">
 					<methods/>
@@ -667,7 +667,7 @@
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 					</lines>
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-				<class name="babel_add_hydrogens.py" filename="biobb_chemistry/babelm/babel_add_hydrogens.py" complexity="0" line-rate="0.84" branch-rate="0">
+				<class name="babel_add_hydrogens.py" filename="biobb_chemistry/babelm/babel_add_hydrogens.py" complexity="0" line-rate="0.8372" branch-rate="0">
 					<methods/>
 					<lines>
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@@ -676,78 +676,89 @@
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 						<line number="8" hits="1"/>
 						<line number="11" hits="1"/>
-						<line number="61" hits="1"/>
-						<line number="63" hits="1"/>
+						<line number="64" hits="1"/>
 						<line number="66" hits="1"/>
-						<line number="67" hits="1"/>
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 						<line number="70" hits="1"/>
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-						<line number="77" hits="1"/>
-						<line number="78" hits="1"/>
+						<line number="73" hits="1"/>
 						<line number="79" hits="1"/>
 						<line number="80" hits="1"/>
 						<line number="81" hits="1"/>
+						<line number="82" hits="1"/>
+						<line number="83" hits="1"/>
 						<line number="84" hits="1"/>
 						<line number="85" hits="1"/>
+						<line number="86" hits="1"/>
 						<line number="87" hits="1"/>
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 						<line number="90" hits="1"/>
-						<line number="92" hits="1"/>
-						<line number="94" hits="1"/>
-						<line number="97" hits="1"/>
+						<line number="91" hits="1"/>
+						<line number="93" hits="1"/>
+						<line number="95" hits="1"/>
+						<line number="96" hits="1"/>
+						<line number="98" hits="1"/>
 						<line number="100" hits="1"/>
-						<line number="101" hits="1"/>
-						<line number="102" hits="1"/>
 						<line number="103" hits="1"/>
-						<line number="104" hits="1"/>
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 						<line number="107" hits="1"/>
 						<line number="108" hits="1"/>
 						<line number="109" hits="1"/>
 						<line number="110" hits="1"/>
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 						<line number="114" hits="1"/>
 						<line number="115" hits="1"/>
 						<line number="116" hits="1"/>
 						<line number="117" hits="1"/>
-						<line number="119" hits="1"/>
+						<line number="120" hits="1"/>
+						<line number="121" hits="1"/>
 						<line number="122" hits="1"/>
-						<line number="125" hits="1"/>
-						<line number="128" hits="1"/>
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+						<line number="123" hits="1"/>
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+						<line number="127" hits="1"/>
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+						<line number="133" hits="1"/>
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 						<line number="135" hits="1"/>
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-						<line number="138" hits="1"/>
-						<line number="142" hits="1"/>
-						<line number="145" hits="1"/>
-						<line number="146" hits="0"/>
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+						<line number="141" hits="1"/>
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-						<line number="150" hits="1"/>
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+						<line number="148" hits="1"/>
+						<line number="151" hits="1"/>
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-						<line number="159" hits="1"/>
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-						<line number="181" hits="0"/>
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-						<line number="185" hits="0"/>
-						<line number="186" hits="0"/>
-						<line number="188" hits="0"/>
-						<line number="189" hits="0"/>
-						<line number="190" hits="0"/>
-						<line number="193" hits="0"/>
-						<line number="198" hits="1"/>
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+						<line number="183" hits="1"/>
+						<line number="185" hits="1"/>
+						<line number="188" hits="1"/>
+						<line number="192" hits="1"/>
+						<line number="197" hits="1"/>
 						<line number="199" hits="0"/>
+						<line number="200" hits="0"/>
+						<line number="203" hits="0"/>
+						<line number="204" hits="0"/>
+						<line number="205" hits="0"/>
+						<line number="207" hits="0"/>
+						<line number="208" hits="0"/>
+						<line number="209" hits="0"/>
+						<line number="212" hits="0"/>
+						<line number="217" hits="1"/>
+						<line number="218" hits="0"/>
 					</lines>
 				</class>
-				<class name="babel_convert.py" filename="biobb_chemistry/babelm/babel_convert.py" complexity="0" line-rate="0.859" branch-rate="0">
+				<class name="babel_convert.py" filename="biobb_chemistry/babelm/babel_convert.py" complexity="0" line-rate="0.8202" branch-rate="0">
 					<methods/>
 					<lines>
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@@ -756,78 +767,89 @@
 						<line number="7" hits="1"/>
 						<line number="8" hits="1"/>
 						<line number="11" hits="1"/>
-						<line number="62" hits="1"/>
-						<line number="64" hits="1"/>
+						<line number="65" hits="1"/>
 						<line number="67" hits="1"/>
-						<line number="68" hits="1"/>
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 						<line number="71" hits="1"/>
-						<line number="77" hits="1"/>
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diff --git a/coverage/coveragebadge.svg b/coverage/coveragebadge.svg
index 0d30c019..13801e69 100644
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diff --git a/coverage/function_index.html b/coverage/function_index.html
index b2e7a882..3927ba35 100644
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@@ -54,8 +54,8 @@ <h2>
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.5.4">coverage.py v7.5.4</a>,
-            created at 2024-07-03 19:03 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
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         </p>
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@@ -585,48 +585,48 @@ <h2>
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             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t61">biobb_chemistry/babelm/babel_add_hydrogens.py</a></td>
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t61"><data value='init__'>BabelAddHydrogens.__init__</data></a></td>
-                <td>12</td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t64">biobb_chemistry/babelm/babel_add_hydrogens.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t64"><data value='init__'>BabelAddHydrogens.__init__</data></a></td>
+                <td>15</td>
                 <td>0</td>
                 <td>0</td>
-                <td class="right" data-ratio="12 12">100%</td>
+                <td class="right" data-ratio="15 15">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t87">biobb_chemistry/babelm/babel_add_hydrogens.py</a></td>
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t87"><data value='check_data_params'>BabelAddHydrogens.check_data_params</data></a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t93">biobb_chemistry/babelm/babel_add_hydrogens.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t93"><data value='check_data_params'>BabelAddHydrogens.check_data_params</data></a></td>
                 <td>2</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="2 2">100%</td>
             </tr>
             <tr class="region">
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-                <td>25</td>
-                <td>1</td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t98">biobb_chemistry/babelm/babel_add_hydrogens.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t98"><data value='create_cmd'>BabelAddHydrogens.create_cmd</data></a></td>
+                <td>33</td>
+                <td>3</td>
                 <td>0</td>
-                <td class="right" data-ratio="24 25">96%</td>
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             </tr>
             <tr class="region">
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-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t138"><data value='launch'>BabelAddHydrogens.launch</data></a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t157">biobb_chemistry/babelm/babel_add_hydrogens.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t157"><data value='launch'>BabelAddHydrogens.launch</data></a></td>
                 <td>11</td>
                 <td>1</td>
                 <td>0</td>
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             </tr>
             <tr class="region">
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+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t188">biobb_chemistry/babelm/babel_add_hydrogens.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t188"><data value='babel_add_hydrogens'>babel_add_hydrogens</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
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             </tr>
             <tr class="region">
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+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t197">biobb_chemistry/babelm/babel_add_hydrogens.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html#t197"><data value='main'>main</data></a></td>
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                 <td>9</td>
                 <td>0</td>
@@ -641,48 +641,48 @@ <h2>
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             </tr>
             <tr class="region">
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-                <td>13</td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t65">biobb_chemistry/babelm/babel_convert.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t65"><data value='init__'>BabelConvert.__init__</data></a></td>
+                <td>16</td>
                 <td>0</td>
                 <td>0</td>
-                <td class="right" data-ratio="13 13">100%</td>
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             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t89">biobb_chemistry/babelm/babel_convert.py</a></td>
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t89"><data value='check_data_params'>BabelConvert.check_data_params</data></a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t95">biobb_chemistry/babelm/babel_convert.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t95"><data value='check_data_params'>BabelConvert.check_data_params</data></a></td>
                 <td>2</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="2 2">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t94">biobb_chemistry/babelm/babel_convert.py</a></td>
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t94"><data value='create_cmd'>BabelConvert.create_cmd</data></a></td>
-                <td>27</td>
-                <td>0</td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t100">biobb_chemistry/babelm/babel_convert.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t100"><data value='create_cmd'>BabelConvert.create_cmd</data></a></td>
+                <td>35</td>
+                <td>5</td>
                 <td>0</td>
-                <td class="right" data-ratio="27 27">100%</td>
+                <td class="right" data-ratio="30 35">86%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t141">biobb_chemistry/babelm/babel_convert.py</a></td>
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t141"><data value='launch'>BabelConvert.launch</data></a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t158">biobb_chemistry/babelm/babel_convert.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t158"><data value='launch'>BabelConvert.launch</data></a></td>
                 <td>11</td>
                 <td>1</td>
                 <td>0</td>
                 <td class="right" data-ratio="10 11">91%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t172">biobb_chemistry/babelm/babel_convert.py</a></td>
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t172"><data value='babel_convert'>babel_convert</data></a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t189">biobb_chemistry/babelm/babel_convert.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t189"><data value='babel_convert'>babel_convert</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t181">biobb_chemistry/babelm/babel_convert.py</a></td>
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t181"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t198">biobb_chemistry/babelm/babel_convert.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html#t198"><data value='main'>main</data></a></td>
                 <td>9</td>
                 <td>9</td>
                 <td>0</td>
@@ -753,48 +753,48 @@ <h2>
                 <td class="right" data-ratio="15 16">94%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t61">biobb_chemistry/babelm/babel_remove_hydrogens.py</a></td>
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t61"><data value='init__'>BabelRemoveHydrogens.__init__</data></a></td>
-                <td>12</td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t64">biobb_chemistry/babelm/babel_remove_hydrogens.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t64"><data value='init__'>BabelRemoveHydrogens.__init__</data></a></td>
+                <td>15</td>
                 <td>0</td>
                 <td>0</td>
-                <td class="right" data-ratio="12 12">100%</td>
+                <td class="right" data-ratio="15 15">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t87">biobb_chemistry/babelm/babel_remove_hydrogens.py</a></td>
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t87"><data value='check_data_params'>BabelRemoveHydrogens.check_data_params</data></a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t93">biobb_chemistry/babelm/babel_remove_hydrogens.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t93"><data value='check_data_params'>BabelRemoveHydrogens.check_data_params</data></a></td>
                 <td>2</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="2 2">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t92">biobb_chemistry/babelm/babel_remove_hydrogens.py</a></td>
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t92"><data value='create_cmd'>BabelRemoveHydrogens.create_cmd</data></a></td>
-                <td>25</td>
-                <td>0</td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t98">biobb_chemistry/babelm/babel_remove_hydrogens.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t98"><data value='create_cmd'>BabelRemoveHydrogens.create_cmd</data></a></td>
+                <td>33</td>
+                <td>4</td>
                 <td>0</td>
-                <td class="right" data-ratio="25 25">100%</td>
+                <td class="right" data-ratio="29 33">88%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t136">biobb_chemistry/babelm/babel_remove_hydrogens.py</a></td>
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t136"><data value='launch'>BabelRemoveHydrogens.launch</data></a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t154">biobb_chemistry/babelm/babel_remove_hydrogens.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t154"><data value='launch'>BabelRemoveHydrogens.launch</data></a></td>
                 <td>11</td>
                 <td>1</td>
                 <td>0</td>
                 <td class="right" data-ratio="10 11">91%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t167">biobb_chemistry/babelm/babel_remove_hydrogens.py</a></td>
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t167"><data value='babel_remove_hydrogens'>babel_remove_hydrogens</data></a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t185">biobb_chemistry/babelm/babel_remove_hydrogens.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t185"><data value='babel_remove_hydrogens'>babel_remove_hydrogens</data></a></td>
                 <td>1</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="1 1">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t176">biobb_chemistry/babelm/babel_remove_hydrogens.py</a></td>
-                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t176"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t194">biobb_chemistry/babelm/babel_remove_hydrogens.py</a></td>
+                <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html#t194"><data value='main'>main</data></a></td>
                 <td>9</td>
                 <td>9</td>
                 <td>0</td>
@@ -1269,10 +1269,10 @@ <h2>
             <tr class="total">
                 <td class="name left">Total</td>
                 <td class="name left">&nbsp;</td>
-                <td>1153</td>
-                <td>215</td>
+                <td>1186</td>
+                <td>226</td>
                 <td>0</td>
-                <td class="right" data-ratio="938 1153">81%</td>
+                <td class="right" data-ratio="960 1186">81%</td>
             </tr>
         </tfoot>
     </table>
@@ -1283,8 +1283,8 @@ <h2>
 <footer>
     <div class="content">
         <p>
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.5.4">coverage.py v7.5.4</a>,
-            created at 2024-07-03 19:03 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
+            created at 2024-07-16 13:32 +0000
         </p>
     </div>
     <aside class="hidden">
diff --git a/coverage/index.html b/coverage/index.html
index 095f3356..5f917dc7 100644
--- a/coverage/index.html
+++ b/coverage/index.html
@@ -53,8 +53,8 @@ <h2>
                 <a class="button" href="class_index.html">Classes</a>
         </h2>
         <p class="text">
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.5.4">coverage.py v7.5.4</a>,
-            created at 2024-07-03 19:03 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
+            created at 2024-07-16 13:32 +0000
         </p>
     </div>
 </header>
@@ -156,17 +156,17 @@ <h2>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_add_hydrogens_py.html">biobb_chemistry/babelm/babel_add_hydrogens.py</a></td>
-                <td>75</td>
-                <td>12</td>
+                <td>86</td>
+                <td>14</td>
                 <td>0</td>
-                <td class="right" data-ratio="63 75">84%</td>
+                <td class="right" data-ratio="72 86">84%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_convert_py.html">biobb_chemistry/babelm/babel_convert.py</a></td>
-                <td>78</td>
-                <td>11</td>
+                <td>89</td>
+                <td>16</td>
                 <td>0</td>
-                <td class="right" data-ratio="67 78">86%</td>
+                <td class="right" data-ratio="73 89">82%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_8e6f3ef91f4b94fc_babel_minimize_py.html">biobb_chemistry/babelm/babel_minimize.py</a></td>
@@ -177,10 +177,10 @@ <h2>
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-                <td>75</td>
-                <td>11</td>
+                <td>86</td>
+                <td>15</td>
                 <td>0</td>
-                <td class="right" data-ratio="64 75">85%</td>
+                <td class="right" data-ratio="71 86">83%</td>
             </tr>
             <tr class="region">
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@@ -270,10 +270,10 @@ <h2>
         <tfoot>
             <tr class="total">
                 <td class="name left">Total</td>
-                <td>1153</td>
-                <td>215</td>
+                <td>1186</td>
+                <td>226</td>
                 <td>0</td>
-                <td class="right" data-ratio="938 1153">81%</td>
+                <td class="right" data-ratio="960 1186">81%</td>
             </tr>
         </tfoot>
     </table>
@@ -284,8 +284,8 @@ <h2>
 <footer>
     <div class="content">
         <p>
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.5.4">coverage.py v7.5.4</a>,
-            created at 2024-07-03 19:03 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
+            created at 2024-07-16 13:32 +0000
         </p>
     </div>
     <aside class="hidden">
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index 2206a2a5..dc5295a8 100644
--- a/coverage/status.json
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@@ -1 +1 @@
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
+            created at 2024-07-16 13:32 +0000
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
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index 6e1643bb..90192866 100644
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+            created at 2024-07-16 13:32 +0000
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
+            created at 2024-07-16 13:32 +0000
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
+            created at 2024-07-16 13:32 +0000
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
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index b2792e6c..853c9378 100644
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+            created at 2024-07-16 13:32 +0000
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@@ -90,8 +90,8 @@ <h2>
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
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-            <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">12<span class="text"> missing</span></button>
+            <span class="text">86 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">72<span class="text"> run</span></button>
+            <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">14<span class="text"> missing</span></button>
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
+            created at 2024-07-16 13:32 +0000
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@@ -102,183 +102,202 @@ <h2>
     <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">        properties (dic - Python dictionary object containing the tool parameters, not input/output files):</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">            * **input_format** (*str*) - (None) Format of input file. If not provided, input_path extension will be taken. Values: dat (Information represented in a data record), ent (Protein Data Bank format), fa (FASTA sequence format), fasta (FASTA sequence format), gro (GROMACS structure), inp (AMBER trajectory format), log (Events file), mcif (Entry format of PDB database in mmCIF format), mdl (file format for holding information about the atoms; bonds; connectivity and coordinates of a molecule), mmcif (Entry format of PDB database in mmCIF format), mol (file format for holding information about the atoms; bonds; connectivity and coordinates of a molecule), mol2 (Complete and portable representation of a SYBYL molecule), pdb (Protein Data Bank format), pdbqt (Protein Data Bank format with charges), png (File format for image compression), sdf (One of a family of chemical-data file formats developed by MDL Information Systems), smi (Chemical structure specified in Simplified Molecular Input Line Entry System line notation.), smiles (Chemical structure specified in Simplified Molecular Input Line Entry System line notation.), txt (Textual format), xml (eXtensible Markup Language), xtc (Portable binary format for trajectories produced by GROMACS package).</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">            * **output_format** (*str*) - (None) Format of output file. If not provided, output_path extension will be taken. Values: ent (Protein Data Bank format), fa (FASTA sequence format), fasta (FASTA sequence format), gro (GROMACS structure), inp (AMBER trajectory format), mcif (Entry format of PDB database in mmCIF format), mdl (file format for holding information about the atoms; bonds; connectivity and coordinates of a molecule), mmcif (Entry format of PDB database in mmCIF format), mol (file format for holding information about the atoms; bonds; connectivity and coordinates of a molecule), mol2 (Complete and portable representation of a SYBYL molecule), pdb (Protein Data Bank format), pdbqt (Protein Data Bank format with charges), png (File format for image compression), sdf (One of a family of chemical-data file formats developed by MDL Information Systems), smi (Chemical structure specified in Simplified Molecular Input Line Entry System line notation.), smiles (Chemical structure specified in Simplified Molecular Input Line Entry System line notation.), txt (Textual format), xtc (Portable binary format for trajectories produced by GROMACS package).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">            * **coordinates** (*int*) - (None) Type of coordinates: 2D or 3D. Values: 2 (2D coordinates), 3 (3D coordinates).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">            * **ph** (*float*) - (7.4) [0~14|0.1] Add hydrogens appropriate for pH.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">            * **binary_path** (*str*) - ("obabel") Path to the obabel executable binary.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **container_path** (*str*) - (None) Container path definition.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **container_image** (*str*) - ('informaticsmatters/obabel:latest') Container image definition.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **container_working_dir** (*str*) - (None) Container working directory definition.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **container_user_id** (*str*) - (None) Container user_id definition.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">            * **fs_input** (*list*) - (None) Format-specific input options. Values: b (disable automatic bonding), d (input file is in dlg -AutoDock docking log- format).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">            * **fs_output** (*list*) - (["h"]) Format-specific output options. Values: b (enable automatic bonding), r (output as a rigid molecule), c (combine separate molecular pieces of input into a single rigid molecule), s (output as a flexible residue), p (preserve atom indices from input file), h (preserve hydrogens), n (preserve atom names).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">            * **coordinates** (*int*) - (None) Type of coordinates: 2D or 3D. Values: 2 (2D coordinates), 3 (3D coordinates).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">            * **effort** (*str*) - ("medium") Computational effort wanted to dedicate for the conformer generation coordinates calculations, only for 3D coordinates. Values: fastest (only generate coordinates, no force field or conformer search), fast (perform quick forcefield optimization), medium (forcefield optimization + fast conformer search), better (more optimization + fast conformer search), best (more optimization + significant conformer search).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">            * **ph** (*float*) - (7.4) [0~14|0.1] Add hydrogens appropriate for pH.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">            * **binary_path** (*str*) - ("obabel") Path to the obabel executable binary.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **container_path** (*str*) - (None) Container path definition.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **container_image** (*str*) - ('informaticsmatters/obabel:latest') Container image definition.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **container_working_dir** (*str*) - (None) Container working directory definition.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **container_user_id** (*str*) - (None) Container user_id definition.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            from biobb_chemistry.babelm.babel_add_hydrogens import babel_add_hydrogens</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">                'input_format': 'pdb',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">                'output_format': 'pdb',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">                'coordinates': 3,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">                'ph': 7.4</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            babel_add_hydrogens(input_path='/path/to/myStructure.pdb',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                                output_path='/path/to/newStructure.pdb',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">            * name: Open Babel</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">            * version: 2.4.1</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">            * license: GNU</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_path</span><span class="op">,</span> <span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">            <span class="str">"in"</span><span class="op">:</span> <span class="op">{</span><span class="str">"input_path"</span><span class="op">:</span> <span class="nam">input_path</span><span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">            <span class="str">"out"</span><span class="op">:</span> <span class="op">{</span><span class="str">"output_path"</span><span class="op">:</span> <span class="nam">output_path</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">input_format</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'input_format'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">output_format</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'output_format'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">coordinates</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'coordinates'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">ph</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'ph'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'binary_path'</span><span class="op">,</span> <span class="str">'obabel'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">    <span class="key">def</span> <span class="nam">check_data_params</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">err_log</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="str">""" Checks all the input/output paths and parameters """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">check_input_path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">__class__</span><span class="op">.</span><span class="nam">__name__</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">check_output_path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">__class__</span><span class="op">.</span><span class="nam">__name__</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">    <span class="key">def</span> <span class="nam">create_cmd</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">err_log</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="str">"""Creates the command line instruction using the properties file settings"""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">instructions_list</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="com"># executable path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="com"># generating input</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="nam">infr</span> <span class="op">=</span> <span class="nam">get_input_format</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">input_format</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="nam">iformat</span> <span class="op">=</span> <span class="str">'-i'</span> <span class="op">+</span> <span class="nam">infr</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">iformat</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="nam">ipath</span> <span class="op">=</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">ipath</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="com"># generating output</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="nam">oufr</span> <span class="op">=</span> <span class="nam">get_output_format</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">output_format</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="nam">oformat</span> <span class="op">=</span> <span class="str">'-o'</span> <span class="op">+</span> <span class="nam">oufr</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">oformat</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="nam">opath</span> <span class="op">=</span> <span class="str">'-O'</span> <span class="op">+</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">opath</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="com"># adding coordinates</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="nam">crd</span> <span class="op">=</span> <span class="nam">get_coordinates</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">coordinates</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="nam">coordinates</span> <span class="op">=</span> <span class="str">''</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="key">if</span> <span class="nam">crd</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">            <span class="nam">coordinates</span> <span class="op">=</span> <span class="str">'--gen'</span> <span class="op">+</span> <span class="nam">crd</span> <span class="op">+</span> <span class="str">'d'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">            from biobb_chemistry.babelm.babel_add_hydrogens import babel_add_hydrogens</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">                'input_format': 'pdb',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">                'output_format': 'pdb',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                'coordinates': 3,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                'ph': 7.4</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">            babel_add_hydrogens(input_path='/path/to/myStructure.pdb',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                                output_path='/path/to/newStructure.pdb',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                                properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">            * name: Open Babel</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * version: 2.4.1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * license: GNU</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_path</span><span class="op">,</span> <span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">            <span class="str">"in"</span><span class="op">:</span> <span class="op">{</span><span class="str">"input_path"</span><span class="op">:</span> <span class="nam">input_path</span><span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">            <span class="str">"out"</span><span class="op">:</span> <span class="op">{</span><span class="str">"output_path"</span><span class="op">:</span> <span class="nam">output_path</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">input_format</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'input_format'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">output_format</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'output_format'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">fs_input</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'fs_input'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">fs_output</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'fs_output'</span><span class="op">,</span> <span class="op">[</span><span class="str">"h"</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">coordinates</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'coordinates'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">effort</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'effort'</span><span class="op">,</span> <span class="str">'medium'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">ph</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'ph'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'binary_path'</span><span class="op">,</span> <span class="str">'obabel'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">    <span class="key">def</span> <span class="nam">check_data_params</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">err_log</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="str">""" Checks all the input/output paths and parameters """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">check_input_path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">__class__</span><span class="op">.</span><span class="nam">__name__</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">check_output_path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">__class__</span><span class="op">.</span><span class="nam">__name__</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">    <span class="key">def</span> <span class="nam">create_cmd</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">err_log</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="str">"""Creates the command line instruction using the properties file settings"""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="nam">instructions_list</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="com"># executable path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="com"># generating input</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="nam">infr</span> <span class="op">=</span> <span class="nam">get_input_format</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">input_format</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="nam">iformat</span> <span class="op">=</span> <span class="str">'-i'</span> <span class="op">+</span> <span class="nam">infr</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">iformat</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="nam">ipath</span> <span class="op">=</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">ipath</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="com"># generating output</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="nam">oufr</span> <span class="op">=</span> <span class="nam">get_output_format</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">output_format</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="nam">oformat</span> <span class="op">=</span> <span class="str">'-o'</span> <span class="op">+</span> <span class="nam">oufr</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">oformat</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="nam">opath</span> <span class="op">=</span> <span class="str">'-O'</span> <span class="op">+</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">opath</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">coordinates</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="com"># checking pH</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="nam">p</span> <span class="op">=</span> <span class="nam">get_ph</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">ph</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="com"># adding H</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="nam">hydrogens</span> <span class="op">=</span> <span class="str">'-h'</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="com"># adding pH</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="nam">ph</span> <span class="op">=</span> <span class="str">''</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="key">if</span> <span class="nam">p</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">            <span class="nam">ph</span> <span class="op">=</span> <span class="str">'-p '</span> <span class="op">+</span> <span class="nam">p</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">ph</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">hydrogens</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="key">return</span> <span class="nam">instructions_list</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="str">"""Execute the :class:`BabelAddHydrogens &lt;babelm.babel_add_hydrogens.BabelAddHydrogens>` babelm.babel_add_hydrogens.BabelAddHydrogens object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="com"># check input/output paths and parameters</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_data_params</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">err_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">        <span class="com"># create command line instruction</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">create_cmd</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">err_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">run_biobb</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="com"># Copy files to host</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="com"># remove temporary folder(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="com"># adding coordinates</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="nam">crd</span> <span class="op">=</span> <span class="nam">get_coordinates</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">coordinates</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="nam">coordinates</span> <span class="op">=</span> <span class="str">''</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="key">if</span> <span class="nam">crd</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="nam">coordinates</span> <span class="op">=</span> <span class="str">'--gen'</span> <span class="op">+</span> <span class="nam">crd</span> <span class="op">+</span> <span class="str">'d'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">coordinates</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="com"># checking pH</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="nam">p</span> <span class="op">=</span> <span class="nam">get_ph</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">ph</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="com"># adding H</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="nam">hydrogens</span> <span class="op">=</span> <span class="str">'-h'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="com"># adding pH</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="nam">ph</span> <span class="op">=</span> <span class="str">''</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="key">if</span> <span class="nam">p</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">ph</span> <span class="op">=</span> <span class="str">'-p '</span> <span class="op">+</span> <span class="nam">p</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">ph</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">hydrogens</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="com"># fs_input</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fs_input</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">            <span class="key">for</span> <span class="nam">fsi</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fs_input</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">                <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'-a'</span> <span class="op">+</span> <span class="nam">fsi</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="com"># fs_output</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fs_output</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">            <span class="key">for</span> <span class="nam">fso</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fs_output</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">                <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'-x'</span> <span class="op">+</span> <span class="nam">fso</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="com"># adding effort (only for 3D coordinates)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="key">if</span> <span class="nam">crd</span> <span class="op">==</span> <span class="str">'3'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'--'</span> <span class="op">+</span> <span class="nam">self</span><span class="op">.</span><span class="nam">effort</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="key">return</span> <span class="nam">instructions_list</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="str">"""Execute the :class:`BabelAddHydrogens &lt;babelm.babel_add_hydrogens.BabelAddHydrogens>` babelm.babel_add_hydrogens.BabelAddHydrogens object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="com"># check input/output paths and parameters</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_data_params</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">err_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t"><span class="key">def</span> <span class="nam">babel_add_hydrogens</span><span class="op">(</span><span class="nam">input_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">    <span class="str">"""Execute the :class:`BabelAddHydrogens &lt;babelm.babel_add_hydrogens.BabelAddHydrogens>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;babelm.babel_add_hydrogens.BabelAddHydrogens.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">    <span class="key">return</span> <span class="nam">BabelAddHydrogens</span><span class="op">(</span><span class="nam">input_path</span><span class="op">=</span><span class="nam">input_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">                             <span class="nam">output_path</span><span class="op">=</span><span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">                             <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="com"># create command line instruction</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">create_cmd</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">err_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">run_biobb</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="com"># Copy files to host</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">"Adds hydrogen atoms to small molecules."</span><span class="op">,</span> <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="com"># remove temporary folder(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Path to the input file. Accepted formats: dat, ent, fa, fasta, gro, inp, log, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt, xml, xtc.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Path to the output file. Accepted formats: ent, fa, fasta, gro, inp, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t"><span class="key">def</span> <span class="nam">babel_add_hydrogens</span><span class="op">(</span><span class="nam">input_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">    <span class="str">"""Execute the :class:`BabelAddHydrogens &lt;babelm.babel_add_hydrogens.BabelAddHydrogens>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;babelm.babel_add_hydrogens.BabelAddHydrogens.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">    <span class="nam">babel_add_hydrogens</span><span class="op">(</span><span class="nam">input_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">                        <span class="nam">output_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">                        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">    <span class="key">return</span> <span class="nam">BabelAddHydrogens</span><span class="op">(</span><span class="nam">input_path</span><span class="op">=</span><span class="nam">input_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">                             <span class="nam">output_path</span><span class="op">=</span><span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">                             <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">"Adds hydrogen atoms to small molecules."</span><span class="op">,</span> <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Path to the input file. Accepted formats: dat, ent, fa, fasta, gro, inp, log, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt, xml, xtc.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Path to the output file. Accepted formats: ent, fa, fasta, gro, inp, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">    <span class="nam">babel_add_hydrogens</span><span class="op">(</span><span class="nam">input_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">                        <span class="nam">output_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">                        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -287,8 +306,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_8e6f3ef91f4b94fc_babel_convert_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.5.4">coverage.py v7.5.4</a>,
-            created at 2024-07-03 19:03 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
+            created at 2024-07-16 13:32 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8e6f3ef91f4b94fc_babel_convert_py.html b/coverage/z_8e6f3ef91f4b94fc_babel_convert_py.html
index c37c4e83..3cee9a0f 100644
--- a/coverage/z_8e6f3ef91f4b94fc_babel_convert_py.html
+++ b/coverage/z_8e6f3ef91f4b94fc_babel_convert_py.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-    <title>Coverage for biobb_chemistry/babelm/babel_convert.py: 86%</title>
+    <title>Coverage for biobb_chemistry/babelm/babel_convert.py: 82%</title>
     <link rel="icon" sizes="32x32" href="favicon_32_cb_58284776.png">
     <link rel="stylesheet" href="style_cb_8e611ae1.css" type="text/css">
     <script src="coverage_html_cb_6fb7b396.js" defer></script>
@@ -12,7 +12,7 @@
     <div class="content">
         <h1>
             <span class="text">Coverage for </span><b>biobb_chemistry/babelm/babel_convert.py</b>:
-            <span class="pc_cov">86%</span>
+            <span class="pc_cov">82%</span>
         </h1>
         <aside id="help_panel_wrapper">
             <input id="help_panel_state" type="checkbox">
@@ -54,9 +54,9 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">78 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">67<span class="text"> run</span></button>
-            <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">11<span class="text"> missing</span></button>
+            <span class="text">89 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">73<span class="text"> run</span></button>
+            <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">16<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
         <p class="text">
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_8e6f3ef91f4b94fc_babel_minimize_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.5.4">coverage.py v7.5.4</a>,
-            created at 2024-07-03 19:03 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
+            created at 2024-07-16 13:32 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -102,186 +102,203 @@ <h2>
     <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">        properties (dic - Python dictionary object containing the tool parameters, not input/output files):</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">            * **input_format** (*str*) - (None) Format of input file. If not provided, input_path extension will be taken. Values: dat (Information represented in a data record), ent (Protein Data Bank format), fa (FASTA sequence format), fasta (FASTA sequence format), gro (GROMACS structure), inp (AMBER trajectory format), log (Events file), mcif (Entry format of PDB database in mmCIF format), mdl (file format for holding information about the atoms; bonds; connectivity and coordinates of a molecule), mmcif (Entry format of PDB database in mmCIF format), mol (file format for holding information about the atoms; bonds; connectivity and coordinates of a molecule), mol2 (Complete and portable representation of a SYBYL molecule), pdb (Protein Data Bank format), pdbqt (Protein Data Bank format with charges), png (File format for image compression), sdf (One of a family of chemical-data file formats developed by MDL Information Systems), smi (Chemical structure specified in Simplified Molecular Input Line Entry System line notation.), smiles (Chemical structure specified in Simplified Molecular Input Line Entry System line notation.), txt (Textual format), xml (eXtensible Markup Language), xtc (Portable binary format for trajectories produced by GROMACS package).</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">            * **output_format** (*str*) - (None) Format of output file. If not provided, output_path extension will be taken. Values: ent (Protein Data Bank format), fa (FASTA sequence format), fasta (FASTA sequence format), gro (GROMACS structure), inp (AMBER trajectory format), mcif (Entry format of PDB database in mmCIF format), mdl (file format for holding information about the atoms; bonds; connectivity and coordinates of a molecule), mmcif (Entry format of PDB database in mmCIF format), mol (file format for holding information about the atoms; bonds; connectivity and coordinates of a molecule), mol2 (Complete and portable representation of a SYBYL molecule), pdb (Protein Data Bank format), pdbqt (Protein Data Bank format with charges), png (File format for image compression), sdf (One of a family of chemical-data file formats developed by MDL Information Systems), smi (Chemical structure specified in Simplified Molecular Input Line Entry System line notation.), smiles (Chemical structure specified in Simplified Molecular Input Line Entry System line notation.), txt (Textual format), xtc (Portable binary format for trajectories produced by GROMACS package).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">            * **coordinates** (*int*) - (None) Type of coordinates: 2D or 3D. Values: 2 (2D coordinates), 3 (3D coordinates).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">            * **ph** (*float*) - (7.4) [0~14|0.1] Add hydrogens appropriate for pH.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">            * **flex** (*bool*) - (False) Remove all but the largest contiguous fragment (strip salts).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">            * **binary_path** (*str*) - ("obabel") Path to the obabel executable binary.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **container_path** (*str*) - (None) Container path definition.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **container_image** (*str*) - ('informaticsmatters/obabel:latest') Container image definition.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **container_working_dir** (*str*) - (None) Container working directory definition.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **container_user_id** (*str*) - (None) Container user_id definition.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">            * **fs_input** (*list*) - (None) Format-specific input options. Values: b (disable automatic bonding), d (input file is in dlg -AutoDock docking log- format).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">            * **fs_output** (*list*) - (None) Format-specific output options. Values: b (enable automatic bonding), r (output as a rigid molecule), c (combine separate molecular pieces of input into a single rigid molecule), s (output as a flexible residue), p (preserve atom indices from input file), h (preserve hydrogens), n (preserve atom names).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">            * **coordinates** (*int*) - (None) Type of coordinates: 2D or 3D. Values: 2 (2D coordinates), 3 (3D coordinates).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">            * **effort** (*str*) - ("medium") Computational effort wanted to dedicate for the conformer generation coordinates calculations, only for 3D coordinates. Values: fastest (only generate coordinates, no force field or conformer search), fast (perform quick forcefield optimization), medium (forcefield optimization + fast conformer search), better (more optimization + fast conformer search), best (more optimization + significant conformer search).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">            * **ph** (*float*) - (7.4) [0~14|0.1] Add hydrogens appropriate for pH.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">            * **flex** (*bool*) - (False) Remove all but the largest contiguous fragment (strip salts).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **binary_path** (*str*) - ("obabel") Path to the obabel executable binary.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **container_path** (*str*) - (None) Container path definition.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **container_image** (*str*) - ('informaticsmatters/obabel:latest') Container image definition.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **container_working_dir** (*str*) - (None) Container working directory definition.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **container_user_id** (*str*) - (None) Container user_id definition.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t"><span class="str">            * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            from biobb_chemistry.babelm.babel_convert import babel_convert</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">                'input_format': 'smi',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">                'output_format': 'mol2',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">                'coordinates': 3,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">                'ph': 7.4</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">            babel_convert(input_path='/path/to/my2DMolecule.smi',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                        output_path='/path/to/new3DMolecule.mol2',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">                        properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">            * name: Open Babel</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">            * version: 2.4.1</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">            * license: GNU</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_path</span><span class="op">,</span> <span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">            <span class="str">"in"</span><span class="op">:</span> <span class="op">{</span><span class="str">"input_path"</span><span class="op">:</span> <span class="nam">input_path</span><span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">            <span class="str">"out"</span><span class="op">:</span> <span class="op">{</span><span class="str">"output_path"</span><span class="op">:</span> <span class="nam">output_path</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">input_format</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'input_format'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">output_format</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'output_format'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">coordinates</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'coordinates'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">ph</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'ph'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">flex</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'flex'</span><span class="op">,</span> <span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'binary_path'</span><span class="op">,</span> <span class="str">'obabel'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">    <span class="key">def</span> <span class="nam">check_data_params</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">err_log</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="str">""" Checks all the input/output paths and parameters """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">check_input_path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">__class__</span><span class="op">.</span><span class="nam">__name__</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">check_output_path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">__class__</span><span class="op">.</span><span class="nam">__name__</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">    <span class="key">def</span> <span class="nam">create_cmd</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">err_log</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="str">"""Creates the command line instruction using the properties file settings"""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="nam">instructions_list</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="com"># executable path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="com"># generating input</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="nam">infr</span> <span class="op">=</span> <span class="nam">get_input_format</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">input_format</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="nam">iformat</span> <span class="op">=</span> <span class="str">'-i'</span> <span class="op">+</span> <span class="nam">infr</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">iformat</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="nam">ipath</span> <span class="op">=</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">ipath</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="com"># generating output</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="nam">oufr</span> <span class="op">=</span> <span class="nam">get_output_format</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">output_format</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="nam">oformat</span> <span class="op">=</span> <span class="str">'-o'</span> <span class="op">+</span> <span class="nam">oufr</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">oformat</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="nam">opath</span> <span class="op">=</span> <span class="str">'-O'</span> <span class="op">+</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">opath</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="com"># adding coordinates</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="nam">crd</span> <span class="op">=</span> <span class="nam">get_coordinates</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">coordinates</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="nam">coordinates</span> <span class="op">=</span> <span class="str">''</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="key">if</span> <span class="nam">crd</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">            <span class="nam">coordinates</span> <span class="op">=</span> <span class="str">'--gen'</span> <span class="op">+</span> <span class="nam">crd</span> <span class="op">+</span> <span class="str">'d'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">            from biobb_chemistry.babelm.babel_convert import babel_convert</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">                'input_format': 'smi',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                'output_format': 'mol2',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                'coordinates': 3,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                'ph': 7.4</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">            babel_convert(input_path='/path/to/my2DMolecule.smi',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                        output_path='/path/to/new3DMolecule.mol2',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">                        properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * name: Open Babel</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * version: 2.4.1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">            * license: GNU</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_path</span><span class="op">,</span> <span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">            <span class="str">"in"</span><span class="op">:</span> <span class="op">{</span><span class="str">"input_path"</span><span class="op">:</span> <span class="nam">input_path</span><span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">            <span class="str">"out"</span><span class="op">:</span> <span class="op">{</span><span class="str">"output_path"</span><span class="op">:</span> <span class="nam">output_path</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">input_format</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'input_format'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">output_format</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'output_format'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">fs_input</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'fs_input'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">fs_output</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'fs_output'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">coordinates</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'coordinates'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">effort</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'effort'</span><span class="op">,</span> <span class="str">'medium'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">ph</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'ph'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">flex</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'flex'</span><span class="op">,</span> <span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'binary_path'</span><span class="op">,</span> <span class="str">'obabel'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">    <span class="key">def</span> <span class="nam">check_data_params</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">err_log</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="str">""" Checks all the input/output paths and parameters """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">check_input_path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">__class__</span><span class="op">.</span><span class="nam">__name__</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">check_output_path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">__class__</span><span class="op">.</span><span class="nam">__name__</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">    <span class="key">def</span> <span class="nam">create_cmd</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">err_log</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="str">"""Creates the command line instruction using the properties file settings"""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="nam">instructions_list</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="com"># executable path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="com"># generating input</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="nam">infr</span> <span class="op">=</span> <span class="nam">get_input_format</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">input_format</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="nam">iformat</span> <span class="op">=</span> <span class="str">'-i'</span> <span class="op">+</span> <span class="nam">infr</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">iformat</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="nam">ipath</span> <span class="op">=</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">ipath</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="com"># generating output</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="nam">oufr</span> <span class="op">=</span> <span class="nam">get_output_format</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">output_format</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="nam">oformat</span> <span class="op">=</span> <span class="str">'-o'</span> <span class="op">+</span> <span class="nam">oufr</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">oformat</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">        <span class="nam">opath</span> <span class="op">=</span> <span class="str">'-O'</span> <span class="op">+</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">opath</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">coordinates</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">        <span class="com"># adding pH</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="nam">p</span> <span class="op">=</span> <span class="nam">get_ph</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">ph</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="nam">ph</span> <span class="op">=</span> <span class="str">''</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="key">if</span> <span class="nam">p</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="nam">ph</span> <span class="op">=</span> <span class="str">'-p '</span> <span class="op">+</span> <span class="nam">p</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">ph</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="com"># flex</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">flex</span> <span class="op">=</span> <span class="str">''</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="key">if</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">flex</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">            <span class="nam">flex</span> <span class="op">=</span> <span class="str">'-r'</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">flex</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="key">return</span> <span class="nam">instructions_list</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="str">"""Execute the :class:`BabelConvert &lt;babelm.babel_convert.BabelConvert>` babelm.babel_convert.BabelConvert object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">        <span class="com"># check input/output paths and parameters</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_data_params</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">err_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="com"># create command line instruction</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">create_cmd</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">err_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="com"># adding coordinates</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="nam">crd</span> <span class="op">=</span> <span class="nam">get_coordinates</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">coordinates</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">        <span class="nam">coordinates</span> <span class="op">=</span> <span class="str">''</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">        <span class="key">if</span> <span class="nam">crd</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">            <span class="nam">coordinates</span> <span class="op">=</span> <span class="str">'--gen'</span> <span class="op">+</span> <span class="nam">crd</span> <span class="op">+</span> <span class="str">'d'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">coordinates</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="com"># adding pH</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">        <span class="nam">p</span> <span class="op">=</span> <span class="nam">get_ph</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">ph</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="nam">ph</span> <span class="op">=</span> <span class="str">''</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="key">if</span> <span class="nam">p</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">            <span class="nam">ph</span> <span class="op">=</span> <span class="str">'-p '</span> <span class="op">+</span> <span class="nam">p</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">ph</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">        <span class="com"># flex</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="nam">flex</span> <span class="op">=</span> <span class="str">''</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="key">if</span> <span class="key">not</span> <span class="nam">self</span><span class="op">.</span><span class="nam">flex</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">            <span class="nam">flex</span> <span class="op">=</span> <span class="str">'-r'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">flex</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">        <span class="com"># fs_input</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fs_input</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">            <span class="key">for</span> <span class="nam">fsi</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fs_input</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">                <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'-a'</span> <span class="op">+</span> <span class="nam">fsi</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">        <span class="com"># fs_output</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fs_output</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">            <span class="key">for</span> <span class="nam">fso</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fs_output</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">                <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'-x'</span> <span class="op">+</span> <span class="nam">fso</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="com"># adding effort (only for 3D coordinates)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">        <span class="key">if</span> <span class="nam">crd</span> <span class="op">==</span> <span class="str">'3'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'--'</span> <span class="op">+</span> <span class="nam">self</span><span class="op">.</span><span class="nam">effort</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">run_biobb</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="com"># Copy files to host</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="key">return</span> <span class="nam">instructions_list</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="str">"""Execute the :class:`BabelConvert &lt;babelm.babel_convert.BabelConvert>` babelm.babel_convert.BabelConvert object."""</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="com"># remove temporary folder(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="com"># check input/output paths and parameters</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_data_params</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">err_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="com"># create command line instruction</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">create_cmd</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">err_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t"><span class="key">def</span> <span class="nam">babel_convert</span><span class="op">(</span><span class="nam">input_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">    <span class="str">"""Execute the :class:`BabelConvert &lt;babelm.babel_convert.BabelConvert>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;babelm.babel_convert.BabelConvert.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">    <span class="key">return</span> <span class="nam">BabelConvert</span><span class="op">(</span><span class="nam">input_path</span><span class="op">=</span><span class="nam">input_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">                        <span class="nam">output_path</span><span class="op">=</span><span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">                        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">"Small molecule format conversion."</span><span class="op">,</span> <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">run_biobb</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="com"># Copy files to host</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="com"># remove temporary folder(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Path to the input file. Accepted formats: dat, ent, fa, fasta, gro, inp, log, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt, xml, xtc.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Path to the output file. Accepted formats: ent, fa, fasta, gro, inp, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">    <span class="nam">babel_convert</span><span class="op">(</span><span class="nam">input_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">                  <span class="nam">output_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">                  <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t"><span class="key">def</span> <span class="nam">babel_convert</span><span class="op">(</span><span class="nam">input_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">    <span class="str">"""Execute the :class:`BabelConvert &lt;babelm.babel_convert.BabelConvert>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;babelm.babel_convert.BabelConvert.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">    <span class="key">return</span> <span class="nam">BabelConvert</span><span class="op">(</span><span class="nam">input_path</span><span class="op">=</span><span class="nam">input_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">                        <span class="nam">output_path</span><span class="op">=</span><span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">                        <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">"Small molecule format conversion."</span><span class="op">,</span> <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Path to the input file. Accepted formats: dat, ent, fa, fasta, gro, inp, log, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt, xml, xtc.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Path to the output file. Accepted formats: ent, fa, fasta, gro, inp, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">    <span class="nam">babel_convert</span><span class="op">(</span><span class="nam">input_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t">                  <span class="nam">output_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">                  <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -290,8 +307,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_8e6f3ef91f4b94fc_babel_minimize_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.5.4">coverage.py v7.5.4</a>,
-            created at 2024-07-03 19:03 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
+            created at 2024-07-16 13:32 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8e6f3ef91f4b94fc_babel_minimize_py.html b/coverage/z_8e6f3ef91f4b94fc_babel_minimize_py.html
index f730e72a..1fc758d9 100644
--- a/coverage/z_8e6f3ef91f4b94fc_babel_minimize_py.html
+++ b/coverage/z_8e6f3ef91f4b94fc_babel_minimize_py.html
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.5.4">coverage.py v7.5.4</a>,
-            created at 2024-07-03 19:03 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
+            created at 2024-07-16 13:32 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -300,8 +300,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.5.4">coverage.py v7.5.4</a>,
-            created at 2024-07-03 19:03 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
+            created at 2024-07-16 13:32 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html b/coverage/z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html
index faa53a47..988bab67 100644
--- a/coverage/z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html
+++ b/coverage/z_8e6f3ef91f4b94fc_babel_remove_hydrogens_py.html
@@ -2,7 +2,7 @@
 <html lang="en">
 <head>
     <meta http-equiv="Content-Type" content="text/html; charset=utf-8">
-    <title>Coverage for biobb_chemistry/babelm/babel_remove_hydrogens.py: 85%</title>
+    <title>Coverage for biobb_chemistry/babelm/babel_remove_hydrogens.py: 83%</title>
     <link rel="icon" sizes="32x32" href="favicon_32_cb_58284776.png">
     <link rel="stylesheet" href="style_cb_8e611ae1.css" type="text/css">
     <script src="coverage_html_cb_6fb7b396.js" defer></script>
@@ -12,7 +12,7 @@
     <div class="content">
         <h1>
             <span class="text">Coverage for </span><b>biobb_chemistry/babelm/babel_remove_hydrogens.py</b>:
-            <span class="pc_cov">85%</span>
+            <span class="pc_cov">83%</span>
         </h1>
         <aside id="help_panel_wrapper">
             <input id="help_panel_state" type="checkbox">
@@ -54,9 +54,9 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">75 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">64<span class="text"> run</span></button>
-            <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">11<span class="text"> missing</span></button>
+            <span class="text">86 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">71<span class="text"> run</span></button>
+            <button type="button" class="mis show_mis button_toggle_mis" value="mis" data-shortcut="m" title="Toggle lines missing">15<span class="text"> missing</span></button>
             <button type="button" class="exc show_exc button_toggle_exc" value="exc" data-shortcut="x" title="Toggle lines excluded">0<span class="text"> excluded</span></button>
         </h2>
         <p class="text">
@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_8e6f3ef91f4b94fc_common_py.html">&#xbb; next</a>
             &nbsp; &nbsp; &nbsp;
-            <a class="nav" href="https://coverage.readthedocs.io/en/7.5.4">coverage.py v7.5.4</a>,
-            created at 2024-07-03 19:03 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
+            created at 2024-07-16 13:32 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -102,181 +102,199 @@ <h2>
     <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">        properties (dic - Python dictionary object containing the tool parameters, not input/output files):</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t21" href="#t21">21</a></span><span class="t"><span class="str">            * **input_format** (*str*) - (None) Format of input file. If not provided, input_path extension will be taken. Values: dat (Information represented in a data record), ent (Protein Data Bank format), fa (FASTA sequence format), fasta (FASTA sequence format), gro (GROMACS structure), inp (AMBER trajectory format), log (Events file), mcif (Entry format of PDB database in mmCIF format), mdl (file format for holding information about the atoms; bonds; connectivity and coordinates of a molecule), mmcif (Entry format of PDB database in mmCIF format), mol (file format for holding information about the atoms; bonds; connectivity and coordinates of a molecule), mol2 (Complete and portable representation of a SYBYL molecule), pdb (Protein Data Bank format), pdbqt (Protein Data Bank format with charges), png (File format for image compression), sdf (One of a family of chemical-data file formats developed by MDL Information Systems), smi (Chemical structure specified in Simplified Molecular Input Line Entry System line notation.), smiles (Chemical structure specified in Simplified Molecular Input Line Entry System line notation.), txt (Textual format), xml (eXtensible Markup Language), xtc (Portable binary format for trajectories produced by GROMACS package).</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t22" href="#t22">22</a></span><span class="t"><span class="str">            * **output_format** (*str*) - (None) Format of output file. If not provided, output_path extension will be taken. Values: ent (Protein Data Bank format), fa (FASTA sequence format), fasta (FASTA sequence format), gro (GROMACS structure), inp (AMBER trajectory format), mcif (Entry format of PDB database in mmCIF format), mdl (file format for holding information about the atoms; bonds; connectivity and coordinates of a molecule), mmcif (Entry format of PDB database in mmCIF format), mol (file format for holding information about the atoms; bonds; connectivity and coordinates of a molecule), mol2 (Complete and portable representation of a SYBYL molecule), pdb (Protein Data Bank format), pdbqt (Protein Data Bank format with charges), png (File format for image compression), sdf (One of a family of chemical-data file formats developed by MDL Information Systems), smi (Chemical structure specified in Simplified Molecular Input Line Entry System line notation.), smiles (Chemical structure specified in Simplified Molecular Input Line Entry System line notation.), txt (Textual format), xtc (Portable binary format for trajectories produced by GROMACS package).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">            * **coordinates** (*int*) - (None) Type of coordinates: 2D or 3D. Values: 2 (2D coordinates), 3 (3D coordinates).</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">            * **ph** (*float*) - (7.4) [0~14|0.1] Add hydrogens appropriate for pH.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">            * **binary_path** (*str*) - ("obabel") Path to the obabel executable binary.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **container_path** (*str*) - (None) Container path definition.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **container_image** (*str*) - ('informaticsmatters/obabel:latest') Container image definition.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **container_working_dir** (*str*) - (None) Container working directory definition.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **container_user_id** (*str*) - (None) Container user_id definition.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t23" href="#t23">23</a></span><span class="t"><span class="str">            * **fs_input** (*list*) - (None) Format-specific input options. Values: b (disable automatic bonding), d (input file is in dlg -AutoDock docking log- format).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t24" href="#t24">24</a></span><span class="t"><span class="str">            * **fs_output** (*list*) - (None) Format-specific output options. Values: b (enable automatic bonding), r (output as a rigid molecule), c (combine separate molecular pieces of input into a single rigid molecule), s (output as a flexible residue), p (preserve atom indices from input file), h (preserve hydrogens), n (preserve atom names).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t25" href="#t25">25</a></span><span class="t"><span class="str">            * **coordinates** (*int*) - (None) Type of coordinates: 2D or 3D. Values: 2 (2D coordinates), 3 (3D coordinates).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t26" href="#t26">26</a></span><span class="t"><span class="str">            * **effort** (*str*) - ("medium") Computational effort wanted to dedicate for the conformer generation coordinates calculations, only for 3D coordinates. Values: fastest (only generate coordinates, no force field or conformer search), fast (perform quick forcefield optimization), medium (forcefield optimization + fast conformer search), better (more optimization + fast conformer search), best (more optimization + significant conformer search).</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t27" href="#t27">27</a></span><span class="t"><span class="str">            * **ph** (*float*) - (7.4) [0~14|0.1] Add hydrogens appropriate for pH.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t28" href="#t28">28</a></span><span class="t"><span class="str">            * **binary_path** (*str*) - ("obabel") Path to the obabel executable binary.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t29" href="#t29">29</a></span><span class="t"><span class="str">            * **remove_tmp** (*bool*) - (True) [WF property] Remove temporal files.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t30" href="#t30">30</a></span><span class="t"><span class="str">            * **restart** (*bool*) - (False) [WF property] Do not execute if output files exist.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **sandbox_path** (*str*) - ("./") [WF property] Parent path to the sandbox directory.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **container_path** (*str*) - (None) Container path definition.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t33" href="#t33">33</a></span><span class="t"><span class="str">            * **container_image** (*str*) - ('informaticsmatters/obabel:latest') Container image definition.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t34" href="#t34">34</a></span><span class="t"><span class="str">            * **container_volume_path** (*str*) - ('/tmp') Container volume path definition.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t35" href="#t35">35</a></span><span class="t"><span class="str">            * **container_working_dir** (*str*) - (None) Container working directory definition.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t36" href="#t36">36</a></span><span class="t"><span class="str">            * **container_user_id** (*str*) - (None) Container user_id definition.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t37" href="#t37">37</a></span><span class="t"><span class="str">            * **container_shell_path** (*str*) - ('/bin/bash') Path to default shell inside the container.</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t38" href="#t38">38</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">            from biobb_chemistry.babelm.babel_remove_hydrogens import babel_remove_hydrogens</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t"><span class="str">                'input_format': 'pdb',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">                'output_format': 'pdb',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">                'coordinates': 3,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">                'ph': 7.4</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">            babel_remove_hydrogens(input_path='/path/to/myStructure.pdb',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                                    output_path='/path/to/newStructure.pdb',</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">                                    properties=prop)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t"><span class="str">            * name: Open Babel</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">            * version: 2.4.1</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">            * license: GNU</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_path</span><span class="op">,</span> <span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">            <span class="str">"in"</span><span class="op">:</span> <span class="op">{</span><span class="str">"input_path"</span><span class="op">:</span> <span class="nam">input_path</span><span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">            <span class="str">"out"</span><span class="op">:</span> <span class="op">{</span><span class="str">"output_path"</span><span class="op">:</span> <span class="nam">output_path</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">input_format</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'input_format'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">output_format</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'output_format'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">coordinates</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'coordinates'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">ph</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'ph'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'binary_path'</span><span class="op">,</span> <span class="str">'obabel'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">    <span class="key">def</span> <span class="nam">check_data_params</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">err_log</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">        <span class="str">""" Checks all the input/output paths and parameters """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">check_input_path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">__class__</span><span class="op">.</span><span class="nam">__name__</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">check_output_path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">__class__</span><span class="op">.</span><span class="nam">__name__</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">    <span class="key">def</span> <span class="nam">create_cmd</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">err_log</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">        <span class="str">"""Creates the command line instruction using the properties file settings"""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="nam">instructions_list</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="com"># executable path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="com"># generating input</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="nam">infr</span> <span class="op">=</span> <span class="nam">get_input_format</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">input_format</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">        <span class="nam">iformat</span> <span class="op">=</span> <span class="str">'-i'</span> <span class="op">+</span> <span class="nam">infr</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">iformat</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="nam">ipath</span> <span class="op">=</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">ipath</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="com"># generating output</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="nam">oufr</span> <span class="op">=</span> <span class="nam">get_output_format</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">output_format</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="nam">oformat</span> <span class="op">=</span> <span class="str">'-o'</span> <span class="op">+</span> <span class="nam">oufr</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">oformat</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="nam">opath</span> <span class="op">=</span> <span class="str">'-O'</span> <span class="op">+</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">opath</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="com"># adding coordinates</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="nam">crd</span> <span class="op">=</span> <span class="nam">get_coordinates</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">coordinates</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="nam">coordinates</span> <span class="op">=</span> <span class="str">''</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="key">if</span> <span class="nam">crd</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">            <span class="nam">coordinates</span> <span class="op">=</span> <span class="str">'--gen'</span> <span class="op">+</span> <span class="nam">crd</span> <span class="op">+</span> <span class="str">'d'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t39" href="#t39">39</a></span><span class="t"><span class="str">    Examples:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t40" href="#t40">40</a></span><span class="t"><span class="str">        This is a use example of how to use the building block from Python::</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t41" href="#t41">41</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t42" href="#t42">42</a></span><span class="t"><span class="str">            from biobb_chemistry.babelm.babel_remove_hydrogens import babel_remove_hydrogens</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t43" href="#t43">43</a></span><span class="t"><span class="str">            prop = {</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t44" href="#t44">44</a></span><span class="t"><span class="str">                'input_format': 'pdb',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t45" href="#t45">45</a></span><span class="t"><span class="str">                'output_format': 'pdb',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t46" href="#t46">46</a></span><span class="t"><span class="str">                'coordinates': 3,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t47" href="#t47">47</a></span><span class="t"><span class="str">                'ph': 7.4</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t48" href="#t48">48</a></span><span class="t"><span class="str">            }</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t49" href="#t49">49</a></span><span class="t"><span class="str">            babel_remove_hydrogens(input_path='/path/to/myStructure.pdb',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t50" href="#t50">50</a></span><span class="t"><span class="str">                                    output_path='/path/to/newStructure.pdb',</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t51" href="#t51">51</a></span><span class="t"><span class="str">                                    properties=prop)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t52" href="#t52">52</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t53" href="#t53">53</a></span><span class="t"><span class="str">    Info:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t54" href="#t54">54</a></span><span class="t"><span class="str">        * wrapped_software:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t55" href="#t55">55</a></span><span class="t"><span class="str">            * name: Open Babel</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t56" href="#t56">56</a></span><span class="t"><span class="str">            * version: 2.4.1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t57" href="#t57">57</a></span><span class="t"><span class="str">            * license: GNU</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t58" href="#t58">58</a></span><span class="t"><span class="str">        * ontology:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t59" href="#t59">59</a></span><span class="t"><span class="str">            * name: EDAM</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t60" href="#t60">60</a></span><span class="t"><span class="str">            * schema: http://edamontology.org/EDAM.owl</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t61" href="#t61">61</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t62" href="#t62">62</a></span><span class="t"><span class="str">    """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t63" href="#t63">63</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t">    <span class="key">def</span> <span class="nam">__init__</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">input_path</span><span class="op">,</span> <span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t65" href="#t65">65</a></span><span class="t">                 <span class="nam">properties</span><span class="op">=</span><span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t66" href="#t66">66</a></span><span class="t">        <span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span> <span class="key">or</span> <span class="op">{</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t67" href="#t67">67</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t68" href="#t68">68</a></span><span class="t">        <span class="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t69" href="#t69">69</a></span><span class="t">        <span class="nam">super</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">__init__</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">locals_var_dict</span> <span class="op">=</span> <span class="nam">locals</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">copy</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t71" href="#t71">71</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t72" href="#t72">72</a></span><span class="t">        <span class="com"># Input/Output files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t73" href="#t73">73</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span> <span class="op">=</span> <span class="op">{</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t74" href="#t74">74</a></span><span class="t">            <span class="str">"in"</span><span class="op">:</span> <span class="op">{</span><span class="str">"input_path"</span><span class="op">:</span> <span class="nam">input_path</span><span class="op">}</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t75" href="#t75">75</a></span><span class="t">            <span class="str">"out"</span><span class="op">:</span> <span class="op">{</span><span class="str">"output_path"</span><span class="op">:</span> <span class="nam">output_path</span><span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t76" href="#t76">76</a></span><span class="t">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t77" href="#t77">77</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t78" href="#t78">78</a></span><span class="t">        <span class="com"># Properties specific for BB</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t79" href="#t79">79</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">input_format</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'input_format'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">output_format</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'output_format'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">fs_input</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'fs_input'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t82" href="#t82">82</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">fs_output</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'fs_output'</span><span class="op">,</span> <span class="key">None</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t83" href="#t83">83</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">coordinates</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'coordinates'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t84" href="#t84">84</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">effort</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'effort'</span><span class="op">,</span> <span class="str">'medium'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t85" href="#t85">85</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">ph</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'ph'</span><span class="op">,</span> <span class="str">''</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t86" href="#t86">86</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span> <span class="op">=</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'binary_path'</span><span class="op">,</span> <span class="str">'obabel'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">properties</span> <span class="op">=</span> <span class="nam">properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t88" href="#t88">88</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">        <span class="com"># Check the properties</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t90" href="#t90">90</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_properties</span><span class="op">(</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t91" href="#t91">91</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t92" href="#t92">92</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t93" href="#t93">93</a></span><span class="t">    <span class="key">def</span> <span class="nam">check_data_params</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">err_log</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t94" href="#t94">94</a></span><span class="t">        <span class="str">""" Checks all the input/output paths and parameters """</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">check_input_path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">__class__</span><span class="op">.</span><span class="nam">__name__</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t96" href="#t96">96</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span> <span class="op">=</span> <span class="nam">check_output_path</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">__class__</span><span class="op">.</span><span class="nam">__name__</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t98" href="#t98">98</a></span><span class="t">    <span class="key">def</span> <span class="nam">create_cmd</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">,</span> <span class="nam">err_log</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t99" href="#t99">99</a></span><span class="t">        <span class="str">"""Creates the command line instruction using the properties file settings"""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="nam">instructions_list</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t101" href="#t101">101</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t102" href="#t102">102</a></span><span class="t">        <span class="com"># executable path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t103" href="#t103">103</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">binary_path</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t104" href="#t104">104</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t105" href="#t105">105</a></span><span class="t">        <span class="com"># generating input</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t106" href="#t106">106</a></span><span class="t">        <span class="nam">infr</span> <span class="op">=</span> <span class="nam">get_input_format</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">input_format</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="nam">iformat</span> <span class="op">=</span> <span class="str">'-i'</span> <span class="op">+</span> <span class="nam">infr</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t108" href="#t108">108</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">iformat</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="nam">ipath</span> <span class="op">=</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t110" href="#t110">110</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">ipath</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t111" href="#t111">111</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t112" href="#t112">112</a></span><span class="t">        <span class="com"># generating output</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t113" href="#t113">113</a></span><span class="t">        <span class="nam">oufr</span> <span class="op">=</span> <span class="nam">get_output_format</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">output_format</span><span class="op">,</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t114" href="#t114">114</a></span><span class="t">        <span class="nam">oformat</span> <span class="op">=</span> <span class="str">'-o'</span> <span class="op">+</span> <span class="nam">oufr</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t115" href="#t115">115</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">oformat</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="nam">opath</span> <span class="op">=</span> <span class="str">'-O'</span> <span class="op">+</span> <span class="nam">container_io_dict</span><span class="op">[</span><span class="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">opath</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t118" href="#t118">118</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">coordinates</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="nam">hydrogens</span> <span class="op">=</span> <span class="str">'-d'</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">hydrogens</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">        <span class="com"># adding pH</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="nam">p</span> <span class="op">=</span> <span class="nam">get_ph</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">ph</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">        <span class="nam">ph</span> <span class="op">=</span> <span class="str">''</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="key">if</span> <span class="nam">p</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="nam">ph</span> <span class="op">=</span> <span class="str">'-p '</span> <span class="op">+</span> <span class="nam">p</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">ph</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="key">return</span> <span class="nam">instructions_list</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="str">"""Execute the :class:`BabelRemoveHydrogens &lt;babelm.babel_remove_hydrogens.BabelRemoveHydrogens>` babelm.babel_remove_hydrogens.BabelRemoveHydrogens object."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">        <span class="com"># check input/output paths and parameters</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_data_params</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">err_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="com"># adding coordinates</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t120" href="#t120">120</a></span><span class="t">        <span class="nam">crd</span> <span class="op">=</span> <span class="nam">get_coordinates</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">coordinates</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t121" href="#t121">121</a></span><span class="t">        <span class="nam">coordinates</span> <span class="op">=</span> <span class="str">''</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t122" href="#t122">122</a></span><span class="t">        <span class="key">if</span> <span class="nam">crd</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t123" href="#t123">123</a></span><span class="t">            <span class="nam">coordinates</span> <span class="op">=</span> <span class="str">'--gen'</span> <span class="op">+</span> <span class="nam">crd</span> <span class="op">+</span> <span class="str">'d'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t124" href="#t124">124</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">coordinates</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t125" href="#t125">125</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t126" href="#t126">126</a></span><span class="t">        <span class="nam">hydrogens</span> <span class="op">=</span> <span class="str">'-d'</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">        <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">hydrogens</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">        <span class="com"># adding pH</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">        <span class="nam">p</span> <span class="op">=</span> <span class="nam">get_ph</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">ph</span><span class="op">,</span> <span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">        <span class="nam">ph</span> <span class="op">=</span> <span class="str">''</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">        <span class="key">if</span> <span class="nam">p</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">            <span class="nam">ph</span> <span class="op">=</span> <span class="str">'-p '</span> <span class="op">+</span> <span class="nam">p</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t135" href="#t135">135</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">ph</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t137" href="#t137">137</a></span><span class="t">        <span class="com"># fs_input</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t138" href="#t138">138</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fs_input</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t139" href="#t139">139</a></span><span class="t">            <span class="key">for</span> <span class="nam">fsi</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fs_input</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t140" href="#t140">140</a></span><span class="t">                <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'-a'</span> <span class="op">+</span> <span class="nam">fsi</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t141" href="#t141">141</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t142" href="#t142">142</a></span><span class="t">        <span class="com"># fs_output</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t143" href="#t143">143</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fs_output</span> <span class="key">is</span> <span class="key">not</span> <span class="key">None</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">            <span class="key">for</span> <span class="nam">fso</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">fs_output</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t145" href="#t145">145</a></span><span class="t">                <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'-x'</span> <span class="op">+</span> <span class="nam">fso</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t146" href="#t146">146</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="com"># create command line instruction</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">create_cmd</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">err_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">run_biobb</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">        <span class="com"># adding effort (only for 3D coordinates)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t148" href="#t148">148</a></span><span class="t">        <span class="key">if</span> <span class="nam">crd</span> <span class="op">==</span> <span class="str">'3'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t149" href="#t149">149</a></span><span class="t">            <span class="nam">instructions_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'--'</span> <span class="op">+</span> <span class="nam">self</span><span class="op">.</span><span class="nam">effort</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">        <span class="key">return</span> <span class="nam">instructions_list</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t152" href="#t152">152</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">        <span class="com"># Copy files to host</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">        <span class="com"># remove temporary folder(s)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t"><span class="key">def</span> <span class="nam">babel_remove_hydrogens</span><span class="op">(</span><span class="nam">input_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">    <span class="str">"""Execute the :class:`BabelRemoveHydrogens &lt;babelm.babel_remove_hydrogens.BabelRemoveHydrogens>` class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;babelm.babel_remove_hydrogens.BabelRemoveHydrogens.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t153" href="#t153">153</a></span><span class="t">    <span class="op">@</span><span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">    <span class="key">def</span> <span class="nam">launch</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="str">"""Execute the :class:`BabelRemoveHydrogens &lt;babelm.babel_remove_hydrogens.BabelRemoveHydrogens>` babelm.babel_remove_hydrogens.BabelRemoveHydrogens object."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t157" href="#t157">157</a></span><span class="t">        <span class="com"># check input/output paths and parameters</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_data_params</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">err_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t159" href="#t159">159</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="com"># Setup Biobb</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t161" href="#t161">161</a></span><span class="t">        <span class="key">if</span> <span class="nam">self</span><span class="op">.</span><span class="nam">check_restart</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">            <span class="key">return</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t163" href="#t163">163</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">stage_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t164" href="#t164">164</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t165" href="#t165">165</a></span><span class="t">        <span class="com"># create command line instruction</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t166" href="#t166">166</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">cmd</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">create_cmd</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">err_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t167" href="#t167">167</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="com"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t169" href="#t169">169</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">run_biobb</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t170" href="#t170">170</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">    <span class="key">return</span> <span class="nam">BabelRemoveHydrogens</span><span class="op">(</span><span class="nam">input_path</span><span class="op">=</span><span class="nam">input_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">                                <span class="nam">output_path</span><span class="op">=</span><span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">                                <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">"Removes hydrogen atoms to small molecules."</span><span class="op">,</span> <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Path to the input file. Accepted formats: dat, ent, fa, fasta, gro, inp, log, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt, xml, xtc.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Path to the output file. Accepted formats: ent, fa, fasta, gro, inp, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">    <span class="nam">babel_remove_hydrogens</span><span class="op">(</span><span class="nam">input_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">                           <span class="nam">output_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">                           <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t171" href="#t171">171</a></span><span class="t">        <span class="com"># Copy files to host</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t172" href="#t172">172</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">copy_to_host</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t173" href="#t173">173</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="com"># remove temporary folder(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t175" href="#t175">175</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">tmp_files</span><span class="op">.</span><span class="nam">extend</span><span class="op">(</span><span class="op">[</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t176" href="#t176">176</a></span><span class="t">            <span class="nam">self</span><span class="op">.</span><span class="nam">stage_io_dict</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">"unique_dir"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t178" href="#t178">178</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">remove_tmp_files</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t179" href="#t179">179</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t180" href="#t180">180</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">check_arguments</span><span class="op">(</span><span class="nam">output_files_created</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">raise_exception</span><span class="op">=</span><span class="key">False</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t181" href="#t181">181</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t182" href="#t182">182</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">return_code</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t183" href="#t183">183</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t184" href="#t184">184</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t185" href="#t185">185</a></span><span class="t"><span class="key">def</span> <span class="nam">babel_remove_hydrogens</span><span class="op">(</span><span class="nam">input_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">properties</span><span class="op">:</span> <span class="nam">dict</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span> <span class="op">-></span> <span class="nam">int</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t186" href="#t186">186</a></span><span class="t">    <span class="str">"""Execute the :class:`BabelRemoveHydrogens &lt;babelm.babel_remove_hydrogens.BabelRemoveHydrogens>` class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t"><span class="str">    execute the :meth:`launch() &lt;babelm.babel_remove_hydrogens.BabelRemoveHydrogens.launch>` method."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t188" href="#t188">188</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t189" href="#t189">189</a></span><span class="t">    <span class="key">return</span> <span class="nam">BabelRemoveHydrogens</span><span class="op">(</span><span class="nam">input_path</span><span class="op">=</span><span class="nam">input_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">                                <span class="nam">output_path</span><span class="op">=</span><span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">                                <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">kwargs</span><span class="op">)</span><span class="op">.</span><span class="nam">launch</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t192" href="#t192">192</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t193" href="#t193">193</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t194" href="#t194">194</a></span><span class="t"><span class="key">def</span> <span class="nam">main</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">    <span class="str">"""Command line execution of this building block. Please check the command line documentation."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t196" href="#t196">196</a></span><span class="t">    <span class="nam">parser</span> <span class="op">=</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">ArgumentParser</span><span class="op">(</span><span class="nam">description</span><span class="op">=</span><span class="str">"Removes hydrogen atoms to small molecules."</span><span class="op">,</span> <span class="nam">formatter_class</span><span class="op">=</span><span class="key">lambda</span> <span class="nam">prog</span><span class="op">:</span> <span class="nam">argparse</span><span class="op">.</span><span class="nam">RawTextHelpFormatter</span><span class="op">(</span><span class="nam">prog</span><span class="op">,</span> <span class="nam">width</span><span class="op">=</span><span class="num">99999</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t197" href="#t197">197</a></span><span class="t">    <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--config'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">False</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Configuration file'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t198" href="#t198">198</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">    <span class="com"># Specific args of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">    <span class="nam">required_args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">add_argument_group</span><span class="op">(</span><span class="str">'required arguments'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t201" href="#t201">201</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--input_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Path to the input file. Accepted formats: dat, ent, fa, fasta, gro, inp, log, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt, xml, xtc.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">    <span class="nam">required_args</span><span class="op">.</span><span class="nam">add_argument</span><span class="op">(</span><span class="str">'--output_path'</span><span class="op">,</span> <span class="nam">required</span><span class="op">=</span><span class="key">True</span><span class="op">,</span> <span class="nam">help</span><span class="op">=</span><span class="str">'Path to the output file. Accepted formats: ent, fa, fasta, gro, inp, mcif, mdl, mmcif, mol, mol2, pdb, pdbqt, png, sdf, smi, smiles, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">    <span class="nam">args</span> <span class="op">=</span> <span class="nam">parser</span><span class="op">.</span><span class="nam">parse_args</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">    <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="op">=</span> <span class="nam">args</span><span class="op">.</span><span class="nam">config</span> <span class="key">or</span> <span class="str">"{}"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t206" href="#t206">206</a></span><span class="t">    <span class="nam">properties</span> <span class="op">=</span> <span class="nam">settings</span><span class="op">.</span><span class="nam">ConfReader</span><span class="op">(</span><span class="nam">config</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">config</span><span class="op">)</span><span class="op">.</span><span class="nam">get_prop_dic</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">    <span class="com"># Specific call of each building block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">    <span class="nam">babel_remove_hydrogens</span><span class="op">(</span><span class="nam">input_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">                           <span class="nam">output_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t211" href="#t211">211</a></span><span class="t">                           <span class="nam">properties</span><span class="op">=</span><span class="nam">properties</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t212" href="#t212">212</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t214" href="#t214">214</a></span><span class="t"><span class="key">if</span> <span class="nam">__name__</span> <span class="op">==</span> <span class="str">'__main__'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">    <span class="nam">main</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -285,8 +303,8 @@ <h2>
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.5.4">coverage.py v7.5.4</a>,
-            created at 2024-07-03 19:03 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
+            created at 2024-07-16 13:32 +0000
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@@ -64,8 +64,8 @@ <h2>
             <a id="indexLink" class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a id="nextFileLink" class="nav" href="z_6aaa09282563964e___init___py.html">&#xbb; next</a>
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.5.4">coverage.py v7.5.4</a>,
-            created at 2024-07-03 19:03 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.0">coverage.py v7.6.0</a>,
+            created at 2024-07-16 13:32 +0000
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+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="10" time="338.485" timestamp="2024-07-16T13:27:05.755190" hostname="biobb-runners"><testcase classname="biobb_chemistry.test.unitests.test_acpype.test_acpype_params_ac.TestAcpypeParamsAC" name="test_params_ac" time="124.798" /><testcase classname="biobb_chemistry.test.unitests.test_acpype.test_acpype_params_cns.TestAcpypeParamsCNS" name="test_params_cns" time="69.567" /><testcase classname="biobb_chemistry.test.unitests.test_acpype.test_acpype_params_gmx.TestAcpypeParamsGMX" name="test_params_gmx" time="70.852" /><testcase classname="biobb_chemistry.test.unitests.test_acpype.test_acpype_params_gmx_opls.TestAcpypeParamsGMXOPLS" name="test_params_gmx_opls" time="71.482" /><testcase classname="biobb_chemistry.test.unitests.test_ambertools.test_reduce_add_hydrogens.TestReduceAddHydrogens" name="test_add_hydrogens" time="0.478" /><testcase classname="biobb_chemistry.test.unitests.test_ambertools.test_reduce_remove_hydrogens.TestReduceRemoveHydrogens" name="test_remove_hydrogens" time="0.081" /><testcase classname="biobb_chemistry.test.unitests.test_babel.test_babel_add_hydrogens.TestBabelAddHydrogens" name="test_add_hydrogens" time="0.238" /><testcase classname="biobb_chemistry.test.unitests.test_babel.test_babel_convert.TestBabelConvert" name="test_convert" time="0.099" /><testcase classname="biobb_chemistry.test.unitests.test_babel.test_babel_minimize.TestBabelMinimize" name="test_minimize" time="0.158" /><testcase classname="biobb_chemistry.test.unitests.test_babel.test_babel_remove_hydrogens.TestBabelRemoveHydrogens" name="test_remove_hydrogens" time="0.239" /></testsuite></testsuites>
\ No newline at end of file
diff --git a/junit/report.html b/junit/report.html
index eb113df6..3fea4ea5 100644
--- a/junit/report.html
+++ b/junit/report.html
@@ -7,7 +7,7 @@
   </head>
   <body>
     <h1 id="title">report.html</h1>
-    <p>Report generated on 03-Jul-2024 at 19:02:59 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
+    <p>Report generated on 16-Jul-2024 at 13:32:44 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
         v4.1.1</p>
     <div id="environment-header">
       <h2>Environment</h2>
@@ -61,7 +61,7 @@ <h2>Environment</h2>
         <h2>Summary</h2>
         <div class="additional-summary prefix">
         </div>
-        <p class="run-count">10 tests took 00:07:06.</p>
+        <p class="run-count">10 tests took 00:05:38.</p>
         <p class="filter">(Un)check the boxes to filter the results.</p>
         <div class="summary__reload">
           <div class="summary__reload__button hidden" onclick="location.reload()">
@@ -108,7 +108,7 @@ <h2>Summary</h2>
     </table>
   </body>
   <footer>
-    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.9.19&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-159-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.2.2&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;html&#34;: &#34;4.1.1&#34;, &#34;cov&#34;: &#34;5.0.0&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_ac.py::TestAcpypeParamsAC::test_params_ac&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_ac.py::TestAcpypeParamsAC::test_params_ac&#34;, &#34;duration&#34;: &#34;00:03:33&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_ac.py::TestAcpypeParamsAC::test_params_ac&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:03:33&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-03 18:55:53,759 [MainThread  ] [INFO ]  Executing biobb_chemistry.acpype.acpype_params_ac Version: 4.2.0\n2024-07-03 18:55:53,759 [MainThread  ] [INFO ]  /tmp/biobb/unitests_208/acpype_params_ac/sandbox_7a59aa36-51ce-4f6c-bf32-fa9107aab93f directory successfully created\n2024-07-03 18:55:53,760 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_208/acpype_params_ac/sandbox_7a59aa36-51ce-4f6c-bf32-fa9107aab93f\n2024-07-03 18:55:53,760 [MainThread  ] [INFO ]  acpype -i /tmp/biobb/unitests_208/acpype_params_ac/sandbox_7a59aa36-51ce-4f6c-bf32-fa9107aab93f/acpype.params.pdb -b BBB.sDkDFa -n 0\n\n2024-07-03 18:59:27,007 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-03 18:59:27,008 [MainThread  ] [INFO ]  ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.sDkDFa.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 3m 33s\n\n2024-07-03 18:59:27,010 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_208/acpype_params_ac/output.lib succesfully created\n2024-07-03 18:59:27,010 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_208/acpype_params_ac/output.inpcrd succesfully created\n2024-07-03 18:59:27,011 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_208/acpype_params_ac/output.prmtop succesfully created\n2024-07-03 18:59:27,012 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_208/acpype_params_ac/output.frcmod succesfully created\n2024-07-03 18:59:27,013 [MainThread  ] [INFO ]  Removed temporary folder: BBB.sDkDFa.acpype\nChecking if empty file: /tmp/biobb/unitests_208/acpype_params_ac/output.frcmod\nChecking if empty file: /tmp/biobb/unitests_208/acpype_params_ac/output.inpcrd\nChecking if empty file: /tmp/biobb/unitests_208/acpype_params_ac/output.lib\nChecking if empty file: /tmp/biobb/unitests_208/acpype_params_ac/output.prmtop\nComparing: \n        File_A: /tmp/biobb/unitests_208/acpype_params_ac/output.frcmod\n        File_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.ac.frcmod\n        File_A hash: b&amp;#x27;\\xed\\x1db\\xfb\\x1c,\\xe4\\x03\\x02\\xf9\\xcb\\x08)\\xe2\\xe3c\\\\T\\x9a\\xe4G\\x87\\xf7#\\xe7\\xe1\\xf0a\\xb3p\\x12\\xa8&amp;#x27;\n        File_B hash: b&amp;#x27;\\xed\\x1db\\xfb\\x1c,\\xe4\\x03\\x02\\xf9\\xcb\\x08)\\xe2\\xe3c\\\\T\\x9a\\xe4G\\x87\\xf7#\\xe7\\xe1\\xf0a\\xb3p\\x12\\xa8&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_208/acpype_params_ac/output.inpcrd\n        File_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.ac.inpcrd\n        File_A hash: b&amp;#x27;\\r\\xeb\\x17\\x04\\xb4\\xb1\\xe8\\xd6\\xef\\x0c[\\xc19[\\x16kXm\\xeceQ\\xba,,\\x12$\\x03\\xa0\\xb5=\\xd2\\xa3&amp;#x27;\n        File_B hash: b&amp;#x27;\\r\\xeb\\x17\\x04\\xb4\\xb1\\xe8\\xd6\\xef\\x0c[\\xc19[\\x16kXm\\xeceQ\\xba,,\\x12$\\x03\\xa0\\xb5=\\xd2\\xa3&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_208/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:391 Executing biobb_chemistry.acpype.acpype_params_ac Version: 4.2.0\nINFO     /tmp/biobb/unitests_208/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:82 /tmp/biobb/unitests_208/acpype_params_ac/sandbox_7a59aa36-51ce-4f6c-bf32-fa9107aab93f directory successfully created\nINFO     /tmp/biobb/unitests_208/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_208/acpype_params_ac/sandbox_7a59aa36-51ce-4f6c-bf32-fa9107aab93f\nINFO     /tmp/biobb/unitests_208/acpype_params_ac/acpype_params_ac_log.out:cmd_wrapper.py:33 acpype -i /tmp/biobb/unitests_208/acpype_params_ac/sandbox_7a59aa36-51ce-4f6c-bf32-fa9107aab93f/acpype.params.pdb -b BBB.sDkDFa -n 0\n\nINFO     /tmp/biobb/unitests_208/acpype_params_ac/acpype_params_ac_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_208/acpype_params_ac/acpype_params_ac_log.out:cmd_wrapper.py:52 ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.sDkDFa.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 3m 33s\n\nINFO     /tmp/biobb/unitests_208/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:391 File /tmp/biobb/unitests_208/acpype_params_ac/output.lib succesfully created\nINFO     /tmp/biobb/unitests_208/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:391 File /tmp/biobb/unitests_208/acpype_params_ac/output.inpcrd succesfully created\nINFO     /tmp/biobb/unitests_208/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:391 File /tmp/biobb/unitests_208/acpype_params_ac/output.prmtop succesfully created\nINFO     /tmp/biobb/unitests_208/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:391 File /tmp/biobb/unitests_208/acpype_params_ac/output.frcmod succesfully created\nINFO     /tmp/biobb/unitests_208/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:391 Removed temporary folder: BBB.sDkDFa.acpype\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_208\n&#34;}], &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_cns.py::TestAcpypeParamsCNS::test_params_cns&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_cns.py::TestAcpypeParamsCNS::test_params_cns&#34;, &#34;duration&#34;: &#34;00:01:10&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_cns.py::TestAcpypeParamsCNS::test_params_cns&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:10&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-03 18:59:27,109 [MainThread  ] [INFO ]  Executing biobb_chemistry.acpype.acpype_params_cns Version: 4.2.0\n2024-07-03 18:59:27,110 [MainThread  ] [INFO ]  /tmp/biobb/unitests_208/acpype_params_cns/sandbox_328f7178-8e0b-4d73-93d3-ec9b15c2ac2a directory successfully created\n2024-07-03 18:59:27,110 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_208/acpype_params_cns/sandbox_328f7178-8e0b-4d73-93d3-ec9b15c2ac2a\n2024-07-03 18:59:27,110 [MainThread  ] [INFO ]  acpype -i /tmp/biobb/unitests_208/acpype_params_cns/sandbox_328f7178-8e0b-4d73-93d3-ec9b15c2ac2a/acpype.params.pdb -b BBB.VhxVaY -n 0\n\n2024-07-03 19:00:37,200 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-03 19:00:37,200 [MainThread  ] [INFO ]  ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.VhxVaY.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 10s\n\n2024-07-03 19:00:37,202 [MainThread  ] [INFO ]  Files: BBB.VhxVaY.acpype/BBB.VhxVaY_CNS.par\n2024-07-03 19:00:37,202 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_208/acpype_params_cns/output.par succesfully created\n2024-07-03 19:00:37,203 [MainThread  ] [INFO ]  Files: BBB.VhxVaY.acpype/BBB.VhxVaY_CNS.inp\n2024-07-03 19:00:37,203 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_208/acpype_params_cns/output.inp succesfully created\n2024-07-03 19:00:37,203 [MainThread  ] [INFO ]  Files: BBB.VhxVaY.acpype/BBB.VhxVaY_CNS.top\n2024-07-03 19:00:37,204 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_208/acpype_params_cns/output.top succesfully created\n2024-07-03 19:00:37,204 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_208/acpype_params_cns/output.pdb succesfully created\n2024-07-03 19:00:37,232 [MainThread  ] [INFO ]  Removed temporary folder: BBB.VhxVaY.acpype\nChecking if empty file: /tmp/biobb/unitests_208/acpype_params_cns/output.par\nChecking if empty file: /tmp/biobb/unitests_208/acpype_params_cns/output.inp\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_208/acpype_params_cns/output.inp\n     FILE_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.cns.inp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_208/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 Executing biobb_chemistry.acpype.acpype_params_cns Version: 4.2.0\nINFO     /tmp/biobb/unitests_208/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:82 /tmp/biobb/unitests_208/acpype_params_cns/sandbox_328f7178-8e0b-4d73-93d3-ec9b15c2ac2a directory successfully created\nINFO     /tmp/biobb/unitests_208/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_208/acpype_params_cns/sandbox_328f7178-8e0b-4d73-93d3-ec9b15c2ac2a\nINFO     /tmp/biobb/unitests_208/acpype_params_cns/acpype_params_cns_log.out:cmd_wrapper.py:33 acpype -i /tmp/biobb/unitests_208/acpype_params_cns/sandbox_328f7178-8e0b-4d73-93d3-ec9b15c2ac2a/acpype.params.pdb -b BBB.VhxVaY -n 0\n\nINFO     /tmp/biobb/unitests_208/acpype_params_cns/acpype_params_cns_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_208/acpype_params_cns/acpype_params_cns_log.out:cmd_wrapper.py:52 ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.VhxVaY.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 10s\n\nINFO     /tmp/biobb/unitests_208/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 Files: BBB.VhxVaY.acpype/BBB.VhxVaY_CNS.par\nINFO     /tmp/biobb/unitests_208/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 File /tmp/biobb/unitests_208/acpype_params_cns/output.par succesfully created\nINFO     /tmp/biobb/unitests_208/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 Files: BBB.VhxVaY.acpype/BBB.VhxVaY_CNS.inp\nINFO     /tmp/biobb/unitests_208/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 File /tmp/biobb/unitests_208/acpype_params_cns/output.inp succesfully created\nINFO     /tmp/biobb/unitests_208/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 Files: BBB.VhxVaY.acpype/BBB.VhxVaY_CNS.top\nINFO     /tmp/biobb/unitests_208/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 File /tmp/biobb/unitests_208/acpype_params_cns/output.top succesfully created\nINFO     /tmp/biobb/unitests_208/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 File /tmp/biobb/unitests_208/acpype_params_cns/output.pdb succesfully created\nINFO     /tmp/biobb/unitests_208/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 Removed temporary folder: BBB.VhxVaY.acpype\n\n&#34;}], &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx.py::TestAcpypeParamsGMX::test_params_gmx&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx.py::TestAcpypeParamsGMX::test_params_gmx&#34;, &#34;duration&#34;: &#34;00:01:11&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx.py::TestAcpypeParamsGMX::test_params_gmx&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:11&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-03 19:00:37,307 [MainThread  ] [INFO ]  Executing biobb_chemistry.acpype.acpype_params_gmx Version: 4.2.0\n2024-07-03 19:00:37,307 [MainThread  ] [INFO ]  /tmp/biobb/unitests_209/acpype_params_gmx/sandbox_69fbd309-c822-49ec-8d04-d09493056551 directory successfully created\n2024-07-03 19:00:37,307 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_209/acpype_params_gmx/sandbox_69fbd309-c822-49ec-8d04-d09493056551\n2024-07-03 19:00:37,308 [MainThread  ] [INFO ]  acpype -i /tmp/biobb/unitests_209/acpype_params_gmx/sandbox_69fbd309-c822-49ec-8d04-d09493056551/acpype.params.pdb -b BBB.H3mqlB -n 0\n\n2024-07-03 19:01:47,748 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-03 19:01:47,749 [MainThread  ] [INFO ]  ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.H3mqlB.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 10s\n\n2024-07-03 19:01:47,750 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_209/acpype_params_gmx/ref_acpype.gmx.top succesfully created\n2024-07-03 19:01:47,751 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_209/acpype_params_gmx/ref_acpype.gmx.itp succesfully created\n2024-07-03 19:01:47,752 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_209/acpype_params_gmx/ref_acpype.gmx.gro succesfully created\nChecking if empty file: /tmp/biobb/unitests_209/acpype_params_gmx/ref_acpype.gmx.gro\nChecking if empty file: /tmp/biobb/unitests_209/acpype_params_gmx/ref_acpype.gmx.itp\nChecking if empty file: /tmp/biobb/unitests_209/acpype_params_gmx/ref_acpype.gmx.top\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_209/acpype_params_gmx/ref_acpype.gmx.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.gro\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_209/acpype_params_gmx/ref_acpype.gmx.top\n     FILE_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.top\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_209/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:391 Executing biobb_chemistry.acpype.acpype_params_gmx Version: 4.2.0\nINFO     /tmp/biobb/unitests_209/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:82 /tmp/biobb/unitests_209/acpype_params_gmx/sandbox_69fbd309-c822-49ec-8d04-d09493056551 directory successfully created\nINFO     /tmp/biobb/unitests_209/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_209/acpype_params_gmx/sandbox_69fbd309-c822-49ec-8d04-d09493056551\nINFO     /tmp/biobb/unitests_209/acpype_params_gmx/acpype_params_gmx_log.out:cmd_wrapper.py:33 acpype -i /tmp/biobb/unitests_209/acpype_params_gmx/sandbox_69fbd309-c822-49ec-8d04-d09493056551/acpype.params.pdb -b BBB.H3mqlB -n 0\n\nINFO     /tmp/biobb/unitests_209/acpype_params_gmx/acpype_params_gmx_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_209/acpype_params_gmx/acpype_params_gmx_log.out:cmd_wrapper.py:52 ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.H3mqlB.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 10s\n\nINFO     /tmp/biobb/unitests_209/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:391 File /tmp/biobb/unitests_209/acpype_params_gmx/ref_acpype.gmx.top succesfully created\nINFO     /tmp/biobb/unitests_209/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:391 File /tmp/biobb/unitests_209/acpype_params_gmx/ref_acpype.gmx.itp succesfully created\nINFO     /tmp/biobb/unitests_209/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:391 File /tmp/biobb/unitests_209/acpype_params_gmx/ref_acpype.gmx.gro succesfully created\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_209\n&#34;}], &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx_opls.py::TestAcpypeParamsGMXOPLS::test_params_gmx_opls&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx_opls.py::TestAcpypeParamsGMXOPLS::test_params_gmx_opls&#34;, &#34;duration&#34;: &#34;00:01:10&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx_opls.py::TestAcpypeParamsGMXOPLS::test_params_gmx_opls&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:10&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-03 19:01:47,828 [MainThread  ] [INFO ]  Executing biobb_chemistry.acpype.acpype_params_gmx_opls Version: 4.2.0\n2024-07-03 19:01:47,828 [MainThread  ] [INFO ]  /tmp/biobb/unitests_209/acpype_params_gmx_opls/sandbox_55392a00-cf15-4f9b-9aeb-c08e7919f5b2 directory successfully created\n2024-07-03 19:01:47,828 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_209/acpype_params_gmx_opls/sandbox_55392a00-cf15-4f9b-9aeb-c08e7919f5b2\n2024-07-03 19:01:47,829 [MainThread  ] [INFO ]  acpype -i /tmp/biobb/unitests_209/acpype_params_gmx_opls/sandbox_55392a00-cf15-4f9b-9aeb-c08e7919f5b2/acpype.params.pdb -b BBB.9yzu6j -n 0\n\n2024-07-03 19:02:57,883 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-03 19:02:57,883 [MainThread  ] [INFO ]  ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.9yzu6j.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 10s\n\n2024-07-03 19:02:57,885 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_209/acpype_params_gmx_opls/ref_acpype.gmx.opls.top succesfully created\n2024-07-03 19:02:57,886 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_209/acpype_params_gmx_opls/ref_acpype.gmx.opls.itp succesfully created\nChecking if empty file: /tmp/biobb/unitests_209/acpype_params_gmx_opls/ref_acpype.gmx.opls.itp\nChecking if empty file: /tmp/biobb/unitests_209/acpype_params_gmx_opls/ref_acpype.gmx.opls.top\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_209/acpype_params_gmx_opls/ref_acpype.gmx.opls.top\n     FILE_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.opls.top\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_209/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:391 Executing biobb_chemistry.acpype.acpype_params_gmx_opls Version: 4.2.0\nINFO     /tmp/biobb/unitests_209/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:82 /tmp/biobb/unitests_209/acpype_params_gmx_opls/sandbox_55392a00-cf15-4f9b-9aeb-c08e7919f5b2 directory successfully created\nINFO     /tmp/biobb/unitests_209/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_209/acpype_params_gmx_opls/sandbox_55392a00-cf15-4f9b-9aeb-c08e7919f5b2\nINFO     /tmp/biobb/unitests_209/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:cmd_wrapper.py:33 acpype -i /tmp/biobb/unitests_209/acpype_params_gmx_opls/sandbox_55392a00-cf15-4f9b-9aeb-c08e7919f5b2/acpype.params.pdb -b BBB.9yzu6j -n 0\n\nINFO     /tmp/biobb/unitests_209/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_209/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:cmd_wrapper.py:52 ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.9yzu6j.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 10s\n\nINFO     /tmp/biobb/unitests_209/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:391 File /tmp/biobb/unitests_209/acpype_params_gmx_opls/ref_acpype.gmx.opls.top succesfully created\nINFO     /tmp/biobb/unitests_209/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:391 File /tmp/biobb/unitests_209/acpype_params_gmx_opls/ref_acpype.gmx.opls.itp succesfully created\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_209\n&#34;}], &#34;biobb_chemistry/test/unitests/test_ambertools/test_reduce_add_hydrogens.py::TestReduceAddHydrogens::test_add_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_ambertools/test_reduce_add_hydrogens.py::TestReduceAddHydrogens::test_add_hydrogens&#34;, &#34;duration&#34;: &#34;506 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_ambertools/test_reduce_add_hydrogens.py::TestReduceAddHydrogens::test_add_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;506 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-03 19:02:57,966 [MainThread  ] [INFO ]  Executing biobb_chemistry.ambertools.reduce_add_hydrogens Version: 4.2.0\n2024-07-03 19:02:57,966 [MainThread  ] [INFO ]  /tmp/biobb/unitests_209/reduce_add_hydrogens/sandbox_d72e2531-226c-46ac-a260-daf0b928750d directory successfully created\n2024-07-03 19:02:57,966 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/ambertools/reduce.no.H.pdb to /tmp/biobb/unitests_209/reduce_add_hydrogens/sandbox_d72e2531-226c-46ac-a260-daf0b928750d\n2024-07-03 19:02:57,966 [MainThread  ] [INFO ]  reduce -NOOH -OH -ROTNH3 -ALLALT /tmp/biobb/unitests_209/reduce_add_hydrogens/sandbox_d72e2531-226c-46ac-a260-daf0b928750d/reduce.no.H.pdb &amp;gt; /tmp/biobb/unitests_209/reduce_add_hydrogens/sandbox_d72e2531-226c-46ac-a260-daf0b928750d/output.pdb\n\n2024-07-03 19:02:58,395 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-03 19:02:58,395 [MainThread  ] [INFO ]  Processing file: &amp;quot;/tmp/biobb/unitests_209/reduce_add_hydrogens/sandbox_d72e2531-226c-46ac-a260-daf0b928750d/reduce.no.H.pdb&amp;quot;\nBuilding or keeping OH &amp;amp; SH Hydrogens.\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nVDW dot density = 16/A^2\nProbe radius = 0.25A\nOrientation penalty scale = 1 (100%)\nEliminate contacts within 3 bonds.\nIgnore atoms with |occupancy| &amp;lt;= 0.01 during adjustments.\nWaters ignored if B-Factor &amp;gt;= 40 or |occupancy| &amp;lt; 0.66\nAromatic rings in amino acids accept hydrogen bonds.\nRotating NH3 Hydrogens.\nNot processing Met methyls.\nFound 0 hydrogens (0 hets)\nStandardized 0 hydrogens (0 hets)\nAdded 27 hydrogens (27 hets)\nIf you publish work which uses reduce, please cite:\nWord, et. al. (1999) J. Mol. Biol. 285, 1735-1747.\nFor more information see http://kinemage.biochem.duke.edu\n\n2024-07-03 19:02:58,396 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_209/reduce_add_hydrogens/sandbox_d72e2531-226c-46ac-a260-daf0b928750d&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_209/reduce_add_hydrogens/output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_209/reduce_add_hydrogens/reduce_add_hydrogens_log.out:file_utils.py:391 Executing biobb_chemistry.ambertools.reduce_add_hydrogens Version: 4.2.0\nINFO     /tmp/biobb/unitests_209/reduce_add_hydrogens/reduce_add_hydrogens_log.out:file_utils.py:82 /tmp/biobb/unitests_209/reduce_add_hydrogens/sandbox_d72e2531-226c-46ac-a260-daf0b928750d directory successfully created\nINFO     /tmp/biobb/unitests_209/reduce_add_hydrogens/reduce_add_hydrogens_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/ambertools/reduce.no.H.pdb to /tmp/biobb/unitests_209/reduce_add_hydrogens/sandbox_d72e2531-226c-46ac-a260-daf0b928750d\nINFO     /tmp/biobb/unitests_209/reduce_add_hydrogens/reduce_add_hydrogens_log.out:cmd_wrapper.py:33 reduce -NOOH -OH -ROTNH3 -ALLALT /tmp/biobb/unitests_209/reduce_add_hydrogens/sandbox_d72e2531-226c-46ac-a260-daf0b928750d/reduce.no.H.pdb &amp;gt; /tmp/biobb/unitests_209/reduce_add_hydrogens/sandbox_d72e2531-226c-46ac-a260-daf0b928750d/output.pdb\n\nINFO     /tmp/biobb/unitests_209/reduce_add_hydrogens/reduce_add_hydrogens_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_209/reduce_add_hydrogens/reduce_add_hydrogens_log.err:cmd_wrapper.py:60 Processing file: &amp;quot;/tmp/biobb/unitests_209/reduce_add_hydrogens/sandbox_d72e2531-226c-46ac-a260-daf0b928750d/reduce.no.H.pdb&amp;quot;\nBuilding or keeping OH &amp;amp; SH Hydrogens.\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nVDW dot density = 16/A^2\nProbe radius = 0.25A\nOrientation penalty scale = 1 (100%)\nEliminate contacts within 3 bonds.\nIgnore atoms with |occupancy| &amp;lt;= 0.01 during adjustments.\nWaters ignored if B-Factor &amp;gt;= 40 or |occupancy| &amp;lt; 0.66\nAromatic rings in amino acids accept hydrogen bonds.\nRotating NH3 Hydrogens.\nNot processing Met methyls.\nFound 0 hydrogens (0 hets)\nStandardized 0 hydrogens (0 hets)\nAdded 27 hydrogens (27 hets)\nIf you publish work which uses reduce, please cite:\nWord, et. al. (1999) J. Mol. Biol. 285, 1735-1747.\nFor more information see http://kinemage.biochem.duke.edu\n\nINFO     /tmp/biobb/unitests_209/reduce_add_hydrogens/reduce_add_hydrogens_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_209/reduce_add_hydrogens/sandbox_d72e2531-226c-46ac-a260-daf0b928750d&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_209\n&#34;}], &#34;biobb_chemistry/test/unitests/test_ambertools/test_reduce_remove_hydrogens.py::TestReduceRemoveHydrogens::test_remove_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_ambertools/test_reduce_remove_hydrogens.py::TestReduceRemoveHydrogens::test_remove_hydrogens&#34;, &#34;duration&#34;: &#34;87 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_ambertools/test_reduce_remove_hydrogens.py::TestReduceRemoveHydrogens::test_remove_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;87 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-03 19:02:58,473 [MainThread  ] [INFO ]  Executing biobb_chemistry.ambertools.reduce_remove_hydrogens Version: 4.2.0\n2024-07-03 19:02:58,474 [MainThread  ] [INFO ]  /tmp/biobb/unitests_209/reduce_remove_hydrogens/sandbox_7542169b-972f-4960-b16e-9d41727d0f73 directory successfully created\n2024-07-03 19:02:58,474 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/ambertools/reduce.H.pdb to /tmp/biobb/unitests_209/reduce_remove_hydrogens/sandbox_7542169b-972f-4960-b16e-9d41727d0f73\n2024-07-03 19:02:58,474 [MainThread  ] [INFO ]  reduce -Trim /tmp/biobb/unitests_209/reduce_remove_hydrogens/sandbox_7542169b-972f-4960-b16e-9d41727d0f73/reduce.H.pdb &amp;gt; /tmp/biobb/unitests_209/reduce_remove_hydrogens/sandbox_7542169b-972f-4960-b16e-9d41727d0f73/output.pdb\n\n2024-07-03 19:02:58,485 [MainThread  ] [INFO ]  Exit code 255\n\n2024-07-03 19:02:58,485 [MainThread  ] [INFO ]  Processing file: &amp;quot;/tmp/biobb/unitests_209/reduce_remove_hydrogens/sandbox_7542169b-972f-4960-b16e-9d41727d0f73/reduce.H.pdb&amp;quot;\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nTrimming: removed 27 hydrogens (27 hets)\nRemoved 27 hydrogens (27 hets)\nIf you publish work which uses reduce, please cite:\nWord, et. al. (1999) J. Mol. Biol. 285, 1735-1747.\nFor more information see http://kinemage.biochem.duke.edu\n\nChecking if empty file: /tmp/biobb/unitests_209/reduce_remove_hydrogens/output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_209/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:file_utils.py:391 Executing biobb_chemistry.ambertools.reduce_remove_hydrogens Version: 4.2.0\nINFO     /tmp/biobb/unitests_209/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:file_utils.py:82 /tmp/biobb/unitests_209/reduce_remove_hydrogens/sandbox_7542169b-972f-4960-b16e-9d41727d0f73 directory successfully created\nINFO     /tmp/biobb/unitests_209/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/ambertools/reduce.H.pdb to /tmp/biobb/unitests_209/reduce_remove_hydrogens/sandbox_7542169b-972f-4960-b16e-9d41727d0f73\nINFO     /tmp/biobb/unitests_209/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:cmd_wrapper.py:33 reduce -Trim /tmp/biobb/unitests_209/reduce_remove_hydrogens/sandbox_7542169b-972f-4960-b16e-9d41727d0f73/reduce.H.pdb &amp;gt; /tmp/biobb/unitests_209/reduce_remove_hydrogens/sandbox_7542169b-972f-4960-b16e-9d41727d0f73/output.pdb\n\nINFO     /tmp/biobb/unitests_209/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:cmd_wrapper.py:50 Exit code 255\n\nINFO     /tmp/biobb/unitests_209/reduce_remove_hydrogens/reduce_remove_hydrogens_log.err:cmd_wrapper.py:60 Processing file: &amp;quot;/tmp/biobb/unitests_209/reduce_remove_hydrogens/sandbox_7542169b-972f-4960-b16e-9d41727d0f73/reduce.H.pdb&amp;quot;\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nTrimming: removed 27 hydrogens (27 hets)\nRemoved 27 hydrogens (27 hets)\nIf you publish work which uses reduce, please cite:\nWord, et. al. (1999) J. Mol. Biol. 285, 1735-1747.\nFor more information see http://kinemage.biochem.duke.edu\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_209\n&#34;}], &#34;biobb_chemistry/test/unitests/test_babel/test_babel_add_hydrogens.py::TestBabelAddHydrogens::test_add_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_babel/test_babel_add_hydrogens.py::TestBabelAddHydrogens::test_add_hydrogens&#34;, &#34;duration&#34;: &#34;246 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_babel/test_babel_add_hydrogens.py::TestBabelAddHydrogens::test_add_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;246 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-03 19:02:58,559 [MainThread  ] [INFO ]  Executing biobb_chemistry.babelm.babel_add_hydrogens Version: 4.2.0\n2024-07-03 19:02:58,560 [MainThread  ] [INFO ]  /tmp/biobb/unitests_209/babel_add_hydrogens/sandbox_93dba836-2419-41a5-8463-786cf45d6a4d directory successfully created\n2024-07-03 19:02:58,560 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babelm/babel.no.H.pdb to /tmp/biobb/unitests_209/babel_add_hydrogens/sandbox_93dba836-2419-41a5-8463-786cf45d6a4d\n2024-07-03 19:02:58,560 [MainThread  ] [INFO ]  obabel -ipdb /tmp/biobb/unitests_209/babel_add_hydrogens/sandbox_93dba836-2419-41a5-8463-786cf45d6a4d/babel.no.H.pdb -opdb -O/tmp/biobb/unitests_209/babel_add_hydrogens/sandbox_93dba836-2419-41a5-8463-786cf45d6a4d/output.pdb --gen3d -p 7.4\n\n2024-07-03 19:02:58,732 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-03 19:02:58,733 [MainThread  ] [INFO ]  1 molecule converted\n\n2024-07-03 19:02:58,733 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_209/babel_add_hydrogens/sandbox_93dba836-2419-41a5-8463-786cf45d6a4d&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_209/babel_add_hydrogens/output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_209/babel_add_hydrogens/babel_add_hydrogens_log.out:file_utils.py:391 Executing biobb_chemistry.babelm.babel_add_hydrogens Version: 4.2.0\nINFO     /tmp/biobb/unitests_209/babel_add_hydrogens/babel_add_hydrogens_log.out:file_utils.py:82 /tmp/biobb/unitests_209/babel_add_hydrogens/sandbox_93dba836-2419-41a5-8463-786cf45d6a4d directory successfully created\nINFO     /tmp/biobb/unitests_209/babel_add_hydrogens/babel_add_hydrogens_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babelm/babel.no.H.pdb to /tmp/biobb/unitests_209/babel_add_hydrogens/sandbox_93dba836-2419-41a5-8463-786cf45d6a4d\nINFO     /tmp/biobb/unitests_209/babel_add_hydrogens/babel_add_hydrogens_log.out:cmd_wrapper.py:33 obabel -ipdb /tmp/biobb/unitests_209/babel_add_hydrogens/sandbox_93dba836-2419-41a5-8463-786cf45d6a4d/babel.no.H.pdb -opdb -O/tmp/biobb/unitests_209/babel_add_hydrogens/sandbox_93dba836-2419-41a5-8463-786cf45d6a4d/output.pdb --gen3d -p 7.4\n\nINFO     /tmp/biobb/unitests_209/babel_add_hydrogens/babel_add_hydrogens_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_209/babel_add_hydrogens/babel_add_hydrogens_log.err:cmd_wrapper.py:60 1 molecule converted\n\nINFO     /tmp/biobb/unitests_209/babel_add_hydrogens/babel_add_hydrogens_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_209/babel_add_hydrogens/sandbox_93dba836-2419-41a5-8463-786cf45d6a4d&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_209\n&#34;}], &#34;biobb_chemistry/test/unitests/test_babel/test_babel_convert.py::TestBabelConvert::test_convert&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_babel/test_babel_convert.py::TestBabelConvert::test_convert&#34;, &#34;duration&#34;: &#34;102 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_babel/test_babel_convert.py::TestBabelConvert::test_convert&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;102 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-03 19:02:58,807 [MainThread  ] [INFO ]  Executing biobb_chemistry.babelm.babel_convert Version: 4.2.0\n2024-07-03 19:02:58,807 [MainThread  ] [INFO ]  /tmp/biobb/unitests_209/babel_convert/sandbox_f6916244-a3f6-4ab8-9047-d36cb265cc9f directory successfully created\n2024-07-03 19:02:58,808 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babelm/babel.smi to /tmp/biobb/unitests_209/babel_convert/sandbox_f6916244-a3f6-4ab8-9047-d36cb265cc9f\n2024-07-03 19:02:58,808 [MainThread  ] [INFO ]  obabel -ismi /tmp/biobb/unitests_209/babel_convert/sandbox_f6916244-a3f6-4ab8-9047-d36cb265cc9f/babel.smi -omol2 -O/tmp/biobb/unitests_209/babel_convert/sandbox_f6916244-a3f6-4ab8-9047-d36cb265cc9f/output.mol2 --gen2d -p 7.4 -r\n\n2024-07-03 19:02:58,837 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-03 19:02:58,837 [MainThread  ] [INFO ]  1 molecule converted\n\n2024-07-03 19:02:58,838 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_209/babel_convert/sandbox_f6916244-a3f6-4ab8-9047-d36cb265cc9f&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_209/babel_convert/output.mol2\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_209/babel_convert/babel_convert_log.out:file_utils.py:391 Executing biobb_chemistry.babelm.babel_convert Version: 4.2.0\nINFO     /tmp/biobb/unitests_209/babel_convert/babel_convert_log.out:file_utils.py:82 /tmp/biobb/unitests_209/babel_convert/sandbox_f6916244-a3f6-4ab8-9047-d36cb265cc9f directory successfully created\nINFO     /tmp/biobb/unitests_209/babel_convert/babel_convert_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babelm/babel.smi to /tmp/biobb/unitests_209/babel_convert/sandbox_f6916244-a3f6-4ab8-9047-d36cb265cc9f\nINFO     /tmp/biobb/unitests_209/babel_convert/babel_convert_log.out:cmd_wrapper.py:33 obabel -ismi /tmp/biobb/unitests_209/babel_convert/sandbox_f6916244-a3f6-4ab8-9047-d36cb265cc9f/babel.smi -omol2 -O/tmp/biobb/unitests_209/babel_convert/sandbox_f6916244-a3f6-4ab8-9047-d36cb265cc9f/output.mol2 --gen2d -p 7.4 -r\n\nINFO     /tmp/biobb/unitests_209/babel_convert/babel_convert_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_209/babel_convert/babel_convert_log.err:cmd_wrapper.py:60 1 molecule converted\n\nINFO     /tmp/biobb/unitests_209/babel_convert/babel_convert_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_209/babel_convert/sandbox_f6916244-a3f6-4ab8-9047-d36cb265cc9f&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_209\n&#34;}], &#34;biobb_chemistry/test/unitests/test_babel/test_babel_minimize.py::TestBabelMinimize::test_minimize&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_babel/test_babel_minimize.py::TestBabelMinimize::test_minimize&#34;, &#34;duration&#34;: &#34;161 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_babel/test_babel_minimize.py::TestBabelMinimize::test_minimize&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;161 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-03 19:02:58,913 [MainThread  ] [INFO ]  Executing biobb_chemistry.babelm.babel_minimize Version: 4.2.0\n2024-07-03 19:02:58,913 [MainThread  ] [INFO ]  /tmp/biobb/unitests_209/babel_minimize/sandbox_340752a8-023f-491f-8ea7-636c9324e33f directory successfully created\n2024-07-03 19:02:58,913 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babelm/babel.minimize.pdb to /tmp/biobb/unitests_209/babel_minimize/sandbox_340752a8-023f-491f-8ea7-636c9324e33f\n2024-07-03 19:02:58,914 [MainThread  ] [INFO ]  obminimize -c 1e-6 -cg -ff GAFF -h -n 2500 -cut -rvdw 6.0 -rele 10.0 -pf 10 -ipdb /tmp/biobb/unitests_209/babel_minimize/sandbox_340752a8-023f-491f-8ea7-636c9324e33f/babel.minimize.pdb -opdb &amp;gt; /tmp/biobb/unitests_209/babel_minimize/sandbox_340752a8-023f-491f-8ea7-636c9324e33f/output.pdb\n\n2024-07-03 19:02:58,998 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-03 19:02:58,998 [MainThread  ] [INFO ]  \nA T O M   T Y P E S\n\nIDX\tTYPE\tRING\n1\tc3\tNO\n2\toh\tNO\n3\tc3\tNO\n4\tc3\tNO\n5\tc3\tNO\n6\tna\tAR\n7\tcc\tAR\n8\tnb\tAR\n9\tca\tAR\n10\tnh\tNO\n11\tca\tAR\n12\tca\tAR\n13\tca\tAR\n14\tca\tAR\n15\tca\tAR\n16\tca\tAR\n17\tn\tAR\n18\thn\tNO\n19\tc\tAR\n20\to\tNO\n21\tcd\tAR\n22\tnb\tAR\n23\tcc\tAR\n24\th1\tNO\n25\th1\tNO\n26\tho\tNO\n27\thc\tNO\n28\thc\tNO\n29\thc\tNO\n30\thc\tNO\n31\th1\tNO\n32\th1\tNO\n33\thn\tNO\n34\tha\tNO\n35\tha\tNO\n36\tha\tNO\n37\tha\tNO\n38\tha\tNO\n39\th5\tNO\n\nC H A R G E S\n\nIDX\tCHARGE\n1\t0.044262\n2\t-0.395006\n3\t-0.028107\n4\t-0.032802\n5\t0.026134\n6\t-0.314804\n7\t0.169132\n8\t-0.195940\n9\t0.201912\n10\t-0.285012\n11\t0.033522\n12\t-0.040471\n13\t-0.060007\n14\t-0.061645\n15\t-0.060007\n16\t-0.040471\n17\t-0.293020\n18\t0.171657\n19\t0.280327\n20\t-0.265372\n21\t0.171984\n22\t-0.228637\n23\t0.098390\n24\t0.055697\n25\t0.055697\n26\t0.209395\n27\t0.028779\n28\t0.028779\n29\t0.028309\n30\t0.028309\n31\t0.049254\n32\t0.049254\n33\t0.154976\n34\t0.063605\n35\t0.061815\n36\t0.061760\n37\t0.061815\n38\t0.063605\n39\t0.102930\n\nS E T T I N G   U P   C A L C U L A T I O N S\n\nSETTING UP BOND CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR BOND cc-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR BOND nb-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR BOND nb-cd, USING DEFAULT PARAMETERS\nSETTING UP ANGLE CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR ANGLE na-cc-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-cc-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cc-nb-ca, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-ca-n, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cc-cd-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE c-cd-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cd-nb-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-cc-h5, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE na-cc-nb, USING DEFAULT PARAMETERS\nSETTING UP TORSION CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR TORSION h5-cc-nb-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION na-cc-nb-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION ca-nb-cc-na, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION ca-nb-cc-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-c, USING DEFAULT PARAMETERS\nSETTING UP IMPROPER TORSION CALCULATIONS...\nSETTING UP VAN DER WAALS CALCULATIONS...\nSETTING UP ELECTROSTATIC CALCULATIONS...\n\nC O N J U G A T E   G R A D I E N T S\n\nSTEPS = 2500\n\nSTEP n     E(n)       E(n-1)    \n--------------------------------\n    1     190.026     471.088\n   10      89.911      91.650\n   20      76.628      77.475\n   30      73.331      73.681\n   40      72.126      72.251\n   50      71.119      71.211\n   60      70.489      70.522\n   70      70.050      70.054\n   80      69.701      69.706\n   90      69.456      69.463\n  100      69.246      69.283\n  110      69.025      69.030\n  120      68.820      68.861\n  130      68.699      68.726\n  140      68.566      68.592\n  150      68.456      68.460\n  153      68.419      68.419\n    CONJUGATE GRADIENTS HAS CONVERGED\nTime: 0.04812seconds. Iterations per second: 3200.33\n\n2024-07-03 19:02:58,999 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_209/babel_minimize/sandbox_340752a8-023f-491f-8ea7-636c9324e33f&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_209/babel_minimize/output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_209/babel_minimize/output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/babelm/ref_babel.minimize.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 3\n     Atoms ALIGNED in PDB_B: 3\n     RMS: 0.0021526397693638504\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_209/babel_minimize/babel_minimize_log.out:file_utils.py:391 Executing biobb_chemistry.babelm.babel_minimize Version: 4.2.0\nINFO     /tmp/biobb/unitests_209/babel_minimize/babel_minimize_log.out:file_utils.py:82 /tmp/biobb/unitests_209/babel_minimize/sandbox_340752a8-023f-491f-8ea7-636c9324e33f directory successfully created\nINFO     /tmp/biobb/unitests_209/babel_minimize/babel_minimize_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babelm/babel.minimize.pdb to /tmp/biobb/unitests_209/babel_minimize/sandbox_340752a8-023f-491f-8ea7-636c9324e33f\nINFO     /tmp/biobb/unitests_209/babel_minimize/babel_minimize_log.out:cmd_wrapper.py:33 obminimize -c 1e-6 -cg -ff GAFF -h -n 2500 -cut -rvdw 6.0 -rele 10.0 -pf 10 -ipdb /tmp/biobb/unitests_209/babel_minimize/sandbox_340752a8-023f-491f-8ea7-636c9324e33f/babel.minimize.pdb -opdb &amp;gt; /tmp/biobb/unitests_209/babel_minimize/sandbox_340752a8-023f-491f-8ea7-636c9324e33f/output.pdb\n\nINFO     /tmp/biobb/unitests_209/babel_minimize/babel_minimize_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_209/babel_minimize/babel_minimize_log.err:cmd_wrapper.py:60 \nA T O M   T Y P E S\n\nIDX\tTYPE\tRING\n1\tc3\tNO\n2\toh\tNO\n3\tc3\tNO\n4\tc3\tNO\n5\tc3\tNO\n6\tna\tAR\n7\tcc\tAR\n8\tnb\tAR\n9\tca\tAR\n10\tnh\tNO\n11\tca\tAR\n12\tca\tAR\n13\tca\tAR\n14\tca\tAR\n15\tca\tAR\n16\tca\tAR\n17\tn\tAR\n18\thn\tNO\n19\tc\tAR\n20\to\tNO\n21\tcd\tAR\n22\tnb\tAR\n23\tcc\tAR\n24\th1\tNO\n25\th1\tNO\n26\tho\tNO\n27\thc\tNO\n28\thc\tNO\n29\thc\tNO\n30\thc\tNO\n31\th1\tNO\n32\th1\tNO\n33\thn\tNO\n34\tha\tNO\n35\tha\tNO\n36\tha\tNO\n37\tha\tNO\n38\tha\tNO\n39\th5\tNO\n\nC H A R G E S\n\nIDX\tCHARGE\n1\t0.044262\n2\t-0.395006\n3\t-0.028107\n4\t-0.032802\n5\t0.026134\n6\t-0.314804\n7\t0.169132\n8\t-0.195940\n9\t0.201912\n10\t-0.285012\n11\t0.033522\n12\t-0.040471\n13\t-0.060007\n14\t-0.061645\n15\t-0.060007\n16\t-0.040471\n17\t-0.293020\n18\t0.171657\n19\t0.280327\n20\t-0.265372\n21\t0.171984\n22\t-0.228637\n23\t0.098390\n24\t0.055697\n25\t0.055697\n26\t0.209395\n27\t0.028779\n28\t0.028779\n29\t0.028309\n30\t0.028309\n31\t0.049254\n32\t0.049254\n33\t0.154976\n34\t0.063605\n35\t0.061815\n36\t0.061760\n37\t0.061815\n38\t0.063605\n39\t0.102930\n\nS E T T I N G   U P   C A L C U L A T I O N S\n\nSETTING UP BOND CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR BOND cc-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR BOND nb-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR BOND nb-cd, USING DEFAULT PARAMETERS\nSETTING UP ANGLE CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR ANGLE na-cc-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-cc-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cc-nb-ca, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-ca-n, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cc-cd-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE c-cd-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cd-nb-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-cc-h5, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE na-cc-nb, USING DEFAULT PARAMETERS\nSETTING UP TORSION CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR TORSION h5-cc-nb-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION na-cc-nb-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION ca-nb-cc-na, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION ca-nb-cc-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-c, USING DEFAULT PARAMETERS\nSETTING UP IMPROPER TORSION CALCULATIONS...\nSETTING UP VAN DER WAALS CALCULATIONS...\nSETTING UP ELECTROSTATIC CALCULATIONS...\n\nC O N J U G A T E   G R A D I E N T S\n\nSTEPS = 2500\n\nSTEP n     E(n)       E(n-1)    \n--------------------------------\n    1     190.026     471.088\n   10      89.911      91.650\n   20      76.628      77.475\n   30      73.331      73.681\n   40      72.126      72.251\n   50      71.119      71.211\n   60      70.489      70.522\n   70      70.050      70.054\n   80      69.701      69.706\n   90      69.456      69.463\n  100      69.246      69.283\n  110      69.025      69.030\n  120      68.820      68.861\n  130      68.699      68.726\n  140      68.566      68.592\n  150      68.456      68.460\n  153      68.419      68.419\n    CONJUGATE GRADIENTS HAS CONVERGED\nTime: 0.04812seconds. Iterations per second: 3200.33\n\nINFO     /tmp/biobb/unitests_209/babel_minimize/babel_minimize_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_209/babel_minimize/sandbox_340752a8-023f-491f-8ea7-636c9324e33f&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_209\n&#34;}], &#34;biobb_chemistry/test/unitests/test_babel/test_babel_remove_hydrogens.py::TestBabelRemoveHydrogens::test_remove_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_babel/test_babel_remove_hydrogens.py::TestBabelRemoveHydrogens::test_remove_hydrogens&#34;, &#34;duration&#34;: &#34;241 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_babel/test_babel_remove_hydrogens.py::TestBabelRemoveHydrogens::test_remove_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;241 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-03 19:02:59,076 [MainThread  ] [INFO ]  Executing biobb_chemistry.babelm.babel_remove_hydrogens Version: 4.2.0\n2024-07-03 19:02:59,077 [MainThread  ] [INFO ]  /tmp/biobb/unitests_209/babel_remove_hydrogens/sandbox_2b392935-1528-4bd8-a225-e28269107f69 directory successfully created\n2024-07-03 19:02:59,077 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babelm/babel.H.pdb to /tmp/biobb/unitests_209/babel_remove_hydrogens/sandbox_2b392935-1528-4bd8-a225-e28269107f69\n2024-07-03 19:02:59,077 [MainThread  ] [INFO ]  obabel -ipdb /tmp/biobb/unitests_209/babel_remove_hydrogens/sandbox_2b392935-1528-4bd8-a225-e28269107f69/babel.H.pdb -opdb -O/tmp/biobb/unitests_209/babel_remove_hydrogens/sandbox_2b392935-1528-4bd8-a225-e28269107f69/output.pdb --gen3d -d -p 7.4\n\n2024-07-03 19:02:59,244 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-03 19:02:59,245 [MainThread  ] [INFO ]  1 molecule converted\n\n2024-07-03 19:02:59,245 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_209/babel_remove_hydrogens/sandbox_2b392935-1528-4bd8-a225-e28269107f69&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_209/babel_remove_hydrogens/output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_209/babel_remove_hydrogens/babel_remove_hydrogens_log.out:file_utils.py:391 Executing biobb_chemistry.babelm.babel_remove_hydrogens Version: 4.2.0\nINFO     /tmp/biobb/unitests_209/babel_remove_hydrogens/babel_remove_hydrogens_log.out:file_utils.py:82 /tmp/biobb/unitests_209/babel_remove_hydrogens/sandbox_2b392935-1528-4bd8-a225-e28269107f69 directory successfully created\nINFO     /tmp/biobb/unitests_209/babel_remove_hydrogens/babel_remove_hydrogens_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babelm/babel.H.pdb to /tmp/biobb/unitests_209/babel_remove_hydrogens/sandbox_2b392935-1528-4bd8-a225-e28269107f69\nINFO     /tmp/biobb/unitests_209/babel_remove_hydrogens/babel_remove_hydrogens_log.out:cmd_wrapper.py:33 obabel -ipdb /tmp/biobb/unitests_209/babel_remove_hydrogens/sandbox_2b392935-1528-4bd8-a225-e28269107f69/babel.H.pdb -opdb -O/tmp/biobb/unitests_209/babel_remove_hydrogens/sandbox_2b392935-1528-4bd8-a225-e28269107f69/output.pdb --gen3d -d -p 7.4\n\nINFO     /tmp/biobb/unitests_209/babel_remove_hydrogens/babel_remove_hydrogens_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_209/babel_remove_hydrogens/babel_remove_hydrogens_log.err:cmd_wrapper.py:60 1 molecule converted\n\nINFO     /tmp/biobb/unitests_209/babel_remove_hydrogens/babel_remove_hydrogens_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_209/babel_remove_hydrogens/sandbox_2b392935-1528-4bd8-a225-e28269107f69&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_209\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
+    <div id="data-container" data-jsonblob="{&#34;environment&#34;: {&#34;Python&#34;: &#34;3.10.14&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-159-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.2.2&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;html&#34;: &#34;4.1.1&#34;, &#34;cov&#34;: &#34;5.0.0&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_ac.py::TestAcpypeParamsAC::test_params_ac&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_ac.py::TestAcpypeParamsAC::test_params_ac&#34;, &#34;duration&#34;: &#34;00:02:05&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_ac.py::TestAcpypeParamsAC::test_params_ac&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:02:05&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-16 13:27:06,210 [MainThread  ] [INFO ]  Executing biobb_chemistry.acpype.acpype_params_ac Version: 4.2.0\n2024-07-16 13:27:06,210 [MainThread  ] [INFO ]  /tmp/biobb/unitests_212/acpype_params_ac/sandbox_e60cbf13-04d7-4d45-b639-6443860b819c directory successfully created\n2024-07-16 13:27:06,210 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_212/acpype_params_ac/sandbox_e60cbf13-04d7-4d45-b639-6443860b819c\n2024-07-16 13:27:06,211 [MainThread  ] [INFO ]  acpype -i /tmp/biobb/unitests_212/acpype_params_ac/sandbox_e60cbf13-04d7-4d45-b639-6443860b819c/acpype.params.pdb -b BBB.wuGgTG -n 0\n\n2024-07-16 13:29:10,855 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-16 13:29:10,855 [MainThread  ] [INFO ]  ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.wuGgTG.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 2m 5s\n\n2024-07-16 13:29:10,857 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_212/acpype_params_ac/output.frcmod succesfully created\n2024-07-16 13:29:10,858 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_212/acpype_params_ac/output.lib succesfully created\n2024-07-16 13:29:10,858 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_212/acpype_params_ac/output.inpcrd succesfully created\n2024-07-16 13:29:10,859 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_212/acpype_params_ac/output.prmtop succesfully created\n2024-07-16 13:29:10,860 [MainThread  ] [INFO ]  Removed temporary folder: BBB.wuGgTG.acpype\nChecking if empty file: /tmp/biobb/unitests_212/acpype_params_ac/output.frcmod\nChecking if empty file: /tmp/biobb/unitests_212/acpype_params_ac/output.inpcrd\nChecking if empty file: /tmp/biobb/unitests_212/acpype_params_ac/output.lib\nChecking if empty file: /tmp/biobb/unitests_212/acpype_params_ac/output.prmtop\nComparing: \n        File_A: /tmp/biobb/unitests_212/acpype_params_ac/output.frcmod\n        File_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.ac.frcmod\n        File_A hash: b&amp;#x27;\\xed\\x1db\\xfb\\x1c,\\xe4\\x03\\x02\\xf9\\xcb\\x08)\\xe2\\xe3c\\\\T\\x9a\\xe4G\\x87\\xf7#\\xe7\\xe1\\xf0a\\xb3p\\x12\\xa8&amp;#x27;\n        File_B hash: b&amp;#x27;\\xed\\x1db\\xfb\\x1c,\\xe4\\x03\\x02\\xf9\\xcb\\x08)\\xe2\\xe3c\\\\T\\x9a\\xe4G\\x87\\xf7#\\xe7\\xe1\\xf0a\\xb3p\\x12\\xa8&amp;#x27;\nComparing: \n        File_A: /tmp/biobb/unitests_212/acpype_params_ac/output.inpcrd\n        File_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.ac.inpcrd\n        File_A hash: b&amp;#x27;\\r\\xeb\\x17\\x04\\xb4\\xb1\\xe8\\xd6\\xef\\x0c[\\xc19[\\x16kXm\\xeceQ\\xba,,\\x12$\\x03\\xa0\\xb5=\\xd2\\xa3&amp;#x27;\n        File_B hash: b&amp;#x27;\\r\\xeb\\x17\\x04\\xb4\\xb1\\xe8\\xd6\\xef\\x0c[\\xc19[\\x16kXm\\xeceQ\\xba,,\\x12$\\x03\\xa0\\xb5=\\xd2\\xa3&amp;#x27;\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_212/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:391 Executing biobb_chemistry.acpype.acpype_params_ac Version: 4.2.0\nINFO     /tmp/biobb/unitests_212/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:82 /tmp/biobb/unitests_212/acpype_params_ac/sandbox_e60cbf13-04d7-4d45-b639-6443860b819c directory successfully created\nINFO     /tmp/biobb/unitests_212/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_212/acpype_params_ac/sandbox_e60cbf13-04d7-4d45-b639-6443860b819c\nINFO     /tmp/biobb/unitests_212/acpype_params_ac/acpype_params_ac_log.out:cmd_wrapper.py:33 acpype -i /tmp/biobb/unitests_212/acpype_params_ac/sandbox_e60cbf13-04d7-4d45-b639-6443860b819c/acpype.params.pdb -b BBB.wuGgTG -n 0\n\nINFO     /tmp/biobb/unitests_212/acpype_params_ac/acpype_params_ac_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_212/acpype_params_ac/acpype_params_ac_log.out:cmd_wrapper.py:52 ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.wuGgTG.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 2m 5s\n\nINFO     /tmp/biobb/unitests_212/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:391 File /tmp/biobb/unitests_212/acpype_params_ac/output.frcmod succesfully created\nINFO     /tmp/biobb/unitests_212/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:391 File /tmp/biobb/unitests_212/acpype_params_ac/output.lib succesfully created\nINFO     /tmp/biobb/unitests_212/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:391 File /tmp/biobb/unitests_212/acpype_params_ac/output.inpcrd succesfully created\nINFO     /tmp/biobb/unitests_212/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:391 File /tmp/biobb/unitests_212/acpype_params_ac/output.prmtop succesfully created\nINFO     /tmp/biobb/unitests_212/acpype_params_ac/acpype_params_ac_log.out:file_utils.py:391 Removed temporary folder: BBB.wuGgTG.acpype\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_212\n&#34;}], &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_cns.py::TestAcpypeParamsCNS::test_params_cns&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_cns.py::TestAcpypeParamsCNS::test_params_cns&#34;, &#34;duration&#34;: &#34;00:01:10&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_cns.py::TestAcpypeParamsCNS::test_params_cns&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:10&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-16 13:29:10,979 [MainThread  ] [INFO ]  Executing biobb_chemistry.acpype.acpype_params_cns Version: 4.2.0\n2024-07-16 13:29:10,979 [MainThread  ] [INFO ]  /tmp/biobb/unitests_212/acpype_params_cns/sandbox_fcb217e8-cd03-42b7-9648-31567e55ddb8 directory successfully created\n2024-07-16 13:29:10,979 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_212/acpype_params_cns/sandbox_fcb217e8-cd03-42b7-9648-31567e55ddb8\n2024-07-16 13:29:10,980 [MainThread  ] [INFO ]  acpype -i /tmp/biobb/unitests_212/acpype_params_cns/sandbox_fcb217e8-cd03-42b7-9648-31567e55ddb8/acpype.params.pdb -b BBB.GBx57t -n 0\n\n2024-07-16 13:30:20,422 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-16 13:30:20,423 [MainThread  ] [INFO ]  ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.GBx57t.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 9s\n\n2024-07-16 13:30:20,424 [MainThread  ] [INFO ]  Files: BBB.GBx57t.acpype/BBB.GBx57t_CNS.inp\n2024-07-16 13:30:20,424 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_212/acpype_params_cns/output.inp succesfully created\n2024-07-16 13:30:20,425 [MainThread  ] [INFO ]  Files: BBB.GBx57t.acpype/BBB.GBx57t_CNS.par\n2024-07-16 13:30:20,425 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_212/acpype_params_cns/output.par succesfully created\n2024-07-16 13:30:20,426 [MainThread  ] [INFO ]  Files: BBB.GBx57t.acpype/BBB.GBx57t_CNS.top\n2024-07-16 13:30:20,427 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_212/acpype_params_cns/output.top succesfully created\n2024-07-16 13:30:20,427 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_212/acpype_params_cns/output.pdb succesfully created\n2024-07-16 13:30:20,444 [MainThread  ] [INFO ]  Removed temporary folder: BBB.GBx57t.acpype\nChecking if empty file: /tmp/biobb/unitests_212/acpype_params_cns/output.par\nChecking if empty file: /tmp/biobb/unitests_212/acpype_params_cns/output.inp\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_212/acpype_params_cns/output.inp\n     FILE_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.cns.inp\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_212/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 Executing biobb_chemistry.acpype.acpype_params_cns Version: 4.2.0\nINFO     /tmp/biobb/unitests_212/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:82 /tmp/biobb/unitests_212/acpype_params_cns/sandbox_fcb217e8-cd03-42b7-9648-31567e55ddb8 directory successfully created\nINFO     /tmp/biobb/unitests_212/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_212/acpype_params_cns/sandbox_fcb217e8-cd03-42b7-9648-31567e55ddb8\nINFO     /tmp/biobb/unitests_212/acpype_params_cns/acpype_params_cns_log.out:cmd_wrapper.py:33 acpype -i /tmp/biobb/unitests_212/acpype_params_cns/sandbox_fcb217e8-cd03-42b7-9648-31567e55ddb8/acpype.params.pdb -b BBB.GBx57t -n 0\n\nINFO     /tmp/biobb/unitests_212/acpype_params_cns/acpype_params_cns_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_212/acpype_params_cns/acpype_params_cns_log.out:cmd_wrapper.py:52 ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.GBx57t.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 9s\n\nINFO     /tmp/biobb/unitests_212/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 Files: BBB.GBx57t.acpype/BBB.GBx57t_CNS.inp\nINFO     /tmp/biobb/unitests_212/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 File /tmp/biobb/unitests_212/acpype_params_cns/output.inp succesfully created\nINFO     /tmp/biobb/unitests_212/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 Files: BBB.GBx57t.acpype/BBB.GBx57t_CNS.par\nINFO     /tmp/biobb/unitests_212/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 File /tmp/biobb/unitests_212/acpype_params_cns/output.par succesfully created\nINFO     /tmp/biobb/unitests_212/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 Files: BBB.GBx57t.acpype/BBB.GBx57t_CNS.top\nINFO     /tmp/biobb/unitests_212/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 File /tmp/biobb/unitests_212/acpype_params_cns/output.top succesfully created\nINFO     /tmp/biobb/unitests_212/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 File /tmp/biobb/unitests_212/acpype_params_cns/output.pdb succesfully created\nINFO     /tmp/biobb/unitests_212/acpype_params_cns/acpype_params_cns_log.out:file_utils.py:391 Removed temporary folder: BBB.GBx57t.acpype\n\n&#34;}], &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx.py::TestAcpypeParamsGMX::test_params_gmx&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx.py::TestAcpypeParamsGMX::test_params_gmx&#34;, &#34;duration&#34;: &#34;00:01:11&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx.py::TestAcpypeParamsGMX::test_params_gmx&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:11&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-16 13:30:20,541 [MainThread  ] [INFO ]  Executing biobb_chemistry.acpype.acpype_params_gmx Version: 4.2.0\n2024-07-16 13:30:20,542 [MainThread  ] [INFO ]  /tmp/biobb/unitests_213/acpype_params_gmx/sandbox_d87eb9ab-2dcb-48d7-b806-27c76ce3d214 directory successfully created\n2024-07-16 13:30:20,542 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_213/acpype_params_gmx/sandbox_d87eb9ab-2dcb-48d7-b806-27c76ce3d214\n2024-07-16 13:30:20,542 [MainThread  ] [INFO ]  acpype -i /tmp/biobb/unitests_213/acpype_params_gmx/sandbox_d87eb9ab-2dcb-48d7-b806-27c76ce3d214/acpype.params.pdb -b BBB.0GJLWJ -n 0\n\n2024-07-16 13:31:31,286 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-16 13:31:31,286 [MainThread  ] [INFO ]  ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.0GJLWJ.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 11s\n\n2024-07-16 13:31:31,288 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_213/acpype_params_gmx/ref_acpype.gmx.gro succesfully created\n2024-07-16 13:31:31,289 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_213/acpype_params_gmx/ref_acpype.gmx.itp succesfully created\n2024-07-16 13:31:31,289 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_213/acpype_params_gmx/ref_acpype.gmx.top succesfully created\nChecking if empty file: /tmp/biobb/unitests_213/acpype_params_gmx/ref_acpype.gmx.gro\nChecking if empty file: /tmp/biobb/unitests_213/acpype_params_gmx/ref_acpype.gmx.itp\nChecking if empty file: /tmp/biobb/unitests_213/acpype_params_gmx/ref_acpype.gmx.top\nComparing ignoring first line of both files:\n     FILE_A: /tmp/biobb/unitests_213/acpype_params_gmx/ref_acpype.gmx.gro\n     FILE_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.gro\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_213/acpype_params_gmx/ref_acpype.gmx.top\n     FILE_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.top\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_213/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:391 Executing biobb_chemistry.acpype.acpype_params_gmx Version: 4.2.0\nINFO     /tmp/biobb/unitests_213/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:82 /tmp/biobb/unitests_213/acpype_params_gmx/sandbox_d87eb9ab-2dcb-48d7-b806-27c76ce3d214 directory successfully created\nINFO     /tmp/biobb/unitests_213/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_213/acpype_params_gmx/sandbox_d87eb9ab-2dcb-48d7-b806-27c76ce3d214\nINFO     /tmp/biobb/unitests_213/acpype_params_gmx/acpype_params_gmx_log.out:cmd_wrapper.py:33 acpype -i /tmp/biobb/unitests_213/acpype_params_gmx/sandbox_d87eb9ab-2dcb-48d7-b806-27c76ce3d214/acpype.params.pdb -b BBB.0GJLWJ -n 0\n\nINFO     /tmp/biobb/unitests_213/acpype_params_gmx/acpype_params_gmx_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_213/acpype_params_gmx/acpype_params_gmx_log.out:cmd_wrapper.py:52 ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.0GJLWJ.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 11s\n\nINFO     /tmp/biobb/unitests_213/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:391 File /tmp/biobb/unitests_213/acpype_params_gmx/ref_acpype.gmx.gro succesfully created\nINFO     /tmp/biobb/unitests_213/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:391 File /tmp/biobb/unitests_213/acpype_params_gmx/ref_acpype.gmx.itp succesfully created\nINFO     /tmp/biobb/unitests_213/acpype_params_gmx/acpype_params_gmx_log.out:file_utils.py:391 File /tmp/biobb/unitests_213/acpype_params_gmx/ref_acpype.gmx.top succesfully created\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_213\n&#34;}], &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx_opls.py::TestAcpypeParamsGMXOPLS::test_params_gmx_opls&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx_opls.py::TestAcpypeParamsGMXOPLS::test_params_gmx_opls&#34;, &#34;duration&#34;: &#34;00:01:11&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_acpype/test_acpype_params_gmx_opls.py::TestAcpypeParamsGMXOPLS::test_params_gmx_opls&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:01:11&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-16 13:31:31,372 [MainThread  ] [INFO ]  Executing biobb_chemistry.acpype.acpype_params_gmx_opls Version: 4.2.0\n2024-07-16 13:31:31,372 [MainThread  ] [INFO ]  /tmp/biobb/unitests_213/acpype_params_gmx_opls/sandbox_fdbd6143-4965-4d20-9048-a90c92a3d198 directory successfully created\n2024-07-16 13:31:31,373 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_213/acpype_params_gmx_opls/sandbox_fdbd6143-4965-4d20-9048-a90c92a3d198\n2024-07-16 13:31:31,373 [MainThread  ] [INFO ]  acpype -i /tmp/biobb/unitests_213/acpype_params_gmx_opls/sandbox_fdbd6143-4965-4d20-9048-a90c92a3d198/acpype.params.pdb -b BBB.7TAmOi -n 0\n\n2024-07-16 13:32:42,768 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-16 13:32:42,768 [MainThread  ] [INFO ]  ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.7TAmOi.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 11s\n\n2024-07-16 13:32:42,769 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_213/acpype_params_gmx_opls/ref_acpype.gmx.opls.top succesfully created\n2024-07-16 13:32:42,771 [MainThread  ] [INFO ]  File /tmp/biobb/unitests_213/acpype_params_gmx_opls/ref_acpype.gmx.opls.itp succesfully created\nChecking if empty file: /tmp/biobb/unitests_213/acpype_params_gmx_opls/ref_acpype.gmx.opls.itp\nChecking if empty file: /tmp/biobb/unitests_213/acpype_params_gmx_opls/ref_acpype.gmx.opls.top\nComparing TOP/ITP:\n     FILE_A: /tmp/biobb/unitests_213/acpype_params_gmx_opls/ref_acpype.gmx.opls.top\n     FILE_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/acpype/ref_acpype.gmx.opls.top\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_213/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:391 Executing biobb_chemistry.acpype.acpype_params_gmx_opls Version: 4.2.0\nINFO     /tmp/biobb/unitests_213/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:82 /tmp/biobb/unitests_213/acpype_params_gmx_opls/sandbox_fdbd6143-4965-4d20-9048-a90c92a3d198 directory successfully created\nINFO     /tmp/biobb/unitests_213/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/acpype/acpype.params.pdb to /tmp/biobb/unitests_213/acpype_params_gmx_opls/sandbox_fdbd6143-4965-4d20-9048-a90c92a3d198\nINFO     /tmp/biobb/unitests_213/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:cmd_wrapper.py:33 acpype -i /tmp/biobb/unitests_213/acpype_params_gmx_opls/sandbox_fdbd6143-4965-4d20-9048-a90c92a3d198/acpype.params.pdb -b BBB.7TAmOi -n 0\n\nINFO     /tmp/biobb/unitests_213/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_213/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:cmd_wrapper.py:52 ==========================================================================\n| ACPYPE: AnteChamber PYthon Parser interfacE v. 2022.6.6 (c) 2024 AWSdS |\n==========================================================================\n==&amp;gt; ... charge set to 0\n==&amp;gt; ... converting pdb input file to mol2 input file\n==&amp;gt; * Babel OK *\n==&amp;gt; Executing Antechamber...\n==&amp;gt; * Antechamber OK *\n==&amp;gt; * Parmchk OK *\n==&amp;gt; Executing Tleap...\n==&amp;gt; * Tleap OK *\n==&amp;gt; Removing temporary files...\n==&amp;gt; Using OpenBabel v.3.1.0\n\n==&amp;gt; Writing NEW PDB file\n\n==&amp;gt; Writing CNS/XPLOR files\n\n==&amp;gt; Writing GROMACS files\n\n==&amp;gt; Disambiguating lower and uppercase atomtypes in GMX top file, even if identical.\n\n==&amp;gt; Writing GMX dihedrals for GMX 4.5 and higher.\n\n==&amp;gt; Writing CHARMM files\n\n==&amp;gt; Writing pickle file BBB.7TAmOi.pkl\n==&amp;gt; Removing temporary files...\nTotal time of execution: 1m 11s\n\nINFO     /tmp/biobb/unitests_213/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:391 File /tmp/biobb/unitests_213/acpype_params_gmx_opls/ref_acpype.gmx.opls.top succesfully created\nINFO     /tmp/biobb/unitests_213/acpype_params_gmx_opls/acpype_params_gmx_opls_log.out:file_utils.py:391 File /tmp/biobb/unitests_213/acpype_params_gmx_opls/ref_acpype.gmx.opls.itp succesfully created\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_213\n&#34;}], &#34;biobb_chemistry/test/unitests/test_ambertools/test_reduce_add_hydrogens.py::TestReduceAddHydrogens::test_add_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_ambertools/test_reduce_add_hydrogens.py::TestReduceAddHydrogens::test_add_hydrogens&#34;, &#34;duration&#34;: &#34;478 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_ambertools/test_reduce_add_hydrogens.py::TestReduceAddHydrogens::test_add_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;478 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-16 13:32:42,854 [MainThread  ] [INFO ]  Executing biobb_chemistry.ambertools.reduce_add_hydrogens Version: 4.2.0\n2024-07-16 13:32:42,854 [MainThread  ] [INFO ]  /tmp/biobb/unitests_213/reduce_add_hydrogens/sandbox_c222078b-0e21-4f03-8f01-c2becaff0160 directory successfully created\n2024-07-16 13:32:42,855 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/ambertools/reduce.no.H.pdb to /tmp/biobb/unitests_213/reduce_add_hydrogens/sandbox_c222078b-0e21-4f03-8f01-c2becaff0160\n2024-07-16 13:32:42,855 [MainThread  ] [INFO ]  reduce -NOOH -OH -ROTNH3 -ALLALT /tmp/biobb/unitests_213/reduce_add_hydrogens/sandbox_c222078b-0e21-4f03-8f01-c2becaff0160/reduce.no.H.pdb &amp;gt; /tmp/biobb/unitests_213/reduce_add_hydrogens/sandbox_c222078b-0e21-4f03-8f01-c2becaff0160/output.pdb\n\n2024-07-16 13:32:43,260 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-16 13:32:43,261 [MainThread  ] [INFO ]  Processing file: &amp;quot;/tmp/biobb/unitests_213/reduce_add_hydrogens/sandbox_c222078b-0e21-4f03-8f01-c2becaff0160/reduce.no.H.pdb&amp;quot;\nBuilding or keeping OH &amp;amp; SH Hydrogens.\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nVDW dot density = 16/A^2\nProbe radius = 0.25A\nOrientation penalty scale = 1 (100%)\nEliminate contacts within 3 bonds.\nIgnore atoms with |occupancy| &amp;lt;= 0.01 during adjustments.\nWaters ignored if B-Factor &amp;gt;= 40 or |occupancy| &amp;lt; 0.66\nAromatic rings in amino acids accept hydrogen bonds.\nRotating NH3 Hydrogens.\nNot processing Met methyls.\nFound 0 hydrogens (0 hets)\nStandardized 0 hydrogens (0 hets)\nAdded 27 hydrogens (27 hets)\nIf you publish work which uses reduce, please cite:\nWord, et. al. (1999) J. Mol. Biol. 285, 1735-1747.\nFor more information see http://kinemage.biochem.duke.edu\n\n2024-07-16 13:32:43,261 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_213/reduce_add_hydrogens/sandbox_c222078b-0e21-4f03-8f01-c2becaff0160&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_213/reduce_add_hydrogens/output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_213/reduce_add_hydrogens/reduce_add_hydrogens_log.out:file_utils.py:391 Executing biobb_chemistry.ambertools.reduce_add_hydrogens Version: 4.2.0\nINFO     /tmp/biobb/unitests_213/reduce_add_hydrogens/reduce_add_hydrogens_log.out:file_utils.py:82 /tmp/biobb/unitests_213/reduce_add_hydrogens/sandbox_c222078b-0e21-4f03-8f01-c2becaff0160 directory successfully created\nINFO     /tmp/biobb/unitests_213/reduce_add_hydrogens/reduce_add_hydrogens_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/ambertools/reduce.no.H.pdb to /tmp/biobb/unitests_213/reduce_add_hydrogens/sandbox_c222078b-0e21-4f03-8f01-c2becaff0160\nINFO     /tmp/biobb/unitests_213/reduce_add_hydrogens/reduce_add_hydrogens_log.out:cmd_wrapper.py:33 reduce -NOOH -OH -ROTNH3 -ALLALT /tmp/biobb/unitests_213/reduce_add_hydrogens/sandbox_c222078b-0e21-4f03-8f01-c2becaff0160/reduce.no.H.pdb &amp;gt; /tmp/biobb/unitests_213/reduce_add_hydrogens/sandbox_c222078b-0e21-4f03-8f01-c2becaff0160/output.pdb\n\nINFO     /tmp/biobb/unitests_213/reduce_add_hydrogens/reduce_add_hydrogens_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_213/reduce_add_hydrogens/reduce_add_hydrogens_log.err:cmd_wrapper.py:60 Processing file: &amp;quot;/tmp/biobb/unitests_213/reduce_add_hydrogens/sandbox_c222078b-0e21-4f03-8f01-c2becaff0160/reduce.no.H.pdb&amp;quot;\nBuilding or keeping OH &amp;amp; SH Hydrogens.\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nVDW dot density = 16/A^2\nProbe radius = 0.25A\nOrientation penalty scale = 1 (100%)\nEliminate contacts within 3 bonds.\nIgnore atoms with |occupancy| &amp;lt;= 0.01 during adjustments.\nWaters ignored if B-Factor &amp;gt;= 40 or |occupancy| &amp;lt; 0.66\nAromatic rings in amino acids accept hydrogen bonds.\nRotating NH3 Hydrogens.\nNot processing Met methyls.\nFound 0 hydrogens (0 hets)\nStandardized 0 hydrogens (0 hets)\nAdded 27 hydrogens (27 hets)\nIf you publish work which uses reduce, please cite:\nWord, et. al. (1999) J. Mol. Biol. 285, 1735-1747.\nFor more information see http://kinemage.biochem.duke.edu\n\nINFO     /tmp/biobb/unitests_213/reduce_add_hydrogens/reduce_add_hydrogens_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_213/reduce_add_hydrogens/sandbox_c222078b-0e21-4f03-8f01-c2becaff0160&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_213\n&#34;}], &#34;biobb_chemistry/test/unitests/test_ambertools/test_reduce_remove_hydrogens.py::TestReduceRemoveHydrogens::test_remove_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_ambertools/test_reduce_remove_hydrogens.py::TestReduceRemoveHydrogens::test_remove_hydrogens&#34;, &#34;duration&#34;: &#34;81 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_ambertools/test_reduce_remove_hydrogens.py::TestReduceRemoveHydrogens::test_remove_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;81 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-16 13:32:43,334 [MainThread  ] [INFO ]  Executing biobb_chemistry.ambertools.reduce_remove_hydrogens Version: 4.2.0\n2024-07-16 13:32:43,334 [MainThread  ] [INFO ]  /tmp/biobb/unitests_213/reduce_remove_hydrogens/sandbox_52e80657-4603-4e9a-92bb-817008ee22cd directory successfully created\n2024-07-16 13:32:43,334 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/ambertools/reduce.H.pdb to /tmp/biobb/unitests_213/reduce_remove_hydrogens/sandbox_52e80657-4603-4e9a-92bb-817008ee22cd\n2024-07-16 13:32:43,335 [MainThread  ] [INFO ]  reduce -Trim /tmp/biobb/unitests_213/reduce_remove_hydrogens/sandbox_52e80657-4603-4e9a-92bb-817008ee22cd/reduce.H.pdb &amp;gt; /tmp/biobb/unitests_213/reduce_remove_hydrogens/sandbox_52e80657-4603-4e9a-92bb-817008ee22cd/output.pdb\n\n2024-07-16 13:32:43,344 [MainThread  ] [INFO ]  Exit code 255\n\n2024-07-16 13:32:43,344 [MainThread  ] [INFO ]  Processing file: &amp;quot;/tmp/biobb/unitests_213/reduce_remove_hydrogens/sandbox_52e80657-4603-4e9a-92bb-817008ee22cd/reduce.H.pdb&amp;quot;\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nTrimming: removed 27 hydrogens (27 hets)\nRemoved 27 hydrogens (27 hets)\nIf you publish work which uses reduce, please cite:\nWord, et. al. (1999) J. Mol. Biol. 285, 1735-1747.\nFor more information see http://kinemage.biochem.duke.edu\n\nChecking if empty file: /tmp/biobb/unitests_213/reduce_remove_hydrogens/output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_213/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:file_utils.py:391 Executing biobb_chemistry.ambertools.reduce_remove_hydrogens Version: 4.2.0\nINFO     /tmp/biobb/unitests_213/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:file_utils.py:82 /tmp/biobb/unitests_213/reduce_remove_hydrogens/sandbox_52e80657-4603-4e9a-92bb-817008ee22cd directory successfully created\nINFO     /tmp/biobb/unitests_213/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/ambertools/reduce.H.pdb to /tmp/biobb/unitests_213/reduce_remove_hydrogens/sandbox_52e80657-4603-4e9a-92bb-817008ee22cd\nINFO     /tmp/biobb/unitests_213/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:cmd_wrapper.py:33 reduce -Trim /tmp/biobb/unitests_213/reduce_remove_hydrogens/sandbox_52e80657-4603-4e9a-92bb-817008ee22cd/reduce.H.pdb &amp;gt; /tmp/biobb/unitests_213/reduce_remove_hydrogens/sandbox_52e80657-4603-4e9a-92bb-817008ee22cd/output.pdb\n\nINFO     /tmp/biobb/unitests_213/reduce_remove_hydrogens/reduce_remove_hydrogens_log.out:cmd_wrapper.py:50 Exit code 255\n\nINFO     /tmp/biobb/unitests_213/reduce_remove_hydrogens/reduce_remove_hydrogens_log.err:cmd_wrapper.py:60 Processing file: &amp;quot;/tmp/biobb/unitests_213/reduce_remove_hydrogens/sandbox_52e80657-4603-4e9a-92bb-817008ee22cd/reduce.H.pdb&amp;quot;\nWARNING: atom H192 from ZEN will be treated as hydrogen\nWARNING: atom H191 from ZEN will be treated as hydrogen\nWARNING: atom H182 from ZEN will be treated as hydrogen\nWARNING: atom H181 from ZEN will be treated as hydrogen\nWARNING: atom H162 from ZEN will be treated as hydrogen\nWARNING: atom H161 from ZEN will be treated as hydrogen\nWARNING: atom H152 from ZEN will be treated as hydrogen\nWARNING: atom H151 from ZEN will be treated as hydrogen\nWARNING: atom H122 from ZEN will be treated as hydrogen\nWARNING: atom H121 from ZEN will be treated as hydrogen\nWARNING: atom H112 from ZEN will be treated as hydrogen\nWARNING: atom H111 from ZEN will be treated as hydrogen\nTrimming: removed 27 hydrogens (27 hets)\nRemoved 27 hydrogens (27 hets)\nIf you publish work which uses reduce, please cite:\nWord, et. al. (1999) J. Mol. Biol. 285, 1735-1747.\nFor more information see http://kinemage.biochem.duke.edu\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_213\n&#34;}], &#34;biobb_chemistry/test/unitests/test_babel/test_babel_add_hydrogens.py::TestBabelAddHydrogens::test_add_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_babel/test_babel_add_hydrogens.py::TestBabelAddHydrogens::test_add_hydrogens&#34;, &#34;duration&#34;: &#34;238 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_babel/test_babel_add_hydrogens.py::TestBabelAddHydrogens::test_add_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;238 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-16 13:32:43,416 [MainThread  ] [INFO ]  Executing biobb_chemistry.babelm.babel_add_hydrogens Version: 4.2.0\n2024-07-16 13:32:43,416 [MainThread  ] [INFO ]  /tmp/biobb/unitests_213/babel_add_hydrogens/sandbox_91eb3f5b-7dae-48c8-9fc9-88d4b3675ac4 directory successfully created\n2024-07-16 13:32:43,417 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babelm/babel.no.H.pdb to /tmp/biobb/unitests_213/babel_add_hydrogens/sandbox_91eb3f5b-7dae-48c8-9fc9-88d4b3675ac4\n2024-07-16 13:32:43,417 [MainThread  ] [INFO ]  obabel -ipdb /tmp/biobb/unitests_213/babel_add_hydrogens/sandbox_91eb3f5b-7dae-48c8-9fc9-88d4b3675ac4/babel.no.H.pdb -opdb -O/tmp/biobb/unitests_213/babel_add_hydrogens/sandbox_91eb3f5b-7dae-48c8-9fc9-88d4b3675ac4/output.pdb --gen3d -p 7.4 -xh --medium\n\n2024-07-16 13:32:43,583 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-16 13:32:43,583 [MainThread  ] [INFO ]  1 molecule converted\n\n2024-07-16 13:32:43,583 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_213/babel_add_hydrogens/sandbox_91eb3f5b-7dae-48c8-9fc9-88d4b3675ac4&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_213/babel_add_hydrogens/output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_213/babel_add_hydrogens/babel_add_hydrogens_log.out:file_utils.py:391 Executing biobb_chemistry.babelm.babel_add_hydrogens Version: 4.2.0\nINFO     /tmp/biobb/unitests_213/babel_add_hydrogens/babel_add_hydrogens_log.out:file_utils.py:82 /tmp/biobb/unitests_213/babel_add_hydrogens/sandbox_91eb3f5b-7dae-48c8-9fc9-88d4b3675ac4 directory successfully created\nINFO     /tmp/biobb/unitests_213/babel_add_hydrogens/babel_add_hydrogens_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babelm/babel.no.H.pdb to /tmp/biobb/unitests_213/babel_add_hydrogens/sandbox_91eb3f5b-7dae-48c8-9fc9-88d4b3675ac4\nINFO     /tmp/biobb/unitests_213/babel_add_hydrogens/babel_add_hydrogens_log.out:cmd_wrapper.py:33 obabel -ipdb /tmp/biobb/unitests_213/babel_add_hydrogens/sandbox_91eb3f5b-7dae-48c8-9fc9-88d4b3675ac4/babel.no.H.pdb -opdb -O/tmp/biobb/unitests_213/babel_add_hydrogens/sandbox_91eb3f5b-7dae-48c8-9fc9-88d4b3675ac4/output.pdb --gen3d -p 7.4 -xh --medium\n\nINFO     /tmp/biobb/unitests_213/babel_add_hydrogens/babel_add_hydrogens_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_213/babel_add_hydrogens/babel_add_hydrogens_log.err:cmd_wrapper.py:60 1 molecule converted\n\nINFO     /tmp/biobb/unitests_213/babel_add_hydrogens/babel_add_hydrogens_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_213/babel_add_hydrogens/sandbox_91eb3f5b-7dae-48c8-9fc9-88d4b3675ac4&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_213\n&#34;}], &#34;biobb_chemistry/test/unitests/test_babel/test_babel_convert.py::TestBabelConvert::test_convert&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_babel/test_babel_convert.py::TestBabelConvert::test_convert&#34;, &#34;duration&#34;: &#34;99 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_babel/test_babel_convert.py::TestBabelConvert::test_convert&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;99 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-16 13:32:43,655 [MainThread  ] [INFO ]  Executing biobb_chemistry.babelm.babel_convert Version: 4.2.0\n2024-07-16 13:32:43,655 [MainThread  ] [INFO ]  /tmp/biobb/unitests_213/babel_convert/sandbox_1e9840a7-ee8c-4621-a17f-38efd4de2012 directory successfully created\n2024-07-16 13:32:43,655 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babelm/babel.smi to /tmp/biobb/unitests_213/babel_convert/sandbox_1e9840a7-ee8c-4621-a17f-38efd4de2012\n2024-07-16 13:32:43,656 [MainThread  ] [INFO ]  obabel -ismi /tmp/biobb/unitests_213/babel_convert/sandbox_1e9840a7-ee8c-4621-a17f-38efd4de2012/babel.smi -omol2 -O/tmp/biobb/unitests_213/babel_convert/sandbox_1e9840a7-ee8c-4621-a17f-38efd4de2012/output.mol2 --gen2d -p 7.4 -r\n\n2024-07-16 13:32:43,683 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-16 13:32:43,683 [MainThread  ] [INFO ]  1 molecule converted\n\n2024-07-16 13:32:43,684 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_213/babel_convert/sandbox_1e9840a7-ee8c-4621-a17f-38efd4de2012&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_213/babel_convert/output.mol2\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_213/babel_convert/babel_convert_log.out:file_utils.py:391 Executing biobb_chemistry.babelm.babel_convert Version: 4.2.0\nINFO     /tmp/biobb/unitests_213/babel_convert/babel_convert_log.out:file_utils.py:82 /tmp/biobb/unitests_213/babel_convert/sandbox_1e9840a7-ee8c-4621-a17f-38efd4de2012 directory successfully created\nINFO     /tmp/biobb/unitests_213/babel_convert/babel_convert_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babelm/babel.smi to /tmp/biobb/unitests_213/babel_convert/sandbox_1e9840a7-ee8c-4621-a17f-38efd4de2012\nINFO     /tmp/biobb/unitests_213/babel_convert/babel_convert_log.out:cmd_wrapper.py:33 obabel -ismi /tmp/biobb/unitests_213/babel_convert/sandbox_1e9840a7-ee8c-4621-a17f-38efd4de2012/babel.smi -omol2 -O/tmp/biobb/unitests_213/babel_convert/sandbox_1e9840a7-ee8c-4621-a17f-38efd4de2012/output.mol2 --gen2d -p 7.4 -r\n\nINFO     /tmp/biobb/unitests_213/babel_convert/babel_convert_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_213/babel_convert/babel_convert_log.err:cmd_wrapper.py:60 1 molecule converted\n\nINFO     /tmp/biobb/unitests_213/babel_convert/babel_convert_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_213/babel_convert/sandbox_1e9840a7-ee8c-4621-a17f-38efd4de2012&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_213\n&#34;}], &#34;biobb_chemistry/test/unitests/test_babel/test_babel_minimize.py::TestBabelMinimize::test_minimize&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_babel/test_babel_minimize.py::TestBabelMinimize::test_minimize&#34;, &#34;duration&#34;: &#34;158 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_babel/test_babel_minimize.py::TestBabelMinimize::test_minimize&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;158 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-16 13:32:43,755 [MainThread  ] [INFO ]  Executing biobb_chemistry.babelm.babel_minimize Version: 4.2.0\n2024-07-16 13:32:43,755 [MainThread  ] [INFO ]  /tmp/biobb/unitests_213/babel_minimize/sandbox_b22cd05b-2c07-4040-8645-ed91d8b8d025 directory successfully created\n2024-07-16 13:32:43,755 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babelm/babel.minimize.pdb to /tmp/biobb/unitests_213/babel_minimize/sandbox_b22cd05b-2c07-4040-8645-ed91d8b8d025\n2024-07-16 13:32:43,756 [MainThread  ] [INFO ]  obminimize -c 1e-6 -cg -ff GAFF -h -n 2500 -cut -rvdw 6.0 -rele 10.0 -pf 10 -ipdb /tmp/biobb/unitests_213/babel_minimize/sandbox_b22cd05b-2c07-4040-8645-ed91d8b8d025/babel.minimize.pdb -opdb &amp;gt; /tmp/biobb/unitests_213/babel_minimize/sandbox_b22cd05b-2c07-4040-8645-ed91d8b8d025/output.pdb\n\n2024-07-16 13:32:43,839 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-16 13:32:43,839 [MainThread  ] [INFO ]  \nA T O M   T Y P E S\n\nIDX\tTYPE\tRING\n1\tc3\tNO\n2\toh\tNO\n3\tc3\tNO\n4\tc3\tNO\n5\tc3\tNO\n6\tna\tAR\n7\tcc\tAR\n8\tnb\tAR\n9\tca\tAR\n10\tnh\tNO\n11\tca\tAR\n12\tca\tAR\n13\tca\tAR\n14\tca\tAR\n15\tca\tAR\n16\tca\tAR\n17\tn\tAR\n18\thn\tNO\n19\tc\tAR\n20\to\tNO\n21\tcd\tAR\n22\tnb\tAR\n23\tcc\tAR\n24\th1\tNO\n25\th1\tNO\n26\tho\tNO\n27\thc\tNO\n28\thc\tNO\n29\thc\tNO\n30\thc\tNO\n31\th1\tNO\n32\th1\tNO\n33\thn\tNO\n34\tha\tNO\n35\tha\tNO\n36\tha\tNO\n37\tha\tNO\n38\tha\tNO\n39\th5\tNO\n\nC H A R G E S\n\nIDX\tCHARGE\n1\t0.044262\n2\t-0.395006\n3\t-0.028107\n4\t-0.032802\n5\t0.026134\n6\t-0.314804\n7\t0.169132\n8\t-0.195940\n9\t0.201912\n10\t-0.285012\n11\t0.033522\n12\t-0.040471\n13\t-0.060007\n14\t-0.061645\n15\t-0.060007\n16\t-0.040471\n17\t-0.293020\n18\t0.171657\n19\t0.280327\n20\t-0.265372\n21\t0.171984\n22\t-0.228637\n23\t0.098390\n24\t0.055697\n25\t0.055697\n26\t0.209395\n27\t0.028779\n28\t0.028779\n29\t0.028309\n30\t0.028309\n31\t0.049254\n32\t0.049254\n33\t0.154976\n34\t0.063605\n35\t0.061815\n36\t0.061760\n37\t0.061815\n38\t0.063605\n39\t0.102930\n\nS E T T I N G   U P   C A L C U L A T I O N S\n\nSETTING UP BOND CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR BOND cc-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR BOND nb-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR BOND nb-cd, USING DEFAULT PARAMETERS\nSETTING UP ANGLE CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR ANGLE na-cc-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-cc-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cc-nb-ca, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-ca-n, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cc-cd-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE c-cd-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cd-nb-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-cc-h5, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE na-cc-nb, USING DEFAULT PARAMETERS\nSETTING UP TORSION CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR TORSION h5-cc-nb-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION na-cc-nb-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION ca-nb-cc-na, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION ca-nb-cc-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-c, USING DEFAULT PARAMETERS\nSETTING UP IMPROPER TORSION CALCULATIONS...\nSETTING UP VAN DER WAALS CALCULATIONS...\nSETTING UP ELECTROSTATIC CALCULATIONS...\n\nC O N J U G A T E   G R A D I E N T S\n\nSTEPS = 2500\n\nSTEP n     E(n)       E(n-1)    \n--------------------------------\n    1     190.026     471.088\n   10      89.911      91.650\n   20      76.628      77.475\n   30      73.331      73.681\n   40      72.126      72.251\n   50      71.119      71.211\n   60      70.489      70.522\n   70      70.050      70.054\n   80      69.701      69.706\n   90      69.456      69.463\n  100      69.246      69.283\n  110      69.025      69.030\n  120      68.820      68.861\n  130      68.699      68.726\n  140      68.566      68.592\n  150      68.456      68.460\n  153      68.419      68.419\n    CONJUGATE GRADIENTS HAS CONVERGED\nTime: 0.048677seconds. Iterations per second: 3163.71\n\n2024-07-16 13:32:43,839 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_213/babel_minimize/sandbox_b22cd05b-2c07-4040-8645-ed91d8b8d025&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_213/babel_minimize/output.pdb\nChecking RMSD between:\n     PDB_A: /tmp/biobb/unitests_213/babel_minimize/output.pdb\n     PDB_B: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/reference/babelm/ref_babel.minimize.pdb\n     Ignoring HETAMT in RMSD\n     Ignoring Hydrogen atoms in RMSD\n     Atoms ALIGNED in PDB_A: 3\n     Atoms ALIGNED in PDB_B: 3\n     RMS: 0.0021526397693638504\n     RMS_CUTOFF: 1\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_213/babel_minimize/babel_minimize_log.out:file_utils.py:391 Executing biobb_chemistry.babelm.babel_minimize Version: 4.2.0\nINFO     /tmp/biobb/unitests_213/babel_minimize/babel_minimize_log.out:file_utils.py:82 /tmp/biobb/unitests_213/babel_minimize/sandbox_b22cd05b-2c07-4040-8645-ed91d8b8d025 directory successfully created\nINFO     /tmp/biobb/unitests_213/babel_minimize/babel_minimize_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babelm/babel.minimize.pdb to /tmp/biobb/unitests_213/babel_minimize/sandbox_b22cd05b-2c07-4040-8645-ed91d8b8d025\nINFO     /tmp/biobb/unitests_213/babel_minimize/babel_minimize_log.out:cmd_wrapper.py:33 obminimize -c 1e-6 -cg -ff GAFF -h -n 2500 -cut -rvdw 6.0 -rele 10.0 -pf 10 -ipdb /tmp/biobb/unitests_213/babel_minimize/sandbox_b22cd05b-2c07-4040-8645-ed91d8b8d025/babel.minimize.pdb -opdb &amp;gt; /tmp/biobb/unitests_213/babel_minimize/sandbox_b22cd05b-2c07-4040-8645-ed91d8b8d025/output.pdb\n\nINFO     /tmp/biobb/unitests_213/babel_minimize/babel_minimize_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_213/babel_minimize/babel_minimize_log.err:cmd_wrapper.py:60 \nA T O M   T Y P E S\n\nIDX\tTYPE\tRING\n1\tc3\tNO\n2\toh\tNO\n3\tc3\tNO\n4\tc3\tNO\n5\tc3\tNO\n6\tna\tAR\n7\tcc\tAR\n8\tnb\tAR\n9\tca\tAR\n10\tnh\tNO\n11\tca\tAR\n12\tca\tAR\n13\tca\tAR\n14\tca\tAR\n15\tca\tAR\n16\tca\tAR\n17\tn\tAR\n18\thn\tNO\n19\tc\tAR\n20\to\tNO\n21\tcd\tAR\n22\tnb\tAR\n23\tcc\tAR\n24\th1\tNO\n25\th1\tNO\n26\tho\tNO\n27\thc\tNO\n28\thc\tNO\n29\thc\tNO\n30\thc\tNO\n31\th1\tNO\n32\th1\tNO\n33\thn\tNO\n34\tha\tNO\n35\tha\tNO\n36\tha\tNO\n37\tha\tNO\n38\tha\tNO\n39\th5\tNO\n\nC H A R G E S\n\nIDX\tCHARGE\n1\t0.044262\n2\t-0.395006\n3\t-0.028107\n4\t-0.032802\n5\t0.026134\n6\t-0.314804\n7\t0.169132\n8\t-0.195940\n9\t0.201912\n10\t-0.285012\n11\t0.033522\n12\t-0.040471\n13\t-0.060007\n14\t-0.061645\n15\t-0.060007\n16\t-0.040471\n17\t-0.293020\n18\t0.171657\n19\t0.280327\n20\t-0.265372\n21\t0.171984\n22\t-0.228637\n23\t0.098390\n24\t0.055697\n25\t0.055697\n26\t0.209395\n27\t0.028779\n28\t0.028779\n29\t0.028309\n30\t0.028309\n31\t0.049254\n32\t0.049254\n33\t0.154976\n34\t0.063605\n35\t0.061815\n36\t0.061760\n37\t0.061815\n38\t0.063605\n39\t0.102930\n\nS E T T I N G   U P   C A L C U L A T I O N S\n\nSETTING UP BOND CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR BOND cc-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR BOND nb-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR BOND nb-cd, USING DEFAULT PARAMETERS\nSETTING UP ANGLE CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR ANGLE na-cc-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-cc-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cc-nb-ca, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-ca-n, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cc-cd-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE c-cd-nb, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE cd-nb-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE nb-cc-h5, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR ANGLE na-cc-nb, USING DEFAULT PARAMETERS\nSETTING UP TORSION CALCULATIONS...\nCOULD NOT FIND PARAMETERS FOR TORSION h5-cc-nb-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION na-cc-nb-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION ca-nb-cc-na, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION ca-nb-cc-cd, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-cc, USING DEFAULT PARAMETERS\nCOULD NOT FIND PARAMETERS FOR TORSION cc-nb-cd-c, USING DEFAULT PARAMETERS\nSETTING UP IMPROPER TORSION CALCULATIONS...\nSETTING UP VAN DER WAALS CALCULATIONS...\nSETTING UP ELECTROSTATIC CALCULATIONS...\n\nC O N J U G A T E   G R A D I E N T S\n\nSTEPS = 2500\n\nSTEP n     E(n)       E(n-1)    \n--------------------------------\n    1     190.026     471.088\n   10      89.911      91.650\n   20      76.628      77.475\n   30      73.331      73.681\n   40      72.126      72.251\n   50      71.119      71.211\n   60      70.489      70.522\n   70      70.050      70.054\n   80      69.701      69.706\n   90      69.456      69.463\n  100      69.246      69.283\n  110      69.025      69.030\n  120      68.820      68.861\n  130      68.699      68.726\n  140      68.566      68.592\n  150      68.456      68.460\n  153      68.419      68.419\n    CONJUGATE GRADIENTS HAS CONVERGED\nTime: 0.048677seconds. Iterations per second: 3163.71\n\nINFO     /tmp/biobb/unitests_213/babel_minimize/babel_minimize_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_213/babel_minimize/sandbox_b22cd05b-2c07-4040-8645-ed91d8b8d025&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_213\n&#34;}], &#34;biobb_chemistry/test/unitests/test_babel/test_babel_remove_hydrogens.py::TestBabelRemoveHydrogens::test_remove_hydrogens&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_chemistry/test/unitests/test_babel/test_babel_remove_hydrogens.py::TestBabelRemoveHydrogens::test_remove_hydrogens&#34;, &#34;duration&#34;: &#34;239 ms&#34;, &#34;resultsTableRow&#34;: [&#34;&lt;td class=\&#34;col-result\&#34;&gt;Passed&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-testId\&#34;&gt;biobb_chemistry/test/unitests/test_babel/test_babel_remove_hydrogens.py::TestBabelRemoveHydrogens::test_remove_hydrogens&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;239 ms&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-07-16 13:32:43,915 [MainThread  ] [INFO ]  Executing biobb_chemistry.babelm.babel_remove_hydrogens Version: 4.2.0\n2024-07-16 13:32:43,915 [MainThread  ] [INFO ]  /tmp/biobb/unitests_213/babel_remove_hydrogens/sandbox_36083eaf-2972-48c9-aa74-5b3567010c2b directory successfully created\n2024-07-16 13:32:43,915 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babelm/babel.H.pdb to /tmp/biobb/unitests_213/babel_remove_hydrogens/sandbox_36083eaf-2972-48c9-aa74-5b3567010c2b\n2024-07-16 13:32:43,915 [MainThread  ] [INFO ]  obabel -ipdb /tmp/biobb/unitests_213/babel_remove_hydrogens/sandbox_36083eaf-2972-48c9-aa74-5b3567010c2b/babel.H.pdb -opdb -O/tmp/biobb/unitests_213/babel_remove_hydrogens/sandbox_36083eaf-2972-48c9-aa74-5b3567010c2b/output.pdb --gen3d -d -p 7.4 --medium\n\n2024-07-16 13:32:44,082 [MainThread  ] [INFO ]  Exit code 0\n\n2024-07-16 13:32:44,082 [MainThread  ] [INFO ]  1 molecule converted\n\n2024-07-16 13:32:44,083 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_213/babel_remove_hydrogens/sandbox_36083eaf-2972-48c9-aa74-5b3567010c2b&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_213/babel_remove_hydrogens/output.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_213/babel_remove_hydrogens/babel_remove_hydrogens_log.out:file_utils.py:391 Executing biobb_chemistry.babelm.babel_remove_hydrogens Version: 4.2.0\nINFO     /tmp/biobb/unitests_213/babel_remove_hydrogens/babel_remove_hydrogens_log.out:file_utils.py:82 /tmp/biobb/unitests_213/babel_remove_hydrogens/sandbox_36083eaf-2972-48c9-aa74-5b3567010c2b directory successfully created\nINFO     /tmp/biobb/unitests_213/babel_remove_hydrogens/babel_remove_hydrogens_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_chemistry/biobb_chemistry/biobb_chemistry/test/data/babelm/babel.H.pdb to /tmp/biobb/unitests_213/babel_remove_hydrogens/sandbox_36083eaf-2972-48c9-aa74-5b3567010c2b\nINFO     /tmp/biobb/unitests_213/babel_remove_hydrogens/babel_remove_hydrogens_log.out:cmd_wrapper.py:33 obabel -ipdb /tmp/biobb/unitests_213/babel_remove_hydrogens/sandbox_36083eaf-2972-48c9-aa74-5b3567010c2b/babel.H.pdb -opdb -O/tmp/biobb/unitests_213/babel_remove_hydrogens/sandbox_36083eaf-2972-48c9-aa74-5b3567010c2b/output.pdb --gen3d -d -p 7.4 --medium\n\nINFO     /tmp/biobb/unitests_213/babel_remove_hydrogens/babel_remove_hydrogens_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_213/babel_remove_hydrogens/babel_remove_hydrogens_log.err:cmd_wrapper.py:60 1 molecule converted\n\nINFO     /tmp/biobb/unitests_213/babel_remove_hydrogens/babel_remove_hydrogens_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_213/babel_remove_hydrogens/sandbox_36083eaf-2972-48c9-aa74-5b3567010c2b&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_213\n&#34;}]}, &#34;renderCollapsed&#34;: [&#34;passed&#34;], &#34;initialSort&#34;: &#34;result&#34;, &#34;title&#34;: &#34;report.html&#34;}"></div>
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