Fix handling of positive formal charge when writing SDF. [closes #274]

OpenBioSim · Jan 17, 2025 · 50dc2de · 50dc2de
1 parent 964a670
commit 50dc2de
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diff --git a/corelib/src/libs/SireIO/sdf.cpp b/corelib/src/libs/SireIO/sdf.cpp
@@ -959,6 +959,13 @@ SDFMolecule parseMolecule(const Molecule &molecule, QStringList &errors, const P
                 sdfmol.addProperty("CHG", i + 1, QString::number(charge));
                 charge = 0;
             }
+            else if (charge > 0)
+            {
+                if (charge < 4)
+                {
+                    charge = 4 - charge;
+                }
+            }
             else if (charge < 0)
             {
                 switch (charge)

diff --git a/doc/source/changelog.rst b/doc/source/changelog.rst
@@ -27,6 +27,8 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
 
 * Add support for Replica Exchange with Solute Tempering (REST2) simulations.
 
+* Fix handling of positive formal charge when writing SDF files.
+
 `2024.3.1 <https://github.com/openbiosim/sire/compare/2024.3.0...2024.3.1>`__ - December 2024
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@@ Expand Up @@
     * Add support for Replica Exchange with Solute Tempering (REST2) simulations.
+    * Fix handling of positive formal charge when writing SDF files.
     `2024.3.1 <https://github.com/openbiosim/sire/compare/2024.3.0...2024.3.1>`__ - December 2024
     --------------------------------------------------------------------------------------------
@@ Expand Down @@