Merge pull request #167 from OpenBioSim/fix_166

Fix issue #166

Author: chryswoods

corelib/src/libs/SireIO/mol2.cpp

@@ -2623,10 +2623,8 @@ MolEditor Mol2::getMolecule(int imol, const PropertyMap &map) const
         types.set(cgatomidx, atom.getType());
         status_bits.set(cgatomidx, atom.getStatusBits());
 
-        // Try to infer the element from the name of the atom.
-        // We'll strip all numeric digits and use a maximum of two characters.
-        auto name = atom.getName().remove(QRegExp("[0-9]")).mid(0, 2);
-        elements.set(cgatomidx, Element::biologicalElement(name));
+        // Infer the element from the SYBYL atom type.
+        elements.set(cgatomidx, Element::biologicalElement(atom.getType()));
     }
 
     // Instantiate the residue property objects that we need.

doc/source/changelog.rst

@@ -151,6 +151,10 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
   extension for Amber RST7 files, and changes the scoring logic of the SDF parser
   to equal the number of molecules times the number of atoms.
 
+* Switched to using the SYBL atom type to infer the element of an atom
+  when reading Mol2 files. This is more robust than using the atom name.
+  Fixes issue #166.
+
 * Please add an item to this changelog when you create your PR
 
 `2023.5.1 <https://github.com/openbiosim/sire/compare/2023.5.0...2023.5.1>`__ - January 2024