Source code for MDAnalysis.topology.MMTFParser
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"""
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:
Atoms:
- altLoc
- atom ID
- tempfactor
- bonds
- charge
- masses (guessed)
- name
- occupancy
- type
Residues:
- icode
- resname
- resid
- resnum
Segments:
- segid
- model
Classes
-------
.. autoclass:: MMTFParser
:members:
.. _Macromolecular Transmission Format (MMTF) format: https://mmtf.rcsb.org/
"""
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 (
AltLocs,
Atomids,
Atomnames,
Atomtypes,
Tempfactors,
Bonds,
Charges,
ICodes,
Masses,
Occupancies,
Resids,
Resnames,
Resnums,
Segids,
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)
else:
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.
Returns
-------
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]
transplants['Universe'].append(
('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
else:
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