Source code for MDAnalysis.topology.PDBParser
# -*- Mode: python; tab-width: 4; indent-tabs-mode:nil; coding:utf-8 -*-
# vim: tabstop=4 expandtab shiftwidth=4 softtabstop=4
#
# MDAnalysis --- https://www.mdanalysis.org
# 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
#
"""
PDB Topology Parser
=========================================================================
This topology parser uses a standard PDB file to build a minimum
internal structure representation (list of atoms).
The topology reader reads a PDB file line by line and ignores atom
numbers but only reads residue numbers up to 9,999 correctly. If you
have systems containing at least 10,000 residues then you need to use
a different file format (e.g. the "extended" PDB, *XPDB* format, see
:mod:`~MDAnalysis.topology.ExtendedPDBParser`) that can handle residue
numbers up to 99,999.
.. Note::
The parser processes atoms and their names. Masses are guessed and set to 0
if unknown. Partial charges are not set. Elements are parsed if they are
valid. If partially missing or incorrect, empty records are assigned.
See Also
--------
* :mod:`MDAnalysis.topology.ExtendedPDBParser`
* :class:`MDAnalysis.coordinates.PDB.PDBReader`
* :class:`MDAnalysis.core.universe.Universe`
Classes
-------
.. autoclass:: PDBParser
:members:
:inherited-members:
"""
import numpy as np
import warnings
from .guessers import guess_masses, guess_types
from .tables import SYMB2Z
from ..lib import util
from .base import TopologyReaderBase, change_squash
from ..core.topology import Topology
from ..core.topologyattrs import (
Atomnames,
Atomids,
AltLocs,
Bonds,
ChainIDs,
Atomtypes,
Elements,
ICodes,
Masses,
Occupancies,
RecordTypes,
Resids,
Resnames,
Resnums,
Segids,
Tempfactors,
FormalCharges,
)
def float_or_default(val, default):
try:
return float(val)
except ValueError:
return default
DIGITS_UPPER = "0123456789ABCDEFGHIJKLMNOPQRSTUVWXYZ"
DIGITS_LOWER = DIGITS_UPPER.lower()
DIGITS_UPPER_VALUES = dict([pair for pair in zip(DIGITS_UPPER, range(36))])
DIGITS_LOWER_VALUES = dict([pair for pair in zip(DIGITS_LOWER, range(36))])
def decode_pure(digits_values, s):
"""Decodes the string s using the digit, value associations for each
character.
Parameters
----------
digits_values: dict
A dictionary containing the base-10 numbers that each hexadecimal
number corresponds to.
s: str
The contents of the pdb index columns.
Returns
-------
The integer in base-10 corresponding to traditional base-36.
"""
result = 0
n = len(digits_values)
for c in s:
result *= n
result += digits_values[c]
return result
def hy36decode(width, s):
"""
Decodes base-10/upper-case base-36/lower-case base-36 hybrid.
Parameters
----------
width: int
The number of columns in the pdb file store atom index.
s: str
The contents of the pdb index columns.
Returns
-------
int
Base-10 integer corresponding to hybrid36.
"""
if (len(s) == width):
f = s[0]
if (f == "-" or f == " " or f.isdigit()):
return int(s)
elif (f in DIGITS_UPPER_VALUES):
return decode_pure(digits_values=DIGITS_UPPER_VALUES,
s=s) - 10 * 36 ** (width - 1) + 10 ** width
elif (f in DIGITS_LOWER_VALUES):
return decode_pure(digits_values=DIGITS_LOWER_VALUES,
s=s) + 16 * 36 ** (width - 1) + 10 ** width
raise ValueError("invalid number literal.")
[docs]
class PDBParser(TopologyReaderBase):
"""Parser that obtains a list of atoms from a standard PDB file.
Creates the following Attributes (if present):
- names
- chainids
- tempfactors
- occupancies
- record_types (ATOM/HETATM)
- resids
- resnames
- segids
- elements
- bonds
- formalcharges
Guesses the following Attributes:
- masses
See Also
--------
:class:`MDAnalysis.coordinates.PDB.PDBReader`
.. versionadded:: 0.8
.. versionchanged:: 0.18.0
Added parsing of Record types
.. versionchanged:: 1.0.0
Added parsing of valid Elements
.. versionchanged:: 2.0.0
Bonds attribute is not added if no bonds are present in PDB file.
If elements are invalid or partially missing, empty elements records
are now assigned (Issue #2422).
Aliased ``bfactors`` topologyattribute to ``tempfactors``.
``bfactors`` is deprecated and will be removed in 3.0 (Issue #1901)
.. versionchanged:: 2.3.0
Formal charges are now read from PDB files if present. No formalcharge
attribute is created if no formal charges are present in the PDB file.
Any formal charges not set are assumed to have a value of 0.
Raise `UserWarning` instead `RuntimeError`
when CONECT records are corrupt.
.. versionchanged:: 2.5.0
Formal charges will not be populated if an unknown entry is encountered,
instead a UserWarning is emitted.
"""
format = ['PDB', 'ENT']
[docs]
def parse(self, **kwargs):
"""Parse atom information from PDB file
Returns
-------
MDAnalysis Topology object
"""
top = self._parseatoms()
try:
bonds = self._parsebonds(top.ids.values)
except AttributeError:
warnings.warn("Invalid atom serials were present, "
"bonds will not be parsed")
except RuntimeError:
warnings.warn("CONECT records was corrupt, "
"bonds will not be parsed")
else:
# Issue 2832: don't append Bonds if there are no bonds
if bonds:
top.add_TopologyAttr(bonds)
return top
def _parseatoms(self):
"""Create the initial Topology object"""
resid_prev = 0 # resid looping hack
record_types = []
serials = []
names = []
altlocs = []
chainids = []
icodes = []
tempfactors = []
occupancies = []
resids = []
resnames = []
segids = []
elements = []
formalcharges = []
self._wrapped_serials = False # did serials go over 100k?
last_wrapped_serial = 100000 # if serials wrap, start from here
with util.openany(self.filename) as f:
for line in f:
line = line.strip() # Remove extra spaces
if not line: # Skip line if empty
continue
if line.startswith('END'):
break
if not line.startswith(('ATOM', 'HETATM')):
continue
record_types.append(line[:6].strip())
try:
serial = int(line[6:11])
except:
try:
serial = hy36decode(5, line[6:11])
except ValueError:
# serial can become '***' when they get too high
self._wrapped_serials = True
serial = last_wrapped_serial
last_wrapped_serial += 1
finally:
serials.append(serial)
names.append(line[12:16].strip())
altlocs.append(line[16:17].strip())
resnames.append(line[17:21].strip())
chainids.append(line[21:22].strip())
elements.append(line[76:78].strip())
formalcharges.append(line[78:80].strip())
# Resids are optional
try:
if self.format == "XPDB": # fugly but keeps code DRY
# extended non-standard format used by VMD
resid = int(line[22:27])
else:
resid = int(line[22:26])
# Wrapping
while resid - resid_prev < -5000:
resid += 10000
resid_prev = resid
except ValueError:
warnings.warn("PDB file is missing resid information. "
"Defaulted to '1'")
resid = 1
finally:
resids.append(resid)
icodes.append(line[26:27].strip())
occupancies.append(float_or_default(line[54:60], 0.0))
tempfactors.append(float_or_default(line[60:66], 1.0)) # AKA bfactor
segids.append(line[66:76].strip())
# Warn about wrapped serials
if self._wrapped_serials:
warnings.warn("Serial numbers went over 100,000. "
"Higher serials have been guessed")
# If segids not present, try to use chainids
if not any(segids):
segids = chainids
n_atoms = len(serials)
attrs = []
# Make Atom TopologyAttrs
for vals, Attr, dtype in (
(names, Atomnames, object),
(altlocs, AltLocs, object),
(chainids, ChainIDs, object),
(record_types, RecordTypes, object),
(serials, Atomids, np.int32),
(tempfactors, Tempfactors, np.float32),
(occupancies, Occupancies, np.float32),
):
attrs.append(Attr(np.array(vals, dtype=dtype)))
# Guessed attributes
# masses from types if they exist
# OPT: We do this check twice, maybe could refactor to avoid this
if not any(elements):
atomtypes = guess_types(names)
attrs.append(Atomtypes(atomtypes, guessed=True))
warnings.warn("Element information is missing, elements attribute "
"will not be populated. If needed these can be "
"guessed using MDAnalysis.topology.guessers.")
else:
# Feed atomtypes as raw element column, but validate elements
atomtypes = elements
attrs.append(Atomtypes(np.array(elements, dtype=object)))
validated_elements = []
for elem in elements:
if elem.capitalize() in SYMB2Z:
validated_elements.append(elem.capitalize())
else:
wmsg = (f"Unknown element {elem} found for some atoms. "
f"These have been given an empty element record. "
f"If needed they can be guessed using "
f"MDAnalysis.topology.guessers.")
warnings.warn(wmsg)
validated_elements.append('')
attrs.append(Elements(np.array(validated_elements, dtype=object)))
if any(formalcharges):
try:
for i, entry in enumerate(formalcharges):
if not entry == '':
if entry == '0':
# Technically a lack of charge shouldn't be in the
# PDB but MDA has a few files that specifically
# have 0 entries, indicating that some folks
# interpret 0 as an allowed entry
formalcharges[i] = 0
elif ('+' in entry) or ('-' in entry):
formalcharges[i] = int(entry[::-1])
else:
raise ValueError
else:
formalcharges[i] = 0
except ValueError:
wmsg = (f"Unknown entry {entry} encountered in formal charge "
"field. This likely indicates that the PDB file is "
"not fully standard compliant. The formalcharges "
"attribute will not be populated.")
warnings.warn(wmsg)
else:
attrs.append(FormalCharges(np.array(formalcharges, dtype=int)))
masses = guess_masses(atomtypes)
attrs.append(Masses(masses, guessed=True))
# Residue level stuff from here
resids = np.array(resids, dtype=np.int32)
resnames = np.array(resnames, dtype=object)
if self.format == 'XPDB': # XPDB doesn't have icodes
icodes = [''] * n_atoms
icodes = np.array(icodes, dtype=object)
resnums = resids.copy()
segids = np.array(segids, dtype=object)
residx, (resids, resnames, icodes, resnums, segids) = change_squash(
(resids, resnames, icodes, segids), (resids, resnames, icodes, resnums, segids))
n_residues = len(resids)
attrs.append(Resnums(resnums))
attrs.append(Resids(resids))
attrs.append(Resnums(resids.copy()))
attrs.append(ICodes(icodes))
attrs.append(Resnames(resnames))
if any(segids) and not any(val is None for val in segids):
segidx, (segids,) = change_squash((segids,), (segids,))
n_segments = len(segids)
attrs.append(Segids(segids))
else:
n_segments = 1
attrs.append(Segids(np.array(['SYSTEM'], dtype=object)))
segidx = None
top = Topology(n_atoms, n_residues, n_segments,
attrs=attrs,
atom_resindex=residx,
residue_segindex=segidx)
return top
def _parsebonds(self, serials):
# Could optimise this by saving lines in the main loop
# then doing post processing after all Atoms have been read
# ie do one pass through the file only
# Problem is that in multiframe PDB, the CONECT is at end of file,
# so the "break" call happens before bonds are reached.
# If the serials wrapped, this won't work
if self._wrapped_serials:
warnings.warn("Invalid atom serials were present, bonds will not"
" be parsed")
raise AttributeError # gets caught in parse
# Mapping between the atom array indicies a.index and atom ids
# (serial) in the original PDB file
mapping = dict((s, i) for i, s in enumerate(serials))
bonds = set()
with util.openany(self.filename) as f:
lines = (line for line in f if line[:6] == "CONECT")
for line in lines:
atom, atoms = _parse_conect(line.strip())
for a in atoms:
try:
bond = tuple([mapping[atom], mapping[a]])
except KeyError:
# Bonds to TER records have no mapping
# Ignore these as they are not real atoms
warnings.warn(
"PDB file contained CONECT record to TER entry. "
"These are not included in bonds.")
else:
bonds.add(bond)
bonds = tuple(bonds)
return Bonds(bonds)
def _parse_conect(conect):
"""parse a CONECT record from pdbs
Parameters
----------
conect : str
white space striped CONECT record
Returns
-------
atom_id : int
atom index of bond
bonds : set
atom ids of bonded atoms
Raises
------
RuntimeError
Raised if ``conect`` is not a valid CONECT record
"""
atom_id = int(conect[6:11])
n_bond_atoms = len(conect[11:]) // 5
try:
if len(conect[11:]) % n_bond_atoms != 0:
raise RuntimeError("Bond atoms aren't aligned proberly for CONECT "
"record: {}".format(conect))
except ZeroDivisionError:
# Conect record with only one entry (CONECT A\n)
warnings.warn("Found CONECT record with single entry, ignoring this")
return atom_id, [] # return empty list to allow iteration over nothing
bond_atoms = (int(conect[11 + i * 5: 16 + i * 5]) for i in
range(n_bond_atoms))
return atom_id, bond_atoms