Merge pull request #18 from martimunicoy/propers_fix

Fix proper and improper constructors
martimunicoy · Aug 5, 2020 · 784f8ef · 784f8ef
2 parents 006b514 + e20bd26
commit 784f8ef
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Showing 2 changed files with 19 additions and 17 deletions.
diff --git a/offpele/main.py b/offpele/main.py
@@ -143,7 +143,7 @@ def run_offpele(pdb_file, forcefield=DEFAULT_OFF_FORCEFIELD,
         not
     """
     print('-' * 60)
-    print('Open Force Field parameterizer for PELE v'
+    print('Open Force Field parameterizer for PELE '
           '{}'.format(offpele.__version__))
     print('-' * 60)
     print(' - PDB to parameterize: {}'.format(pdb_file))

diff --git a/offpele/topology/molecule.py b/offpele/topology/molecule.py
@@ -748,16 +748,17 @@ def _build_propers(self):
         ks = self.parameters.get_dihedral_ks()
         idivfs = self.parameters.get_dihedral_idivfs()
 
-        # idivf is a optional parameter in OpenForceField
-        if idivfs is not None:
-            if len(idivfs) == 0:
-                for period_by_index in periodicities:
-                    idivfs.append(dict(zip(
-                        period_by_index.keys(),
-                        [1, ] * len(period_by_index.keys()))))
-        else:
+        # TODO in which situation these dicts are supposed to be None?
+        if periodicities is None or phases is None or ks is None:
             return
 
+        # idivf is a optional parameter in OpenForceField
+        if len(idivfs) == 0:
+            for period_by_index in periodicities:
+                idivfs.append(dict(zip(
+                    period_by_index.keys(),
+                    [1, ] * len(period_by_index.keys()))))
+
         assert len(periodicities) == len(phases) and \
             len(periodicities) == len(ks) and \
             len(periodicities) == len(idivfs), 'Unconsistent set of ' \
@@ -823,16 +824,17 @@ def _build_impropers(self):
         ks = self.parameters.get_improper_ks()
         idivfs = self.parameters.get_improper_idivfs()
 
-        # idivf is a optional parameter in OpenForceField
-        if idivfs is not None:
-            if len(idivfs) == 0:
-                for period_by_index in periodicities:
-                    idivfs.append(dict(zip(
-                        period_by_index.keys(),
-                        [1, ] * len(period_by_index.keys()))))
-        else:
+        # TODO in which situation these dicts are supposed to be None?
+        if periodicities is None or phases is None or ks is None:
             return
 
+        # idivf is a optional parameter in OpenForceField
+        if len(idivfs) == 0:
+            for period_by_index in periodicities:
+                idivfs.append(dict(zip(
+                    period_by_index.keys(),
+                    [1, ] * len(period_by_index.keys()))))
+
         assert len(periodicities) == len(phases) and \
             len(periodicities) == len(ks) and \
             len(periodicities) == len(idivfs), 'Unconsistent set of ' \