def _assignNamesFromForceFieldTemplates(topology, system, openmm_forcefields_to_use):
'''
Assign Amber atom and residue names from specified forcefield templates.
Requires OpenMM version >= 5.2.
ARGUMENTS
topology
system
openmm_forcefields_to_use (list of strings) - list of XML files of forcefields containing templates
RETURNS
atoms - list of atom information
sorted_atom_indices (list of int) - atom indices in order that they appear in forcefield templates, in case re-sorting is required
'''
# Assign AMBER atom and residue names.
from simtk.openmm.app import ForceField
import simtk.openmm.app.forcefield
forcefield = ForceField(*openmm_forcefields_to_use)
data = ForceField._SystemData()
atomIndices = {}
for index, atom in enumerate(topology.atoms()):
data.atoms.append(atom)
atomIndices[atom] = index
# Make a list of all bonds
for bond in topology.bonds():
if bond[0] in atomIndices and bond[1] in atomIndices:
data.bonds.append(ForceField._BondData(atomIndices[bond[0]], atomIndices[bond[1]]))
# Record which atoms are bonded to each other atom
bondedToAtom = []
for i in range(len(data.atoms)):
bondedToAtom.append(set())
data.atomBonds.append([])
for i in range(len(data.bonds)):
bond = data.bonds[i]
bondedToAtom[bond.atom1].add(bond.atom2)
bondedToAtom[bond.atom2].add(bond.atom1)
data.atomBonds[bond.atom1].append(i)
data.atomBonds[bond.atom2].append(i)
# Find the template matching each residue and assign atom types.
sorted_atom_indices = list()
for chain in topology.chains():
for res in chain.residues():
template = None
matches = None
# NOTE: Before OpenMM 5.2, was necessary to convert output of _createResidueSignature using the method simtk.openmm.app.forcefield._signatureToString - this is now done within _createResidueSignature
sig = simtk.openmm.app.forcefield._createResidueSignature([atom.element for atom in res.atoms()])
if sig != '':
if sig in forcefield._templateSignatures:
for t in forcefield._templateSignatures[sig]:
# NOTE: No longer necessary to pass atomIndices in OpenMM > 5.2
matches = simtk.openmm.app.forcefield._matchResidue(res, t, bondedToAtom)
if matches is not None:
template = t
break
if matches is None:
# Check templates involving virtual sites
for t in forcefield._templateSignatures[None]:
matches = simtk.openmm.app.forcefield._matchResidue(res, t, bondedToAtom)
if matches is not None:
template = t
break
if matches is None:
raise ValueError('No template found for residue %d (%s). This might mean your input topology is missing some atoms or bonds, or possibly that you are using the wrong force field.' % (res.index+1, res.name))
# Sort matches by order in template.
atom_indices = [ atom.index for atom in res.atoms() ]
for local_index in range(len(template.atoms)):
if local_index in matches:
sorted_atom_indices.append(min(atom_indices) + matches.index(local_index))
for (atom, match) in zip(res.atoms(), matches):
data.atomType[atom] = template.atoms[match].type
# Rename atom (JDC).
atom.name = template.atoms[match].name
atom.resname = template.name
for site in template.virtualSites:
if match == site.index:
data.virtualSites[atom] = site
return (data.atoms, sorted_atom_indices)
