Source code for MDAnalysis.topology.PDBParser

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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`


.. autoclass:: PDBParser

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 (

def float_or_default(val, default):
        return float(val)
    except ValueError:
        return default

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

    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.

    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.

    width: int
        The number of columns in the pdb file store atom index.
    s: str
        The contents of the pdb index columns.

        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: - names - chainids - tempfactors - occupancies - record_types (ATOM/HETATM) - resids - resnames - segids - elements - bonds 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) """ 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") 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 = [] 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()) # 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))) 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