From 7909930c4b8df6c69557c8818e97379109f36406 Mon Sep 17 00:00:00 2001
From: PauAndrio <andriopau@gmail.com>
Date: Mon, 4 Nov 2024 13:16:13 +0000
Subject: [PATCH] =?UTF-8?q?Deploying=20to=20gh-pages=20from=20@=20bioexcel?=
 =?UTF-8?q?/biobb=5Fgodmd@617c1f63ac908a6ccbd3d9662d887c6ec7091c12=20?=
 =?UTF-8?q?=F0=9F=9A=80?=
MIME-Version: 1.0
Content-Type: text/plain; charset=UTF-8
Content-Transfer-Encoding: 8bit

---
 coverage/class_index.html                     |  58 +-
 coverage/coverage.xml                         | 251 +++---
 coverage/coveragebadge.svg                    |   2 +-
 coverage/function_index.html                  | 104 +--
 coverage/index.html                           |  28 +-
 coverage/status.json                          |   2 +-
 coverage/z_1594175cfefe9933___init___py.html  |  19 +-
 ...z_b3ec5c7564c25379_test_godmd_prep_py.html |  43 +-
 .../z_b3ec5c7564c25379_test_godmd_run_py.html |  47 +-
 coverage/z_c296ee536f0b791d___init___py.html  |  18 +-
 coverage/z_c296ee536f0b791d_common_py.html    |   8 +-
 .../z_c296ee536f0b791d_godmd_prep_py.html     | 720 +++++++++---------
 coverage/z_c296ee536f0b791d_godmd_run_py.html | 520 ++++++-------
 flake8/index.html                             |   4 +-
 junit/junit.xml                               |   2 +-
 junit/report.html                             |   6 +-
 16 files changed, 923 insertions(+), 909 deletions(-)

diff --git a/coverage/class_index.html b/coverage/class_index.html
index 261cc0f..d1f7f5b 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 2024-06-27 09:20 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
+            created at 2024-11-04 13:16 +0000
         </p>
     </div>
 </header>
@@ -75,30 +75,30 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_1594175cfefe9933___init___py.html">biobb_godmd/__init__.py</a></td>
                 <td class="name left"><a href="z_1594175cfefe9933___init___py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>3</td>
+                <td>4</td>
                 <td>0</td>
                 <td>0</td>
-                <td class="right" data-ratio="3 3">100%</td>
+                <td class="right" data-ratio="4 4">100%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_c296ee536f0b791d___init___py.html">biobb_godmd/godmd/__init__.py</a></td>
                 <td class="name left"><a href="z_c296ee536f0b791d___init___py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>2</td>
+                <td>4</td>
                 <td>0</td>
                 <td>0</td>
-                <td class="right" data-ratio="2 2">100%</td>
+                <td class="right" data-ratio="4 4">100%</td>
             </tr>
             <tr class="region">
                 <td class="name left"><a href="z_c296ee536f0b791d_common_py.html">biobb_godmd/godmd/common.py</a></td>
                 <td class="name left"><a href="z_c296ee536f0b791d_common_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>5</td>
-                <td>0</td>
+                <td>28</td>
+                <td>11</td>
                 <td>0</td>
-                <td class="right" data-ratio="5 5">100%</td>
+                <td class="right" data-ratio="17 28">61%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t13">biobb_godmd/godmd/godmd_prep.py</a></td>
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t13"><data value='GOdMDPrep'>GOdMDPrep</data></a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t14">biobb_godmd/godmd/godmd_prep.py</a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t14"><data value='GOdMDPrep'>GOdMDPrep</data></a></td>
                 <td>132</td>
                 <td>9</td>
                 <td>0</td>
@@ -107,14 +107,14 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html">biobb_godmd/godmd/godmd_prep.py</a></td>
                 <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html"><data value=''><span class='no-noun'>(no class)</span></data></a></td>
-                <td>18</td>
-                <td>1</td>
+                <td>31</td>
+                <td>12</td>
                 <td>0</td>
-                <td class="right" data-ratio="17 18">94%</td>
+                <td class="right" data-ratio="19 31">61%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t14">biobb_godmd/godmd/godmd_run.py</a></td>
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t14"><data value='GOdMDRun'>GOdMDRun</data></a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t15">biobb_godmd/godmd/godmd_run.py</a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t15"><data value='GOdMDRun'>GOdMDRun</data></a></td>
                 <td>56</td>
                 <td>11</td>
                 <td>0</td>
@@ -123,14 +123,14 @@ <h2>
             <tr class="region">
                 <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html">biobb_godmd/godmd/godmd_run.py</a></td>
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-                <td>18</td>
-                <td>1</td>
+                <td>36</td>
+                <td>17</td>
                 <td>0</td>
-                <td class="right" data-ratio="17 18">94%</td>
+                <td class="right" data-ratio="19 36">53%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_b3ec5c7564c25379_test_godmd_prep_py.html#t5">biobb_godmd/test/unitests/test_godmd/test_godmd_prep.py</a></td>
-                <td class="name left"><a href="z_b3ec5c7564c25379_test_godmd_prep_py.html#t5"><data value='TestGOdMDPrep'>TestGOdMDPrep</data></a></td>
+                <td class="name left"><a href="z_b3ec5c7564c25379_test_godmd_prep_py.html#t6">biobb_godmd/test/unitests/test_godmd/test_godmd_prep.py</a></td>
+                <td class="name left"><a href="z_b3ec5c7564c25379_test_godmd_prep_py.html#t6"><data value='TestGOdMDPrep'>TestGOdMDPrep</data></a></td>
                 <td>5</td>
                 <td>0</td>
                 <td>0</td>
@@ -145,8 +145,8 @@ <h2>
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             <tr class="region">
-                <td class="name left"><a href="z_b3ec5c7564c25379_test_godmd_run_py.html#t5">biobb_godmd/test/unitests/test_godmd/test_godmd_run.py</a></td>
-                <td class="name left"><a href="z_b3ec5c7564c25379_test_godmd_run_py.html#t5"><data value='TestGOdMDrun'>TestGOdMDrun</data></a></td>
+                <td class="name left"><a href="z_b3ec5c7564c25379_test_godmd_run_py.html#t6">biobb_godmd/test/unitests/test_godmd/test_godmd_run.py</a></td>
+                <td class="name left"><a href="z_b3ec5c7564c25379_test_godmd_run_py.html#t6"><data value='TestGOdMDrun'>TestGOdMDrun</data></a></td>
                 <td>7</td>
                 <td>0</td>
                 <td>0</td>
@@ -165,10 +165,10 @@ <h2>
             <tr class="total">
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                 <td class="name left">&nbsp;</td>
-                <td>258</td>
-                <td>22</td>
+                <td>315</td>
+                <td>60</td>
                 <td>0</td>
-                <td class="right" data-ratio="236 258">91%</td>
+                <td class="right" data-ratio="255 315">81%</td>
             </tr>
         </tfoot>
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@@ -179,8 +179,8 @@ <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 2024-06-27 09:20 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
+            created at 2024-11-04 13:16 +0000
         </p>
     </div>
     <aside class="hidden">
diff --git a/coverage/coverage.xml b/coverage/coverage.xml
index 028a93e..1b6447b 100644
--- a/coverage/coverage.xml
+++ b/coverage/coverage.xml
@@ -1,6 +1,6 @@
 <?xml version="1.0" ?>
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-	<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.5.4 -->
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+	<!-- Generated by coverage.py: https://coverage.readthedocs.io/en/7.6.4 -->
 	<!-- Based on https://raw.githubusercontent.com/cobertura/web/master/htdocs/xml/coverage-04.dtd -->
 	<sources>
 		<source>/home/user/actions-runner/_work/biobb_godmd/biobb_godmd</source>
@@ -14,17 +14,20 @@
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 						<line number="2" hits="1"/>
 						<line number="3" hits="1"/>
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 				</class>
 			</classes>
 		</package>
-		<package name="biobb_godmd.godmd" line-rate="0.788" branch-rate="0" complexity="0">
+		<package name="biobb_godmd.godmd" line-rate="0.7909" branch-rate="0" complexity="0">
 			<classes>
 				<class name="__init__.py" filename="biobb_godmd/godmd/__init__.py" complexity="0" line-rate="1" branch-rate="0">
 					<methods/>
 					<lines>
 						<line number="1" hits="1"/>
 						<line number="2" hits="1"/>
+						<line number="3" hits="1"/>
+						<line number="4" hits="1"/>
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 				<class name="common.py" filename="biobb_godmd/godmd/common.py" complexity="0" line-rate="0.6071" branch-rate="0">
@@ -60,7 +63,7 @@
 						<line number="51" hits="1"/>
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-				<class name="godmd_prep.py" filename="biobb_godmd/godmd/godmd_prep.py" complexity="0" line-rate="0.8704" branch-rate="0">
+				<class name="godmd_prep.py" filename="biobb_godmd/godmd/godmd_prep.py" complexity="0" line-rate="0.8712" branch-rate="0">
 					<methods/>
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 						<line number="2" hits="1"/>
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diff --git a/coverage/coveragebadge.svg b/coverage/coveragebadge.svg
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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>,
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+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
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         </p>
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             <tr class="region">
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-                <td>3</td>
+                <td>4</td>
                 <td>0</td>
                 <td>0</td>
-                <td class="right" data-ratio="3 3">100%</td>
+                <td class="right" data-ratio="4 4">100%</td>
             </tr>
             <tr class="region">
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-                <td>2</td>
+                <td>4</td>
                 <td>0</td>
                 <td>0</td>
-                <td class="right" data-ratio="2 2">100%</td>
+                <td class="right" data-ratio="4 4">100%</td>
             </tr>
             <tr class="region">
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@@ -121,56 +121,56 @@ <h2>
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             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t56">biobb_godmd/godmd/godmd_prep.py</a></td>
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t56"><data value='init__'>GOdMDPrep.__init__</data></a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t58">biobb_godmd/godmd/godmd_prep.py</a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t58"><data value='init__'>GOdMDPrep.__init__</data></a></td>
                 <td>12</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="12 12">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t116">biobb_godmd/godmd/godmd_prep.py</a></td>
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t116"><data value='check_data_params'>GOdMDPrep.check_data_params</data></a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t118">biobb_godmd/godmd/godmd_prep.py</a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t118"><data value='check_data_params'>GOdMDPrep.check_data_params</data></a></td>
                 <td>4</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="4 4">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t127">biobb_godmd/godmd/godmd_prep.py</a></td>
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t127"><data value='extract_sequence'>GOdMDPrep.extract_sequence</data></a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t129">biobb_godmd/godmd/godmd_prep.py</a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t129"><data value='extract_sequence'>GOdMDPrep.extract_sequence</data></a></td>
                 <td>24</td>
                 <td>3</td>
                 <td>0</td>
                 <td class="right" data-ratio="21 24">88%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t157">biobb_godmd/godmd/godmd_prep.py</a></td>
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t157"><data value='retrieve_alignment'>GOdMDPrep.retrieve_alignment</data></a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t159">biobb_godmd/godmd/godmd_prep.py</a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t159"><data value='retrieve_alignment'>GOdMDPrep.retrieve_alignment</data></a></td>
                 <td>51</td>
                 <td>3</td>
                 <td>0</td>
                 <td class="right" data-ratio="48 51">94%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t232">biobb_godmd/godmd/godmd_prep.py</a></td>
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t232"><data value='launch'>GOdMDPrep.launch</data></a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t234">biobb_godmd/godmd/godmd_prep.py</a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t234"><data value='launch'>GOdMDPrep.launch</data></a></td>
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                 <td>3</td>
                 <td>0</td>
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             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t325">biobb_godmd/godmd/godmd_prep.py</a></td>
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t325"><data value='godmd_prep'>godmd_prep</data></a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t327">biobb_godmd/godmd/godmd_prep.py</a></td>
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                 <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_c296ee536f0b791d_godmd_prep_py.html#t338"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t340">biobb_godmd/godmd/godmd_prep.py</a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_prep_py.html#t340"><data value='main'>main</data></a></td>
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                 <td>11</td>
                 <td>0</td>
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                 <td>1</td>
                 <td>0</td>
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             <tr class="region">
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t64">biobb_godmd/godmd/godmd_run.py</a></td>
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t64"><data value='init__'>GOdMDRun.__init__</data></a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t66">biobb_godmd/godmd/godmd_run.py</a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t66"><data value='init__'>GOdMDRun.__init__</data></a></td>
                 <td>8</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="8 8">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t97">biobb_godmd/godmd/godmd_run.py</a></td>
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t97"><data value='check_data_params'>GOdMDRun.check_data_params</data></a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t99">biobb_godmd/godmd/godmd_run.py</a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t99"><data value='check_data_params'>GOdMDRun.check_data_params</data></a></td>
                 <td>9</td>
                 <td>0</td>
                 <td>0</td>
                 <td class="right" data-ratio="9 9">100%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t113">biobb_godmd/godmd/godmd_run.py</a></td>
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t113"><data value='create_godmdin'>GOdMDRun.create_godmdin</data></a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t115">biobb_godmd/godmd/godmd_run.py</a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t115"><data value='create_godmdin'>GOdMDRun.create_godmdin</data></a></td>
                 <td>26</td>
                 <td>10</td>
                 <td>0</td>
                 <td class="right" data-ratio="16 26">62%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t161">biobb_godmd/godmd/godmd_run.py</a></td>
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t161"><data value='launch'>GOdMDRun.launch</data></a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t163">biobb_godmd/godmd/godmd_run.py</a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t163"><data value='launch'>GOdMDRun.launch</data></a></td>
                 <td>13</td>
                 <td>1</td>
                 <td>0</td>
                 <td class="right" data-ratio="12 13">92%</td>
             </tr>
             <tr class="region">
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t208">biobb_godmd/godmd/godmd_run.py</a></td>
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t208"><data value='godmd_run'>godmd_run</data></a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t210">biobb_godmd/godmd/godmd_run.py</a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t210"><data value='godmd_run'>godmd_run</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_c296ee536f0b791d_godmd_run_py.html#t227">biobb_godmd/godmd/godmd_run.py</a></td>
-                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t227"><data value='main'>main</data></a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t229">biobb_godmd/godmd/godmd_run.py</a></td>
+                <td class="name left"><a href="z_c296ee536f0b791d_godmd_run_py.html#t229"><data value='main'>main</data></a></td>
                 <td>16</td>
                 <td>16</td>
                 <td>0</td>
@@ -235,30 +235,30 @@ <h2>
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-                <td class="name left"><a href="z_b3ec5c7564c25379_test_godmd_prep_py.html#t13">biobb_godmd/test/unitests/test_godmd/test_godmd_prep.py</a></td>
-                <td class="name left"><a href="z_b3ec5c7564c25379_test_godmd_prep_py.html#t13"><data value='test_godmd_prep'>TestGOdMDPrep.test_godmd_prep</data></a></td>
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                 <td>0</td>
                 <td>0</td>
@@ -273,24 +273,24 @@ <h2>
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             <tr class="region">
-                <td class="name left"><a href="z_b3ec5c7564c25379_test_godmd_run_py.html#t6">biobb_godmd/test/unitests/test_godmd/test_godmd_run.py</a></td>
-                <td class="name left"><a href="z_b3ec5c7564c25379_test_godmd_run_py.html#t6"><data value='setup_class'>TestGOdMDrun.setup_class</data></a></td>
+                <td class="name left"><a href="z_b3ec5c7564c25379_test_godmd_run_py.html#t7">biobb_godmd/test/unitests/test_godmd/test_godmd_run.py</a></td>
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-                <td class="name left"><a href="z_b3ec5c7564c25379_test_godmd_run_py.html#t9">biobb_godmd/test/unitests/test_godmd/test_godmd_run.py</a></td>
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-            created at 2024-06-27 09:20 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
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-                <td class="right" data-ratio="3 3">100%</td>
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                 <td>0</td>
-                <td class="right" data-ratio="2 2">100%</td>
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-                <td>162</td>
+                <td>163</td>
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                 <td>0</td>
-                <td class="right" data-ratio="141 162">87%</td>
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                 <td>0</td>
-                <td class="right" data-ratio="63 91">69%</td>
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             <tr class="region">
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@@ -123,10 +123,10 @@ <h2>
         <tfoot>
             <tr class="total">
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-                <td>310</td>
+                <td>315</td>
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                 <td>0</td>
-                <td class="right" data-ratio="250 310">81%</td>
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     <div class="content">
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.5.4">coverage.py v7.5.4</a>,
-            created at 2024-06-27 09:20 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
+            created at 2024-11-04 13:16 +0000
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     </div>
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index 4e83a82..98e2c1f 100644
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-            <a class="nav" href="https://coverage.readthedocs.io/en/7.5.4">coverage.py v7.5.4</a>,
-            created at 2024-06-27 09:20 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
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-            created at 2024-06-27 09:20 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</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 2024-06-27 09:20 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
+            created at 2024-11-04 13:16 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -80,24 +80,25 @@ <h2>
     </div>
 </header>
 <main id="source">
-    <p class="run"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span> <span class="key">import</span> <span class="nam">test_fixtures</span> <span class="key">as</span> <span class="nam">fx</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_godmd</span><span class="op">.</span><span class="nam">godmd</span><span class="op">.</span><span class="nam">godmd_prep</span> <span class="key">import</span> <span class="nam">godmd_prep</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="com"># type: ignore</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span> <span class="key">import</span> <span class="nam">test_fixtures</span> <span class="key">as</span> <span class="nam">fx</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_godmd</span><span class="op">.</span><span class="nam">godmd</span><span class="op">.</span><span class="nam">godmd_prep</span> <span class="key">import</span> <span class="nam">godmd_prep</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">class</span> <span class="nam">TestGOdMDPrep</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t">    <span class="key">def</span> <span class="nam">setup_class</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t">        <span class="nam">fx</span><span class="op">.</span><span class="nam">test_setup</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="str">'godmd_prep'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t">    <span class="key">def</span> <span class="nam">teardown_class</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t">        <span class="nam">fx</span><span class="op">.</span><span class="nam">test_teardown</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t">        <span class="com"># pass</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t">    <span class="key">def</span> <span class="nam">test_godmd_prep</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t">        <span class="nam">godmd_prep</span><span class="op">(</span><span class="nam">properties</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">not_empty</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">'output_aln_orig_path'</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">not_empty</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">'output_aln_target_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="t17" href="#t17">17</a></span><span class="t">        <span class="com"># assert fx.equal(self.paths['output_traj_path'], self.paths['ref_output_traj_path'])</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t">        <span class="com"># assert fx.equal(self.paths['output_rst_path'], self.paths['ref_output_rst_path'])</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">class</span> <span class="nam">TestGOdMDPrep</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t">    <span class="key">def</span> <span class="nam">setup_class</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t">        <span class="nam">fx</span><span class="op">.</span><span class="nam">test_setup</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="str">'godmd_prep'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t">    <span class="key">def</span> <span class="nam">teardown_class</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t">        <span class="nam">fx</span><span class="op">.</span><span class="nam">test_teardown</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t">        <span class="com"># pass</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t">    <span class="key">def</span> <span class="nam">test_godmd_prep</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t">        <span class="nam">godmd_prep</span><span class="op">(</span><span class="nam">properties</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">not_empty</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">'output_aln_orig_path'</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">not_empty</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">'output_aln_target_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="t18" href="#t18">18</a></span><span class="t">        <span class="com"># assert fx.equal(self.paths['output_traj_path'], self.paths['ref_output_traj_path'])</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">        <span class="com"># assert fx.equal(self.paths['output_rst_path'], self.paths['ref_output_rst_path'])</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -106,8 +107,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_b3ec5c7564c25379_test_godmd_run_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 2024-06-27 09:20 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
+            created at 2024-11-04 13:16 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_b3ec5c7564c25379_test_godmd_run_py.html b/coverage/z_b3ec5c7564c25379_test_godmd_run_py.html
index 87d8c83..ca8f91d 100644
--- a/coverage/z_b3ec5c7564c25379_test_godmd_run_py.html
+++ b/coverage/z_b3ec5c7564c25379_test_godmd_run_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="index.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 2024-06-27 09:20 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
+            created at 2024-11-04 13:16 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -80,26 +80,27 @@ <h2>
     </div>
 </header>
 <main id="source">
-    <p class="run"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span> <span class="key">import</span> <span class="nam">test_fixtures</span> <span class="key">as</span> <span class="nam">fx</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_godmd</span><span class="op">.</span><span class="nam">godmd</span><span class="op">.</span><span class="nam">godmd_run</span> <span class="key">import</span> <span class="nam">godmd_run</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="com"># type: ignore</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span> <span class="key">import</span> <span class="nam">test_fixtures</span> <span class="key">as</span> <span class="nam">fx</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_godmd</span><span class="op">.</span><span class="nam">godmd</span><span class="op">.</span><span class="nam">godmd_run</span> <span class="key">import</span> <span class="nam">godmd_run</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">class</span> <span class="nam">TestGOdMDrun</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t">    <span class="key">def</span> <span class="nam">setup_class</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t">        <span class="nam">fx</span><span class="op">.</span><span class="nam">test_setup</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="str">'godmd_run'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t">    <span class="key">def</span> <span class="nam">teardown_class</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t">        <span class="nam">fx</span><span class="op">.</span><span class="nam">test_teardown</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t">        <span class="com"># pass</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t">    <span class="key">def</span> <span class="nam">test_godmd_run</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t">        <span class="nam">godmd_run</span><span class="op">(</span><span class="nam">properties</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">not_empty</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">'output_log_path'</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">not_empty</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">'output_ene_path'</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">not_empty</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">'output_trj_path'</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">not_empty</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">'output_pdb_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="t19" href="#t19">19</a></span><span class="t">        <span class="com"># assert fx.equal(self.paths['output_traj_path'], self.paths['ref_output_traj_path'])</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t">        <span class="com"># assert fx.equal(self.paths['output_rst_path'], self.paths['ref_output_rst_path'])</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">class</span> <span class="nam">TestGOdMDrun</span><span class="op">(</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t">    <span class="key">def</span> <span class="nam">setup_class</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t">        <span class="nam">fx</span><span class="op">.</span><span class="nam">test_setup</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="str">'godmd_run'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t">    <span class="key">def</span> <span class="nam">teardown_class</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t">        <span class="com"># fx.test_teardown(self)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t">        <span class="key">pass</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t">    <span class="key">def</span> <span class="nam">test_godmd_run</span><span class="op">(</span><span class="nam">self</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t">        <span class="nam">godmd_run</span><span class="op">(</span><span class="nam">properties</span><span class="op">=</span><span class="nam">self</span><span class="op">.</span><span class="nam">properties</span><span class="op">,</span> <span class="op">**</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">not_empty</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">'output_log_path'</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">not_empty</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">'output_ene_path'</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">not_empty</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">'output_trj_path'</span><span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">        <span class="key">assert</span> <span class="nam">fx</span><span class="op">.</span><span class="nam">not_empty</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">paths</span><span class="op">[</span><span class="str">'output_pdb_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="t20" href="#t20">20</a></span><span class="t">        <span class="com"># assert fx.equal(self.paths['output_traj_path'], self.paths['ref_output_traj_path'])</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="com"># assert fx.equal(self.paths['output_rst_path'], self.paths['ref_output_rst_path'])</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -108,8 +109,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="index.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 2024-06-27 09:20 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
+            created at 2024-11-04 13:16 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_c296ee536f0b791d___init___py.html b/coverage/z_c296ee536f0b791d___init___py.html
index 714c8c7..77014ac 100644
--- a/coverage/z_c296ee536f0b791d___init___py.html
+++ b/coverage/z_c296ee536f0b791d___init___py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">2 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">2<span class="text"> run</span></button>
+            <span class="text">4 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">4<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">0<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>
@@ -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_c296ee536f0b791d_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 2024-06-27 09:20 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
+            created at 2024-11-04 13:16 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -80,8 +80,10 @@ <h2>
     </div>
 </header>
 <main id="source">
-    <p class="run"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="nam">name</span> <span class="op">=</span> <span class="str">"godmd"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t"><span class="nam">__all__</span> <span class="op">=</span> <span class="op">[</span><span class="str">"godmd_run"</span><span class="op">,</span> <span class="str">"godmd_prep"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t1" href="#t1">1</a></span><span class="t"><span class="key">from</span> <span class="op">.</span> <span class="key">import</span> <span class="nam">godmd_run</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t"><span class="key">from</span> <span class="op">.</span> <span class="key">import</span> <span class="nam">godmd_prep</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t"><span class="nam">name</span> <span class="op">=</span> <span class="str">"godmd"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t"><span class="nam">__all__</span> <span class="op">=</span> <span class="op">[</span><span class="str">"godmd_run"</span><span class="op">,</span> <span class="str">"godmd_prep"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
 </main>
 <footer>
     <div class="content">
@@ -90,8 +92,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_c296ee536f0b791d_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 2024-06-27 09:20 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
+            created at 2024-11-04 13:16 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_c296ee536f0b791d_common_py.html b/coverage/z_c296ee536f0b791d_common_py.html
index ffa6add..393a6bb 100644
--- a/coverage/z_c296ee536f0b791d_common_py.html
+++ b/coverage/z_c296ee536f0b791d_common_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_c296ee536f0b791d_godmd_prep_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 2024-06-27 09:20 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
+            created at 2024-11-04 13:16 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -139,8 +139,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_c296ee536f0b791d_godmd_prep_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 2024-06-27 09:20 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
+            created at 2024-11-04 13:16 +0000
         </p>
     </div>
 </footer>
diff --git a/coverage/z_c296ee536f0b791d_godmd_prep_py.html b/coverage/z_c296ee536f0b791d_godmd_prep_py.html
index bb8f6e0..40b8ae2 100644
--- a/coverage/z_c296ee536f0b791d_godmd_prep_py.html
+++ b/coverage/z_c296ee536f0b791d_godmd_prep_py.html
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">162 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">141<span class="text"> run</span></button>
+            <span class="text">163 statements &nbsp;</span>
+            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">142<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">21<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>
@@ -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_c296ee536f0b791d_godmd_run_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 2024-06-27 09:20 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
+            created at 2024-11-04 13:16 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -84,366 +84,368 @@ <h2>
     <p class="pln"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t"><span class="str">"""Module containing the GOdMDPrep class and the command line interface."""</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">from</span> <span class="nam">pathlib</span> <span class="key">import</span> <span class="nam">Path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span> <span class="key">import</span> <span class="nam">file_utils</span> <span class="key">as</span> <span class="nam">fu</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_godmd</span><span class="op">.</span><span class="nam">godmd</span><span class="op">.</span><span class="nam">common</span> <span class="key">import</span> <span class="nam">check_input_path</span><span class="op">,</span> <span class="nam">check_output_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">from</span> <span class="nam">pathlib</span> <span class="key">import</span> <span class="nam">Path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span> <span class="key">import</span> <span class="nam">file_utils</span> <span class="key">as</span> <span class="nam">fu</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_godmd</span><span class="op">.</span><span class="nam">godmd</span><span class="op">.</span><span class="nam">common</span> <span class="key">import</span> <span class="nam">check_input_path</span><span class="op">,</span> <span class="nam">check_output_path</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t"><span class="key">class</span> <span class="nam">GOdMDPrep</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t"><span class="str">    | biobb_godmd GOdMDPrep</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t"><span class="str">    | Helper bb to prepare inputs for the `GOdMD tool &lt;http://mmb.irbbarcelona.org/GOdMD/>`_ module.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="str">    | Prepares input files for the GOdMD tool.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t"><span class="str">    Args:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">        input_pdb_orig_path (str): Input PDB file to be used as origin in the conformational transition. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/1ake_A.pdb>`_. Accepted formats: pdb (edam:format_1476).</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_pdb_target_path (str): Input PDB file to be used as target in the conformational transition. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/4ake_A.pdb>`_. Accepted formats: pdb (edam:format_1476).</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_aln_orig_path (str): Output GOdMD alignment file corresponding to the origin structure of the conformational transition. File type: output. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/1ake_A.aln>`_. Accepted formats: aln (edam:format_2330), txt (edam:format_2330).</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">        output_aln_target_path (str): Output GOdMD alignment file corresponding to the target structure of the conformational transition. File type: output. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/4ake_A.aln>`_. Accepted formats: aln (edam:format_2330), txt (edam:format_2330).</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">        properties (dict - 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="t25" href="#t25">25</a></span><span class="t"><span class="str">            * **gapopen** (*float*) - (12.0) Standard gap penalty: score taken away when a gap is created.</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">            * **gapextend** (*float*) - (2.0) Penalty added to the standard gap penalty for each base or residue in the gap.</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">            * **datafile** (*str*) - ("EPAM250") Scoring matrix file used when comparing sequences.</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*) - ("water") Binary path.</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">&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">    Examples:</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">        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="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">            from biobb_godmd.godmd.godmd_prep import godmd_prep</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">            prop = {</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">                'gapopen': 10.0,</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">                'gapextend': 2.0</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">            }</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">            godmd_prep( input_pdb_orig_path='/path/to/input_orig.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">                        input_pdb_target_path='/path/to/input_target.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">                        output_aln_orig_path='/path/to/orig.aln',</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">                        output_aln_target_path='/path/to/target.aln',</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">                        properties=prop)</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">&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">    Info:</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">        * wrapped_software:</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">            * name: In house</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">            * license: Apache-2.0</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">        * ontology:</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: EDAM</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">            * schema: http://edamontology.org/EDAM.owl</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">&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">    """</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t56" href="#t56">56</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_pdb_orig_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_pdb_target_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</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="nam">output_aln_orig_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_aln_target_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</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="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="key">None</span><span class="op">:</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="run"><span class="n"><a id="t60" href="#t60">60</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="t13" href="#t13">13</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">class</span> <span class="nam">GOdMDPrep</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t"><span class="str">    | biobb_godmd GOdMDPrep</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="str">    | Helper bb to prepare inputs for the `GOdMD tool &lt;http://mmb.irbbarcelona.org/GOdMD/>`_ module.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t"><span class="str">    | Prepares input files for the GOdMD tool.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">    Args:</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_pdb_orig_path (str): Input PDB file to be used as origin in the conformational transition. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/1ake_A.pdb>`_. Accepted formats: pdb (edam:format_1476).</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">        input_pdb_target_path (str): Input PDB file to be used as target in the conformational transition. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/4ake_A.pdb>`_. Accepted formats: pdb (edam:format_1476).</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">        output_aln_orig_path (str): Output GOdMD alignment file corresponding to the origin structure of the conformational transition. File type: output. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/1ake_A.aln>`_. Accepted formats: aln (edam:format_2330), txt (edam:format_2330).</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">        output_aln_target_path (str): Output GOdMD alignment file corresponding to the target structure of the conformational transition. File type: output. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/4ake_A.aln>`_. Accepted formats: aln (edam:format_2330), txt (edam:format_2330).</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">        properties (dict - 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="t26" href="#t26">26</a></span><span class="t"><span class="str">            * **gapopen** (*float*) - (12.0) Standard gap penalty: score taken away when a gap is created.</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">            * **gapextend** (*float*) - (2.0) Penalty added to the standard gap penalty for each base or residue in the gap.</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">            * **datafile** (*str*) - ("EPAM250") Scoring matrix file used when comparing sequences.</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*) - ("water") Binary path.</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">&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">    Examples:</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">        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="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">            from biobb_godmd.godmd.godmd_prep import godmd_prep</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">            prop = {</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">                'gapopen': 10.0,</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">                'gapextend': 2.0</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">            }</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">            godmd_prep( input_pdb_orig_path='/path/to/input_orig.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">                        input_pdb_target_path='/path/to/input_target.pdb',</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">                        output_aln_orig_path='/path/to/orig.aln',</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_aln_target_path='/path/to/target.aln',</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">                        properties=prop)</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">&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">    Info:</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">        * wrapped_software:</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">            * name: In house</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">            * license: Apache-2.0</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">        * ontology:</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: EDAM</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">            * schema: http://edamontology.org/EDAM.owl</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">&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">    """</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">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t58" href="#t58">58</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_pdb_orig_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_pdb_target_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</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="nam">output_aln_orig_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_aln_target_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</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="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</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="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="com"># Call parent class constructor</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">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="t64" href="#t64">64</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="t65" href="#t65">65</a></span><span class="t">&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">self</span><span class="op">.</span><span class="nam">AA_TRANSLATOR</span> <span class="op">=</span> <span class="op">{</span><span class="str">'GLY'</span><span class="op">:</span> <span class="str">'G'</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">                              <span class="str">'ALA'</span><span class="op">:</span> <span class="str">'A'</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">                              <span class="str">'VAL'</span><span class="op">:</span> <span class="str">'V'</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">                              <span class="str">'LEU'</span><span class="op">:</span> <span class="str">'L'</span><span class="op">,</span>&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="str">'ILE'</span><span class="op">:</span> <span class="str">'I'</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">'MET'</span><span class="op">:</span> <span class="str">'M'</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">'PHE'</span><span class="op">:</span> <span class="str">'F'</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">'TRP'</span><span class="op">:</span> <span class="str">'W'</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">'PRO'</span><span class="op">:</span> <span class="str">'P'</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">'SER'</span><span class="op">:</span> <span class="str">'S'</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">'THR'</span><span class="op">:</span> <span class="str">'T'</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="str">'CYS'</span><span class="op">:</span> <span class="str">'C'</span><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">                              <span class="str">'CYX'</span><span class="op">:</span> <span class="str">'C'</span><span class="op">,</span>&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="str">'CYM'</span><span class="op">:</span> <span class="str">'C'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                              <span class="str">'TYR'</span><span class="op">:</span> <span class="str">'Y'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                              <span class="str">'TYM'</span><span class="op">:</span> <span class="str">'Y'</span><span class="op">,</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">                              <span class="str">'ASN'</span><span class="op">:</span> <span class="str">'N'</span><span class="op">,</span>&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="str">'GLN'</span><span class="op">:</span> <span class="str">'Q'</span><span class="op">,</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">                              <span class="str">'ASP'</span><span class="op">:</span> <span class="str">'D'</span><span class="op">,</span>&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="str">'ASH'</span><span class="op">:</span> <span class="str">'D'</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">                              <span class="str">'GLU'</span><span class="op">:</span> <span class="str">'E'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">                              <span class="str">'GLH'</span><span class="op">:</span> <span class="str">'E'</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">'LYS'</span><span class="op">:</span> <span class="str">'K'</span><span class="op">,</span>&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="str">'LYN'</span><span class="op">:</span> <span class="str">'K'</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">'ARG'</span><span class="op">:</span> <span class="str">'R'</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">                              <span class="str">'ARN'</span><span class="op">:</span> <span class="str">'R'</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">                              <span class="str">'HIS'</span><span class="op">:</span> <span class="str">'H'</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">'HIE'</span><span class="op">:</span> <span class="str">'H'</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">'HID'</span><span class="op">:</span> <span class="str">'H'</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">'HIP'</span><span class="op">:</span> <span class="str">'H'</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">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t97" href="#t97">97</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="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="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">'in'</span><span class="op">:</span> <span class="op">{</span><span class="str">'input_pdb_orig_path'</span><span class="op">:</span> <span class="nam">input_pdb_orig_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">                   <span class="str">'input_pdb_target_path'</span><span class="op">:</span> <span class="nam">input_pdb_target_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="t101" href="#t101">101</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span><span class="str">'output_aln_orig_path'</span><span class="op">:</span> <span class="nam">output_aln_orig_path</span><span class="op">,</span>&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="str">'output_aln_target_path'</span><span class="op">:</span> <span class="nam">output_aln_target_path</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">        <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"># Properties specific for BB</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">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="run"><span class="n"><a id="t107" href="#t107">107</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">gapopen</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">'gapopen'</span><span class="op">,</span> <span class="num">12.0</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">self</span><span class="op">.</span><span class="nam">gapextend</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">'gapextend'</span><span class="op">,</span> <span class="num">2.0</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">self</span><span class="op">.</span><span class="nam">datafile</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">'datafile'</span><span class="op">,</span> <span class="str">"EPAM250"</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">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">"water"</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"># Check the properties</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">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="t114" href="#t114">114</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="t115" href="#t115">115</a></span><span class="t">&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">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">out_err</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t117" href="#t117">117</a></span><span class="t">        <span class="str">""" Checks input/output paths correctness """</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="pln"><span class="n"><a id="t119" href="#t119">119</a></span><span class="t">        <span class="com"># Check input(s)</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">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_pdb_orig_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_pdb_orig_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"input_pdb_orig_path"</span><span class="op">,</span> <span class="key">False</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="t121" href="#t121">121</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_pdb_target_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_pdb_target_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"input_pdb_target_path"</span><span class="op">,</span> <span class="key">False</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="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"># Check output(s)</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">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_aln_orig_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_aln_orig_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"output_aln_orig_path"</span><span class="op">,</span> <span class="key">False</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="t125" href="#t125">125</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_aln_target_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_aln_target_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"output_aln_target_path"</span><span class="op">,</span> <span class="key">False</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="t126" href="#t126">126</a></span><span class="t">&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="key">def</span> <span class="nam">extract_sequence</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">pdb</span><span class="op">)</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">        <span class="str">'''</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"><span class="str">        Parses a PDB file to retrieve the sequence of a certain chain.</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"><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="nam">seq</span> <span class="op">=</span> <span class="str">''</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">resids</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</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">with</span> <span class="nam">open</span><span class="op">(</span><span class="nam">pdb</span><span class="op">)</span> <span class="key">as</span> <span class="nam">file</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="key">for</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">file</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">line</span> <span class="op">=</span> <span class="nam">line</span><span class="op">.</span><span class="nam">rstrip</span><span class="op">(</span><span class="str">'\n'</span><span class="op">)</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">record</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="op">:</span><span class="num">6</span><span class="op">]</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">" "</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="t137" href="#t137">137</a></span><span class="t">                <span class="key">if</span> <span class="nam">record</span> <span class="op">!=</span> <span class="str">'ATOM'</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="key">continue</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">atomname</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">12</span><span class="op">:</span><span class="num">16</span><span class="op">]</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">atomname</span> <span class="op">=</span> <span class="nam">atomname</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">" "</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="t141" href="#t141">141</a></span><span class="t">                <span class="key">if</span> <span class="nam">atomname</span> <span class="op">!=</span> <span class="str">'CA'</span><span class="op">:</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">continue</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="nam">alternate</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">16</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">                <span class="key">if</span> <span class="nam">alternate</span> <span class="op">!=</span> <span class="str">' '</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="key">if</span> <span class="nam">alternate</span> <span class="op">!=</span> <span class="str">'A'</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">continue</span>  <span class="com"># if alt loc, only A-labeled residues</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">resname</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">17</span><span class="op">:</span><span class="num">20</span><span class="op">]</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">" "</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="t148" href="#t148">148</a></span><span class="t">                <span class="key">if</span> <span class="nam">resname</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">AA_TRANSLATOR</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">continue</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">resnum</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">22</span><span class="op">:</span><span class="num">26</span><span class="op">]</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">" "</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="t151" href="#t151">151</a></span><span class="t">                <span class="nam">icode</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">26</span><span class="op">:</span><span class="num">27</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">seq</span> <span class="op">+=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">AA_TRANSLATOR</span><span class="op">[</span><span class="nam">resname</span><span class="op">]</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">resids</span> <span class="op">+=</span> <span class="op">[</span><span class="op">(</span><span class="str">' '</span><span class="op">,</span> <span class="nam">int</span><span class="op">(</span><span class="nam">resnum</span><span class="op">)</span><span class="op">,</span> <span class="nam">icode</span><span class="op">)</span><span class="op">]</span>  <span class="com"># BioPython's standard PDB atom id (' ',resid,insertioncode) (e.g. (' ',40,'B'))</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="run"><span class="n"><a id="t155" href="#t155">155</a></span><span class="t">        <span class="key">return</span> <span class="nam">seq</span><span class="op">,</span> <span class="nam">resids</span>&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="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="t63" href="#t63">63</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t64" href="#t64">64</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="t65" href="#t65">65</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="t66" href="#t66">66</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="t67" href="#t67">67</a></span><span class="t">&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">AA_TRANSLATOR</span> <span class="op">=</span> <span class="op">{</span><span class="str">'GLY'</span><span class="op">:</span> <span class="str">'G'</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">                              <span class="str">'ALA'</span><span class="op">:</span> <span class="str">'A'</span><span class="op">,</span>&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="str">'VAL'</span><span class="op">:</span> <span class="str">'V'</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">'LEU'</span><span class="op">:</span> <span class="str">'L'</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">'ILE'</span><span class="op">:</span> <span class="str">'I'</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">'MET'</span><span class="op">:</span> <span class="str">'M'</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">'PHE'</span><span class="op">:</span> <span class="str">'F'</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">'TRP'</span><span class="op">:</span> <span class="str">'W'</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">'PRO'</span><span class="op">:</span> <span class="str">'P'</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="str">'SER'</span><span class="op">:</span> <span class="str">'S'</span><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">                              <span class="str">'THR'</span><span class="op">:</span> <span class="str">'T'</span><span class="op">,</span>&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="str">'CYS'</span><span class="op">:</span> <span class="str">'C'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                              <span class="str">'CYX'</span><span class="op">:</span> <span class="str">'C'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                              <span class="str">'CYM'</span><span class="op">:</span> <span class="str">'C'</span><span class="op">,</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">                              <span class="str">'TYR'</span><span class="op">:</span> <span class="str">'Y'</span><span class="op">,</span>&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="str">'TYM'</span><span class="op">:</span> <span class="str">'Y'</span><span class="op">,</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">                              <span class="str">'ASN'</span><span class="op">:</span> <span class="str">'N'</span><span class="op">,</span>&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="str">'GLN'</span><span class="op">:</span> <span class="str">'Q'</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">                              <span class="str">'ASP'</span><span class="op">:</span> <span class="str">'D'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">                              <span class="str">'ASH'</span><span class="op">:</span> <span class="str">'D'</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">'GLU'</span><span class="op">:</span> <span class="str">'E'</span><span class="op">,</span>&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="str">'GLH'</span><span class="op">:</span> <span class="str">'E'</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">'LYS'</span><span class="op">:</span> <span class="str">'K'</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">                              <span class="str">'LYN'</span><span class="op">:</span> <span class="str">'K'</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">                              <span class="str">'ARG'</span><span class="op">:</span> <span class="str">'R'</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">'ARN'</span><span class="op">:</span> <span class="str">'R'</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">'HIS'</span><span class="op">:</span> <span class="str">'H'</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">'HIE'</span><span class="op">:</span> <span class="str">'H'</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">'HID'</span><span class="op">:</span> <span class="str">'H'</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">                              <span class="str">'HIP'</span><span class="op">:</span> <span class="str">'H'</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"># Input/Output files</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">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="t101" href="#t101">101</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span><span class="str">'input_pdb_orig_path'</span><span class="op">:</span> <span class="nam">input_pdb_orig_path</span><span class="op">,</span>&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="str">'input_pdb_target_path'</span><span class="op">:</span> <span class="nam">input_pdb_target_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="t103" href="#t103">103</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span><span class="str">'output_aln_orig_path'</span><span class="op">:</span> <span class="nam">output_aln_orig_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">                    <span class="str">'output_aln_target_path'</span><span class="op">:</span> <span class="nam">output_aln_target_path</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">        <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"># Properties specific for BB</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">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="run"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="nam">self</span><span class="op">.</span><span class="nam">gapopen</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">'gapopen'</span><span class="op">,</span> <span class="num">12.0</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">self</span><span class="op">.</span><span class="nam">gapextend</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">'gapextend'</span><span class="op">,</span> <span class="num">2.0</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">self</span><span class="op">.</span><span class="nam">datafile</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">'datafile'</span><span class="op">,</span> <span class="str">"EPAM250"</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">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">"water"</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"># Check the properties</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">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="t116" href="#t116">116</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="t117" href="#t117">117</a></span><span class="t">&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">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">out_err</span><span class="op">)</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="str">""" Checks input/output paths correctness """</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"># Check input(s)</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">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_pdb_orig_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_pdb_orig_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"input_pdb_orig_path"</span><span class="op">,</span> <span class="key">False</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="t123" href="#t123">123</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_pdb_target_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_pdb_target_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"input_pdb_target_path"</span><span class="op">,</span> <span class="key">False</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="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"># Check output(s)</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">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_aln_orig_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_aln_orig_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"output_aln_orig_path"</span><span class="op">,</span> <span class="key">False</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="t127" href="#t127">127</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_aln_target_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_aln_target_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"output_aln_target_path"</span><span class="op">,</span> <span class="key">False</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="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="key">def</span> <span class="nam">extract_sequence</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">pdb</span><span class="op">)</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">        <span class="str">'''</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"><span class="str">        Parses a PDB file to retrieve the sequence of a certain chain.</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="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="nam">seq</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="nam">resids</span> <span class="op">=</span> <span class="op">[</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="key">with</span> <span class="nam">open</span><span class="op">(</span><span class="nam">pdb</span><span class="op">)</span> <span class="key">as</span> <span class="nam">file</span><span class="op">:</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">for</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">file</span><span class="op">:</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="nam">line</span> <span class="op">=</span> <span class="nam">line</span><span class="op">.</span><span class="nam">rstrip</span><span class="op">(</span><span class="str">'\n'</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">record</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="op">:</span><span class="num">6</span><span class="op">]</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">" "</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="t139" href="#t139">139</a></span><span class="t">                <span class="key">if</span> <span class="nam">record</span> <span class="op">!=</span> <span class="str">'ATOM'</span><span class="op">:</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="key">continue</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="nam">atomname</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">12</span><span class="op">:</span><span class="num">16</span><span class="op">]</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">atomname</span> <span class="op">=</span> <span class="nam">atomname</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">" "</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="t143" href="#t143">143</a></span><span class="t">                <span class="key">if</span> <span class="nam">atomname</span> <span class="op">!=</span> <span class="str">'CA'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t144" href="#t144">144</a></span><span class="t">                    <span class="key">continue</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">alternate</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">16</span><span class="op">]</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">alternate</span> <span class="op">!=</span> <span class="str">' '</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t147" href="#t147">147</a></span><span class="t">                    <span class="key">if</span> <span class="nam">alternate</span> <span class="op">!=</span> <span class="str">'A'</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">continue</span>  <span class="com"># if alt loc, only A-labeled residues</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">resname</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">17</span><span class="op">:</span><span class="num">20</span><span class="op">]</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">" "</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="t150" href="#t150">150</a></span><span class="t">                <span class="key">if</span> <span class="nam">resname</span> <span class="key">not</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">AA_TRANSLATOR</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t151" href="#t151">151</a></span><span class="t">                    <span class="key">continue</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">resnum</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">22</span><span class="op">:</span><span class="num">26</span><span class="op">]</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">" "</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="t153" href="#t153">153</a></span><span class="t">                <span class="nam">icode</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">26</span><span class="op">:</span><span class="num">27</span><span class="op">]</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">seq</span> <span class="op">+=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">AA_TRANSLATOR</span><span class="op">[</span><span class="nam">resname</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="nam">resids</span> <span class="op">+=</span> <span class="op">[</span><span class="op">(</span><span class="str">' '</span><span class="op">,</span> <span class="nam">int</span><span class="op">(</span><span class="nam">resnum</span><span class="op">)</span><span class="op">,</span> <span class="nam">icode</span><span class="op">)</span><span class="op">]</span>  <span class="com"># BioPython's standard PDB atom id (' ',resid,insertioncode) (e.g. (' ',40,'B'))</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="key">def</span> <span class="nam">retrieve_alignment</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">waterFile</span><span class="op">,</span> <span class="nam">resids1</span><span class="op">,</span> <span class="nam">resids2</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="str">'''</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">        Gets the FASTA sequence of two PDB structures and a list of their residues in Biopython residue format.</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="str">        Opens a file containing a local sequence alignment (Water program of EMBOSS package) between those two PDB structures.</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="str">        Returns the sequence identity and the pairs of residues of the alignment.</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"><span class="str">        '''</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="com"># Parsing Water alignment file</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="nam">is_alignment</span> <span class="op">=</span> <span class="num">0</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">is_qseq</span> <span class="op">=</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">is_sseq</span> <span class="op">=</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">qseq</span> <span class="op">=</span> <span class="str">""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">sseq</span> <span class="op">=</span> <span class="str">""</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">ident</span> <span class="op">=</span> <span class="str">""</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">next_seq</span> <span class="op">=</span> <span class="num">0</span>&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="nam">qstart</span> <span class="op">=</span> <span class="str">""</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">sstart</span> <span class="op">=</span> <span class="str">""</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="key">with</span> <span class="nam">open</span><span class="op">(</span><span class="nam">waterFile</span><span class="op">)</span> <span class="key">as</span> <span class="nam">file</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">            <span class="key">for</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">file</span><span class="op">:</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">line</span> <span class="op">=</span> <span class="nam">line</span><span class="op">.</span><span class="nam">rstrip</span><span class="op">(</span><span class="str">"\n"</span><span class="op">)</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="key">if</span> <span class="nam">is_alignment</span> <span class="op">==</span> <span class="num">0</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">                    <span class="key">if</span> <span class="key">not</span> <span class="nam">line</span><span class="op">.</span><span class="nam">startswith</span><span class="op">(</span><span class="str">">>#1"</span><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="key">continue</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="key">else</span><span class="op">:</span>&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">is_alignment</span> <span class="op">=</span> <span class="num">1</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="key">else</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="key">if</span> <span class="nam">line</span><span class="op">.</span><span class="nam">startswith</span><span class="op">(</span><span class="str">"; sw_ident:"</span><span class="op">)</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">ident</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">12</span><span class="op">:</span><span class="op">]</span>&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="key">elif</span> <span class="nam">line</span><span class="op">.</span><span class="nam">startswith</span><span class="op">(</span><span class="str">"; al_start:"</span><span class="op">)</span><span class="op">:</span>&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">if</span> <span class="nam">next_seq</span> <span class="op">==</span> <span class="num">0</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="nam">qstart</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">12</span><span class="op">:</span><span class="op">]</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="key">else</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="nam">sstart</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">12</span><span class="op">:</span><span class="op">]</span>&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">elif</span> <span class="nam">line</span><span class="op">.</span><span class="nam">startswith</span><span class="op">(</span><span class="str">"; al_display_start:"</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">                        <span class="key">if</span> <span class="nam">next_seq</span> <span class="op">==</span> <span class="num">0</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">                            <span class="nam">is_qseq</span> <span class="op">=</span> <span class="num">1</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="key">else</span><span class="op">:</span>&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="nam">is_sseq</span> <span class="op">=</span> <span class="num">1</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="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">                        <span class="key">if</span> <span class="nam">is_qseq</span> <span class="op">==</span> <span class="num">1</span><span class="op">:</span>&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="key">not</span> <span class="nam">line</span><span class="op">.</span><span class="nam">startswith</span><span class="op">(</span><span class="str">">"</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="nam">qseq</span> <span class="op">=</span> <span class="nam">qseq</span> <span class="op">+</span> <span class="nam">line</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="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">                                <span class="nam">is_qseq</span> <span class="op">=</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">                                <span class="nam">next_seq</span> <span class="op">=</span> <span class="num">1</span>&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">is_sseq</span> <span class="op">==</span> <span class="num">1</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">                            <span class="key">if</span> <span class="nam">line</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="t203" href="#t203">203</a></span><span class="t">                                <span class="nam">sseq</span> <span class="op">=</span> <span class="nam">sseq</span> <span class="op">+</span> <span class="nam">line</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">                            <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t205" href="#t205">205</a></span><span class="t">                                <span class="nam">is_sseq</span> <span class="op">=</span> <span class="num">0</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="pln"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">        <span class="com"># Get the Sequence Identity of the alignment</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">        <span class="nam">seq_id</span> <span class="op">=</span> <span class="nam">float</span><span class="op">(</span><span class="nam">ident</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">&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="com"># Get the residues of the alignment.</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="com"># -2 is applied because in the first iteration of next loop all values will always be increased by 1 (local alignment)</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">        <span class="com"># and we also need to convert the number into a python index to retrieve the proper token in the list</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t213" href="#t213">213</a></span><span class="t">        <span class="nam">resid_pairs</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span>&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="nam">idx1</span> <span class="op">=</span> <span class="nam">int</span><span class="op">(</span><span class="nam">qstart</span><span class="op">)</span><span class="op">-</span><span class="num">2</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">idx2</span> <span class="op">=</span> <span class="nam">int</span><span class="op">(</span><span class="nam">sstart</span><span class="op">)</span><span class="op">-</span><span class="num">2</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="key">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">qseq</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>  <span class="com"># it could be also len(sseq)</span>&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">qseq</span><span class="op">[</span><span class="nam">i</span><span class="op">]</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="t218" href="#t218">218</a></span><span class="t">                <span class="nam">idx1</span> <span class="op">+=</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">            <span class="key">if</span> <span class="nam">sseq</span><span class="op">[</span><span class="nam">i</span><span class="op">]</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="t220" href="#t220">220</a></span><span class="t">                <span class="nam">idx2</span> <span class="op">+=</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">            <span class="key">if</span> <span class="nam">qseq</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="op">==</span> <span class="str">'-'</span> <span class="key">or</span> <span class="nam">sseq</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="op">==</span> <span class="str">'-'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">                <span class="key">continue</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">            <span class="nam">resid_pairs</span> <span class="op">+=</span> <span class="op">[</span><span class="op">(</span><span class="nam">resids1</span><span class="op">[</span><span class="nam">idx1</span><span class="op">]</span><span class="op">,</span> <span class="nam">resids2</span><span class="op">[</span><span class="nam">idx2</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="t224" href="#t224">224</a></span><span class="t">        <span class="com"># Check contents of the residues of the alignment</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">        <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">resid_pairs</span><span class="op">)</span> <span class="op">==</span> <span class="num">0</span><span class="op">:</span>  <span class="com"># Alignment file was empty or there was no possible matching residues between the PDBs</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Alignment file was empty or there was no possible matching residues between the PDBs'</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="str">"unique_dir"</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">            <span class="key">return</span> <span class="key">False</span><span class="op">,</span> <span class="key">False</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">            <span class="key">return</span> <span class="nam">seq_id</span><span class="op">,</span> <span class="nam">resid_pairs</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t231" href="#t231">231</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="t232" href="#t232">232</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>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">        <span class="str">"""Launches the execution of the GOdMDPrep module."""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t234" href="#t234">234</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t235" href="#t235">235</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="t236" href="#t236">236</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="t237" href="#t237">237</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t238" href="#t238">238</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="t239" href="#t239">239</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="t240" href="#t240">240</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="t241" href="#t241">241</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="t242" href="#t242">242</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t243" href="#t243">243</a></span><span class="t">        <span class="com"># Starting the work...</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">        <span class="com"># Parsing the input PDB files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="nam">pdb1</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_pdb_orig_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="nam">pdb2</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_pdb_target_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">        <span class="com"># Generate sequence of first PDB</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">        <span class="nam">seq1</span><span class="op">,</span> <span class="nam">resids1</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">extract_sequence</span><span class="op">(</span><span class="nam">pdb1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="com"># Generate sequence of second PDB</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">        <span class="nam">seq2</span><span class="op">,</span> <span class="nam">resids2</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">extract_sequence</span><span class="op">(</span><span class="nam">pdb2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">        <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">seq1</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">50</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'WARNING: Short sequence (ORIGIN)'</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="str">"unique_dir"</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</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="t256" href="#t256">256</a></span><span class="t">        <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">seq2</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">50</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'WARNING: Short sequence (TARGET)'</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="str">"unique_dir"</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</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="t258" href="#t258">258</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">        <span class="com"># Produce FASTA files</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">        <span class="nam">name1</span> <span class="op">=</span> <span class="str">"fasta1.fa"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">        <span class="nam">name2</span> <span class="op">=</span> <span class="str">"fasta2.fa"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">        <span class="nam">fasta1Filename</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">Path</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="str">"unique_dir"</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="nam">name1</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">        <span class="nam">fasta1File</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">fasta1Filename</span><span class="op">,</span> <span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">        <span class="nam">fasta1File</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">">"</span><span class="op">+</span><span class="nam">pdb1</span><span class="op">+</span><span class="str">"\n"</span><span class="op">+</span><span class="nam">seq1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">        <span class="nam">fasta1File</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">        <span class="nam">fasta2Filename</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">Path</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="str">"unique_dir"</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="nam">name2</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">        <span class="nam">fasta2File</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">fasta2Filename</span><span class="op">,</span> <span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">        <span class="nam">fasta2File</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">">"</span><span class="op">+</span><span class="nam">pdb2</span><span class="op">+</span><span class="str">"\n"</span><span class="op">+</span><span class="nam">seq2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">        <span class="nam">fasta2File</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">        <span class="nam">waterFilename</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">Path</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="str">"unique_dir"</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="str">"water_align.out"</span><span class="op">)</span><span class="op">)</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">return</span> <span class="nam">seq</span><span class="op">,</span> <span class="nam">resids</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">&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="key">def</span> <span class="nam">retrieve_alignment</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">waterFile</span><span class="op">,</span> <span class="nam">resids1</span><span class="op">,</span> <span class="nam">resids2</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="str">'''</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="str">        Gets the FASTA sequence of two PDB structures and a list of their residues in Biopython residue format.</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"><span class="str">        Opens a file containing a local sequence alignment (Water program of EMBOSS package) between those two PDB structures.</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="str">        Returns the sequence identity and the pairs of residues of the alignment.</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="str">        '''</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">        <span class="com"># Parsing Water alignment file</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">is_alignment</span> <span class="op">=</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">is_qseq</span> <span class="op">=</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t168" href="#t168">168</a></span><span class="t">        <span class="nam">is_sseq</span> <span class="op">=</span> <span class="num">0</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">qseq</span> <span class="op">=</span> <span class="str">""</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">sseq</span> <span class="op">=</span> <span class="str">""</span>&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="nam">ident</span> <span class="op">=</span> <span class="str">""</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">next_seq</span> <span class="op">=</span> <span class="num">0</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">qstart</span> <span class="op">=</span> <span class="str">""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t174" href="#t174">174</a></span><span class="t">        <span class="nam">sstart</span> <span class="op">=</span> <span class="str">""</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="key">with</span> <span class="nam">open</span><span class="op">(</span><span class="nam">waterFile</span><span class="op">)</span> <span class="key">as</span> <span class="nam">file</span><span class="op">:</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="key">for</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">file</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t177" href="#t177">177</a></span><span class="t">                <span class="nam">line</span> <span class="op">=</span> <span class="nam">line</span><span class="op">.</span><span class="nam">rstrip</span><span class="op">(</span><span class="str">"\n"</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="key">if</span> <span class="nam">is_alignment</span> <span class="op">==</span> <span class="num">0</span><span class="op">:</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="key">if</span> <span class="key">not</span> <span class="nam">line</span><span class="op">.</span><span class="nam">startswith</span><span class="op">(</span><span class="str">">>#1"</span><span class="op">)</span><span class="op">:</span>&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="key">continue</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="key">else</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">is_alignment</span> <span class="op">=</span> <span class="num">1</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">                <span class="key">else</span><span class="op">:</span>&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="key">if</span> <span class="nam">line</span><span class="op">.</span><span class="nam">startswith</span><span class="op">(</span><span class="str">"; sw_ident:"</span><span class="op">)</span><span class="op">:</span>&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="nam">ident</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">12</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">elif</span> <span class="nam">line</span><span class="op">.</span><span class="nam">startswith</span><span class="op">(</span><span class="str">"; al_start:"</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t187" href="#t187">187</a></span><span class="t">                        <span class="key">if</span> <span class="nam">next_seq</span> <span class="op">==</span> <span class="num">0</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="nam">qstart</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">12</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">                        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t190" href="#t190">190</a></span><span class="t">                            <span class="nam">sstart</span> <span class="op">=</span> <span class="nam">line</span><span class="op">[</span><span class="num">12</span><span class="op">:</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t191" href="#t191">191</a></span><span class="t">                    <span class="key">elif</span> <span class="nam">line</span><span class="op">.</span><span class="nam">startswith</span><span class="op">(</span><span class="str">"; al_display_start:"</span><span class="op">)</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">if</span> <span class="nam">next_seq</span> <span class="op">==</span> <span class="num">0</span><span class="op">:</span>&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="nam">is_qseq</span> <span class="op">=</span> <span class="num">1</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="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t195" href="#t195">195</a></span><span class="t">                            <span class="nam">is_sseq</span> <span class="op">=</span> <span class="num">1</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">                    <span class="key">else</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">if</span> <span class="nam">is_qseq</span> <span class="op">==</span> <span class="num">1</span><span class="op">:</span>&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="key">not</span> <span class="nam">line</span><span class="op">.</span><span class="nam">startswith</span><span class="op">(</span><span class="str">">"</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t199" href="#t199">199</a></span><span class="t">                                <span class="nam">qseq</span> <span class="op">=</span> <span class="nam">qseq</span> <span class="op">+</span> <span class="nam">line</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t200" href="#t200">200</a></span><span class="t">                            <span class="key">else</span><span class="op">:</span>&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="nam">is_qseq</span> <span class="op">=</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t202" href="#t202">202</a></span><span class="t">                                <span class="nam">next_seq</span> <span class="op">=</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t203" href="#t203">203</a></span><span class="t">                        <span class="key">if</span> <span class="nam">is_sseq</span> <span class="op">==</span> <span class="num">1</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t204" href="#t204">204</a></span><span class="t">                            <span class="key">if</span> <span class="nam">line</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="t205" href="#t205">205</a></span><span class="t">                                <span class="nam">sseq</span> <span class="op">=</span> <span class="nam">sseq</span> <span class="op">+</span> <span class="nam">line</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">                            <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t207" href="#t207">207</a></span><span class="t">                                <span class="nam">is_sseq</span> <span class="op">=</span> <span class="num">0</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">        <span class="com"># Get the Sequence Identity of the alignment</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t">        <span class="nam">seq_id</span> <span class="op">=</span> <span class="nam">float</span><span class="op">(</span><span class="nam">ident</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"># Get the residues of the alignment.</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="com"># -2 is applied because in the first iteration of next loop all values will always be increased by 1 (local alignment)</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="com"># and we also need to convert the number into a python index to retrieve the proper token in the list</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">        <span class="nam">resid_pairs</span> <span class="op">=</span> <span class="op">[</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t216" href="#t216">216</a></span><span class="t">        <span class="nam">idx1</span> <span class="op">=</span> <span class="nam">int</span><span class="op">(</span><span class="nam">qstart</span><span class="op">)</span><span class="op">-</span><span class="num">2</span>&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="nam">idx2</span> <span class="op">=</span> <span class="nam">int</span><span class="op">(</span><span class="nam">sstart</span><span class="op">)</span><span class="op">-</span><span class="num">2</span>&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">for</span> <span class="nam">i</span> <span class="key">in</span> <span class="nam">range</span><span class="op">(</span><span class="nam">len</span><span class="op">(</span><span class="nam">qseq</span><span class="op">)</span><span class="op">)</span><span class="op">:</span>  <span class="com"># it could be also len(sseq)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">            <span class="key">if</span> <span class="nam">qseq</span><span class="op">[</span><span class="nam">i</span><span class="op">]</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="t220" href="#t220">220</a></span><span class="t">                <span class="nam">idx1</span> <span class="op">+=</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">            <span class="key">if</span> <span class="nam">sseq</span><span class="op">[</span><span class="nam">i</span><span class="op">]</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="t222" href="#t222">222</a></span><span class="t">                <span class="nam">idx2</span> <span class="op">+=</span> <span class="num">1</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">            <span class="key">if</span> <span class="nam">qseq</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="op">==</span> <span class="str">'-'</span> <span class="key">or</span> <span class="nam">sseq</span><span class="op">[</span><span class="nam">i</span><span class="op">]</span> <span class="op">==</span> <span class="str">'-'</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">                <span class="key">continue</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">            <span class="nam">resid_pairs</span> <span class="op">+=</span> <span class="op">[</span><span class="op">(</span><span class="nam">resids1</span><span class="op">[</span><span class="nam">idx1</span><span class="op">]</span><span class="op">,</span> <span class="nam">resids2</span><span class="op">[</span><span class="nam">idx2</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="t226" href="#t226">226</a></span><span class="t">        <span class="com"># Check contents of the residues of the alignment</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t227" href="#t227">227</a></span><span class="t">        <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">resid_pairs</span><span class="op">)</span> <span class="op">==</span> <span class="num">0</span><span class="op">:</span>  <span class="com"># Alignment file was empty or there was no possible matching residues between the PDBs</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'Alignment file was empty or there was no possible matching residues between the PDBs'</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="str">"unique_dir"</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">out_log</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t229" href="#t229">229</a></span><span class="t">            <span class="key">return</span> <span class="key">False</span><span class="op">,</span> <span class="key">False</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t230" href="#t230">230</a></span><span class="t">        <span class="key">else</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">            <span class="key">return</span> <span class="nam">seq_id</span><span class="op">,</span> <span class="nam">resid_pairs</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t232" href="#t232">232</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t233" href="#t233">233</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="t234" href="#t234">234</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>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t235" href="#t235">235</a></span><span class="t">        <span class="str">"""Launches the execution of the GOdMDPrep module."""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t236" href="#t236">236</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t237" href="#t237">237</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="t238" href="#t238">238</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="t239" href="#t239">239</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t240" href="#t240">240</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="t241" href="#t241">241</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="t242" href="#t242">242</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="t243" href="#t243">243</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="t244" href="#t244">244</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t245" href="#t245">245</a></span><span class="t">        <span class="com"># Starting the work...</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">        <span class="com"># Parsing the input PDB files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t247" href="#t247">247</a></span><span class="t">        <span class="nam">pdb1</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_pdb_orig_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">        <span class="nam">pdb2</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_pdb_target_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">        <span class="com"># Generate sequence of first PDB</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">        <span class="nam">seq1</span><span class="op">,</span> <span class="nam">resids1</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">extract_sequence</span><span class="op">(</span><span class="nam">pdb1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">        <span class="com"># Generate sequence of second PDB</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">        <span class="nam">seq2</span><span class="op">,</span> <span class="nam">resids2</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">extract_sequence</span><span class="op">(</span><span class="nam">pdb2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">        <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">seq1</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">50</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'WARNING: Short sequence (ORIGIN)'</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="str">"unique_dir"</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</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="t258" href="#t258">258</a></span><span class="t">        <span class="key">if</span> <span class="nam">len</span><span class="op">(</span><span class="nam">seq2</span><span class="op">)</span> <span class="op">&lt;</span> <span class="num">50</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">            <span class="nam">fu</span><span class="op">.</span><span class="nam">log</span><span class="op">(</span><span class="str">'WARNING: Short sequence (TARGET)'</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="str">"unique_dir"</span><span class="op">]</span><span class="op">,</span> <span class="nam">self</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="t260" href="#t260">260</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">        <span class="com"># Produce FASTA files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t262" href="#t262">262</a></span><span class="t">        <span class="nam">name1</span> <span class="op">=</span> <span class="str">"fasta1.fa"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">        <span class="nam">name2</span> <span class="op">=</span> <span class="str">"fasta2.fa"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t264" href="#t264">264</a></span><span class="t">        <span class="nam">fasta1Filename</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">Path</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="str">"unique_dir"</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="nam">name1</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t265" href="#t265">265</a></span><span class="t">        <span class="nam">fasta1File</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">fasta1Filename</span><span class="op">,</span> <span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t266" href="#t266">266</a></span><span class="t">        <span class="nam">fasta1File</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">">"</span><span class="op">+</span><span class="nam">pdb1</span><span class="op">+</span><span class="str">"\n"</span><span class="op">+</span><span class="nam">seq1</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t267" href="#t267">267</a></span><span class="t">        <span class="nam">fasta1File</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t268" href="#t268">268</a></span><span class="t">        <span class="nam">fasta2Filename</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">Path</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="str">"unique_dir"</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="nam">name2</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t269" href="#t269">269</a></span><span class="t">        <span class="nam">fasta2File</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">fasta2Filename</span><span class="op">,</span> <span class="str">"w"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t270" href="#t270">270</a></span><span class="t">        <span class="nam">fasta2File</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">">"</span><span class="op">+</span><span class="nam">pdb2</span><span class="op">+</span><span class="str">"\n"</span><span class="op">+</span><span class="nam">seq2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t271" href="#t271">271</a></span><span class="t">        <span class="nam">fasta2File</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t272" href="#t272">272</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">        <span class="com"># water -auto -outfile=water_align.out -asequence=1ake.chains.nolig.pdb.fa</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">        <span class="com"># -bsequence=4ake.chains.pdb.fa -gapopen=12 -gapextend=2</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">        <span class="com"># -datafile=EPAM250 -aformat=markx10</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">        <span class="com"># Command line</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t278" href="#t278">278</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="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="t279" href="#t279">279</a></span><span class="t">                    <span class="str">'-auto'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t280" href="#t280">280</a></span><span class="t">                    <span class="str">'-outfile'</span><span class="op">,</span> <span class="nam">waterFilename</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t281" href="#t281">281</a></span><span class="t">                    <span class="str">'-asequence'</span><span class="op">,</span> <span class="nam">fasta1Filename</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t">                    <span class="str">'-bsequence'</span><span class="op">,</span> <span class="nam">fasta2Filename</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">                    <span class="str">'-gapopen'</span><span class="op">,</span> <span class="nam">str</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">gapopen</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t284" href="#t284">284</a></span><span class="t">                    <span class="str">'-gapextend'</span><span class="op">,</span> <span class="nam">str</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">gapextend</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t">                    <span class="str">'-datafile'</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">datafile</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t286" href="#t286">286</a></span><span class="t">                    <span class="str">'-aformat'</span><span class="op">,</span> <span class="str">"markx10"</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t287" href="#t287">287</a></span><span class="t">                    <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t288" href="#t288">288</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t289" href="#t289">289</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="t290" href="#t290">290</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="t291" href="#t291">291</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t292" href="#t292">292</a></span><span class="t">        <span class="com"># Starting post-alignment process: generating .aln files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t273" href="#t273">273</a></span><span class="t">        <span class="nam">waterFilename</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">Path</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="str">"unique_dir"</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="str">"water_align.out"</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t274" href="#t274">274</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t275" href="#t275">275</a></span><span class="t">        <span class="com"># water -auto -outfile=water_align.out -asequence=1ake.chains.nolig.pdb.fa</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t276" href="#t276">276</a></span><span class="t">        <span class="com"># -bsequence=4ake.chains.pdb.fa -gapopen=12 -gapextend=2</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t277" href="#t277">277</a></span><span class="t">        <span class="com"># -datafile=EPAM250 -aformat=markx10</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t278" href="#t278">278</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t279" href="#t279">279</a></span><span class="t">        <span class="com"># Command line</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t280" href="#t280">280</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="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="t281" href="#t281">281</a></span><span class="t">                    <span class="str">'-auto'</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t282" href="#t282">282</a></span><span class="t">                    <span class="str">'-outfile'</span><span class="op">,</span> <span class="nam">waterFilename</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t283" href="#t283">283</a></span><span class="t">                    <span class="str">'-asequence'</span><span class="op">,</span> <span class="nam">fasta1Filename</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t284" href="#t284">284</a></span><span class="t">                    <span class="str">'-bsequence'</span><span class="op">,</span> <span class="nam">fasta2Filename</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t285" href="#t285">285</a></span><span class="t">                    <span class="str">'-gapopen'</span><span class="op">,</span> <span class="nam">str</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">gapopen</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t286" href="#t286">286</a></span><span class="t">                    <span class="str">'-gapextend'</span><span class="op">,</span> <span class="nam">str</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">gapextend</span><span class="op">)</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t287" href="#t287">287</a></span><span class="t">                    <span class="str">'-datafile'</span><span class="op">,</span> <span class="nam">self</span><span class="op">.</span><span class="nam">datafile</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t288" href="#t288">288</a></span><span class="t">                    <span class="str">'-aformat'</span><span class="op">,</span> <span class="str">"markx10"</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t289" href="#t289">289</a></span><span class="t">                    <span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t290" href="#t290">290</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t291" href="#t291">291</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="t292" href="#t292">292</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="t293" href="#t293">293</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t294" href="#t294">294</a></span><span class="t">        <span class="com"># Retrieve sequence identity of the pair, based on local sequence alignment</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t295" href="#t295">295</a></span><span class="t">        <span class="com"># previously computed, and generate the pairs of residues from both structres</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t296" href="#t296">296</a></span><span class="t">        <span class="com"># to drive the superimposition</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t297" href="#t297">297</a></span><span class="t">        <span class="nam">seq_id</span><span class="op">,</span> <span class="nam">resid_pairs</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">retrieve_alignment</span><span class="op">(</span><span class="nam">waterFilename</span><span class="op">,</span> <span class="nam">resids1</span><span class="op">,</span> <span class="nam">resids2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t298" href="#t298">298</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t299" href="#t299">299</a></span><span class="t">        <span class="nam">aln1Filename</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_aln_orig_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t300" href="#t300">300</a></span><span class="t">        <span class="nam">aln1File</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">aln1Filename</span><span class="op">,</span> <span class="str">'w'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t301" href="#t301">301</a></span><span class="t">        <span class="key">for</span> <span class="nam">pair</span> <span class="key">in</span> <span class="nam">resid_pairs</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t302" href="#t302">302</a></span><span class="t">            <span class="nam">aln1File</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"%s%s\n"</span> <span class="op">%</span> <span class="op">(</span><span class="nam">pair</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">,</span> <span class="nam">pair</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">[</span><span class="num">2</span><span class="op">]</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">" "</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t303" href="#t303">303</a></span><span class="t">        <span class="nam">aln1File</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t304" href="#t304">304</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t305" href="#t305">305</a></span><span class="t">        <span class="nam">aln2Filename</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_aln_target_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t306" href="#t306">306</a></span><span class="t">        <span class="nam">aln2File</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">aln2Filename</span><span class="op">,</span> <span class="str">'w'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t307" href="#t307">307</a></span><span class="t">        <span class="key">for</span> <span class="nam">pair</span> <span class="key">in</span> <span class="nam">resid_pairs</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t308" href="#t308">308</a></span><span class="t">            <span class="nam">aln2File</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"%s%s\n"</span> <span class="op">%</span> <span class="op">(</span><span class="nam">pair</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">,</span> <span class="nam">pair</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">[</span><span class="num">2</span><span class="op">]</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">" "</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t309" href="#t309">309</a></span><span class="t">        <span class="nam">aln2File</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t310" href="#t310">310</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t311" href="#t311">311</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="t312" href="#t312">312</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="t313" href="#t313">313</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t314" href="#t314">314</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="t315" href="#t315">315</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="t316" href="#t316">316</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="t317" href="#t317">317</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="t318" href="#t318">318</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="t319" href="#t319">319</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t320" href="#t320">320</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="t294" href="#t294">294</a></span><span class="t">        <span class="com"># Starting post-alignment process: generating .aln files</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t295" href="#t295">295</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t296" href="#t296">296</a></span><span class="t">        <span class="com"># Retrieve sequence identity of the pair, based on local sequence alignment</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t297" href="#t297">297</a></span><span class="t">        <span class="com"># previously computed, and generate the pairs of residues from both structres</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t298" href="#t298">298</a></span><span class="t">        <span class="com"># to drive the superimposition</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t299" href="#t299">299</a></span><span class="t">        <span class="nam">seq_id</span><span class="op">,</span> <span class="nam">resid_pairs</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">retrieve_alignment</span><span class="op">(</span><span class="nam">waterFilename</span><span class="op">,</span> <span class="nam">resids1</span><span class="op">,</span> <span class="nam">resids2</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t300" href="#t300">300</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t301" href="#t301">301</a></span><span class="t">        <span class="nam">aln1Filename</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_aln_orig_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t302" href="#t302">302</a></span><span class="t">        <span class="nam">aln1File</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">aln1Filename</span><span class="op">,</span> <span class="str">'w'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t303" href="#t303">303</a></span><span class="t">        <span class="key">for</span> <span class="nam">pair</span> <span class="key">in</span> <span class="nam">resid_pairs</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t304" href="#t304">304</a></span><span class="t">            <span class="nam">aln1File</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"%s%s\n"</span> <span class="op">%</span> <span class="op">(</span><span class="nam">pair</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">,</span> <span class="nam">pair</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">[</span><span class="num">2</span><span class="op">]</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">" "</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t305" href="#t305">305</a></span><span class="t">        <span class="nam">aln1File</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t306" href="#t306">306</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t307" href="#t307">307</a></span><span class="t">        <span class="nam">aln2Filename</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_aln_target_path"</span><span class="op">]</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t308" href="#t308">308</a></span><span class="t">        <span class="nam">aln2File</span> <span class="op">=</span> <span class="nam">open</span><span class="op">(</span><span class="nam">aln2Filename</span><span class="op">,</span> <span class="str">'w'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t309" href="#t309">309</a></span><span class="t">        <span class="key">for</span> <span class="nam">pair</span> <span class="key">in</span> <span class="nam">resid_pairs</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t310" href="#t310">310</a></span><span class="t">            <span class="nam">aln2File</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"%s%s\n"</span> <span class="op">%</span> <span class="op">(</span><span class="nam">pair</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">,</span> <span class="nam">pair</span><span class="op">[</span><span class="num">1</span><span class="op">]</span><span class="op">[</span><span class="num">2</span><span class="op">]</span><span class="op">.</span><span class="nam">replace</span><span class="op">(</span><span class="str">" "</span><span class="op">,</span> <span class="str">""</span><span class="op">)</span><span class="op">)</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t311" href="#t311">311</a></span><span class="t">        <span class="nam">aln2File</span><span class="op">.</span><span class="nam">close</span><span class="op">(</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t312" href="#t312">312</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t313" href="#t313">313</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="t314" href="#t314">314</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="t315" href="#t315">315</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t316" href="#t316">316</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="t317" href="#t317">317</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="t318" href="#t318">318</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> <span class="str">""</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t319" href="#t319">319</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="t320" href="#t320">320</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="t321" href="#t321">321</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t322" href="#t322">322</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="run"><span class="n"><a id="t322" href="#t322">322</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="t323" href="#t323">323</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t324" href="#t324">324</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t325" href="#t325">325</a></span><span class="t"><span class="key">def</span> <span class="nam">godmd_prep</span><span class="op">(</span><span class="nam">input_pdb_orig_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_pdb_target_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t326" href="#t326">326</a></span><span class="t">               <span class="nam">output_aln_orig_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_aln_target_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t327" href="#t327">327</a></span><span class="t">               <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="t328" href="#t328">328</a></span><span class="t">    <span class="str">"""Create :class:`GOdMDPrep &lt;godmd.godmd_prep.GOdMDPrep>`godmd.godmd_prep.GOdMDPrep class and</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t329" href="#t329">329</a></span><span class="t"><span class="str">    execute :meth:`launch() &lt;godmd.godmd_prep.GOdMDPrep.launch>` method"""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t330" href="#t330">330</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t331" href="#t331">331</a></span><span class="t">    <span class="key">return</span> <span class="nam">GOdMDPrep</span><span class="op">(</span><span class="nam">input_pdb_orig_path</span><span class="op">=</span><span class="nam">input_pdb_orig_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t332" href="#t332">332</a></span><span class="t">                     <span class="nam">input_pdb_target_path</span><span class="op">=</span><span class="nam">input_pdb_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t333" href="#t333">333</a></span><span class="t">                     <span class="nam">output_aln_orig_path</span><span class="op">=</span><span class="nam">output_aln_orig_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t334" href="#t334">334</a></span><span class="t">                     <span class="nam">output_aln_target_path</span><span class="op">=</span><span class="nam">output_aln_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t335" href="#t335">335</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">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="t336" href="#t336">336</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t337" href="#t337">337</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t338" href="#t338">338</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="mis show_mis"><span class="n"><a id="t339" href="#t339">339</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">'Prepares input files for the GOdMD tool.'</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="t340" href="#t340">340</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="t341" href="#t341">341</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t342" href="#t342">342</a></span><span class="t">    <span class="com"># Specific args</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t343" href="#t343">343</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="t344" href="#t344">344</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_pdb_orig_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">'Input PDB file to be used as origin in the conformational transition. Accepted formats: pdb.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t345" href="#t345">345</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_pdb_target_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">'Input PDB file to be used as target in the conformational transition. Accepted formats: pdb.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t346" href="#t346">346</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_aln_orig_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">'Output GOdMD alignment file corresponding to the origin structure of the conformational transition. Accepted formats: aln, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t347" href="#t347">347</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_aln_target_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">'Output GOdMD alignment file corresponding to the target structure of the conformational transition. Accepted formats: aln, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t348" href="#t348">348</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t349" href="#t349">349</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="pln"><span class="n"><a id="t350" href="#t350">350</a></span><span class="t">    <span class="com"># config = args.config if args.config else None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t351" href="#t351">351</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="pln"><span class="n"><a id="t352" href="#t352">352</a></span><span class="t">    <span class="com"># properties = settings.ConfReader(config=config).get_prop_dic()</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t353" href="#t353">353</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="t354" href="#t354">354</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t355" href="#t355">355</a></span><span class="t">    <span class="com"># Specific call</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t356" href="#t356">356</a></span><span class="t">    <span class="nam">godmd_prep</span><span class="op">(</span><span class="nam">input_pdb_orig_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_pdb_orig_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t357" href="#t357">357</a></span><span class="t">               <span class="nam">input_pdb_target_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_pdb_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t358" href="#t358">358</a></span><span class="t">               <span class="nam">output_aln_orig_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_aln_orig_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t359" href="#t359">359</a></span><span class="t">               <span class="nam">output_aln_target_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_aln_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t360" href="#t360">360</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="t361" href="#t361">361</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t362" href="#t362">362</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t363" href="#t363">363</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="t364" href="#t364">364</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="t324" href="#t324">324</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="t325" href="#t325">325</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t326" href="#t326">326</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t327" href="#t327">327</a></span><span class="t"><span class="key">def</span> <span class="nam">godmd_prep</span><span class="op">(</span><span class="nam">input_pdb_orig_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_pdb_target_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t328" href="#t328">328</a></span><span class="t">               <span class="nam">output_aln_orig_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_aln_target_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t329" href="#t329">329</a></span><span class="t">               <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</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="t330" href="#t330">330</a></span><span class="t">    <span class="str">"""Create :class:`GOdMDPrep &lt;godmd.godmd_prep.GOdMDPrep>`godmd.godmd_prep.GOdMDPrep class and</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t331" href="#t331">331</a></span><span class="t"><span class="str">    execute :meth:`launch() &lt;godmd.godmd_prep.GOdMDPrep.launch>` method"""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t332" href="#t332">332</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t333" href="#t333">333</a></span><span class="t">    <span class="key">return</span> <span class="nam">GOdMDPrep</span><span class="op">(</span><span class="nam">input_pdb_orig_path</span><span class="op">=</span><span class="nam">input_pdb_orig_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t334" href="#t334">334</a></span><span class="t">                     <span class="nam">input_pdb_target_path</span><span class="op">=</span><span class="nam">input_pdb_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t335" href="#t335">335</a></span><span class="t">                     <span class="nam">output_aln_orig_path</span><span class="op">=</span><span class="nam">output_aln_orig_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t336" href="#t336">336</a></span><span class="t">                     <span class="nam">output_aln_target_path</span><span class="op">=</span><span class="nam">output_aln_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t337" href="#t337">337</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">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="t338" href="#t338">338</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t339" href="#t339">339</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t340" href="#t340">340</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="mis show_mis"><span class="n"><a id="t341" href="#t341">341</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">'Prepares input files for the GOdMD tool.'</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="t342" href="#t342">342</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="t343" href="#t343">343</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t344" href="#t344">344</a></span><span class="t">    <span class="com"># Specific args</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t345" href="#t345">345</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="t346" href="#t346">346</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_pdb_orig_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">'Input PDB file to be used as origin in the conformational transition. Accepted formats: pdb.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t347" href="#t347">347</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_pdb_target_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">'Input PDB file to be used as target in the conformational transition. Accepted formats: pdb.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t348" href="#t348">348</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_aln_orig_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">'Output GOdMD alignment file corresponding to the origin structure of the conformational transition. Accepted formats: aln, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t349" href="#t349">349</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_aln_target_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">'Output GOdMD alignment file corresponding to the target structure of the conformational transition. Accepted formats: aln, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t350" href="#t350">350</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t351" href="#t351">351</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="pln"><span class="n"><a id="t352" href="#t352">352</a></span><span class="t">    <span class="com"># config = args.config if args.config else None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t353" href="#t353">353</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="pln"><span class="n"><a id="t354" href="#t354">354</a></span><span class="t">    <span class="com"># properties = settings.ConfReader(config=config).get_prop_dic()</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t355" href="#t355">355</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="t356" href="#t356">356</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t357" href="#t357">357</a></span><span class="t">    <span class="com"># Specific call</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t358" href="#t358">358</a></span><span class="t">    <span class="nam">godmd_prep</span><span class="op">(</span><span class="nam">input_pdb_orig_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_pdb_orig_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t359" href="#t359">359</a></span><span class="t">               <span class="nam">input_pdb_target_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_pdb_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t360" href="#t360">360</a></span><span class="t">               <span class="nam">output_aln_orig_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_aln_orig_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t361" href="#t361">361</a></span><span class="t">               <span class="nam">output_aln_target_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_aln_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t362" href="#t362">362</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="t363" href="#t363">363</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t364" href="#t364">364</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t365" href="#t365">365</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="t366" href="#t366">366</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>
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diff --git a/coverage/z_c296ee536f0b791d_godmd_run_py.html b/coverage/z_c296ee536f0b791d_godmd_run_py.html
index fd54faf..45cea46 100644
--- a/coverage/z_c296ee536f0b791d_godmd_run_py.html
+++ b/coverage/z_c296ee536f0b791d_godmd_run_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_godmd/godmd/godmd_run.py: 69%</title>
+    <title>Coverage for biobb_godmd/godmd/godmd_run.py: 70%</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_godmd/godmd/godmd_run.py</b>:
-            <span class="pc_cov">69%</span>
+            <span class="pc_cov">70%</span>
         </h1>
         <aside id="help_panel_wrapper">
             <input id="help_panel_state" type="checkbox">
@@ -54,8 +54,8 @@ <h1>
             </div>
         </aside>
         <h2>
-            <span class="text">91 statements &nbsp;</span>
-            <button type="button" class="run button_toggle_run" value="run" data-shortcut="r" title="Toggle lines run">63<span class="text"> run</span></button>
+            <span class="text">92 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">28<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>
@@ -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_b3ec5c7564c25379_test_godmd_prep_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 2024-06-27 09:20 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
+            created at 2024-11-04 13:16 +0000
         </p>
         <aside class="hidden">
             <button type="button" class="button_next_chunk" data-shortcut="j"></button>
@@ -84,265 +84,267 @@ <h2>
     <p class="pln"><span class="n"><a id="t2" href="#t2">2</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t3" href="#t3">3</a></span><span class="t"><span class="str">"""Module containing the GOdMDRun class and the command line interface."""</span>&nbsp;</span><span class="r"></span></p>
     <p class="run"><span class="n"><a id="t4" href="#t4">4</a></span><span class="t"><span class="key">import</span> <span class="nam">argparse</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">import</span> <span class="nam">shutil</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">from</span> <span class="nam">pathlib</span> <span class="key">import</span> <span class="nam">Path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="key">from</span> <span class="nam">pathlib</span> <span class="key">import</span> <span class="nam">PurePath</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_godmd</span><span class="op">.</span><span class="nam">godmd</span><span class="op">.</span><span class="nam">common</span> <span class="key">import</span> <span class="nam">check_input_path</span><span class="op">,</span> <span class="nam">check_output_path</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t5" href="#t5">5</a></span><span class="t"><span class="key">from</span> <span class="nam">typing</span> <span class="key">import</span> <span class="nam">Optional</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t6" href="#t6">6</a></span><span class="t"><span class="key">import</span> <span class="nam">shutil</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t7" href="#t7">7</a></span><span class="t"><span class="key">from</span> <span class="nam">pathlib</span> <span class="key">import</span> <span class="nam">Path</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t8" href="#t8">8</a></span><span class="t"><span class="key">from</span> <span class="nam">pathlib</span> <span class="key">import</span> <span class="nam">PurePath</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t9" href="#t9">9</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">generic</span><span class="op">.</span><span class="nam">biobb_object</span> <span class="key">import</span> <span class="nam">BiobbObject</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t10" href="#t10">10</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">configuration</span> <span class="key">import</span> <span class="nam">settings</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t11" href="#t11">11</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_common</span><span class="op">.</span><span class="nam">tools</span><span class="op">.</span><span class="nam">file_utils</span> <span class="key">import</span> <span class="nam">launchlogger</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t12" href="#t12">12</a></span><span class="t"><span class="key">from</span> <span class="nam">biobb_godmd</span><span class="op">.</span><span class="nam">godmd</span><span class="op">.</span><span class="nam">common</span> <span class="key">import</span> <span class="nam">check_input_path</span><span class="op">,</span> <span class="nam">check_output_path</span>&nbsp;</span><span class="r"></span></p>
     <p class="pln"><span class="n"><a id="t13" href="#t13">13</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t14" href="#t14">14</a></span><span class="t"><span class="key">class</span> <span class="nam">GOdMDRun</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t"><span class="str">    | biobb_godmd GOdMDRun</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="str">    | Wrapper of the `GOdMD tool &lt;http://mmb.irbbarcelona.org/GOdMD/>`_ module.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t"><span class="str">    | Computes conformational transition trajectories for proteins using GOdMD tool.</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t"><span class="str">    Args:</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_pdb_orig_path (str): Input PDB file to be used as origin in the conformational transition. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/1ake_A.pdb>`_. Accepted formats: pdb (edam:format_1476).</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">        input_pdb_target_path (str): Input PDB file to be used as target in the conformational transition. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/4ake_A.pdb>`_. Accepted formats: pdb (edam:format_1476).</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">        input_aln_orig_path (str): Input GOdMD alignment file corresponding to the origin structure of the conformational transition. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/1ake_A.aln>`_. Accepted formats: aln (edam:format_2330), txt (edam:format_2330).</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">        input_aln_target_path (str): Input GOdMD alignment file corresponding to the target structure of the conformational transition. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/4ake_A.aln>`_. Accepted formats: aln (edam:format_2330), txt (edam:format_2330).</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">        input_config_path (str) (Optional): Input GOdMD configuration file. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/params.in>`_. Accepted formats: in (edam:format_2330), txt (edam:format_2330).</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">        output_log_path (str): Output log file. File type: output. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/reference/godmd/godmd.log>`_. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330).</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">        output_ene_path (str): Output energy file. File type: output. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/reference/godmd/godmd_ene.out>`_. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330).</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">        output_trj_path (str): Output trajectory file. File type: output. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/reference/godmd/godmd_trj.mdcrd>`_. Accepted formats: trj (edam:format_3878), crd (edam:format_3878), mdcrd (edam:format_3878), x (edam:format_3878).</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">        output_pdb_path (str): Output structure file. File type: output. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/reference/godmd/godmd_pdb.pdb>`_. Accepted formats: pdb (edam:format_1476).</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">        properties (dict - 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="t31" href="#t31">31</a></span><span class="t"><span class="str">            * **godmdin** (*dict*) - ({}) GOdMD options specification.</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">            * **binary_path** (*str*) - ("discrete") Binary path.</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">            * **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="t34" href="#t34">34</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="t35" href="#t35">35</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="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="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_godmd.godmd.godmd_run import godmd_run</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">                'remove_tmp': True</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">            }</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">            godmd_run(   input_pdb_orig_path='/path/to/pdb_orig.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">                         input_pdb_target_path='/path/to/pdb_target.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">                         input_aln_orig_path='/path/to/aln_orig.aln',</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">                         input_aln_target_path='/path/to/aln_target.aln',</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_log_path='/path/to/godmd_log.log',</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">                         output_ene_path='/path/to/godmd_ene.txt',</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_trj_path='/path/to/godmd_trj.mdcrd',</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_pdb_path='/path/to/godmd_pdb.pdb',</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: GOdMD</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: >=1.0</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: Apache-2.0</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="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_pdb_orig_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_pdb_target_path</span><span class="op">:</span> <span class="nam">str</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">input_aln_orig_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_aln_target_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_config_path</span><span class="op">:</span> <span class="nam">str</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">output_log_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_ene_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_trj_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_pdb_path</span><span class="op">:</span> <span class="nam">str</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">                 <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="key">None</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="run"><span class="n"><a id="t69" href="#t69">69</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="t14" href="#t14">14</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t15" href="#t15">15</a></span><span class="t"><span class="key">class</span> <span class="nam">GOdMDRun</span><span class="op">(</span><span class="nam">BiobbObject</span><span class="op">)</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t16" href="#t16">16</a></span><span class="t">    <span class="str">"""</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t17" href="#t17">17</a></span><span class="t"><span class="str">    | biobb_godmd GOdMDRun</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t18" href="#t18">18</a></span><span class="t"><span class="str">    | Wrapper of the `GOdMD tool &lt;http://mmb.irbbarcelona.org/GOdMD/>`_ module.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t19" href="#t19">19</a></span><span class="t"><span class="str">    | Computes conformational transition trajectories for proteins using GOdMD tool.</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t20" href="#t20">20</a></span><span class="t">&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">    Args:</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">        input_pdb_orig_path (str): Input PDB file to be used as origin in the conformational transition. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/1ake_A.pdb>`_. Accepted formats: pdb (edam:format_1476).</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">        input_pdb_target_path (str): Input PDB file to be used as target in the conformational transition. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/4ake_A.pdb>`_. Accepted formats: pdb (edam:format_1476).</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">        input_aln_orig_path (str): Input GOdMD alignment file corresponding to the origin structure of the conformational transition. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/1ake_A.aln>`_. Accepted formats: aln (edam:format_2330), txt (edam:format_2330).</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">        input_aln_target_path (str): Input GOdMD alignment file corresponding to the target structure of the conformational transition. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/4ake_A.aln>`_. Accepted formats: aln (edam:format_2330), txt (edam:format_2330).</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">        input_config_path (str) (Optional): Input GOdMD configuration file. File type: input. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/data/godmd/params.in>`_. Accepted formats: in (edam:format_2330), txt (edam:format_2330).</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">        output_log_path (str): Output log file. File type: output. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/reference/godmd/godmd.log>`_. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330).</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">        output_ene_path (str): Output energy file. File type: output. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/reference/godmd/godmd_ene.out>`_. Accepted formats: log (edam:format_2330), out (edam:format_2330), txt (edam:format_2330), o (edam:format_2330).</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">        output_trj_path (str): Output trajectory file. File type: output. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/reference/godmd/godmd_trj.mdcrd>`_. Accepted formats: trj (edam:format_3878), crd (edam:format_3878), mdcrd (edam:format_3878), x (edam:format_3878).</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">        output_pdb_path (str): Output structure file. File type: output. `Sample file &lt;https://github.com/bioexcel/biobb_godmd/raw/master/biobb_godmd/test/reference/godmd/godmd_pdb.pdb>`_. Accepted formats: pdb (edam:format_1476).</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">        properties (dict - 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="t32" href="#t32">32</a></span><span class="t"><span class="str">            * **godmdin** (*dict*) - ({}) GOdMD options specification.</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">            * **binary_path** (*str*) - ("discrete") Binary path.</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">            * **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="t35" href="#t35">35</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="t36" href="#t36">36</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="t37" href="#t37">37</a></span><span class="t">&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">    Examples:</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">        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="t40" href="#t40">40</a></span><span class="t">&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">            from biobb_godmd.godmd.godmd_run import godmd_run</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">            prop = {</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">                'remove_tmp': True</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">            }</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">            godmd_run(   input_pdb_orig_path='/path/to/pdb_orig.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">                         input_pdb_target_path='/path/to/pdb_target.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">                         input_aln_orig_path='/path/to/aln_orig.aln',</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">                         input_aln_target_path='/path/to/aln_target.aln',</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">                         output_log_path='/path/to/godmd_log.log',</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_ene_path='/path/to/godmd_ene.txt',</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_trj_path='/path/to/godmd_trj.mdcrd',</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">                         output_pdb_path='/path/to/godmd_pdb.pdb',</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">                         properties=prop)</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">&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">    Info:</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">        * wrapped_software:</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: GOdMD</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">            * version: >=1.0</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">            * license: Apache-2.0</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">        * ontology:</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">            * name: EDAM</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="str">            * schema: http://edamontology.org/EDAM.owl</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="pln"><span class="n"><a id="t64" href="#t64">64</a></span><span class="t"><span class="str">    """</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="run"><span class="n"><a id="t66" href="#t66">66</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_pdb_orig_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_pdb_target_path</span><span class="op">:</span> <span class="nam">str</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">                 <span class="nam">input_aln_orig_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_aln_target_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_config_path</span><span class="op">:</span> <span class="nam">str</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">                 <span class="nam">output_log_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_ene_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_trj_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_pdb_path</span><span class="op">:</span> <span class="nam">str</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">                 <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</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="pln"><span class="n"><a id="t70" href="#t70">70</a></span><span class="t">&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="com"># Call parent class constructor</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t72" href="#t72">72</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="t73" href="#t73">73</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="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"># Input/Output files</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">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="t77" href="#t77">77</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span><span class="str">'input_pdb_orig_path'</span><span class="op">:</span> <span class="nam">input_pdb_orig_path</span><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">                   <span class="str">'input_pdb_target_path'</span><span class="op">:</span> <span class="nam">input_pdb_target_path</span><span class="op">,</span>&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="str">'input_aln_orig_path'</span><span class="op">:</span> <span class="nam">input_aln_orig_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                   <span class="str">'input_aln_target_path'</span><span class="op">:</span> <span class="nam">input_aln_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                   <span class="str">'input_config_path'</span><span class="op">:</span> <span class="nam">input_config_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="t82" href="#t82">82</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span><span class="str">'output_log_path'</span><span class="op">:</span> <span class="nam">output_log_path</span><span class="op">,</span>&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="str">'output_ene_path'</span><span class="op">:</span> <span class="nam">output_ene_path</span><span class="op">,</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">                    <span class="str">'output_trj_path'</span><span class="op">:</span> <span class="nam">output_trj_path</span><span class="op">,</span>&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="str">'output_pdb_path'</span><span class="op">:</span> <span class="nam">output_pdb_path</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">        <span class="op">}</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">&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="com"># Properties specific for BB</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="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">godmdin</span> <span class="op">=</span> <span class="op">{</span><span class="nam">k</span><span class="op">:</span> <span class="nam">str</span><span class="op">(</span><span class="nam">v</span><span class="op">)</span> <span class="key">for</span> <span class="nam">k</span><span class="op">,</span> <span class="nam">v</span> <span class="key">in</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'godmdin'</span><span class="op">,</span> <span class="nam">dict</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">.</span><span class="nam">items</span><span class="op">(</span><span class="op">)</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">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">"discrete"</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="pln"><span class="n"><a id="t93" href="#t93">93</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="t94" href="#t94">94</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="pln"><span class="n"><a id="t95" href="#t95">95</a></span><span class="t">        <span class="com"># self.check_arguments()</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">&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="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">out_err</span><span class="op">)</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">        <span class="str">""" Checks input/output paths correctness """</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="pln"><span class="n"><a id="t100" href="#t100">100</a></span><span class="t">        <span class="com"># Check input(s)</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">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_pdb_orig_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_pdb_orig_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"input_pdb_orig_path"</span><span class="op">,</span> <span class="key">False</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="t102" href="#t102">102</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_pdb_target_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_pdb_target_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"input_pdb_target_path"</span><span class="op">,</span> <span class="key">False</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="t103" href="#t103">103</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_aln_orig_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_aln_orig_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"input_aln_orig_path"</span><span class="op">,</span> <span class="key">False</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="t104" href="#t104">104</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_aln_target_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_aln_target_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"input_aln_target_path"</span><span class="op">,</span> <span class="key">False</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="t105" href="#t105">105</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_config_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_config_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"input_config_path"</span><span class="op">,</span> <span class="key">True</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="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"># Check output(s)</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">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_log_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_log_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"output_log_path"</span><span class="op">,</span> <span class="key">False</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="t109" href="#t109">109</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_ene_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_ene_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"output_ene_path"</span><span class="op">,</span> <span class="key">False</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="t110" href="#t110">110</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_trj_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_trj_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"output_trj_path"</span><span class="op">,</span> <span class="key">False</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="t111" href="#t111">111</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_pdb_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_pdb_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"output_pdb_path"</span><span class="op">,</span> <span class="key">False</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="t112" href="#t112">112</a></span><span class="t">&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="key">def</span> <span class="nam">create_godmdin</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">path</span><span class="op">:</span> <span class="nam">str</span> <span class="op">=</span> <span class="key">None</span><span class="op">)</span> <span class="op">-></span> <span class="nam">str</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">        <span class="str">"""Creates a GOdMD configuration file (godmdin) using the properties file settings"""</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">godmdin_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="t116" href="#t116">116</a></span><span class="t">&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">self</span><span class="op">.</span><span class="nam">output_godmdin_path</span> <span class="op">=</span> <span class="nam">path</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">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="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"># Call parent class constructor</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">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="t75" href="#t75">75</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="t76" href="#t76">76</a></span><span class="t">&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="com"># Input/Output files</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">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="t79" href="#t79">79</a></span><span class="t">            <span class="str">'in'</span><span class="op">:</span> <span class="op">{</span><span class="str">'input_pdb_orig_path'</span><span class="op">:</span> <span class="nam">input_pdb_orig_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t80" href="#t80">80</a></span><span class="t">                   <span class="str">'input_pdb_target_path'</span><span class="op">:</span> <span class="nam">input_pdb_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t81" href="#t81">81</a></span><span class="t">                   <span class="str">'input_aln_orig_path'</span><span class="op">:</span> <span class="nam">input_aln_orig_path</span><span class="op">,</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">                   <span class="str">'input_aln_target_path'</span><span class="op">:</span> <span class="nam">input_aln_target_path</span><span class="op">,</span>&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="str">'input_config_path'</span><span class="op">:</span> <span class="nam">input_config_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="t84" href="#t84">84</a></span><span class="t">            <span class="str">'out'</span><span class="op">:</span> <span class="op">{</span><span class="str">'output_log_path'</span><span class="op">:</span> <span class="nam">output_log_path</span><span class="op">,</span>&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="str">'output_ene_path'</span><span class="op">:</span> <span class="nam">output_ene_path</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">                    <span class="str">'output_trj_path'</span><span class="op">:</span> <span class="nam">output_trj_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t87" href="#t87">87</a></span><span class="t">                    <span class="str">'output_pdb_path'</span><span class="op">:</span> <span class="nam">output_pdb_path</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="op">}</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t89" href="#t89">89</a></span><span class="t">&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="com"># Properties specific for BB</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">properties</span> <span class="op">=</span> <span class="nam">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">godmdin</span> <span class="op">=</span> <span class="op">{</span><span class="nam">k</span><span class="op">:</span> <span class="nam">str</span><span class="op">(</span><span class="nam">v</span><span class="op">)</span> <span class="key">for</span> <span class="nam">k</span><span class="op">,</span> <span class="nam">v</span> <span class="key">in</span> <span class="nam">properties</span><span class="op">.</span><span class="nam">get</span><span class="op">(</span><span class="str">'godmdin'</span><span class="op">,</span> <span class="nam">dict</span><span class="op">(</span><span class="op">)</span><span class="op">)</span><span class="op">.</span><span class="nam">items</span><span class="op">(</span><span class="op">)</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">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">"discrete"</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="pln"><span class="n"><a id="t95" href="#t95">95</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="t96" href="#t96">96</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="pln"><span class="n"><a id="t97" href="#t97">97</a></span><span class="t">        <span class="com"># self.check_arguments()</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="run"><span class="n"><a id="t99" href="#t99">99</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">out_err</span><span class="op">)</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">        <span class="str">""" Checks input/output paths correctness """</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"># Check input(s)</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">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_pdb_orig_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_pdb_orig_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"input_pdb_orig_path"</span><span class="op">,</span> <span class="key">False</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="t104" href="#t104">104</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_pdb_target_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_pdb_target_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"input_pdb_target_path"</span><span class="op">,</span> <span class="key">False</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="t105" href="#t105">105</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_aln_orig_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_aln_orig_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"input_aln_orig_path"</span><span class="op">,</span> <span class="key">False</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="t106" href="#t106">106</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_aln_target_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_aln_target_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"input_aln_target_path"</span><span class="op">,</span> <span class="key">False</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="t107" href="#t107">107</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_config_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_config_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"input_config_path"</span><span class="op">,</span> <span class="key">True</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="t108" href="#t108">108</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t109" href="#t109">109</a></span><span class="t">        <span class="com"># Check output(s)</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">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_log_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_log_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"output_log_path"</span><span class="op">,</span> <span class="key">False</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="t111" href="#t111">111</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_ene_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_ene_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"output_ene_path"</span><span class="op">,</span> <span class="key">False</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="t112" href="#t112">112</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_trj_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_trj_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"output_trj_path"</span><span class="op">,</span> <span class="key">False</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="t113" href="#t113">113</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_pdb_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_pdb_path"</span><span class="op">]</span><span class="op">,</span> <span class="str">"output_pdb_path"</span><span class="op">,</span> <span class="key">False</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="t114" href="#t114">114</a></span><span class="t">&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="key">def</span> <span class="nam">create_godmdin</span><span class="op">(</span><span class="nam">self</span><span class="op">,</span> <span class="nam">path</span><span class="op">:</span> <span class="nam">str</span> <span class="op">=</span> <span class="key">None</span><span class="op">)</span> <span class="op">-></span> <span class="nam">str</span><span class="op">:</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t116" href="#t116">116</a></span><span class="t">        <span class="str">"""Creates a GOdMD configuration file (godmdin) using the properties file settings"""</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">godmdin_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="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="key">if</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_config_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="t120" href="#t120">120</a></span><span class="t">            <span class="com"># GOdMD input parameters read from an input godmdin file</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="key">with</span> <span class="nam">open</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_config_path'</span><span class="op">]</span><span class="op">)</span> <span class="key">as</span> <span class="nam">input_params</span><span class="op">:</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">for</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">input_params</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="key">if</span> <span class="str">'='</span> <span class="key">in</span> <span class="nam">line</span><span class="op">:</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">godmdin_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">line</span><span class="op">.</span><span class="nam">upper</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="t125" href="#t125">125</a></span><span class="t">        <span class="key">else</span><span class="op">:</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">            <span class="com"># Pre-configured simulation type parameters</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t127" href="#t127">127</a></span><span class="t">            <span class="nam">godmdin_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"  TSNAP = 500 ! BioBB GOdMD default params \n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t128" href="#t128">128</a></span><span class="t">            <span class="nam">godmdin_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"  TEMP = 300 ! BioBB GOdMD default params \n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="nam">godmdin_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"  SEED = 2525 ! BioBB GOdMD default params \n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">            <span class="nam">godmdin_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"  ENER_EVO_SIZE = 20 ! BioBB GOdMD default params \n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">            <span class="nam">godmdin_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"  NBLOC = 10000 ! BioBB GOdMD default params \n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">            <span class="nam">godmdin_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"  ERRORACCEPTABLE = 1.5 ! BioBB GOdMD default params \n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t133" href="#t133">133</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">        <span class="com"># Adding the rest of parameters in the config file to the mdin file</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">        <span class="com"># if the parameter has already been added replace the value</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">parameter_keys</span> <span class="op">=</span> <span class="op">[</span><span class="nam">parameter</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">'='</span><span class="op">)</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span> <span class="key">for</span> <span class="nam">parameter</span> <span class="key">in</span> <span class="nam">godmdin_list</span><span class="op">]</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">for</span> <span class="nam">k</span><span class="op">,</span> <span class="nam">v</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">godmdin</span><span class="op">.</span><span class="nam">items</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="t138" href="#t138">138</a></span><span class="t">            <span class="nam">config_parameter_key</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">k</span><span class="op">)</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">upper</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="t139" href="#t139">139</a></span><span class="t">            <span class="key">if</span> <span class="nam">config_parameter_key</span> <span class="key">in</span> <span class="nam">parameter_keys</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">godmdin_list</span><span class="op">[</span><span class="nam">parameter_keys</span><span class="op">.</span><span class="nam">index</span><span class="op">(</span><span class="nam">config_parameter_key</span><span class="op">)</span><span class="op">]</span> <span class="op">=</span> <span class="str">'\t'</span> <span class="op">+</span> <span class="nam">config_parameter_key</span> <span class="op">+</span> <span class="str">' = '</span> <span class="op">+</span> <span class="nam">str</span><span class="op">(</span><span class="nam">v</span><span class="op">)</span> <span class="op">+</span> <span class="str">' ! BioBB property \n'</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">            <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="t142" href="#t142">142</a></span><span class="t">                <span class="nam">godmdin_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'\t'</span> <span class="op">+</span> <span class="nam">config_parameter_key</span> <span class="op">+</span> <span class="str">' = '</span><span class="op">+</span><span class="nam">str</span><span class="op">(</span><span class="nam">v</span><span class="op">)</span> <span class="op">+</span> <span class="str">' ! BioBB property \n'</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"># Writing MD configuration file (mdin)</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">with</span> <span class="nam">open</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">output_godmdin_path</span><span class="op">,</span> <span class="str">'w'</span><span class="op">)</span> <span class="key">as</span> <span class="nam">godmdin</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"># GOdMDIN parameters added by the biobb_godmd module</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">godmdin</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"!This godmdin file has been created by the biobb_godmd module from the BioBB library \n\n"</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="run"><span class="n"><a id="t150" href="#t150">150</a></span><span class="t">            <span class="nam">godmdin</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"&amp;INPUT\n"</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">self</span><span class="op">.</span><span class="nam">output_godmdin_path</span> <span class="op">=</span> <span class="nam">path</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="key">if</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_config_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="t122" href="#t122">122</a></span><span class="t">            <span class="com"># GOdMD input parameters read from an input godmdin file</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="key">with</span> <span class="nam">open</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_config_path'</span><span class="op">]</span><span class="op">)</span> <span class="key">as</span> <span class="nam">input_params</span><span class="op">:</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">for</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">input_params</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="key">if</span> <span class="str">'='</span> <span class="key">in</span> <span class="nam">line</span><span class="op">:</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">godmdin_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="nam">line</span><span class="op">.</span><span class="nam">upper</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="t127" href="#t127">127</a></span><span class="t">        <span class="key">else</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">            <span class="com"># Pre-configured simulation type parameters</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t129" href="#t129">129</a></span><span class="t">            <span class="nam">godmdin_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"  TSNAP = 500 ! BioBB GOdMD default params \n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t130" href="#t130">130</a></span><span class="t">            <span class="nam">godmdin_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"  TEMP = 300 ! BioBB GOdMD default params \n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t131" href="#t131">131</a></span><span class="t">            <span class="nam">godmdin_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"  SEED = 2525 ! BioBB GOdMD default params \n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t132" href="#t132">132</a></span><span class="t">            <span class="nam">godmdin_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"  ENER_EVO_SIZE = 20 ! BioBB GOdMD default params \n"</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">godmdin_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"  NBLOC = 10000 ! BioBB GOdMD default params \n"</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t134" href="#t134">134</a></span><span class="t">            <span class="nam">godmdin_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">"  ERRORACCEPTABLE = 1.5 ! BioBB GOdMD default params \n"</span><span class="op">)</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="pln"><span class="n"><a id="t136" href="#t136">136</a></span><span class="t">        <span class="com"># Adding the rest of parameters in the config file to the mdin file</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="com"># if the parameter has already been added replace the value</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">parameter_keys</span> <span class="op">=</span> <span class="op">[</span><span class="nam">parameter</span><span class="op">.</span><span class="nam">split</span><span class="op">(</span><span class="str">'='</span><span class="op">)</span><span class="op">[</span><span class="num">0</span><span class="op">]</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span> <span class="key">for</span> <span class="nam">parameter</span> <span class="key">in</span> <span class="nam">godmdin_list</span><span class="op">]</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="key">for</span> <span class="nam">k</span><span class="op">,</span> <span class="nam">v</span> <span class="key">in</span> <span class="nam">self</span><span class="op">.</span><span class="nam">godmdin</span><span class="op">.</span><span class="nam">items</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="t140" href="#t140">140</a></span><span class="t">            <span class="nam">config_parameter_key</span> <span class="op">=</span> <span class="nam">str</span><span class="op">(</span><span class="nam">k</span><span class="op">)</span><span class="op">.</span><span class="nam">strip</span><span class="op">(</span><span class="op">)</span><span class="op">.</span><span class="nam">upper</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="t141" href="#t141">141</a></span><span class="t">            <span class="key">if</span> <span class="nam">config_parameter_key</span> <span class="key">in</span> <span class="nam">parameter_keys</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="nam">godmdin_list</span><span class="op">[</span><span class="nam">parameter_keys</span><span class="op">.</span><span class="nam">index</span><span class="op">(</span><span class="nam">config_parameter_key</span><span class="op">)</span><span class="op">]</span> <span class="op">=</span> <span class="str">'\t'</span> <span class="op">+</span> <span class="nam">config_parameter_key</span> <span class="op">+</span> <span class="str">' = '</span> <span class="op">+</span> <span class="nam">str</span><span class="op">(</span><span class="nam">v</span><span class="op">)</span> <span class="op">+</span> <span class="str">' ! BioBB property \n'</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">            <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="t144" href="#t144">144</a></span><span class="t">                <span class="nam">godmdin_list</span><span class="op">.</span><span class="nam">append</span><span class="op">(</span><span class="str">'\t'</span> <span class="op">+</span> <span class="nam">config_parameter_key</span> <span class="op">+</span> <span class="str">' = '</span><span class="op">+</span><span class="nam">str</span><span class="op">(</span><span class="nam">v</span><span class="op">)</span> <span class="op">+</span> <span class="str">' ! BioBB property \n'</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"># Writing MD configuration file (mdin)</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">with</span> <span class="nam">open</span><span class="op">(</span><span class="nam">self</span><span class="op">.</span><span class="nam">output_godmdin_path</span><span class="op">,</span> <span class="str">'w'</span><span class="op">)</span> <span class="key">as</span> <span class="nam">godmdin</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"># GOdMDIN parameters added by the biobb_godmd module</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">godmdin</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"!This godmdin file has been created by the biobb_godmd module from the BioBB library \n\n"</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"># MD config parameters</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="key">for</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">godmdin_list</span><span class="op">:</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">godmdin</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">line</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="run"><span class="n"><a id="t156" href="#t156">156</a></span><span class="t">            <span class="nam">godmdin</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"&amp;END\n"</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">godmdin</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"&amp;INPUT\n"</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="pln"><span class="n"><a id="t154" href="#t154">154</a></span><span class="t">            <span class="com"># MD config parameters</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">for</span> <span class="nam">line</span> <span class="key">in</span> <span class="nam">godmdin_list</span><span class="op">:</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">godmdin</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="nam">line</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="run"><span class="n"><a id="t158" href="#t158">158</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">output_godmdin_path</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">godmdin</span><span class="op">.</span><span class="nam">write</span><span class="op">(</span><span class="str">"&amp;END\n"</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="run"><span class="n"><a id="t160" href="#t160">160</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="t161" href="#t161">161</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>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t162" href="#t162">162</a></span><span class="t">        <span class="str">"""Launches the execution of the GOdMDRun module."""</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"># check input/output paths and parameters</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">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="t166" href="#t166">166</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t167" href="#t167">167</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="t168" href="#t168">168</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="t169" href="#t169">169</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="t170" href="#t170">170</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="t171" href="#t171">171</a></span><span class="t">&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"># Creating GOdMD input file</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">output_godmdin_path</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">create_godmdin</span><span class="op">(</span><span class="nam">path</span><span class="op">=</span><span class="nam">str</span><span class="op">(</span><span class="nam">Path</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="str">"unique_dir"</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="str">"godmd.in"</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="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"># Command line</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="com"># discrete -i $fileName.in -pdbin $pdbch1 -pdbtarg $pdbch2 -ener $fileName.ene -trj $fileName.crd -p1 $alignFile1 -p2 $alignFile2 -o $fileName.log >&amp; $fileName.out</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t177" href="#t177">177</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="op">[</span><span class="str">'cd'</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="str">"unique_dir"</span><span class="op">]</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">binary_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="str">'-i'</span><span class="op">,</span> <span class="str">"godmd.in"</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">'-pdbin'</span><span class="op">,</span> <span class="nam">PurePath</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="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_pdb_orig_path"</span><span class="op">]</span><span class="op">)</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="t180" href="#t180">180</a></span><span class="t">                    <span class="str">'-pdbtarg'</span><span class="op">,</span> <span class="nam">PurePath</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="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_pdb_target_path"</span><span class="op">]</span><span class="op">)</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="t181" href="#t181">181</a></span><span class="t">                    <span class="str">'-p1'</span><span class="op">,</span> <span class="nam">PurePath</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="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_aln_orig_path"</span><span class="op">]</span><span class="op">)</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="t182" href="#t182">182</a></span><span class="t">                    <span class="str">'-p2'</span><span class="op">,</span> <span class="nam">PurePath</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="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_aln_target_path"</span><span class="op">]</span><span class="op">)</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="t183" href="#t183">183</a></span><span class="t">                    <span class="str">'-o'</span><span class="op">,</span> <span class="nam">PurePath</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="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_log_path"</span><span class="op">]</span><span class="op">)</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="t184" href="#t184">184</a></span><span class="t">                    <span class="str">'-ener'</span><span class="op">,</span> <span class="nam">PurePath</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="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_ene_path"</span><span class="op">]</span><span class="op">)</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="t185" href="#t185">185</a></span><span class="t">                    <span class="str">'-trj'</span><span class="op">,</span> <span class="nam">PurePath</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="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_trj_path"</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</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="op">]</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">        <span class="com"># Run Biobb block</span>&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="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="t190" href="#t190">190</a></span><span class="t">&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="com"># Copy outputs from temporary folder to output path</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="nam">shutil</span><span class="op">.</span><span class="nam">copy2</span><span class="op">(</span><span class="nam">str</span><span class="op">(</span><span class="nam">Path</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="str">"unique_dir"</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="str">"reference.pdb"</span><span class="op">)</span><span class="op">)</span><span class="op">,</span> <span class="nam">PurePath</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_pdb_path"</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="t193" href="#t193">193</a></span><span class="t">&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="com"># Copy files to host</span>&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t195" href="#t195">195</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="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">        <span class="com"># remove temporary folder(s)</span>&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="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="t199" href="#t199">199</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><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t200" href="#t200">200</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="t201" href="#t201">201</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="t202" href="#t202">202</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t203" href="#t203">203</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="run"><span class="n"><a id="t160" href="#t160">160</a></span><span class="t">        <span class="key">return</span> <span class="nam">self</span><span class="op">.</span><span class="nam">output_godmdin_path</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="op">@</span><span class="nam">launchlogger</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="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>&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="str">"""Launches the execution of the GOdMDRun module."""</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">        <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="t167" href="#t167">167</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="t168" href="#t168">168</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"># Setup Biobb</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="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="t171" href="#t171">171</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="t172" href="#t172">172</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="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"># Creating GOdMD input file</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">output_godmdin_path</span> <span class="op">=</span> <span class="nam">self</span><span class="op">.</span><span class="nam">create_godmdin</span><span class="op">(</span><span class="nam">path</span><span class="op">=</span><span class="nam">str</span><span class="op">(</span><span class="nam">Path</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="str">"unique_dir"</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="str">"godmd.in"</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="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">        <span class="com"># Command line</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="com"># discrete -i $fileName.in -pdbin $pdbch1 -pdbtarg $pdbch2 -ener $fileName.ene -trj $fileName.crd -p1 $alignFile1 -p2 $alignFile2 -o $fileName.log >&amp; $fileName.out</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">cmd</span> <span class="op">=</span> <span class="op">[</span><span class="str">'cd'</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="str">"unique_dir"</span><span class="op">]</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">binary_path</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="str">'-i'</span><span class="op">,</span> <span class="str">"godmd.in"</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="str">'-pdbin'</span><span class="op">,</span> <span class="nam">PurePath</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="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_pdb_orig_path"</span><span class="op">]</span><span class="op">)</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="t182" href="#t182">182</a></span><span class="t">                    <span class="str">'-pdbtarg'</span><span class="op">,</span> <span class="nam">PurePath</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="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_pdb_target_path"</span><span class="op">]</span><span class="op">)</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="t183" href="#t183">183</a></span><span class="t">                    <span class="str">'-p1'</span><span class="op">,</span> <span class="nam">PurePath</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="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_aln_orig_path"</span><span class="op">]</span><span class="op">)</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="t184" href="#t184">184</a></span><span class="t">                    <span class="str">'-p2'</span><span class="op">,</span> <span class="nam">PurePath</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="str">"in"</span><span class="op">]</span><span class="op">[</span><span class="str">"input_aln_target_path"</span><span class="op">]</span><span class="op">)</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="t185" href="#t185">185</a></span><span class="t">                    <span class="str">'-o'</span><span class="op">,</span> <span class="nam">PurePath</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="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_log_path"</span><span class="op">]</span><span class="op">)</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="t186" href="#t186">186</a></span><span class="t">                    <span class="str">'-ener'</span><span class="op">,</span> <span class="nam">PurePath</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="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_ene_path"</span><span class="op">]</span><span class="op">)</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="t187" href="#t187">187</a></span><span class="t">                    <span class="str">'-trj'</span><span class="op">,</span> <span class="nam">PurePath</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="str">"out"</span><span class="op">]</span><span class="op">[</span><span class="str">"output_trj_path"</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">name</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">                    <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"># Run Biobb block</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t191" href="#t191">191</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="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">        <span class="com"># Copy outputs from temporary folder to output path</span>&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="nam">shutil</span><span class="op">.</span><span class="nam">copy2</span><span class="op">(</span><span class="nam">str</span><span class="op">(</span><span class="nam">Path</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="str">"unique_dir"</span><span class="op">]</span><span class="op">)</span><span class="op">.</span><span class="nam">joinpath</span><span class="op">(</span><span class="str">"reference.pdb"</span><span class="op">)</span><span class="op">)</span><span class="op">,</span> <span class="nam">PurePath</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_pdb_path"</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">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t196" href="#t196">196</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="t197" href="#t197">197</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="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"># remove temporary folder(s)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t200" href="#t200">200</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="t201" href="#t201">201</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> <span class="str">""</span><span class="op">)</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">        <span class="op">]</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t203" href="#t203">203</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="t204" href="#t204">204</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t205" href="#t205">205</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="run"><span class="n"><a id="t205" href="#t205">205</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="t206" href="#t206">206</a></span><span class="t">&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="run"><span class="n"><a id="t208" href="#t208">208</a></span><span class="t"><span class="key">def</span> <span class="nam">godmd_run</span><span class="op">(</span><span class="nam">input_pdb_orig_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_pdb_target_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">              <span class="nam">input_aln_orig_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_aln_target_path</span><span class="op">:</span> <span class="nam">str</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_log_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_ene_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_trj_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_pdb_path</span><span class="op">:</span> <span class="nam">str</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">input_config_path</span><span class="op">:</span> <span class="nam">str</span> <span class="op">=</span> <span class="key">None</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="t212" href="#t212">212</a></span><span class="t">    <span class="str">"""Create :class:`GOdMDRun &lt;godmd.godmd_run.GOdMDRun>`godmd.godmd_run.GOdMDRun class and</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="str">    execute :meth:`launch() &lt;godmd.godmd_run.GOdMDRun.launch>` method"""</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">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t215" href="#t215">215</a></span><span class="t">    <span class="key">return</span> <span class="nam">GOdMDRun</span><span class="op">(</span><span class="nam">input_pdb_orig_path</span><span class="op">=</span><span class="nam">input_pdb_orig_path</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">                    <span class="nam">input_pdb_target_path</span><span class="op">=</span><span class="nam">input_pdb_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">                    <span class="nam">input_aln_orig_path</span><span class="op">=</span><span class="nam">input_aln_orig_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">                    <span class="nam">input_aln_target_path</span><span class="op">=</span><span class="nam">input_aln_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">                    <span class="nam">input_config_path</span><span class="op">=</span><span class="nam">input_config_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">                    <span class="nam">output_log_path</span><span class="op">=</span><span class="nam">output_log_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">                    <span class="nam">output_ene_path</span><span class="op">=</span><span class="nam">output_ene_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">                    <span class="nam">output_trj_path</span><span class="op">=</span><span class="nam">output_trj_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">                    <span class="nam">output_pdb_path</span><span class="op">=</span><span class="nam">output_pdb_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t224" href="#t224">224</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">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="t225" href="#t225">225</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t226" href="#t226">226</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t227" href="#t227">227</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="mis show_mis"><span class="n"><a id="t228" href="#t228">228</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">'Computing conformational transition trajectories for proteins using GOdMD tool.'</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="t229" href="#t229">229</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="t230" href="#t230">230</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t231" href="#t231">231</a></span><span class="t">    <span class="com"># Specific args</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t232" href="#t232">232</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="t233" href="#t233">233</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_pdb_orig_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">'Input PDB file to be used as origin in the conformational transition. Accepted formats: pdb.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t234" href="#t234">234</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_pdb_target_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">'Input PDB file to be used as target in the conformational transition. Accepted formats: pdb.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t235" href="#t235">235</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_aln_orig_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">'Input GOdMD alignment file corresponding to the origin structure of the conformational transition. Accepted formats: aln, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t236" href="#t236">236</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_aln_target_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">'Input GOdMD alignment file corresponding to the target structure of the conformational transition. Accepted formats: aln, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t237" href="#t237">237</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_config_path'</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">'Input configuration file (GOdMD run options). Accepted formats: in, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t238" href="#t238">238</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_log_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">'Output log file. Accepted formats: log, out, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t239" href="#t239">239</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_ene_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">'Output energy file. Accepted formats: log, out, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t240" href="#t240">240</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_trj_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">'Output trajectory file. Accepted formats: mdcrd.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t241" href="#t241">241</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_pdb_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">'Output structure file. Accepted formats: pdb.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t242" href="#t242">242</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t243" href="#t243">243</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="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">    <span class="com"># config = args.config if args.config else None</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t245" href="#t245">245</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="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">    <span class="com"># properties = settings.ConfReader(config=config).get_prop_dic()</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t247" href="#t247">247</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="t248" href="#t248">248</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t249" href="#t249">249</a></span><span class="t">    <span class="com"># Specific call</span>&nbsp;</span><span class="r"></span></p>
-    <p class="mis show_mis"><span class="n"><a id="t250" href="#t250">250</a></span><span class="t">    <span class="nam">godmd_run</span><span class="op">(</span><span class="nam">input_pdb_orig_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_pdb_orig_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">              <span class="nam">input_pdb_target_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_pdb_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">              <span class="nam">input_aln_orig_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_aln_orig_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">              <span class="nam">input_aln_target_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_aln_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">              <span class="nam">input_config_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_config_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">              <span class="nam">output_log_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_log_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">              <span class="nam">output_ene_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_ene_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">              <span class="nam">output_trj_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_trj_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">              <span class="nam">output_pdb_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_pdb_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t259" href="#t259">259</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="t260" href="#t260">260</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="pln"><span class="n"><a id="t261" href="#t261">261</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
-    <p class="run"><span class="n"><a id="t262" href="#t262">262</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="t263" href="#t263">263</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="t207" href="#t207">207</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="t208" href="#t208">208</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t209" href="#t209">209</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t210" href="#t210">210</a></span><span class="t"><span class="key">def</span> <span class="nam">godmd_run</span><span class="op">(</span><span class="nam">input_pdb_orig_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_pdb_target_path</span><span class="op">:</span> <span class="nam">str</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">input_aln_orig_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">input_aln_target_path</span><span class="op">:</span> <span class="nam">str</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">              <span class="nam">output_log_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_ene_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_trj_path</span><span class="op">:</span> <span class="nam">str</span><span class="op">,</span> <span class="nam">output_pdb_path</span><span class="op">:</span> <span class="nam">str</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">input_config_path</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">str</span><span class="op">]</span> <span class="op">=</span> <span class="key">None</span><span class="op">,</span> <span class="nam">properties</span><span class="op">:</span> <span class="nam">Optional</span><span class="op">[</span><span class="nam">dict</span><span class="op">]</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="t214" href="#t214">214</a></span><span class="t">    <span class="str">"""Create :class:`GOdMDRun &lt;godmd.godmd_run.GOdMDRun>`godmd.godmd_run.GOdMDRun class and</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="str">    execute :meth:`launch() &lt;godmd.godmd_run.GOdMDRun.launch>` method"""</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="run"><span class="n"><a id="t217" href="#t217">217</a></span><span class="t">    <span class="key">return</span> <span class="nam">GOdMDRun</span><span class="op">(</span><span class="nam">input_pdb_orig_path</span><span class="op">=</span><span class="nam">input_pdb_orig_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t218" href="#t218">218</a></span><span class="t">                    <span class="nam">input_pdb_target_path</span><span class="op">=</span><span class="nam">input_pdb_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t219" href="#t219">219</a></span><span class="t">                    <span class="nam">input_aln_orig_path</span><span class="op">=</span><span class="nam">input_aln_orig_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t220" href="#t220">220</a></span><span class="t">                    <span class="nam">input_aln_target_path</span><span class="op">=</span><span class="nam">input_aln_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t221" href="#t221">221</a></span><span class="t">                    <span class="nam">input_config_path</span><span class="op">=</span><span class="nam">input_config_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t222" href="#t222">222</a></span><span class="t">                    <span class="nam">output_log_path</span><span class="op">=</span><span class="nam">output_log_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t223" href="#t223">223</a></span><span class="t">                    <span class="nam">output_ene_path</span><span class="op">=</span><span class="nam">output_ene_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t224" href="#t224">224</a></span><span class="t">                    <span class="nam">output_trj_path</span><span class="op">=</span><span class="nam">output_trj_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t225" href="#t225">225</a></span><span class="t">                    <span class="nam">output_pdb_path</span><span class="op">=</span><span class="nam">output_pdb_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t226" href="#t226">226</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">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="t227" href="#t227">227</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t228" href="#t228">228</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t229" href="#t229">229</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="mis show_mis"><span class="n"><a id="t230" href="#t230">230</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">'Computing conformational transition trajectories for proteins using GOdMD tool.'</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="t231" href="#t231">231</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="t232" href="#t232">232</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t233" href="#t233">233</a></span><span class="t">    <span class="com"># Specific args</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t234" href="#t234">234</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="t235" href="#t235">235</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_pdb_orig_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">'Input PDB file to be used as origin in the conformational transition. Accepted formats: pdb.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t236" href="#t236">236</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_pdb_target_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">'Input PDB file to be used as target in the conformational transition. Accepted formats: pdb.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t237" href="#t237">237</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_aln_orig_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">'Input GOdMD alignment file corresponding to the origin structure of the conformational transition. Accepted formats: aln, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t238" href="#t238">238</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_aln_target_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">'Input GOdMD alignment file corresponding to the target structure of the conformational transition. Accepted formats: aln, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t239" href="#t239">239</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_config_path'</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">'Input configuration file (GOdMD run options). Accepted formats: in, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t240" href="#t240">240</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_log_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">'Output log file. Accepted formats: log, out, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t241" href="#t241">241</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_ene_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">'Output energy file. Accepted formats: log, out, txt.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t242" href="#t242">242</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_trj_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">'Output trajectory file. Accepted formats: mdcrd.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t243" href="#t243">243</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_pdb_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">'Output structure file. Accepted formats: pdb.'</span><span class="op">)</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t244" href="#t244">244</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t245" href="#t245">245</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="pln"><span class="n"><a id="t246" href="#t246">246</a></span><span class="t">    <span class="com"># config = args.config if args.config else None</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t247" href="#t247">247</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="pln"><span class="n"><a id="t248" href="#t248">248</a></span><span class="t">    <span class="com"># properties = settings.ConfReader(config=config).get_prop_dic()</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t249" href="#t249">249</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="t250" href="#t250">250</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t251" href="#t251">251</a></span><span class="t">    <span class="com"># Specific call</span>&nbsp;</span><span class="r"></span></p>
+    <p class="mis show_mis"><span class="n"><a id="t252" href="#t252">252</a></span><span class="t">    <span class="nam">godmd_run</span><span class="op">(</span><span class="nam">input_pdb_orig_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_pdb_orig_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t253" href="#t253">253</a></span><span class="t">              <span class="nam">input_pdb_target_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_pdb_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t254" href="#t254">254</a></span><span class="t">              <span class="nam">input_aln_orig_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_aln_orig_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t255" href="#t255">255</a></span><span class="t">              <span class="nam">input_aln_target_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_aln_target_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t256" href="#t256">256</a></span><span class="t">              <span class="nam">input_config_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">input_config_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t257" href="#t257">257</a></span><span class="t">              <span class="nam">output_log_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_log_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t258" href="#t258">258</a></span><span class="t">              <span class="nam">output_ene_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_ene_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t259" href="#t259">259</a></span><span class="t">              <span class="nam">output_trj_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_trj_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t260" href="#t260">260</a></span><span class="t">              <span class="nam">output_pdb_path</span><span class="op">=</span><span class="nam">args</span><span class="op">.</span><span class="nam">output_pdb_path</span><span class="op">,</span>&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t261" href="#t261">261</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="t262" href="#t262">262</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="pln"><span class="n"><a id="t263" href="#t263">263</a></span><span class="t">&nbsp;</span><span class="r"></span></p>
+    <p class="run"><span class="n"><a id="t264" href="#t264">264</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="t265" href="#t265">265</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">
@@ -351,8 +353,8 @@ <h2>
             <a class="nav" href="index.html">&Hat; index</a> &nbsp; &nbsp;
             <a class="nav" href="z_b3ec5c7564c25379_test_godmd_prep_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 2024-06-27 09:20 +0000
+            <a class="nav" href="https://coverage.readthedocs.io/en/7.6.4">coverage.py v7.6.4</a>,
+            created at 2024-11-04 13:16 +0000
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diff --git a/flake8/index.html b/flake8/index.html
index 4d8db75..e47371a 100644
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+++ b/flake8/index.html
@@ -9,8 +9,8 @@
       <div id="masthead" class="sev-4"></div>
       <div id="page">
           <h1>flake8 violations</h1>
-         <p id="versions">Generated on 2024-06-27 09:16
-            with Installed plugins: flake8-html: 0.4.3, mccabe: 0.7.0, pycodestyle: 2.12.0, pyflakes: 3.2.0
+         <p id="versions">Generated on 2024-11-04 13:15
+            with Installed plugins: flake8-html: 0.4.3, mccabe: 0.7.0, pycodestyle: 2.12.1, pyflakes: 3.2.0
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diff --git a/junit/junit.xml b/junit/junit.xml
index 936bb05..6349a43 100644
--- a/junit/junit.xml
+++ b/junit/junit.xml
@@ -1 +1 @@
-<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="2" time="194.677" timestamp="2024-06-27T09:16:59.217793" hostname="biobb-runners"><testcase classname="biobb_godmd.test.unitests.test_godmd.test_godmd_prep.TestGOdMDPrep" name="test_godmd_prep" time="0.042" /><testcase classname="biobb_godmd.test.unitests.test_godmd.test_godmd_run.TestGOdMDrun" name="test_godmd_run" time="194.303" /></testsuite></testsuites>
\ No newline at end of file
+<?xml version="1.0" encoding="utf-8"?><testsuites><testsuite name="pytest" errors="0" failures="0" skipped="0" tests="2" time="15.139" timestamp="2024-11-04T13:15:55.122729+00:00" hostname="biobb-runners"><testcase classname="biobb_godmd.test.unitests.test_godmd.test_godmd_prep.TestGOdMDPrep" name="test_godmd_prep" time="0.047" /><testcase classname="biobb_godmd.test.unitests.test_godmd.test_godmd_run.TestGOdMDrun" name="test_godmd_run" time="14.735" /></testsuite></testsuites>
\ No newline at end of file
diff --git a/junit/report.html b/junit/report.html
index 7aeff86..a8dad9a 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 27-Jun-2024 at 09:20:13 by <a href="https://pypi.python.org/pypi/pytest-html">pytest-html</a>
+    <p>Report generated on 04-Nov-2024 at 13:16:10 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">2 tests took 00:03:14.</p>
+        <p class="run-count">2 tests took 00:00:15.</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_godmd/test/unitests/test_godmd/test_godmd_prep.py::TestGOdMDPrep::test_godmd_prep&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_godmd/test/unitests/test_godmd/test_godmd_prep.py::TestGOdMDPrep::test_godmd_prep&#34;, &#34;duration&#34;: &#34;42 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_godmd/test/unitests/test_godmd/test_godmd_prep.py::TestGOdMDPrep::test_godmd_prep&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;42 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 -----------------------------\n2024-06-27 09:16:59,482 [MainThread  ] [INFO ]  Executing biobb_godmd.godmd.godmd_prep Version: 4.2.0\n2024-06-27 09:16:59,482 [MainThread  ] [INFO ]  /tmp/biobb/unitests_185/godmd_prep/sandbox_cdfedd1b-31ec-4930-866b-623333b2d4a0 directory successfully created\n2024-06-27 09:16:59,483 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/1ake_A.pdb to /tmp/biobb/unitests_185/godmd_prep/sandbox_cdfedd1b-31ec-4930-866b-623333b2d4a0\n2024-06-27 09:16:59,483 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/4ake_A.pdb to /tmp/biobb/unitests_185/godmd_prep/sandbox_cdfedd1b-31ec-4930-866b-623333b2d4a0\n2024-06-27 09:16:59,488 [MainThread  ] [INFO ]  water -auto -outfile /tmp/biobb/unitests_185/godmd_prep/sandbox_cdfedd1b-31ec-4930-866b-623333b2d4a0/water_align.out -asequence /tmp/biobb/unitests_185/godmd_prep/sandbox_cdfedd1b-31ec-4930-866b-623333b2d4a0/fasta1.fa -bsequence /tmp/biobb/unitests_185/godmd_prep/sandbox_cdfedd1b-31ec-4930-866b-623333b2d4a0/fasta2.fa -gapopen 12.0 -gapextend 2 -datafile EPAM250 -aformat markx10\n\n2024-06-27 09:16:59,508 [MainThread  ] [INFO ]  Exit code 0\n\n2024-06-27 09:16:59,509 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_185/godmd_prep/sandbox_cdfedd1b-31ec-4930-866b-623333b2d4a0&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_185/godmd_prep/godmd_orig.aln\nChecking if empty file: /tmp/biobb/unitests_185/godmd_prep/godmd_target.aln\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_185/godmd_prep/godmd_prep_log.out:file_utils.py:391 Executing biobb_godmd.godmd.godmd_prep Version: 4.2.0\nINFO     /tmp/biobb/unitests_185/godmd_prep/godmd_prep_log.out:file_utils.py:82 /tmp/biobb/unitests_185/godmd_prep/sandbox_cdfedd1b-31ec-4930-866b-623333b2d4a0 directory successfully created\nINFO     /tmp/biobb/unitests_185/godmd_prep/godmd_prep_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/1ake_A.pdb to /tmp/biobb/unitests_185/godmd_prep/sandbox_cdfedd1b-31ec-4930-866b-623333b2d4a0\nINFO     /tmp/biobb/unitests_185/godmd_prep/godmd_prep_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/4ake_A.pdb to /tmp/biobb/unitests_185/godmd_prep/sandbox_cdfedd1b-31ec-4930-866b-623333b2d4a0\nINFO     /tmp/biobb/unitests_185/godmd_prep/godmd_prep_log.out:cmd_wrapper.py:33 water -auto -outfile /tmp/biobb/unitests_185/godmd_prep/sandbox_cdfedd1b-31ec-4930-866b-623333b2d4a0/water_align.out -asequence /tmp/biobb/unitests_185/godmd_prep/sandbox_cdfedd1b-31ec-4930-866b-623333b2d4a0/fasta1.fa -bsequence /tmp/biobb/unitests_185/godmd_prep/sandbox_cdfedd1b-31ec-4930-866b-623333b2d4a0/fasta2.fa -gapopen 12.0 -gapextend 2 -datafile EPAM250 -aformat markx10\n\nINFO     /tmp/biobb/unitests_185/godmd_prep/godmd_prep_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_185/godmd_prep/godmd_prep_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_185/godmd_prep/sandbox_cdfedd1b-31ec-4930-866b-623333b2d4a0&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_185\n&#34;}], &#34;biobb_godmd/test/unitests/test_godmd/test_godmd_run.py::TestGOdMDrun::test_godmd_run&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_godmd/test/unitests/test_godmd/test_godmd_run.py::TestGOdMDrun::test_godmd_run&#34;, &#34;duration&#34;: &#34;00:03:14&#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_godmd/test/unitests/test_godmd/test_godmd_run.py::TestGOdMDrun::test_godmd_run&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:03:14&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-06-27 09:16:59,543 [MainThread  ] [INFO ]  Executing biobb_godmd.godmd.godmd_run Version: 4.2.0\n2024-06-27 09:16:59,543 [MainThread  ] [INFO ]  /tmp/biobb/unitests_185/godmd_run/sandbox_bd6b9021-e1ba-486d-a2a2-82f7e81f6185 directory successfully created\n2024-06-27 09:16:59,544 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/1ake_A.pdb to /tmp/biobb/unitests_185/godmd_run/sandbox_bd6b9021-e1ba-486d-a2a2-82f7e81f6185\n2024-06-27 09:16:59,544 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/4ake_A.pdb to /tmp/biobb/unitests_185/godmd_run/sandbox_bd6b9021-e1ba-486d-a2a2-82f7e81f6185\n2024-06-27 09:16:59,544 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/1ake_A.aln to /tmp/biobb/unitests_185/godmd_run/sandbox_bd6b9021-e1ba-486d-a2a2-82f7e81f6185\n2024-06-27 09:16:59,545 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/4ake_A.aln to /tmp/biobb/unitests_185/godmd_run/sandbox_bd6b9021-e1ba-486d-a2a2-82f7e81f6185\n2024-06-27 09:16:59,545 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/params.in to /tmp/biobb/unitests_185/godmd_run/sandbox_bd6b9021-e1ba-486d-a2a2-82f7e81f6185\n2024-06-27 09:16:59,545 [MainThread  ] [INFO ]  cd /tmp/biobb/unitests_185/godmd_run/sandbox_bd6b9021-e1ba-486d-a2a2-82f7e81f6185 ; discrete -i godmd.in -pdbin 1ake_A.pdb -pdbtarg 4ake_A.pdb -p1 1ake_A.aln -p2 4ake_A.aln -o godmd.log -ener godmd_ene.out -trj godmd_trj.mdcrd\n\n2024-06-27 09:20:13,830 [MainThread  ] [INFO ]  Exit code 0\n\n2024-06-27 09:20:13,833 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_185/godmd_run/sandbox_bd6b9021-e1ba-486d-a2a2-82f7e81f6185&amp;#x27;]\nChecking if empty file: /tmp/biobb/unitests_185/godmd_run/godmd.log\nChecking if empty file: /tmp/biobb/unitests_185/godmd_run/godmd_ene.out\nChecking if empty file: /tmp/biobb/unitests_185/godmd_run/godmd_trj.mdcrd\nChecking if empty file: /tmp/biobb/unitests_185/godmd_run/godmd_pdb.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_185/godmd_run/godmd_run_log.out:file_utils.py:391 Executing biobb_godmd.godmd.godmd_run Version: 4.2.0\nINFO     /tmp/biobb/unitests_185/godmd_run/godmd_run_log.out:file_utils.py:82 /tmp/biobb/unitests_185/godmd_run/sandbox_bd6b9021-e1ba-486d-a2a2-82f7e81f6185 directory successfully created\nINFO     /tmp/biobb/unitests_185/godmd_run/godmd_run_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/1ake_A.pdb to /tmp/biobb/unitests_185/godmd_run/sandbox_bd6b9021-e1ba-486d-a2a2-82f7e81f6185\nINFO     /tmp/biobb/unitests_185/godmd_run/godmd_run_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/4ake_A.pdb to /tmp/biobb/unitests_185/godmd_run/sandbox_bd6b9021-e1ba-486d-a2a2-82f7e81f6185\nINFO     /tmp/biobb/unitests_185/godmd_run/godmd_run_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/1ake_A.aln to /tmp/biobb/unitests_185/godmd_run/sandbox_bd6b9021-e1ba-486d-a2a2-82f7e81f6185\nINFO     /tmp/biobb/unitests_185/godmd_run/godmd_run_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/4ake_A.aln to /tmp/biobb/unitests_185/godmd_run/sandbox_bd6b9021-e1ba-486d-a2a2-82f7e81f6185\nINFO     /tmp/biobb/unitests_185/godmd_run/godmd_run_log.out:file_utils.py:391 Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/params.in to /tmp/biobb/unitests_185/godmd_run/sandbox_bd6b9021-e1ba-486d-a2a2-82f7e81f6185\nINFO     /tmp/biobb/unitests_185/godmd_run/godmd_run_log.out:cmd_wrapper.py:33 cd /tmp/biobb/unitests_185/godmd_run/sandbox_bd6b9021-e1ba-486d-a2a2-82f7e81f6185 ; discrete -i godmd.in -pdbin 1ake_A.pdb -pdbtarg 4ake_A.pdb -p1 1ake_A.aln -p2 4ake_A.aln -o godmd.log -ener godmd_ene.out -trj godmd_trj.mdcrd\n\nINFO     /tmp/biobb/unitests_185/godmd_run/godmd_run_log.out:cmd_wrapper.py:50 Exit code 0\n\nINFO     /tmp/biobb/unitests_185/godmd_run/godmd_run_log.out:file_utils.py:391 Removed: [&amp;#x27;/tmp/biobb/unitests_185/godmd_run/sandbox_bd6b9021-e1ba-486d-a2a2-82f7e81f6185&amp;#x27;]\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_185\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;3.10.15&#34;, &#34;Platform&#34;: &#34;Linux-5.4.0-200-generic-x86_64-with-glibc2.31&#34;, &#34;Packages&#34;: {&#34;pytest&#34;: &#34;8.3.3&#34;, &#34;pluggy&#34;: &#34;1.5.0&#34;}, &#34;Plugins&#34;: {&#34;metadata&#34;: &#34;3.1.1&#34;, &#34;cov&#34;: &#34;6.0.0&#34;, &#34;html&#34;: &#34;4.1.1&#34;}, &#34;CI&#34;: &#34;true&#34;}, &#34;tests&#34;: {&#34;biobb_godmd/test/unitests/test_godmd/test_godmd_prep.py::TestGOdMDPrep::test_godmd_prep&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_godmd/test/unitests/test_godmd/test_godmd_prep.py::TestGOdMDPrep::test_godmd_prep&#34;, &#34;duration&#34;: &#34;47 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_godmd/test/unitests/test_godmd/test_godmd_prep.py::TestGOdMDPrep::test_godmd_prep&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;47 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 -----------------------------\n2024-11-04 13:15:55,432 [MainThread  ] [INFO ]  Module: biobb_godmd.godmd.godmd_prep Version: 4.2.0\n2024-11-04 13:15:55,432 [MainThread  ] [INFO ]  /tmp/biobb/unitests_8/godmd_prep/sandbox_1bc613d5-a04d-4391-800c-24911d737647 directory successfully created\n2024-11-04 13:15:55,433 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/1ake_A.pdb to /tmp/biobb/unitests_8/godmd_prep/sandbox_1bc613d5-a04d-4391-800c-24911d737647\n2024-11-04 13:15:55,433 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/4ake_A.pdb to /tmp/biobb/unitests_8/godmd_prep/sandbox_1bc613d5-a04d-4391-800c-24911d737647\n2024-11-04 13:15:55,439 [MainThread  ] [INFO ]  water -auto -outfile /tmp/biobb/unitests_8/godmd_prep/sandbox_1bc613d5-a04d-4391-800c-24911d737647/water_align.out -asequence /tmp/biobb/unitests_8/godmd_prep/sandbox_1bc613d5-a04d-4391-800c-24911d737647/fasta1.fa -bsequence /tmp/biobb/unitests_8/godmd_prep/sandbox_1bc613d5-a04d-4391-800c-24911d737647/fasta2.fa -gapopen 12.0 -gapextend 2 -datafile EPAM250 -aformat markx10\n\n2024-11-04 13:15:55,464 [MainThread  ] [INFO ]  Executing: water -auto -outfile /tmp/biobb/unitests_8/godmd_prep/sandbox_1bc613d5-a04d-4391...\n2024-11-04 13:15:55,464 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 13:15:55,466 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_8/godmd_prep/sandbox_1bc613d5-a04d-4391-800c-24911d737647&amp;#x27;]\n2024-11-04 13:15:55,466 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/godmd_prep/godmd_orig.aln\nChecking if empty file: /tmp/biobb/unitests_8/godmd_prep/godmd_target.aln\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_8/godmd_prep/godmd_prep_log.out:file_utils.py:409 Module: biobb_godmd.godmd.godmd_prep Version: 4.2.0\nINFO     /tmp/biobb/unitests_8/godmd_prep/godmd_prep_log.out:file_utils.py:82 /tmp/biobb/unitests_8/godmd_prep/sandbox_1bc613d5-a04d-4391-800c-24911d737647 directory successfully created\nINFO     /tmp/biobb/unitests_8/godmd_prep/godmd_prep_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/1ake_A.pdb to /tmp/biobb/unitests_8/godmd_prep/sandbox_1bc613d5-a04d-4391-800c-24911d737647\nINFO     /tmp/biobb/unitests_8/godmd_prep/godmd_prep_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/4ake_A.pdb to /tmp/biobb/unitests_8/godmd_prep/sandbox_1bc613d5-a04d-4391-800c-24911d737647\nINFO     /tmp/biobb/unitests_8/godmd_prep/godmd_prep_log.out:cmd_wrapper.py:63 water -auto -outfile /tmp/biobb/unitests_8/godmd_prep/sandbox_1bc613d5-a04d-4391-800c-24911d737647/water_align.out -asequence /tmp/biobb/unitests_8/godmd_prep/sandbox_1bc613d5-a04d-4391-800c-24911d737647/fasta1.fa -bsequence /tmp/biobb/unitests_8/godmd_prep/sandbox_1bc613d5-a04d-4391-800c-24911d737647/fasta2.fa -gapopen 12.0 -gapextend 2 -datafile EPAM250 -aformat markx10\n\nINFO     /tmp/biobb/unitests_8/godmd_prep/godmd_prep_log.out:cmd_wrapper.py:36 Executing: water -auto -outfile /tmp/biobb/unitests_8/godmd_prep/sandbox_1bc613d5-a04d-4391...\nINFO     /tmp/biobb/unitests_8/godmd_prep/godmd_prep_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_8/godmd_prep/godmd_prep_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_8/godmd_prep/sandbox_1bc613d5-a04d-4391-800c-24911d737647&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/godmd_prep/godmd_prep_log.out:file_utils.py:409\n\n--------------------------- Captured stdout teardown ---------------------------\n\nRemoving: /tmp/biobb/unitests_8\n&#34;}], &#34;biobb_godmd/test/unitests/test_godmd/test_godmd_run.py::TestGOdMDrun::test_godmd_run&#34;: [{&#34;extras&#34;: [], &#34;result&#34;: &#34;Passed&#34;, &#34;testId&#34;: &#34;biobb_godmd/test/unitests/test_godmd/test_godmd_run.py::TestGOdMDrun::test_godmd_run&#34;, &#34;duration&#34;: &#34;00:00:15&#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_godmd/test/unitests/test_godmd/test_godmd_run.py::TestGOdMDrun::test_godmd_run&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-duration\&#34;&gt;00:00:15&lt;/td&gt;&#34;, &#34;&lt;td class=\&#34;col-links\&#34;&gt;&lt;/td&gt;&#34;], &#34;log&#34;: &#34;----------------------------- Captured stdout call -----------------------------\n2024-11-04 13:15:55,490 [MainThread  ] [INFO ]  Module: biobb_godmd.godmd.godmd_run Version: 4.2.0\n2024-11-04 13:15:55,491 [MainThread  ] [INFO ]  /tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2 directory successfully created\n2024-11-04 13:15:55,491 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/1ake_A.pdb to /tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2\n2024-11-04 13:15:55,491 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/4ake_A.pdb to /tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2\n2024-11-04 13:15:55,492 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/1ake_A.aln to /tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2\n2024-11-04 13:15:55,492 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/4ake_A.aln to /tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2\n2024-11-04 13:15:55,492 [MainThread  ] [INFO ]  Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/params.in to /tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2\n2024-11-04 13:15:55,493 [MainThread  ] [INFO ]  cd /tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2 ; discrete -i godmd.in -pdbin 1ake_A.pdb -pdbtarg 4ake_A.pdb -p1 1ake_A.aln -p2 4ake_A.aln -o godmd.log -ener godmd_ene.out -trj godmd_trj.mdcrd\n\n2024-11-04 13:16:10,213 [MainThread  ] [INFO ]  Executing: cd /tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2 ...\n2024-11-04 13:16:10,214 [MainThread  ] [INFO ]  Exit code: 0\n2024-11-04 13:16:10,216 [MainThread  ] [INFO ]  Removed: [&amp;#x27;/tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2&amp;#x27;]\n2024-11-04 13:16:10,216 [MainThread  ] [INFO ]  \nChecking if empty file: /tmp/biobb/unitests_8/godmd_run/godmd.log\nChecking if empty file: /tmp/biobb/unitests_8/godmd_run/godmd_ene.out\nChecking if empty file: /tmp/biobb/unitests_8/godmd_run/godmd_trj.mdcrd\nChecking if empty file: /tmp/biobb/unitests_8/godmd_run/godmd_pdb.pdb\n\n------------------------------ Captured log call -------------------------------\nINFO     /tmp/biobb/unitests_8/godmd_run/godmd_run_log.out:file_utils.py:409 Module: biobb_godmd.godmd.godmd_run Version: 4.2.0\nINFO     /tmp/biobb/unitests_8/godmd_run/godmd_run_log.out:file_utils.py:82 /tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2 directory successfully created\nINFO     /tmp/biobb/unitests_8/godmd_run/godmd_run_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/1ake_A.pdb to /tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2\nINFO     /tmp/biobb/unitests_8/godmd_run/godmd_run_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/4ake_A.pdb to /tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2\nINFO     /tmp/biobb/unitests_8/godmd_run/godmd_run_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/1ake_A.aln to /tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2\nINFO     /tmp/biobb/unitests_8/godmd_run/godmd_run_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/4ake_A.aln to /tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2\nINFO     /tmp/biobb/unitests_8/godmd_run/godmd_run_log.out:file_utils.py:409 Copy: /home/user/actions-runner/_work/biobb_godmd/biobb_godmd/biobb_godmd/test/data/godmd/params.in to /tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2\nINFO     /tmp/biobb/unitests_8/godmd_run/godmd_run_log.out:cmd_wrapper.py:63 cd /tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2 ; discrete -i godmd.in -pdbin 1ake_A.pdb -pdbtarg 4ake_A.pdb -p1 1ake_A.aln -p2 4ake_A.aln -o godmd.log -ener godmd_ene.out -trj godmd_trj.mdcrd\n\nINFO     /tmp/biobb/unitests_8/godmd_run/godmd_run_log.out:cmd_wrapper.py:36 Executing: cd /tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2 ...\nINFO     /tmp/biobb/unitests_8/godmd_run/godmd_run_log.out:cmd_wrapper.py:37 Exit code: 0\nINFO     /tmp/biobb/unitests_8/godmd_run/godmd_run_log.out:file_utils.py:409 Removed: [&amp;#x27;/tmp/biobb/unitests_8/godmd_run/sandbox_eee10d2e-4a6f-486e-9c36-5fc5131079c2&amp;#x27;]\nINFO     /tmp/biobb/unitests_8/godmd_run/godmd_run_log.out:file_utils.py:409\n\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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