Source code for MDAnalysis.topology.MMTFParser

# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4 
# MDAnalysis ---
# Copyright (c) 2006-2017 The MDAnalysis Development Team and contributors
# (see the file AUTHORS for the full list of names)
# Released under the GNU Public Licence, v2 or any higher version
# Please cite your use of MDAnalysis in published work:
# R. J. Gowers, M. Linke, J. Barnoud, T. J. E. Reddy, M. N. Melo, S. L. Seyler,
# D. L. Dotson, J. Domanski, S. Buchoux, I. M. Kenney, and O. Beckstein.
# MDAnalysis: A Python package for the rapid analysis of molecular dynamics
# simulations. In S. Benthall and S. Rostrup editors, Proceedings of the 15th
# Python in Science Conference, pages 102-109, Austin, TX, 2016. SciPy.
# doi: 10.25080/majora-629e541a-00e
# N. Michaud-Agrawal, E. J. Denning, T. B. Woolf, and O. Beckstein.
# MDAnalysis: A Toolkit for the Analysis of Molecular Dynamics Simulations.
# J. Comput. Chem. 32 (2011), 2319--2327, doi:10.1002/jcc.21787

MMTF Topology Parser

Reads topology data from the `Macromolecular Transmission Format
(MMTF) format`_.  This should generally be a quicker alternative to PDB.

Makes individual models within the MMTF file available via the `models`
attribute on Universe.

.. versionadded:: 0.16.0
.. versionchanged:: 0.20.0
   Can now read files with optional fields missing/empty

.. versionchanged:: 2.0.0
   Aliased ``bfactors`` topologyattribute to ``tempfactors``.
   ``tempfactors`` is deprecated and will be removed in 3.0 (Issue #1901)

Reads the following topology attributes:

 - altLoc
 - atom ID
 - tempfactor
 - bonds
 - charge
 - masses (guessed)
 - name
 - occupancy
 - type

 - icode
 - resname
 - resid
 - resnum

 - segid
 - model


.. autoclass:: MMTFParser

.. _Macromolecular Transmission Format (MMTF) format:
from collections import defaultdict
import mmtf
import numpy as np

from . import base
from . import guessers
from ..core.topology import Topology
from ..core.topologyattrs import (
    SegmentAttr,  # for model
from ..core.selection import RangeSelection
from ..due import due, Doi

def _parse_mmtf(fn):
    if fn.endswith('gz'):
        return mmtf.parse_gzip(fn)
        return mmtf.parse(fn)

class Models(SegmentAttr):
    attrname = 'models'
    singular = 'model'
    transplants = defaultdict(list)

    def models(self):
        """Models in this Universe.

        The MMTF format can define various models for a given structure. The
        topology (eg residue identity) can change between different models,
        resulting in a different number of atoms in each model.

        A list of AtomGroups, each representing a single model.
        model_ids = np.unique(self.segments.models)

        return [self.select_atoms('model {}'.format(i))
                for i in model_ids]

        ('models', property(models, None, None, models.__doc__)))

class ModelSelection(RangeSelection):
    token = 'model'
    field = 'models'

    def apply(self, group):
        mask = np.zeros(len(group), dtype=bool)
        vals = group.models

        for upper, lower in zip(self.uppers, self.lowers):
            if upper is not None:
                thismask = vals >= lower
                thismask &= vals <= upper
                thismask = vals == lower

            mask |= thismask
        return group[mask].unique

[docs]class MMTFParser(base.TopologyReaderBase): format = 'MMTF' @staticmethod def _format_hint(thing): """Can parser read *thing*? .. versionadded:: 1.0.0 """ return isinstance(thing, mmtf.MMTFDecoder) @due.dcite( Doi('10.1371/journal.pcbi.1005575'), description="MMTF Parser", path='MDAnalysis.topology.MMTFParser', ) def parse(self, **kwargs): if isinstance(self.filename, mmtf.MMTFDecoder): mtop = self.filename else: mtop = _parse_mmtf(self.filename) def iter_atoms(field): # iterate through atoms in groups for i in mtop.group_type_list: g = mtop.group_list[i] for val in g[field]: yield val natoms = mtop.num_atoms nresidues = mtop.num_groups nsegments = mtop.num_chains attrs = [] # required charges = Charges(list(iter_atoms('formalChargeList'))) names = Atomnames(list(iter_atoms('atomNameList'))) types = Atomtypes(list(iter_atoms('elementList'))) masses = Masses(guessers.guess_masses(types.values), guessed=True) attrs.extend([charges, names, types, masses]) #optional are empty list if empty, sometimes arrays if len(mtop.atom_id_list): attrs.append(Atomids(mtop.atom_id_list)) else: # must have this attribute for MDA attrs.append(Atomids(np.arange(natoms), guessed=True)) if mtop.alt_loc_list: attrs.append(AltLocs([val.replace('\x00', '').strip() for val in mtop.alt_loc_list])) else: attrs.append(AltLocs(['']*natoms)) if len(mtop.b_factor_list): attrs.append(Tempfactors(mtop.b_factor_list)) else: attrs.append(Tempfactors([0]*natoms)) if len(mtop.occupancy_list): attrs.append(Occupancies(mtop.occupancy_list)) else: attrs.append(Occupancies([1]*natoms)) # Residue things # required resids = Resids(mtop.group_id_list) resnums = Resnums(resids.values.copy()) resnames = Resnames([mtop.group_list[i]['groupName'] for i in mtop.group_type_list]) attrs.extend([resids, resnums, resnames]) # optional # mmtf empty icode is '\x00' rather than '' if mtop.ins_code_list: attrs.append(ICodes([val.replace('\x00', '').strip() for val in mtop.ins_code_list])) else: attrs.append(ICodes(['']*nresidues)) # Segment things # optional if mtop.chain_name_list: attrs.append(Segids(mtop.chain_name_list)) else: # required for MDAnalysis attrs.append(Segids(['SYSTEM'] * nsegments, guessed=True)) mods = np.repeat(np.arange(mtop.num_models), mtop.chains_per_model) attrs.append(Models(mods)) #attrs.append(chainids) # number of atoms in a given group id groupID_2_natoms = {i:len(g['atomNameList']) for i, g in enumerate(mtop.group_list)} # mapping of atoms to residues resindex = np.repeat(np.arange(nresidues), [groupID_2_natoms[i] for i in mtop.group_type_list]) # mapping of residues to segments segindex = np.repeat(np.arange(nsegments), mtop.groups_per_chain) # Bonds # bonds are listed as indices within a group, # offset pulls out 'global' index offset = 0 bonds = [] for gtype in mtop.group_type_list: g = mtop.group_list[gtype] bondlist = g['bondAtomList'] for x, y in zip(bondlist[1::2], bondlist[::2]): if x > y: x, y = y, x # always have x < y bonds.append((x + offset, y + offset)) offset += groupID_2_natoms[gtype] # add inter group bonds if not mtop.bond_atom_list is None: # optional field for x, y in zip(mtop.bond_atom_list[1::2], mtop.bond_atom_list[::2]): if x > y: x, y = y, x bonds.append((x, y)) attrs.append(Bonds(bonds)) top = Topology(natoms, nresidues, nsegments, atom_resindex=resindex, residue_segindex=segindex, attrs=attrs) return top