fixed error in verbose mode for missing dihedrals (#335)

* fixed error in verbose mode for missing dihedrals

* merged in additional error messages from ray's PR

foyer/forcefield.py

@@ -310,22 +310,38 @@ def _check_dihedrals(data, structure, verbose,
  if verbose:
  for omm_ids in data.propers:
  missing_dihedral = True
+ for pmd_proper in proper_dihedrals:
+ pmd_ids = (pmd_proper.atom1.idx, pmd_proper.atom2.idx, pmd_proper.atom3.idx, pmd_proper.atom4.idx)
+ if pmd_ids == omm_ids:
+ missing_dihedral = False
  for pmd_proper in structure.rb_torsions:
  pmd_ids = (pmd_proper.atom1.idx, pmd_proper.atom2.idx, pmd_proper.atom3.idx, pmd_proper.atom4.idx)
  if pmd_ids == omm_ids:
  missing_dihedral = False
  if missing_dihedral:
- print('missing improper with ids {}'.format(pmd_ids))
+ print("Missing dihedral with ids {} and types {}.".format(
+ omm_ids, [structure.atoms[idx].type for idx in omm_ids]))
 
  if data.propers and len(data.propers) != \
- len(proper_dihedrals) + len(structure.rb_torsions):
- msg = ("Parameters have not been assigned to all proper dihedrals. "
- "Total system dihedrals: {}, Parameterized dihedrals: {}. "
- "Note that if your system contains torsions of Ryckaert-"
- "Bellemans functional form, all of these torsions are "
- "processed as propers.".format(len(data.propers),
- len(proper_dihedrals) + len(structure.rb_torsions)))
- _error_or_warn(assert_dihedral_params, msg)
+ len(proper_dihedrals) + len(structure.rb_torsions):
+ if data.propers and len(data.propers) < \
+ len(proper_dihedrals) + len(structure.rb_torsions):
+ msg = ("Parameters have been assigned to all proper dihedrals. "
+ "However, there are more parameterized dihedrals ({}) "
+ "than total system dihedrals ({}). "
+ "This may be due to having multiple periodic dihedrals "
+ "for a single system dihedral.".format(len(proper_dihedrals) +
+ len(structure.rb_torsions),
+ len(data.propers)))
+ warnings.warn(msg)
+ else:
+ msg = ("Parameters have not been assigned to all proper dihedrals. "
+ "Total system dihedrals: {}, Parameterized dihedrals: {}. "
+ "Note that if your system contains torsions of Ryckaert-"
+ "Bellemans functional form, all of these torsions are "
+ "processed as propers.".format(len(data.propers),
+ len(proper_dihedrals) + len(structure.rb_torsions)))
+ _error_or_warn(assert_dihedral_params, msg)
 
  improper_dihedrals = [dihedral for dihedral in structure.dihedrals
  if dihedral.improper]