Merge branch 'master' into feature/charmm-enhancements

parmed/amber/_amberparm.py

@@ -286,7 +286,7 @@ def from_structure(cls, struct, copy=False):
             return struct
         if struct.unknown_functional:
             raise TypeError('Cannot instantiate an AmberParm from unknown functional')
-        if (struct.urey_bradleys or struct.impropers or struct.cmaps or
+        if (struct.urey_bradleys or struct.impropers or
                 struct.trigonal_angles or struct.pi_torsions or
                 struct.out_of_plane_bends or struct.stretch_bends or
                 struct.torsion_torsions or struct.multipole_frames):

parmed/gromacs/gromacstop.py

@@ -401,7 +401,8 @@ def read(self, fname, defines=None, parametrize=True):
                     dihedral_types = dict()
                     exc_types = dict()
                 elif current_section == 'atoms':
-                    molecule.add_atom(*self._parse_atoms(line, params))
+                    atom, resname, resnum, icode = self._parse_atoms(line, params)
+                    molecule.add_atom(atom, resname, resnum, inscode=icode)
                 elif current_section == 'bonds':
                     bond, bond_type = self._parse_bonds(line, bond_types, molecule.atoms)
                     molecule.bonds.append(bond)
@@ -582,7 +583,15 @@ def _parse_atoms(self, line, params):
         else:
             atom = Atom(atomic_number=atomic_number, name=words[4],
                         type=words[1], charge=charge, mass=mass)
-        return atom, words[3], int(words[2])
+
+        # check for insertion code and negative res number
+        if words[2].isnumeric() or (words[2].startswith('-') and words[2][1:].isnumeric()):
+            icode = ''
+            resnum = int(words[2])
+        else:
+            icode = words[2][-1]
+            resnum = int(words[2][:-1])
+        return atom, words[3], resnum, icode
 
     def _parse_bonds(self, line, bond_types, atoms):
         """ Parses a bond line. Returns a Bond, BondType/None """