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
import warnings

from ..topology.base import TopologyReaderBase
from ..topology.tables import SYMB2Z
from ..topology.guessers import guess_types, guess_masses
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 openmm import app except ImportError: try: # pragma: no cover 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: openmm.Topology Returns ------- top : MDAnalysis.core.topology.Topology Note ---- When none of the elements are present in the openmm topolgy, their atomtypes are guessed using their names and their masses are then guessed using their atomtypes. When partial elements are present, values from available elements are used whereas the absent elements are assigned an empty string with their atomtype set to 'X' and mass set to 0.0. For elements with invalid and unreal symbols, the symbol is used as it is for atomtypes but an empty string is used for elements. .. versionchanged:: 2.2.0 The parser now works when element attribute is missing in some or all the atoms. """ try: from openmm.unit import daltons except ImportError: try: from simtk.unit import daltons except ImportError: msg = ("OpenMM is required for the OpenMMParser but " "it's not installed. Try installing it with \n" "conda install -c conda-forge openmm") raise ImportError(msg) 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()] 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()] attrs = [ Atomids(np.array(atomids, dtype=np.int32)), Atomnames(np.array(atomnames, dtype=object)), Bonds(bonds, types=bond_types, order=bond_orders, guessed=False), ChainIDs(np.array(chainids, dtype=object)), Resids(resids), Resnums(resnums), Resnames(resnames), Segids(segids), ] validated_elements = [] masses = [] atomtypes = [] for a in omm_topology.atoms(): elem = a.element if elem is not None: if elem.symbol.capitalize() in SYMB2Z: validated_elements.append(elem.symbol) else: validated_elements.append('') atomtypes.append(elem.symbol) masses.append(elem.mass.value_in_unit(daltons)) else: validated_elements.append('') masses.append(0.0) atomtypes.append('X') if not all(validated_elements): if any(validated_elements): warnings.warn("Element information missing for some atoms. " "These have been given an empty element record ") if any(i == 'X' for i in atomtypes): warnings.warn("For absent elements, atomtype has been " "set to 'X' and mass has been set to 0.0. " "If needed these can be guessed using " "MDAnalysis.topology.guessers.") attrs.append(Elements(np.array(validated_elements, dtype=object))) else: atomtypes = guess_types(atomnames) masses = guess_masses(atomtypes) wmsg = ("Element information is missing for all the atoms. " "Elements attribute will not be populated. " "Atomtype attribute will be guessed using atom " "name and mass will be guessed using atomtype." "See MDAnalysis.topology.guessers.") warnings.warn(wmsg) else: attrs.append(Elements(np.array(validated_elements, dtype=object))) attrs.append(Atomtypes(np.array(atomtypes, dtype=object))) attrs.append(Masses(np.array(masses))) n_atoms = len(atomids) n_residues = len(resids) n_segments = len(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 openmm import app except ImportError: try: # pragma: no cover 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