Merge pull request #844 from swails/master

Update `Topology` creation from CHARMM parsers and fix Amber prmtop parsing when %COMMENT sections are present

wrappers/python/simtk/openmm/app/charmmpsffile.py

@@ -777,11 +777,12 @@ class CharmmPsfFile(object):
         # Add each chain (separate 'system's) and residue
         for atom in self.atom_list:
             if atom.system != last_chain:
-                chain = topology.addChain()
+                chain = topology.addChain(atom.system)
                 last_chain = atom.system
             if atom.residue.idx != last_residue:
                 last_residue = atom.residue.idx
-                residue = topology.addResidue(atom.residue.resname, chain)
+                residue = topology.addResidue(atom.residue.resname, chain,
+                                              str(atom.residue.idx))
             if atom.type is not None:
                 # This is the most reliable way of determining the element
                 atomic_num = atom.type.atomic_number

wrappers/python/simtk/openmm/app/internal/amber_file_parser.py

@@ -135,6 +135,8 @@ class PrmtopLoader(object):
                     format = format[index0+1:index1]
                     m = FORMAT_RE_PATTERN.search(format)
                     self._raw_format[self._flags[-1]] = (format, m.group(1), m.group(2), m.group(3), m.group(4))
+                elif line.startswith('%COMMENT'):
+                    continue
                 elif self._flags \
                      and 'TITLE'==self._flags[-1] \
                      and not self._raw_data['TITLE']:

wrappers/python/tests/systems/Mg_water.prmtop

@@ -1802,6 +1802,7 @@ WAT WAT
   2.54487941E+01  1.27063907E+02  5.94825035E+02  0.00000000E+00  0.00000000E+00
   0.00000000E+00
 %FLAG LENNARD_JONES_CCOEF
+%COMMENT This is the r^-4 term in the 12-6-4 LJ potential
 %FORMAT(5E16.8)
   0.00000000E+00  1.32908847E+02  0000000000E+00  0.00000000E+00  0.00000000E+00
   0.00000000E+00