Source code for molecupy.pdb.pdbdatafile

"""This module performs the actual parsing of the PDB file, though it does not
process the values that it extracts."""

import datetime
import math
from .pdbfile import PdbRecord, PdbFile

[docs]class PdbDataFile: """This object is essentially a list of values extracted from a PDB file. It functions as a data sheet.""" def __init__(self): self._source = None self._classification = None self._deposition_date = None self._pdb_code = None self._is_obsolete = False self._obsolete_date = None self._replacement_code = None self._title = None self._split_codes = [] self._caveat = None self._compounds = [] self._sources = [] self._keywords = [] self._experimental_techniques = [] self._model_count = 1 self._model_annotations = [] self._authors = [] self._revisions = [] self._supercedes = [] self._supercede_date = None self._journal = None self._remarks = [] self._dbreferences = [] self._sequence_differences = [] self._residue_sequences = [] self._modified_residues = [] self._hets = [] self._het_names = {} self._het_synonyms = {} self._formulae = {} self._helices = [] self._sheets = [] self._ss_bonds = [] self._links = [] self._cis_peptides = [] self._sites = [] self._crystal = None self._origix = None self._scale = None self._matrix = None self._models = [{"model_id": 1, "start_record": -1, "end_record": -1}] self._atoms = [] self._anisou = [] self._termini = [] self._heteroatoms = [] self._connections = [] self._master = None def __repr__(self): return "<PdbDataFile (%s)>" % (self.pdb_code() if self.pdb_code() else "????")
[docs] def source(self): """The object from which this PdbDataFile was created.""" return self._source
[docs] def to_pdb_file(self): """Converts the PdbDataFile to a :py:class:`.PdbFile`.""" from ..converters.pdbdatafile2pdbfile import pdb_file_from_pdb_data_file return pdb_file_from_pdb_data_file(self)
[docs] def classification(self, classification=None): """The classification of the PDB. :param str classification: if given, the classifcation will be set to\ this. :rtype: ``str``""" if classification: if not isinstance(classification, str): raise TypeError( "classification must be str, not '%s'" % str(classification) ) if len(classification) > 40: raise ValueError( "classification must be <40 chars, not '%s'" % classification ) self._classification = classification else: return self._classification
def deposition_date(self, deposition_date=None): if deposition_date: if not isinstance(deposition_date, raise TypeError( "deposition_date must be date, not '%s'" % str(deposition_date) ) self._deposition_date = deposition_date else: return self._deposition_date def pdb_code(self, pdb_code=None): if pdb_code: if not isinstance(pdb_code, str): raise TypeError( "pdb_code must be str, not '%s'" % str(pdb_code) ) if len(pdb_code) != 4: raise ValueError( "pdb_code must be 4 chars, not '%s'" % pdb_code ) self._pdb_code = pdb_code else: return self._pdb_code def is_obsolete(self, is_obsolete=None): if is_obsolete is not None: if not isinstance(is_obsolete, bool): raise TypeError( "is_obsolete must be bool, not '%s'" % str(is_obsolete) ) self._is_obsolete = is_obsolete else: return self._is_obsolete def obsolete_date(self, obsolete_date=None): if obsolete_date: if not isinstance(obsolete_date, raise TypeError( "obsolete_date must be date, not '%s'" % str(obsolete_date) ) self._obsolete_date = obsolete_date else: return self._obsolete_date def replacement_code(self, replacement_code=None): if replacement_code: if not isinstance(replacement_code, str): raise TypeError( "replacement_code must be str, not '%s'" % str(replacement_code) ) if len(replacement_code) != 4: raise ValueError( "replacement_code must be 4 chars, not '%s'" % replacement_code ) self._replacement_code = replacement_code else: return self._replacement_code def title(self, title=None): if title: if not isinstance(title, str): raise TypeError("title must be str, not '%s'" % str(title)) self._title = title else: return self._title def split_codes(self): return self._split_codes def caveat(self, caveat=None): if caveat: if not isinstance(caveat, str): raise TypeError("caveat must be str, not '%s'" % str(caveat)) self._caveat = caveat else: return self._caveat def compounds(self): return self._compounds def sources(self): return self._sources def keywords(self): return self._keywords def experimental_techniques(self): return self._experimental_techniques def model_count(self, model_count=None): if model_count: if not isinstance(model_count, int): raise TypeError( "model_count must be int, not '%s'" % str(model_count) ) self._model_count = model_count else: return self._model_count def model_annotations(self): return self._model_annotations def authors(self): return self._authors def revisions(self): return self._revisions def supercedes(self): return self._supercedes def supercede_date(self, supercede_date=None): if supercede_date: if not isinstance(supercede_date, raise TypeError( "supercede_date must be date, not '%s'" % str(supercede_date) ) self._supercede_date = supercede_date else: return self._supercede_date def journal(self, journal=None): if journal: if not isinstance(journal, dict): raise TypeError( "journal must be dict, not '%s'" % str(journal) ) self._journal = journal else: return self._journal def remarks(self): return self._remarks def get_remark_by_number(self, number): for remark in self.remarks(): if remark["number"] == number: return remark def dbreferences(self): return self._dbreferences def sequence_differences(self): return self._sequence_differences def residue_sequences(self): return self._residue_sequences def modified_residues(self): return self._modified_residues def hets(self): return self._hets def het_names(self): return self._het_names def het_synonyms(self): return self._het_synonyms def formulae(self): return self._formulae def helices(self): return self._helices def sheets(self): return self._sheets def ss_bonds(self): return self._ss_bonds def links(self): return self._links def cis_peptides(self): return self._cis_peptides def sites(self): return self._sites def crystal(self, crystal=None): if crystal: if not isinstance(crystal, dict): raise TypeError( "crystal must be dict, not '%s'" % str(crystal) ) self._crystal = crystal else: return self._crystal def origx(self, origx=None): if origx: if not isinstance(origx, dict): raise TypeError( "origx must be dict, not '%s'" % str(origx) ) self._origx = origx else: return self._origx def scale(self, scale=None): if scale: if not isinstance(scale, dict): raise TypeError( "scale must be dict, not '%s'" % str(scale) ) self._scale = scale else: return self._scale def matrix(self, matrix=None): if matrix: if not isinstance(matrix, dict): raise TypeError( "matrix must be dict, not '%s'" % str(matrix) ) self._matrix = matrix else: return self._matrix def models(self): return self._models def atoms(self): return self._atoms def anisou(self): return self._anisou def termini(self): return self._termini def heteroatoms(self): return self._heteroatoms def connections(self): return self._connections def master(self, master=None): if master: if not isinstance(master, dict): raise TypeError( "master must be dict, not '%s'" % str(master) ) self._master = master else: return self._master