Source code for MDAnalysis.converters.OpenMMParser

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"""OpenMM topology parser :mod:`MDAnalysis.converters.OpenMMParser`

.. versionadded:: 2.0.0

Converts an
`OpenMM topology <>`_
:class:`` into a :class:`MDAnalysis.core.Topology`.

Also converts some objects within the
`OpenMM Application layer <>`_

    - ` <>`_
    - ` <>`_
    - ` <>`_
    - ` <>`_

The :class:`OpenMMTopologyParser` generates a topology from an OpenMM Topology object.


.. autoclass:: OpenMMTopologyParser

.. autoclass:: OpenMMAppTopologyParser


import numpy as np

from ..topology.base import TopologyReaderBase
from ..core.topology import Topology
from ..core.topologyattrs import (

[docs]class OpenMMTopologyParser(TopologyReaderBase): format = "OPENMMTOPOLOGY" @staticmethod def _format_hint(thing): """Can this Parser read object *thing*? """ try: from simtk.openmm import app except ImportError: return False else: return isinstance(thing, app.Topology) def _mda_topology_from_omm_topology(self, omm_topology): """ Construct mda topology from omm topology Can be used for any openmm object that contains a topology object Parameters ---------- omm_topology: simtk.openmm.Topology Returns ------- top : MDAnalysis.core.topology.Topology """ atom_resindex = [a.residue.index for a in omm_topology.atoms()] residue_segindex = [r.chain.index for r in omm_topology.residues()] atomids = [ for a in omm_topology.atoms()] atomnames = [ for a in omm_topology.atoms()] chainids = [ for a in omm_topology.atoms()] elements = [a.element.symbol for a in omm_topology.atoms()] atomtypes = [a.element.symbol for a in omm_topology.atoms()] masses = [a.element.mass._value for a in omm_topology.atoms()] resnames = [ for r in omm_topology.residues()] resids = [r.index + 1 for r in omm_topology.residues()] resnums = resids.copy() segids = [str(c.index) for c in omm_topology.chains()] bonds = [(b.atom1.index, b.atom2.index) for b in omm_topology.bonds()] bond_orders = [b.order for b in omm_topology.bonds()] bond_types = [b.type for b in omm_topology.bonds()] n_atoms = len(atomids) n_residues = len(resids) n_segments = len(segids) attrs = [ Atomids(np.array(atomids, dtype=np.int32)), Atomnames(np.array(atomnames, dtype=object)), Atomtypes(np.array(atomtypes, dtype=object)), Bonds(bonds, types=bond_types, order=bond_orders, guessed=False), ChainIDs(np.array(chainids, dtype=object)), Elements(np.array(elements, dtype=object)), Masses(np.array(masses, dtype=np.float32)), Resids(resids), Resnums(resnums), Resnames(resnames), Segids(segids), ] top = Topology( n_atoms, n_residues, n_segments, attrs=attrs, atom_resindex=atom_resindex, residue_segindex=residue_segindex, ) return top def parse(self, **kwargs): omm_topology = self.filename top = self._mda_topology_from_omm_topology(omm_topology) return top
[docs]class OpenMMAppTopologyParser(OpenMMTopologyParser): format = "OPENMMAPP" @staticmethod def _format_hint(thing): """Can this Parser read object *thing*? """ try: from simtk.openmm import app except ImportError: return False else: return isinstance( thing, ( app.PDBFile, app.Modeller, app.Simulation, app.PDBxFile ) ) def parse(self, **kwargs): try: omm_topology = self.filename.getTopology() except AttributeError: omm_topology = self.filename.topology top = self._mda_topology_from_omm_topology(omm_topology) return top