def GetTopology(self):
"""Determine bonded topology of molecules from coordinates."""
topology.GetBondGraph(self)
topology.GetBonds(self)
topology.GetAngles(self)
topology.GetTorsions(self)
topology.GetOutofplanes(self)
topology.GetNonints(self)
def GetTopology(self):
"""Determine bonded topology of molecules from coordinates."""
self.bond_graph = topology.GetBondGraph(self.atoms)
self.bonds = topology.GetBonds(self.atoms, self.bond_graph)
self.angles = topology.GetAngles(self.atoms, self.bond_graph)
self.torsions = topology.GetTorsions(self.atoms, self.bond_graph)
self.outofplanes = topology.GetOutofplanes(self.atoms, self.bond_graph)
self.nonints = topology.GetNonints(self.bonds, self.angles,
self.torsions)
self.n_bonds = len(self.bonds)
self.n_angles = len(self.angles)
self.n_torsions = len(self.torsions)
self.n_outofplanes = len(self.outofplanes)
def ReadInPrm(self):
"""Read in prm data from .prm input file."""
input_rows = fileio.GetFileStringArray(self.infile)
self.atoms = fileio.GetAtomsFromPrm(input_rows)
self.bonds = fileio.GetBondsFromPrm(input_rows)
self.angles = fileio.GetAnglesFromPrm(input_rows)
self.torsions = fileio.GetTorsionsFromPrm(input_rows)
self.outofplanes = fileio.GetOutofplanesFromPrm(input_rows)
self.n_atoms = len(self.atoms)
self.n_bonds = len(self.bonds)
self.n_angles = len(self.angles)
self.n_torsions = len(self.torsions)
self.n_outofplanes = len(self.outofplanes)
self.bond_graph = topology.GetBondGraphFromBonds(
self.bonds, self.n_atoms)
self.nonints = topology.GetNonints(self.bonds, self.angles,
self.torsions)
def GetPrm(mol):
"""Parse contents of prm file into molecular topology / geometry data.
Reads in and organizes contents of a prm parameter file into given
mmlib.molecule.Molecule object. Contents of molecule object include Atom
objects, Bond objects, Angle objects, Torsion objects, and Outofplane objects
and associated parameters and values.
Args:
mol (mmlib.molecule.Molecule): Molecule to append data
"""
infile_array = _GetFileStringArray(mol.infile)
for i in range(len(infile_array)):
record = infile_array[i]
rec_type = record[0].lower()
if rec_type == 'atom':
_GetAtom(mol, record)
mol.n_atoms = len(mol.atoms)
mol.bond_graph = [{} for i in range(mol.n_atoms)]
for i in range(len(infile_array)):
record = infile_array[i]
rec_type = record[0].lower()
if rec_type == 'bond':
_GetBond(mol, record)
elif rec_type == 'angle':
_GetAngle(mol, record)
elif rec_type == 'torsion':
_GetTorsion(mol, record)
elif rec_type == 'outofplane':
_GetOutofplane(mol, record)
mol.n_bonds = len(mol.bonds)
mol.n_angles = len(mol.angles)
mol.n_torsions = len(mol.torsions)
mol.n_outofplanes = len(mol.outofplanes)
topology.GetNonints(mol)