Source code for moldesign.interfaces.parmed_interface

# Copyright 2016 Autodesk Inc.
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# See the License for the specific language governing permissions and
# limitations under the License.
import collections
import parmed

import moldesign as mdt
from moldesign import units as u

def exports(o):
    return o

__all__ = []

[docs]def parmed_to_mdt(pmdmol): """ Convert parmed object to MDT object Args: pmdmol (parmed.Structure): parmed structure to convert Returns: mdt.Molecule: converted molecule """ atoms = collections.OrderedDict() residues = {} chains = {} for patm in pmdmol.atoms: if patm.residue.chain not in chains: chains[patm.residue.chain] = mdt.Chain(pdbname=patm.residue.chain) chain = chains[patm.residue.chain] if patm.residue not in residues: residues[patm.residue] = mdt.Residue(, pdbindex=patm.residue.number) residues[patm.residue].chain = chain chain.add(residues[patm.residue]) residue = residues[patm.residue] atom = mdt.Atom(, atnum=patm.atomic_number, pdbindex=patm.number, mass=patm.mass * u.dalton) atom.position = [patm.xx, patm.xy, patm.xz]*u.angstrom atom.residue = residue residue.add(atom) atom.chain = chain atoms[patm] = atom for pbnd in pmdmol.bonds: atoms[pbnd.atom1].bond_to(atoms[pbnd.atom2], int(pbnd.order)) return mdt.Molecule(atoms.values(), name=pmdmol.title)
def _parmed_to_ff(topo, atom_map): """ Create an MDT FFParameters object from a ParmEd topology Args: topo (parmed.Structure): ParmEd structure (with FF terms) atom_map (Mapping[parmed.Atom, moldesign.Atom]): mapping between MDT and ParmEd atoms Returns: moldesign.forcefields.FFParameters: parameters in MDT format """ bonds = [mdt.forcefields.HarmonicBondTerm(atom_map[bond.a1], atom_map[bond.a2], bond.type.k*u.kcalpermol/u.angstrom ** 2, bond.type.req*u.angstrom) for bond in topo.bonds] angles = [mdt.forcefields.HarmonicAngleTerm(atom_map[angle.a1], atom_map[angle.a2], atom_map[angle.a3], angle.type.k*u.kcalpermol/u.radian ** 2, angle.type.theta_eq*u.degrees) for angle in topo.angles] dihedrals = [mdt.forcefields.PeriodicTorsionTerm(atom_map[dihedral.a1], atom_map[dihedral.a2], atom_map[dihedral.a3], atom_map[dihedral.a4], dihedral.type.per, dihedral.type.phi_k*u.kcalpermol, dihedral.type.phase*u.degrees) for dihedral in topo.dihedrals]