Fixed the merge code by making sure that the AtomIdx of the added ato…

…m is correct

for its position in the molecule (i.e. is one higher than the AtomIdx of the last
atom in the residue)

corelib/src/libs/SireSystem/merge.cpp

@@ -390,12 +390,26 @@ namespace SireSystem
 
                 auto res = mol.residue(residx);
 
+                // get the AtomIdx of the last atom in this residue
+                AtomIdx last_atomidx(0);
+
+                if (res.nAtoms() > 0)
+                {
+                    last_atomidx = res.atom(res.nAtoms() - 1).index();
+                }
+
                 // add the atom - it has the name "Xxx" as it doesn't exist
                 // in the reference state
                 auto atom = res.add(AtomName("Xxx"));
                 largest_atomnum = AtomNum(largest_atomnum.value() + 1);
                 atom.renumber(largest_atomnum);
 
+                // ensure that its index follows on from the index of the
+                // last atom in the residue - this is so that we keep
+                // the AtomIdx and CGAtomIdx orders in sync, and don't
+                // force a complex reordering of the atoms when we commit
+                atom.reindex(last_atomidx + 1);
+
                 // reparent this atom to the CutGroup for this residue
                 atom.reparent(cgidx);
 

doc/source/changelog.rst

@@ -55,6 +55,19 @@ organisation on `GitHub <https://github.com/openbiosim/sire>`__.
 * Added a map option (fix_perturbable_zero_sigmas) to prevent perturbation of
   the Lennard-Jones sigma parameter for ghost atoms during alchemical free energy simulations.
 
+* [CHANGE IN BEHAVIOUR] - added code that ensures that, when editing molecules,
+  the CGAtomIdx order will always follow the AtomIdx order of atoms. This is
+  because a lot of code had implicitly assumed this, and so it was a cause
+  of bugs when this wasn't the case. Now, when you edit a molecule, on committing,
+  the orders will be checked. If they don't agree, then the CutGroups will be
+  reordered, with atoms reordered as necessary to make the CGAtomIdx order match
+  the AtomIdx order. If this isn't possible (e.g. because atoms in CutGroups
+  are not contiguous), then the molecule will be converted to a single-cutgroup
+  molecule, with the atoms placed in AtomIdx order. As part of this change,
+  the merge code will now also ensure that added atoms are added with the
+  correct AtomIdx, rather than added as the last atoms in the molecule. This
+  is also more natural. This fixes issue #202.
+
 * Please add an item to this changelog when you create your PR
 
 `2024.1.0 <https://github.com/openbiosim/sire/compare/2023.5.2...2024.1.0>`__ - April 2024