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 ReadInXYZQ(self):
"""Read in xyzq data from .xyzq input file."""
input_rows = fileio.GetFileStringArray(self.infile)
self.atoms = fileio.GetAtomsFromXyzq(input_rows)
self.n_atoms = len(self.atoms)