Beispiel #1
0
    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)
Beispiel #2
0
 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)