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.
Note
----
The file format is described in :mod:`MDAnalysis.coordinates.PQR`.
Classes
-------
.. autoclass:: PQRParser
:members:
:inherited-members:
.. _PQR: https://apbs-pdb2pqr.readthedocs.io/en/latest/formats/pqr.html
.. _APBS: https://apbs-pdb2pqr.readthedocs.io/en/latest/apbs/index.html
.. _PDB2PQR: https://apbs-pdb2pqr.readthedocs.io/en/latest/pdb2pqr/index.html
.. _PDB: http://www.wwpdb.org/documentation/file-format
"""
import numpy as np
from ..lib.util import openany
from ..core.topologyattrs import (
Atomids,
Atomnames,
Atomtypes,
Charges,
ICodes,
Radii,
RecordTypes,
Resids,
Resnums,
Resnames,
Segids,
)
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
.. note::
Atomtypes will be read from the input file if they are present
(e.g. GROMACS PQR files). Otherwise, they will be guessed on Universe
creation. By default, masses will also be guessed on Universe creation.
This may change in release 3.0.
See :ref:`Guessers` for more information.
.. 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
.. versionchanged:: 2.8.0
Removed type and mass guessing (attributes guessing takes place now
through universe.guess_TopologyAttrs() API).
"""
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)
attrs = []
if elements:
atomtypes = elements
attrs.append(Atomtypes(atomtypes, False))
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(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