Source code for MDAnalysis.topology.PQRParser

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PQR topology parser

Read atoms with charges from a PQR_ file (as written by PDB2PQR_). No
connectivity is deduced.

The file format is described in :mod:`MDAnalysis.coordinates.PQR`.


.. autoclass:: PQRParser

.. _PQR:
.. _APBS:
.. _PDB2PQR:
.. _PDB:

from __future__ import absolute_import

import numpy as np

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

[docs]class PQRParser(TopologyReaderBase): """Parse atom information from PQR file *filename*. Creates a MDAnalysis Topology with the following attributes - Atomids - Atomnames - Charges - Radii - RecordTypes (ATOM/HETATM) - Resids - Resnames - Segids Guesses the following: - atomtypes (if not present, Gromacs generated PQR files have these) - masses .. versionchanged:: 0.9.0 Read chainID from a PQR file and use it as segid (before we always used 'SYSTEM' as the new segid). .. versionchanged:: 0.16.1 Now reads insertion codes and splits into new residues around these .. versionchanged:: 0.18.0 Added parsing of Record types Can now read PQR files from Gromacs, these provide atom type as last column but don't have segids """ format = 'PQR'
[docs] @staticmethod def guess_flavour(line): """Guess which variant of PQR format this line is Parameters ---------- line : str entire line of PQR file starting with ATOM/HETATM Returns ------- flavour : str ORIGINAL / GROMACS / NO_CHAINID .. versionadded:: 0.18.0 """ fields = line.split() if len(fields) == 11: try: float(fields[-1]) except ValueError: flavour = 'GROMACS' else: flavour = 'ORIGINAL' else: flavour = 'NO_CHAINID' return flavour
[docs] def parse(self, **kwargs): """Parse atom information from PQR file *filename*. Returns ------- A MDAnalysis Topology object """ record_types = [] serials = [] names = [] resnames = [] chainIDs = [] resids = [] icodes = [] charges = [] radii = [] elements = [] flavour = None with openany(self.filename) as f: for line in f: if not line.startswith(("ATOM", "HETATM")): continue fields = line.split() if flavour is None: flavour = self.guess_flavour(line) if flavour == 'ORIGINAL': (recordName, serial, name, resName, chainID, resSeq, x, y, z, charge, radius) = fields elif flavour == 'GROMACS': (recordName, serial, name, resName, resSeq, x, y, z, charge, radius, element) = fields chainID = "SYSTEM" elements.append(element) elif flavour == 'NO_CHAINID': # files without the chainID (recordName, serial, name, resName, resSeq, x, y, z, charge, radius) = fields chainID = "SYSTEM" try: resid = int(resSeq) except ValueError: # has icode present resid = int(resSeq[:-1]) icode = resSeq[-1] else: icode = '' record_types.append(recordName) serials.append(serial) names.append(name) resnames.append(resName) resids.append(resid) icodes.append(icode) charges.append(charge) radii.append(radius) chainIDs.append(chainID) n_atoms = len(serials) if not elements: atomtypes = guessers.guess_types(names) guessed_types = True else: atomtypes = elements guessed_types = False masses = guessers.guess_masses(atomtypes) attrs = [] attrs.append(Atomids(np.array(serials, dtype=np.int32))) attrs.append(Atomnames(np.array(names, dtype=object))) attrs.append(Charges(np.array(charges, dtype=np.float32))) attrs.append(Atomtypes(atomtypes, guessed=guessed_types)) attrs.append(Masses(masses, guessed=True)) attrs.append(RecordTypes(np.array(record_types, dtype=object))) attrs.append(Radii(np.array(radii, dtype=np.float32))) 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, resnames, icodes, chainIDs) = change_squash( (resids, resnames, icodes, chainIDs), (resids, resnames, icodes, chainIDs)) n_residues = len(resids) attrs.append(Resids(resids)) attrs.append(Resnums(resids.copy())) attrs.append(Resnames(resnames)) attrs.append(ICodes(icodes)) segidx, chainIDs = squash_by(chainIDs)[:2] n_segments = len(chainIDs) attrs.append(Segids(chainIDs)) top = Topology(n_atoms, n_residues, n_segments, attrs=attrs, atom_resindex=residx, residue_segindex=segidx) return top