def to_omm_topology(self):
'''
Generate OpenMM topology from this topology
Returns
-------
omm_topology : mm.app.Topology
'''
try:
from simtk.openmm import app as omm_app
from simtk.openmm.app.element import Element as omm_Element
except ImportError:
raise Exception('cannot import openmm')
omm_top = omm_app.Topology()
omm_chain = omm_top.addChain()
for mol in self._molecules:
omm_residue = omm_top.addResidue(mol.name, omm_chain)
for atom in mol.atoms:
try:
omm_element = omm_Element.getBySymbol(atom.symbol)
except:
omm_element = None
omm_top.addAtom(atom.name, omm_element, omm_residue)
if self.cell.volume != 0:
omm_top.setPeriodicBoxVectors(self.cell.vectors)
omm_atoms = list(omm_top.atoms())
for bond in self.bonds:
omm_top.addBond(omm_atoms[bond.atom1.id], omm_atoms[bond.atom2.id])
return omm_top
