Only apply fix when atomic number is negative.

[ref michellab/BioSimSpace#251]
michellab · Dec 3, 2021 · 0122d3f · 0122d3f
1 parent 80c5794
commit 0122d3f
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/corelib/src/libs/SireIO/amber.cpp b/corelib/src/libs/SireIO/amber.cpp
@@ -521,7 +521,9 @@ static void setAtomParameters(AtomEditor &editatom, MolEditor &editmol,
     {
         Element elem;
 
-        if (element[atomNumber-1] <= 0 and mass[atomNumber-1] > 0)
+        // Infer element from mass if atomic number is negative, which
+        // can be the case for files generated by Acellara's "parameterize".
+        if (element[atomNumber-1] < 0 and mass[atomNumber-1] > 0)
         {
             elem = Element::elementWithMass(mass[atomNumber-1] * g_per_mol);
         }

diff --git a/corelib/src/libs/SireIO/amberprm.cpp b/corelib/src/libs/SireIO/amberprm.cpp
@@ -3946,8 +3946,9 @@ AmberParams AmberPrm::getAmberParams(int molidx, const MoleculeInfoData &molinfo
 
             Element element;
 
-            if (int(atomic_num_array[atom_idx]) <= 0 and
-                mass_array[atom_idx] > 0)
+            // Infer element from mass if atomic number is negative, which
+            // can be the case for files generated by Acellara's "parameterize".
+            if (int(atomic_num_array[atom_idx]) < 0 and mass_array[atom_idx] > 0)
             {
                 element = Element::elementWithMass(mass_array[atom_idx] * g_per_mol);
             }