Source code for MDAnalysis.topology.PDBQTParser

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PDBQT topology parser

Use a PDBQT_ file to build a minimum internal structure representation (list of
atoms), including AutoDock_ atom types (stored as :attr:`Atom.type`) and
partial charges (:attr:`Atom.charge`).

* Reads a PDBQT file line by line and does not require sequential atom numbering.
* Multi-model PDBQT files are not supported.

Only reads atoms and their names; connectivity is not
deduced. Masses are guessed and set to 0 if unknown.

See Also

.. autoclass:: PDBQTParser

.. _PDBQT:
.. _AutoDock:
from __future__ import absolute_import

import numpy as np

from . import guessers
from ..lib import util
from .base import TopologyReaderBase, change_squash
from ..core.topology import Topology
from ..core.topologyattrs import (

[docs]class PDBQTParser(TopologyReaderBase): """Read topology from a PDBQT file. Creates the following Attributes: - atom ids (serial) - atom types - atom names - altLocs - resnames - chainIDs (becomes segid) - resids - record_types (ATOM/HETATM) - icodes - occupancies - tempfactors - charges Guesses the following: - elements - masses .. versionchanged:: 0.18.0 Added parsing of Record types """ format = 'PDBQT'
[docs] def parse(self, **kwargs): """Parse atom information from PDBQT file *filename*. Returns ------- MDAnalysis Topology object """ record_types = [] serials = [] names = [] altlocs = [] resnames = [] chainids = [] resids = [] icodes = [] occupancies = [] tempfactors = [] charges = [] atomtypes = [] with util.openany(self.filename) as f: for line in f: line = line.strip() if not line.startswith(('ATOM', 'HETATM')): continue record_types.append(line[:6].strip()) serials.append(int(line[6:11])) names.append(line[12:16].strip()) altlocs.append(line[16:17].strip()) resnames.append(line[17:21].strip()) chainids.append(line[21:22].strip()) resids.append(int(line[22:26])) icodes.append(line[26:27].strip()) occupancies.append(float(line[54:60])) tempfactors.append(float(line[60:66])) charges.append(float(line[66:76])) atomtypes.append(line[77:80].strip()) n_atoms = len(serials) masses = guessers.guess_masses(atomtypes) attrs = [] for attrlist, Attr, dtype in ( (record_types, RecordTypes, object), (serials, Atomids, np.int32), (names, Atomnames, object), (altlocs, AltLocs, object), (occupancies, Occupancies, np.float32), (tempfactors, Tempfactors, np.float32), (charges, Charges, np.float32), (atomtypes, Atomtypes, object), ): attrs.append(Attr(np.array(attrlist, dtype=dtype))) attrs.append(Masses(masses, guessed=True)) resids = np.array(resids, dtype=np.int32) icodes = np.array(icodes, dtype=object) resnames = np.array(resnames, dtype=object) chainids = np.array(chainids, dtype=object) residx, (resids, icodes, resnames, chainids) = change_squash( (resids, icodes), (resids, icodes, resnames, chainids)) n_residues = len(resids) attrs.append(Resids(resids)) attrs.append(Resnums(resids.copy())) attrs.append(ICodes(icodes)) attrs.append(Resnames(resnames)) segidx, (segids,) = change_squash((chainids,), (chainids,)) n_segments = len(segids) attrs.append(Segids(segids)) top = Topology(n_atoms, n_residues, n_segments, attrs=attrs, atom_resindex=residx, residue_segindex=segidx) return top