/usr/lib/python3/dist-packages/csb/bio/io/wwpdb.py is in python3-csb 1.2.2+dfsg-2ubuntu1.
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PDB structure parsers, format builders and database providers.
The most basic usage is:
>>> parser = StructureParser('structure.pdb')
>>> parser.parse_structure()
<Structure> # a Structure object (model)
or if this is an NMR ensemble:
>>> parser.parse_models()
<Ensemble> # an Ensemble object (collection of alternative Structure-s)
This module introduces a family of PDB file parsers. The common interface of all
parsers is defined in L{AbstractStructureParser}. This class has several
implementations:
- L{RegularStructureParser} - handles normal PDB files with SEQRES fields
- L{LegacyStructureParser} - reads structures from legacy or malformed PDB files,
which are lacking SEQRES records (initializes all residues from the ATOMs instead)
- L{PDBHeaderParser} - reads only the headers of the PDB files and produces structures
without coordinates. Useful for reading metadata (e.g. accession numbers or just
plain SEQRES sequences) with minimum overhead
Unless you have a special reason, you should use the L{StructureParser} factory,
which returns a proper L{AbstractStructureParser} implementation, depending on the
input PDB file. If the input file looks like a regular PDB file, the factory
returns a L{RegularStructureParser}, otherwise it instantiates L{LegacyStructureParser}.
L{StructureParser} is in fact an alias for L{AbstractStructureParser.create_parser}.
Writing your own, customized PDB parser is easy. Suppose that you are trying to
parse a PDB-like file which misuses the charge column to store custom info. This
will certainly crash L{RegularStructureParser} (for good), but you can create your
own parser as a workaround. All you need to to is to override the virtual
C{_read_charge} hook method::
class CustomParser(RegularStructureParser):
def _read_charge(self, line):
try:
return super(CustomParser, self)._read_charge(line)
except StructureFormatError:
return None
Another important abstraction in this module is L{StructureProvider}. It has several
implementations which can be used to retrieve PDB L{Structure}s from various sources:
file system directories, remote URLs, etc. You can easily create your own provider as
well. See L{StructureProvider} for details.
Finally, this module gives you some L{FileBuilder}s, used for text serialization
of L{Structure}s and L{Ensemble}s:
>>> builder = PDBFileBuilder(stream)
>>> builder.add_header(structure)
>>> builder.add_structure(structure)
where stream is any Python stream, e.g. an open file or sys.stdout.
See L{Ensemble} and L{Structure} from L{csb.bio.structure} for details on these
objects.
"""
import re
import os
import numpy
import datetime
import multiprocessing
import csb.bio.structure
import csb.bio.sequence
import csb.bio.sequence.alignment as alignment
import csb.core
import csb.io
from abc import ABCMeta, abstractmethod
from csb.bio.sequence import SequenceTypes, SequenceAlphabets
from csb.bio.structure import ChemElements, SecStructures
PDB_AMINOACIDS = {
'PAQ': 'TYR', 'AGM': 'ARG', 'ILE': 'ILE', 'PR3': 'CYS', 'GLN': 'GLN',
'DVA': 'VAL', 'CCS': 'CYS', 'ACL': 'ARG', 'GLX': 'GLX', 'GLY': 'GLY',
'GLZ': 'GLY', 'DTH': 'THR', 'OAS': 'SER', 'C6C': 'CYS', 'NEM': 'HIS',
'DLY': 'LYS', 'MIS': 'SER', 'SMC': 'CYS', 'GLU': 'GLU', 'NEP': 'HIS',
'BCS': 'CYS', 'ASQ': 'ASP', 'ASP': 'ASP', 'SCY': 'CYS', 'SER': 'SER',
'LYS': 'LYS', 'SAC': 'SER', 'PRO': 'PRO', 'ASX': 'ASX', 'DGN': 'GLN',
'DGL': 'GLU', 'MHS': 'HIS', 'ASB': 'ASP', 'ASA': 'ASP', 'NLE': 'LEU',
'DCY': 'CYS', 'ASK': 'ASP', 'GGL': 'GLU', 'STY': 'TYR', 'SEL': 'SER',
'CGU': 'GLU', 'ASN': 'ASN', 'ASL': 'ASP', 'LTR': 'TRP', 'DAR': 'ARG',
'VAL': 'VAL', 'CHG': 'ALA', 'TPO': 'THR', 'CLE': 'LEU', 'GMA': 'GLU',
'HAC': 'ALA', 'AYA': 'ALA', 'THR': 'THR', 'TIH': 'ALA', 'SVA': 'SER',
'MVA': 'VAL', 'SAR': 'GLY', 'LYZ': 'LYS', 'BNN': 'ALA', '5HP': 'GLU',
'IIL': 'ILE', 'SHR': 'LYS', 'HAR': 'ARG', 'FME': 'MET', 'ALO': 'THR',
'PHI': 'PHE', 'ALM': 'ALA', 'PHL': 'PHE', 'MEN': 'ASN', 'TPQ': 'ALA',
'GSC': 'GLY', 'PHE': 'PHE', 'ALA': 'ALA', 'MAA': 'ALA', 'MET': 'MET',
'UNK': 'UNK', 'LEU': 'LEU', 'ALY': 'LYS', 'SET': 'SER', 'GL3': 'GLY',
'TRG': 'LYS', 'CXM': 'MET', 'TYR': 'TYR', 'SCS': 'CYS', 'DIL': 'ILE',
'TYQ': 'TYR', '3AH': 'HIS', 'DPR': 'PRO', 'PRR': 'ALA', 'CME': 'CYS',
'IYR': 'TYR', 'CY1': 'CYS', 'TYY': 'TYR', 'HYP': 'PRO', 'DTY': 'TYR',
'2AS': 'ASP', 'DTR': 'TRP', 'FLA': 'ALA', 'DPN': 'PHE', 'DIV': 'VAL',
'PCA': 'GLU', 'MSE': 'MET', 'MSA': 'GLY', 'AIB': 'ALA', 'CYS': 'CYS',
'NLP': 'LEU', 'CYQ': 'CYS', 'HIS': 'HIS', 'DLE': 'LEU', 'CEA': 'CYS',
'DAL': 'ALA', 'LLP': 'LYS', 'DAH': 'PHE', 'HMR': 'ARG', 'TRO': 'TRP',
'HIC': 'HIS', 'CYG': 'CYS', 'BMT': 'THR', 'DAS': 'ASP', 'TYB': 'TYR',
'BUC': 'CYS', 'PEC': 'CYS', 'BUG': 'LEU', 'CYM': 'CYS', 'NLN': 'LEU',
'CY3': 'CYS', 'HIP': 'HIS', 'CSO': 'CYS', 'TPL': 'TRP', 'LYM': 'LYS',
'DHI': 'HIS', 'MLE': 'LEU', 'CSD': 'ALA', 'HPQ': 'PHE', 'MPQ': 'GLY',
'LLY': 'LYS', 'DHA': 'ALA', 'DSN': 'SER', 'SOC': 'CYS', 'CSX': 'CYS',
'OMT': 'MET', 'DSP': 'ASP', 'PTR': 'TYR', 'TRP': 'TRP', 'CSW': 'CYS',
'EFC': 'CYS', 'CSP': 'CYS', 'CSS': 'CYS', 'SCH': 'CYS', 'OCS': 'CYS',
'NMC': 'GLY', 'SEP': 'SER', 'BHD': 'ASP', 'KCX': 'LYS', 'SHC': 'CYS',
'C5C': 'CYS', 'HTR': 'TRP', 'ARG': 'ARG', 'TYS': 'TYR', 'ARM': 'ARG',
'DNP': 'ALA'
}
"""
Dictionary of non-standard amino acids, which could be found in PDB.
"""
PDB_NUCLEOTIDES = {
'DA': 'Adenine', 'DG': 'Guanine', 'DC': 'Cytosine', 'DT': 'Thymine',
'A': 'Adenine', 'G': 'Guanine', 'C': 'Cytosine', 'T': 'Thymine',
'U': 'Uracil', 'DOC': 'Cytosine', 'R': 'Purine', 'Y': 'Pyrimidine',
'K': 'Ketone', ' M': 'Amino', 'S': 'Strong', 'W': 'Weak',
'B': 'NotA', 'D' : 'NotC', 'H': 'NotG', 'V': 'NotT',
'N': 'Any', 'X' : 'Masked'
}
"""
Dictionary of non-standard nucleotides, which could be found in PDB.
"""
class PDBParseError(ValueError):
pass
class HeaderFormatError(PDBParseError):
pass
class SecStructureFormatError(PDBParseError):
pass
class StructureFormatError(PDBParseError):
pass
class UnknownPDBResidueError(PDBParseError):
pass
class StructureNotFoundError(KeyError):
pass
class InvalidEntryIDError(StructureFormatError):
pass
class ResidueMappingError(StructureFormatError):
pass
class EntryID(object):
"""
Represents a PDB Chain identifier. Implementing classes must define
how the original ID is split into accession number and chain ID.
@param id: identifier
@type id: str
"""
__metaclass__ = ABCMeta
def __init__(self, id):
self._accession = ''
self._chain = ''
id = id.strip()
self._accession, self._chain = self.parse(id)
@staticmethod
def create(id):
"""
Guess the format of C{id} and parse it.
@return: a new PDB ID of the appropriate type
@rtype: L{EntryID}
"""
if len(id) in (4, 5):
return StandardID(id)
elif len(id) == 6 and id[4] == '_':
return SeqResID(id)
else:
return DegenerateID(id)
@abstractmethod
def parse(self, id):
"""
Split C{id} into accession number and chain ID.
@param id: PDB identifier
@type id: str
@return: (accession, chain)
@rtype: tuple of str
@raise InvalidEntryIDError: when C{id} is in an inappropriate format
"""
pass
def format(self):
"""
@return: the identifier in its original format
@rtype: str
"""
return self.entry_id
@property
def accession(self):
"""
Accession number part of the Entry ID
@rtype: str
"""
return self._accession
@property
def chain(self):
"""
Chain ID part of the Entry ID
@rtype: str
"""
return self._chain
@property
def entry_id(self):
"""
Accession number + Chain ID
@rtype: str
"""
return "{0.accession}{0.chain}".format(self)
def __str__(self):
return self.entry_id
class StandardID(EntryID):
"""
Standard PDB ID in the following form: xxxxY, where xxxx is the accession
number (lower case) and Y is an optional chain identifier.
"""
def parse(self, id):
if len(id) not in (4, 5):
raise InvalidEntryIDError(id)
return (id[:4].lower(), id[4:])
class DegenerateID(EntryID):
"""
Looks like a L{StandardID}, except that the accession number may have
arbitrary length.
"""
def parse(self, id):
if len(id) < 2:
raise InvalidEntryIDError(id)
return (id[:-1].lower(), id[-1])
class SeqResID(EntryID):
"""
Same as a L{StandardID}, but contains an additional underscore between
te accession number and the chain identifier.
"""
def parse(self, id):
if not (len(id) == 6 and id[4] == '_'):
raise InvalidEntryIDError(id)
return (id[:4].lower(), id[5:])
def format(self):
return "{0.accession}_{0.chain}".format(self)
class AbstractStructureParser(object):
"""
A base PDB structure format-aware parser. Subclasses must implement the
internal abstract method C{_parse_header} in order to complete the
implementation.
@param structure_file: the input PD file to parse
@type structure_file: str
@param check_ss: if True, secondary structure errors in the file will cause
L{SecStructureFormatError} exceptions
@type check_ss: bool
@param mapper: residue mapper, used to align ATOM records to SEQRES.
If None, use the default (L{CombinedResidueMapper})
@type mapper: L{AbstractResidueMapper}
@raise IOError: when the input file cannot be found
"""
__metaclass__ = ABCMeta
@staticmethod
def create_parser(structure_file, check_ss=False, mapper=None):
"""
A StructureParser factory, which instantiates and returns the proper parser
object based on the contents of the PDB file.
If the file contains a SEQRES section, L{RegularStructureParser} is returned,
otherwise L{LegacyStructureParser} is instantiated. In the latter case
LegacyStructureParser will read the sequence data directly from the ATOMs.
@param structure_file: the PDB file to parse
@type structure_file: str
@param check_ss: if True, secondary structure errors in the file will cause
L{SecStructureFormatError} exceptions
@type check_ss: bool
@param mapper: residue mapper, used to align ATOM records to SEQRES.
If None, use the default (L{CombinedResidueMapper})
@type mapper: L{AbstractResidueMapper}
@rtype: L{AbstractStructureParser}
"""
has_seqres = False
for line in open(structure_file):
if line.startswith('SEQRES'):
has_seqres = True
break
if has_seqres:
return RegularStructureParser(structure_file, check_ss, mapper)
else:
return LegacyStructureParser(structure_file, check_ss, mapper)
def __init__(self, structure_file, check_ss=False, mapper=None):
self._file = None
self._stream = None
self._mapper = CombinedResidueMapper()
self._check_ss = bool(check_ss)
self.filename = structure_file
if mapper is not None:
self.mapper = mapper
def __del__(self):
try:
self._stream.close()
except:
pass
@property
def mapper(self):
"""
Current residue mapping strategy
@rtype: L{AbstractResidueMapper}
"""
return self._mapper
@mapper.setter
def mapper(self, value):
if not isinstance(value, AbstractResidueMapper):
raise TypeError(value)
self._mapper = value
@property
def filename(self):
"""
Current input PDB file name
@rtype: str
"""
return self._file
@filename.setter
def filename(self, name):
try:
stream = open(name)
except IOError:
raise IOError('File not found: {0}'.format(name))
if self._stream:
try:
self._stream.close()
except:
pass
self._stream = stream
self._file = name
def models(self):
"""
Find all available model identifiers in the structure.
@return: a list of model IDs
@rtype: list
"""
models = []
check = set()
with open(self._file, 'r') as f:
for line in f:
if line.startswith('MODEL'):
model_id = int(line[10:14])
if model_id in check:
raise StructureFormatError('Duplicate model identifier: {0}'.format(model_id))
models.append(model_id)
check.add(model_id)
if len(models) > 0:
if not(min(check) == 1 and max(check) == len(models)):
raise StructureFormatError('Non-consecutive model identifier(s) encountered')
return models
else:
return []
def guess_chain_type(self, residue_labels):
"""
Try to guess what is the sequence type of a chunk of PDB
C{residue_label}s. The list of labels is probed starting from the middle
first, because PDB chains often contain modified / unknown residues at
the termini. If none of the probed residues can be used to determine
chain's type, just give up and return L{SequenceTypes.Unknown}.
@param residue_labels: an iterable of PDB residue labels
@type residue_labels: iterable
@return: a L{SequenceTypes} enum member
@rtype: L{csb.core.EnumItem}
"""
labels = list(residue_labels)
middle = int(len(labels) / 2)
reordered = labels[middle:] + list(reversed(labels[:middle]))
for label in reordered:
try:
type = self.guess_sequence_type(label)
if type != SequenceTypes.Unknown:
return type
except UnknownPDBResidueError:
continue
return SequenceTypes.Unknown
def guess_sequence_type(self, residue_label):
"""
Try to guess what is the sequence type of a PDB C{residue_label}.
@param residue_label: a PDB-conforming name of a residue
@type residue_label: str
@return: a L{SequenceTypes} enum member
@rtype: L{csb.core.EnumItem}
@raise UnknownPDBResidueError: when there is no such PDB residue name
in the catalog tables
"""
if residue_label in PDB_AMINOACIDS:
return SequenceTypes.Protein
elif residue_label in PDB_NUCLEOTIDES:
return SequenceTypes.NucleicAcid
else:
raise UnknownPDBResidueError(residue_label)
def parse_residue(self, residue_label, as_type=None):
"""
Try to parse a PDB C{residue_label} and return its closest 'normal'
string representation. If a sequence type (C{as_type}) is defined,
guess the alphabet based on that information, otherwise try first to
parse it as a protein residue.
@param residue_label: a PDB-conforming name of a residue
@type residue_label: str
@param as_type: suggest a sequence type (L{SequenceTypes} member)
@type L{scb.core.EnumItem}
@return: a normalized residue name
@rtype: str
@raise UnknownPDBResidueError: when there is no such PDB residue name
in the catalog table(s)
"""
if as_type is None:
as_type = self.guess_sequence_type(residue_label)
try:
if as_type == SequenceTypes.Protein:
return PDB_AMINOACIDS[residue_label]
elif as_type == SequenceTypes.NucleicAcid:
return PDB_NUCLEOTIDES[residue_label]
else:
raise UnknownPDBResidueError(residue_label)
except KeyError:
raise UnknownPDBResidueError(residue_label)
def parse_residue_safe(self, residue_label, as_type):
"""
Same as C{parse_residue}, but returns UNK/Any instead of raising
UnknownPDBResidueError.
@param residue_label: a PDB-conforming name of a residue
@type residue_label: str
@param as_type: suggest a sequence type (L{SequenceTypes} member)
@type L{scb.core.EnumItem}
@return: a normalized residue name
@rtype: str
"""
try:
return self.parse_residue(residue_label, as_type)
except UnknownPDBResidueError:
if as_type == SequenceTypes.Protein:
return repr(SequenceAlphabets.Protein.UNK)
elif as_type == SequenceTypes.NucleicAcid:
return repr(SequenceAlphabets.Nucleic.Any)
else:
return repr(SequenceAlphabets.Unknown.UNK)
def parse(self, filename=None, model=None):
if filename:
self.filename = filename
return self.parse_structure(model)
def parse_structure(self, model=None):
"""
Parse and return the L{Structure} with the specified model identifier.
If no explicit model is specified, parse the first model in the
structure.
@param model: parse exactly the model with this ID
@type model: str
@return: object representation of the selected model
@rtype: L{Structure}
@raise ValueError: When an invalid model ID is specified
@raise PDBParseError: When the input PDB file suffers from unrecoverable
corruption. More specialized exceptions will be
raised depending on the context (see L{PDBParseError}'s
subclasses).
"""
if model is not None:
model = int(model)
try:
structure = self._parse_header(model)
except PDBParseError:
raise
except ValueError as ex:
raise HeaderFormatError("Malformed header: {0}".format(ex))
self._parse_atoms(structure, model)
self._parse_ss(structure)
return structure
def parse_models(self, models=()):
"""
Parse the specified models in the file and build an L{Ensemble}.
@param models: an iterable object providing model identifiers.
If not specified, all models will be parsed.
@type models: tuple
@return: an ensemble with all parsed models
@rtype: L{Ensemble}
"""
if not models:
models = self.models()
else:
models = list(map(int, models))
ensemble = csb.bio.structure.Ensemble()
if len(models) > 0:
for model_id in models:
model = self.parse_structure(model_id)
ensemble.models.append(model)
else:
model = self.parse_structure()
model.model_id = 1
ensemble.models.append(model)
return ensemble
def parse_biomolecule(self, number=1, single=False):
"""
Parse and return the L{Structure} of the biological unit (quaternary
structure) as annotated by the REMARK 350 BIOMOLECULE record.
@param number: biomolecule number
@type number: int
@param single: if True, assign new single-letter chain
identifiers. If False, assign multi-letter chain identifiers whith a
number appended to the original identifier, like "A1", "A2", ...
@type single: bool
@return: structure of biological unit
@rtype: L{Structure}
"""
remarks = self._parse_remarks()
if 350 not in remarks:
raise PDBParseError('There is no REMARK 350')
current = 1
biomt = {current: {}}
chains = tuple()
def split(line):
return [c.strip() for c in line.split(',') if c.strip() != '']
for line in remarks[350]:
if line.startswith('BIOMOLECULE:'):
current = int(line[12:])
biomt[current] = {}
elif line.startswith('APPLY THE FOLLOWING TO CHAINS:'):
chains = tuple(split(line[30:]))
elif line.startswith(' AND CHAINS:'):
chains += tuple(split(line[30:]))
elif line.startswith(' BIOMT'):
num = int(line[8:12])
vec = line[12:].split()
vec = list(map(float, vec))
biomt[current].setdefault(chains, dict()).setdefault(num, []).extend(vec)
if number not in biomt or len(biomt[number]) == 0:
raise KeyError('no BIOMOLECULE number {0}'.format(number))
asu = self.parse_structure()
structure = csb.bio.structure.Structure('{0}_{1}'.format(asu.accession, number))
newchainiditer = iter('ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789')
for chains, matrices in biomt[number].items():
for num in matrices:
mat = numpy.array(matrices[num][0:12]).reshape((3,4))
R, t = mat[:3,:3], mat[:3,3]
for chain in chains:
if chain not in asu:
raise PDBParseError('chain {0} missing'.format(chain))
copy = asu[chain].clone()
copy.transform(R, t)
if single:
if len(structure.chains) == 62:
raise ValueError('too many chains for single=True')
copy.id = next(newchainiditer)
else:
copy.id = '{0}{1}'.format(chain, num)
structure.chains.append(copy)
return structure
@abstractmethod
def _parse_header(self, model):
"""
An abstract method, which subclasses must use to customize the way the
PDB header (or the absence of a such) is handled. The implementation
must rely on reading character data from the current internal
self._stream and must return a new L{csb.bio.structure.Structure}
instance with properly initialized header data: accession, model,
molecule identifiers, chains and residues. This structure object is
then internally passed to the C{_parse_atoms} hook, responsible for
attachment of the atoms to the residues in the structure.
@param model: model ID to parse
@type model: str
@rtype: L{Structure}
"""
pass
def _scroll_model(self, model, stream):
"""
Scroll the C{stream} to the specified C{model}.
"""
while True:
try:
line = next(stream)
except StopIteration:
raise ValueError('No such model {0} in the structure.'.format(model))
if line.startswith('MODEL'):
model_id = self._read_model(line)
if model == model_id:
return model_id
def _parse_atoms(self, structure, model):
"""
Parse the ATOMs from the specified C{model} and attach them to the
C{structure}.
@param structure: L{Structure} being constructed
@type structure:L{Structure}
@param model: model ID to parse
@type model: str
"""
structure.model_id = None
chains = set()
total_chains = len([c for c in structure.items if c.length > 0])
residues = dict( (chain, []) for chain in structure.chains )
seen_residues = dict( (chain, {}) for chain in structure.chains )
in_ligands = False
in_atom = False
read_model = False
self._stream.seek(0)
while True:
try:
line = next(self._stream)
except StopIteration:
break
if line.startswith('MODEL'):
if read_model:
break
else:
self._parse_model_line(line, structure, model)
model = structure.model_id
read_model = True
elif line.startswith('ATOM') or \
(line.startswith('HETATM') and not in_ligands):
in_atom = True
info = self._parse_atom_line(line, structure)
chains.add(info.chain)
if info.id not in seen_residues[info.chain]:
residues[info.chain].append(info)
seen_residues[info.chain][info.id] = info
else:
atom = info.atoms[0]
seen_residues[info.chain][info.id].atoms.append(atom)
elif in_atom and line.startswith('TER'):
in_atom = False
if len(chains) == total_chains:
in_ligands = True
elif line.startswith('ENDMDL'):
break
elif line.startswith('END'):
break
if structure.model_id != model:
raise ValueError('No such model {0} in the structure.'.format(model))
self._map_residues(structure, residues)
def _parse_model_line(self, line, structure, model):
"""
Handle a new MODEL line. The default implementation will read the model
ID and attach it to the C{structure}.
@param line: raw string line to parse
@type line: str
@param structure: L{Structure} being constructed
@type structure:L{Structure}
@note: this method may have side effects: scrolls the current stream
@return: read model ID
@rtype: int
"""
if model and model != self._read_model(line):
self._scroll_model(model, self._stream)
structure.model_id = model
else:
model = self._read_model(line)
structure.model_id = model
return model
def _parse_atom_line(self, line, structure):
"""
Handle a new ATOM or HETATM line. The default implementation will read
all data fields and create a new L{Atom}.
@param line: raw string line to parse
@type line: str
@param structure: L{Structure} being constructed
@type structure:L{Structure}
@return: newly constructed atom
@rtype: L{ResidueInfo}
"""
atom = self._read_atom(line)
rank = self._read_sequence_number(line)
sequence_number = rank
insertion_code = self._read_insertion_code(line)
id = str(sequence_number)
if insertion_code:
id += insertion_code
chain = self._read_chain_id(line)
if chain not in structure.chains:
raise StructureFormatError("Chain {0} is undefined".format(chain))
type = self._read_residue(line, structure.chains[chain])
label = self._read_residue_raw(line)
atom.alternate = self._read_alternate(line)
atom.occupancy = self._read_occupancy(line)
atom.bfactor = self._read_bfactor(line)
atom.charge = self._read_charge(line)
info = ResidueInfo(chain, rank, id, sequence_number, insertion_code, type, label)
info.atoms = [atom]
return info
def _read_model(self, line):
"""
@return: model identifier
@rtype: int
"""
try:
return int(line[10:14])
except ValueError:
raise StructureFormatError("Invalid model ID: {0}".format(line))
def _read_atom(self, line):
"""
@return: a new atom (serial_number, name, element, vector)
@rtype: L{Atom}
"""
try:
serial_number = int(line[6:11])
name = line[12:16]
x, y, z = line[30:38], line[38:46], line[46:54]
vector = numpy.array([float(x), float(y), float(z)])
except ValueError as ve:
raise StructureFormatError("Invalid ATOM line: {0}".format(ve))
element = self._read_element(line)
return csb.bio.structure.Atom(serial_number, name, element, vector)
def _read_sequence_number(self, line):
"""
@return: PDB sequence number
@rtype: int
"""
try:
return int(line[22:26])
except ValueError:
raise StructureFormatError("Invalid sequence number")
def _read_insertion_code(self, line):
"""
@return: PDB insertion code
@rtype: str or None
"""
code = line[26].strip()
if code:
return code
else:
return None
def _read_chain_id(self, line):
"""
@return: chain identifier
@rtype: str
"""
return line[21].strip()
def _read_residue(self, line, chain):
"""
@param chain: owning L{Chain} object
@type chain: L{Chain}
@return: a member of any alphabet (e.g. L{SequenceAlphabets.Protein})
@rtype: L{EnumItem}
"""
raw = self._read_residue_raw(line)
residue = self.parse_residue_safe(raw, as_type=chain.type)
try:
if chain.type == SequenceTypes.NucleicAcid:
return csb.core.Enum.parsename(SequenceAlphabets.Nucleic, residue)
else:
return csb.core.Enum.parsename(SequenceAlphabets.Protein, residue)
except csb.core.EnumMemberError:
raise StructureFormatError("{0} is not a valid {1} residue".format(raw, chain.type))
def _read_residue_raw(self, line):
"""
@rtype: str
"""
return line[17:20].strip()
def _read_element(self, line):
"""
@return: a member of L{ChemElements}
@rtype: L{EnumItem} or None
"""
element = line[76:78].strip()
if element:
try:
element = csb.core.Enum.parsename(ChemElements, element)
except csb.core.EnumMemberError:
if element in ('D', 'X'):
element = ChemElements.x
else:
raise StructureFormatError('Unknown chemical element: {0}'.format(element))
else:
element = None
return element
def _read_alternate(self, line):
"""
@return: alt identifier
@rtype: str or None
"""
alternate = line[16].strip()
if not alternate:
return None
else:
return alternate
def _read_occupancy(self, line):
"""
@return: occupancy
@rtype: float or None
"""
try:
return float(line[54:60].strip() or 0)
except ValueError:
raise StructureFormatError("Malformed occupancy field")
def _read_bfactor(self, line):
"""
@return: b-factor
@rtype: float or None
"""
try:
return float(line[60:66].strip() or 0)
except ValueError:
raise StructureFormatError("Malformed bfactor field")
def _read_charge(self, line):
"""
@return: charge
@rtype: int or None
"""
charge = line[78:80].strip()
if charge:
if charge in ('+', '-'):
charge += '1'
if charge[-1] in ('+', '-'):
charge = charge[::-1]
try:
return int(charge)
except ValueError:
raise StructureFormatError("Malformed charge field")
else:
return None
def _map_residues(self, structure, residues):
"""
Attach each L{Atom} to its corresponding L{Residue}.
So far we have constructed a sparse (fragmented) chain given the information
we have read from the ATOM/HETATM records. That includes PDB sequence
identifiers and insertion codes, which cover only residues with XYZ coordinates
and often do not correspond to our L{Residue} ranks.
Our job is to find the right correspondence by matching this unreal sequence
to what we have got from the SEQRES fields (the complete, gap-free protein
sequence). Here we delegate this task to the current L{AbstractResidueMapper}
strategy, which does all the magic.
@param structure: L{Structure} being constructed
@type structure:L{Structure}
@param residues: all L{Atom}s which have been constructed so far.
This must be a map of the form:
<chainID: [L{ResidueInfo}1, L{ResidueInfo}2...]>
@type residues: dict of L{ResidueInfo}
"""
if set(structure.chains) != set(residues.keys()):
raise PDBParseError("Corrupt PDB file")
for chain in structure.items:
if chain.length == 0 or len(residues[chain.id]) == 0:
continue
reference = SparseChainSequence.create(chain)
sparse = SparseChainSequence(
"atoms", "", residues[chain.id], chain.type)
aligned = self.mapper.map(sparse, reference)
assert aligned.length == chain.length
for residue, mapped in zip(chain.residues, aligned.residues):
if mapped.type != sparse.alphabet.GAP:
residue.id = (mapped.sequence_number, mapped.insertion_code)
for atom in mapped.atoms:
residue.atoms.append(atom)
def _parse_ss(self, structure):
"""
Parse and attach secondary structure data.
@bug: Currently the PDB helix types are ignored. Each HELIX line is treated
as a regular SecStructures.Helix. This is due to incompatibility
between DSSP and PDB helix types.
@todo: Implement a proper workaround for the previous bug (e.g. skip all
helices types not included in the DSSP enum)
@warning: In this implementation only the start/end positions of the SS
elements are parsed. Additional data like H-bonding is ignored.
@bug: Currently structure.to_pdb() is not writing any SS data.
"""
elements = {}
self._stream.seek(0)
while True:
try:
line = next(self._stream)
except StopIteration:
break
if line.startswith('HELIX'):
chain = structure.chains[line[19].strip()]
if chain.id not in elements:
elements[chain.id] = []
if chain.id != line[31].strip():
if self._check_ss:
raise SecStructureFormatError('Helix {0} spans multiple chains'.format(line[7:10]))
else:
continue
try:
startres = chain.find(line[21:25].strip(), line[25].strip())
endres = chain.find(line[33:37].strip(), line[37].strip())
except csb.core.ItemNotFoundError as ex:
if self._check_ss:
raise SecStructureFormatError(
'Helix {0} refers to an undefined residue ID: {1}'.format(line[7:10], str(ex)))
else:
continue
if not startres.rank <= endres.rank:
if self._check_ss:
raise SecStructureFormatError('Helix {0} is out of range'.format(line[7:10]))
else:
continue
helix = csb.bio.structure.SecondaryStructureElement(startres.rank, endres.rank, SecStructures.Helix)
elements[chain.id].append(helix)
if line.startswith('SHEET'):
chain = structure.chains[line[21].strip()]
if chain.id not in elements:
elements[chain.id] = []
if chain.id != line[32].strip():
if self._check_ss:
raise SecStructureFormatError('Sheet {0} spans multiple chains'.format(line[7:10]))
else:
continue
try:
startres = chain.find(line[22:26].strip(), line[26].strip())
endres = chain.find(line[33:37].strip(), line[37].strip())
except csb.core.ItemNotFoundError as ex:
if self._check_ss:
raise SecStructureFormatError(
'Sheet {0} refers to an undefined residue ID: {1}'.format(line[7:10], str(ex)))
else:
continue
if not startres.rank <= endres.rank:
if self._check_ss:
raise SecStructureFormatError('Sheet {0} is out of range'.format(line[7:10]))
else:
continue
strand = csb.bio.structure.SecondaryStructureElement(startres.rank, endres.rank, SecStructures.Strand)
elements[chain.id].append(strand)
elif line.startswith('MODEL') or line.startswith('ATOM'):
break
for chain_id in elements:
ss = csb.bio.structure.SecondaryStructure()
for e in elements[chain_id]:
ss.append(e)
structure.chains[chain_id].secondary_structure = ss
def _parse_remarks(self):
"""
Read REMARK lines from PDB file.
@return: dictionary with remark numbers as keys, and lists of lines as values.
@rtype: dict
"""
self._stream.seek(0)
remarks = {}
for line in self._stream:
if line.startswith('REMARK'):
num = int(line[7:10])
lstring = line[11:]
remarks.setdefault(num, []).append(lstring)
elif line.startswith('DBREF') or line.startswith('ATOM'):
break
return remarks
class RegularStructureParser(AbstractStructureParser):
"""
This is the de facto PDB parser, which is designed to read SEQRES and ATOM
sections separately, and them map them. Intentionally fails to parse
malformed PDB files, e.g. a PDB file without a HEADER section.
"""
def _parse_header(self, model):
"""
Parse the HEADER section of a regular PDB file.
@return: a L{csb.bio.structure.Structure} instance with properly
initialized residues from the SEQRES.
@rtype: L{csb.bio.structure.Structure}
@raise PDBParseError: if the stream has no HEADER at byte 0
"""
self._stream.seek(0)
header = next(self._stream)
if not header.startswith('HEADER'):
raise PDBParseError('Does not look like a regular PDB file.')
structure = csb.bio.structure.Structure(header.split()[-1])
while True:
try:
line = next(self._stream)
except StopIteration:
break
if line.startswith('COMPND'):
if line[10:].lstrip().startswith('MOL_ID:'):
mol_id = int(line[18:].replace(';', '').strip())
chain_name = ''
chains = ''
while line.startswith('COMPND'):
line = next(self._stream)
if line.split()[2].startswith('MOLECULE:'):
chain_name += line[20:].strip()
while not chain_name.endswith(';'):
line = next(self._stream)
if not line.startswith('COMPND'):
break
chain_name += ' ' + line[11:].strip()
else:
while not line.split()[2].startswith('CHAIN:'):
line = next(self._stream)
if not line.startswith('COMPND'):
raise HeaderFormatError('Missing chain identifier in COMPND section')
chains = line[17:].strip()
while not chains.endswith(';'):
line = next(self._stream)
if not line.startswith('COMPND'):
break
chains += ', ' + line[11:].strip()
break
chain_ids = chains.replace(';', ' ').replace(',', ' ').split() or [''] # the second part deals with an empty chain id
self._add_chains(structure, chain_name, mol_id, *chain_ids)
elif line.startswith('REMARK 2 RESOLUTION'):
structure.resolution = self._read_resolution(line)
elif line.startswith('SEQRES'):
chain_id, residues = self._parse_seqres_line(line, structure)
chain = structure.chains[chain_id]
for residue in residues:
chain.residues.append(residue)
if chain.residues.last_index != residue.rank:
raise HeaderFormatError("Malformed SEQRES")
elif line.startswith('MODEL') or line.startswith('ATOM'):
break
return structure
def _add_chains(self, structure, name, mol_id, *chain_ids):
name = name.strip().rstrip(";")
for chain in chain_ids:
new_chain = csb.bio.structure.Chain(chain, type=SequenceTypes.Unknown,
name=name, accession=structure.accession)
new_chain.molecule_id = mol_id
try:
structure.chains.append(new_chain)
except csb.bio.structure.DuplicateChainIDError:
raise HeaderFormatError('Chain {0} is already defined.'.format(new_chain.id))
def _read_resolution(self, line):
"""
@return: resolution
@rtype: float or None
"""
res = re.search("(\d+(?:\.\d+)?)\s+ANGSTROM", line)
if res and res.groups():
return float(res.group(1))
else:
return None
def _parse_seqres_line(self, line, structure):
"""
Parse a SEQRES line, build and return newly constructed residues.
If the current sequence type of the chain is unknown, try to guess it
before parsing the residues.
@return: parsed chain_id and L{Residue}s
@rtype: 2-tuple: (str, iterable of L{Residue})
"""
residues = []
rownum = int(line[7:10])
chain_id = line[11].strip()
labels = line[18:].split()
if chain_id not in structure.chains:
raise HeaderFormatError('Chain {0} is undefined'.format(chain_id))
chain = structure.chains[chain_id]
if chain.type == SequenceTypes.Unknown:
chain.type = self.guess_chain_type(labels)
for rn, label in enumerate(labels):
rank = rownum * 13 - (13 - (rn + 1))
rtype = self.parse_residue_safe(label, as_type=chain.type)
residue = csb.bio.structure.Residue.create(chain.type, rank=rank, type=rtype)
residue.label = label
residues.append(residue)
return chain_id, residues
class PDBHeaderParser(RegularStructureParser):
"""
Ultra fast PDB HEADER parser. Does not read any structural data.
"""
def _parse_atoms(self, structure, model):
pass
def _parse_ss(self, structure):
pass
def _parse_header(self, model):
return super(PDBHeaderParser, self)._parse_header(model)
class LegacyStructureParser(AbstractStructureParser):
"""
This is a customized PDB parser, which is designed to read both sequence and
atom data from the ATOM section. This is especially useful when parsing PDB
files without a header.
"""
def _parse_header(self, model):
"""
Initialize a structure with residues from the ATOMs section.
@param model: model identifier (e.g. if multiple models exist)
@type model: str
@return: a L{csb.bio.structure.Structure} instance with properly
initialized residues from ATOMs under the specified C{model}.
@rtype: L{csb.bio.structure.Structure}
"""
self._stream.seek(0)
in_atom = False
has_atoms = False
has_model = False
chains = csb.core.OrderedDict()
header = next(self._stream)
if header.startswith('HEADER'):
structure = csb.bio.structure.Structure(header.split()[-1])
else:
self._stream.seek(0)
structure = csb.bio.structure.Structure('NONE')
structure.model_id = None
while True:
try:
line = next(self._stream)
except StopIteration:
break
if line.startswith('MODEL'):
if has_model:
break
else:
self._parse_model_line(line, structure, model)
model = structure.model_id
has_model = True
elif line.startswith('ATOM') \
or (in_atom and line.startswith('HETATM')):
in_atom = True
has_atoms = True
seq_number = self._read_sequence_number(line)
ins_code = self._read_insertion_code(line)
residue_id = (seq_number, ins_code)
label = self._read_residue_raw(line)
chain_id = self._read_chain_id(line)
if chain_id not in chains:
chains[chain_id] = csb.core.OrderedDict()
self._add_chain(structure, chain_id)
if residue_id not in chains[chain_id]:
chains[chain_id][residue_id] = label
chain = structure.chains[chain_id]
if chain.type == SequenceTypes.Unknown:
self._fix_chain(chain, label)
elif in_atom and line.startswith('TER'):
in_atom = False
elif line.startswith('ENDMDL'):
break
elif line.startswith('END'):
break
if not has_atoms:
raise HeaderFormatError("Can't parse legacy structure: no ATOMs found")
for chain in structure.items:
self._build_chain(chain, chains[chain.id])
return structure
def _add_chain(self, structure, chain_id):
new_chain = csb.bio.structure.Chain(chain_id,
type=SequenceTypes.Unknown,
accession=structure.accession)
new_chain.molecule_id = '1'
structure.chains.append(new_chain)
def _build_chain(self, chain, residues):
for residue_id, label in residues.items():
rank = (chain.residues.last_index or 0) + 1
rname = self.parse_residue_safe(label, as_type=chain.type)
residue = csb.bio.structure.Residue.create(chain.type, rank=rank, type=rname)
residue.label = label
residue.id = residue_id
chain.residues.append(residue)
def _fix_chain(self, chain, probe):
try:
chain.type = self.guess_sequence_type(probe)
except UnknownPDBResidueError:
pass
def _map_residues(self, structure, residues):
for chain in structure.items:
for residue_info in residues[chain.id]:
try:
residue = chain.find(residue_info.sequence_number, residue_info.insertion_code)
for atom in residue_info.atoms:
residue.atoms.append(atom)
except csb.bio.structure.EntityNotFoundError:
pass
StructureParser = AbstractStructureParser.create_parser
"""
Alias for L{AbstractStructureParser.create_parser}.
"""
class ResidueInfo(object):
"""
High-performance struct, which functions as a container for unmapped
L{Atom}s.
@note: This object must implement the L{csb.bio.sequence.ResidueInfo}
interface. This is not enforced through inheritance solely
to save some CPU (by exposing public fields and no properties).
However, on an abstract level this object is_a ResidueInfo
and is used to build L{AbstractSequence}s.
"""
__slots__ = ['chain', 'rank', 'id' , 'sequence_number', 'insertion_code', 'type', 'label', 'atoms']
def __init__(self, chain, rank, id, seq_number, ins_code, type, label):
self.chain = chain
self.rank = rank
self.id = id
self.sequence_number = seq_number
self.insertion_code = ins_code
self.type = type
self.label = label
self.atoms = []
@property
def is_modified(self):
if self.type.enum is SequenceAlphabets.Nucleic:
return self.label != str(self.type)
else:
return self.label != repr(self.type)
class SparseChainSequence(csb.bio.sequence.ChainSequence):
"""
Sequence view for reference (SEQRES) or sparse (ATOM) PDB chains.
The residue instances passed to the constructor must be
L{csb.bio.structure.Residue} or L{csb.bio.io.wwpdb.ResidueInfo} objects.
See L{csb.bio.sequence.AbstractSequence} for details.
"""
def _add(self, residue):
if not isinstance(residue, (csb.bio.structure.Residue, ResidueInfo)):
raise TypeError(residue)
else:
self._residues.append(residue)
def _get(self, rank):
return self._residues[rank - 1]
@staticmethod
def create(chain):
"""
Create a new L{SparseChainSequence} from existing L{Chain}.
@type chain: L{csb.bio.structure.Chain}
@rtype: L{SparseChainSequence}
"""
return SparseChainSequence(
chain.entry_id, chain.header, chain.residues, chain.type)
class AbstractResidueMapper(object):
"""
Defines the base interface of all residue mappers, used to align PDB ATOM
records to the real (SEQRES) sequence of a chain.
"""
__metaclass__ = ABCMeta
@abstractmethod
def map(self, sparse, reference):
"""
Map L{sparse}'s residues to L{reference}. Return all C{sparse} residues,
aligned over C{reference}, with artificial gap residues inserted at
relevant positions. The resulting sequence of sparse residues will
always have the same length as the C{reference} sequence.
@note: C{sparse}'s ranks won't be touched because the C{rank} property
of the underlying L{ResidueInfo} implementation is not necessarily r/w.
@param sparse: sparse sequence (e.g. derived from ATOMS records)
@type sparse: L{SparseChainSequence}
@param reference: reference, complete sequence
(e.g. derived from SEQRES records)
@type reference: L{SparseChainSequence}
@return: all C{sparse} residues, optimally aligned over C{reference}
(with gaps)
@rtype: L{SparseChainSequence}
@raise ResidueMappingError: if the specified sequences are not alignable
"""
pass
def create_gap(self, alphabet=SequenceAlphabets.Protein):
"""
Create and return a new gap residue.
@param alphabet: sequence alphabet; a member of L{SequenceAlphabets}
which has GAP item
@type alphabet: L{enum}
@rtype: L{ResidueInfo}
"""
return ResidueInfo(None, -1, None, None, None, alphabet.GAP, "-")
def _build(self, sparse, aligned):
return SparseChainSequence(
sparse.id, sparse.header, aligned, sparse.type)
class FastResidueMapper(AbstractResidueMapper):
"""
RegExp-based residue mapper. Fails on heavily malformed input (i.e. it cannot
insert gaps in the C{reference}), but it is very fast (linear) and memory
efficient.
"""
MAX_FRAGMENTS = 20
MIN_UNICODE_CHAR = 300
FORBIDDEN_CHARS = set('^.*?()-')
CODEC = "utf-8"
DELIMITER = ").*?(".encode(CODEC).decode(CODEC)
PATTERN = "^.*?({0}).*?$".encode(CODEC).decode(CODEC)
def __init__(self):
self._charcode = FastResidueMapper.MIN_UNICODE_CHAR
self._cache = {}
def map(self, sparse, reference):
aligned = []
mapping = {}
residues = list(sparse.residues)
pattern = self._build_pattern(residues)
seqres = self._encode_sequence(reference)
matches = re.match(pattern, seqres)
if matches:
unmapped_item = -1
for fn, fragment in enumerate(matches.groups(), start=1):
assert fragment != ''
for offset in range(1, len(fragment) + 1):
unmapped_item += 1
rank = matches.start(fn) + offset
mapped_residue = residues[unmapped_item]
real_residue = reference.residues[rank]
assert real_residue.type == mapped_residue.type
mapping[real_residue] = mapped_residue
else:
raise ResidueMappingError("Can't map ATOM records")
for rank, residue in enumerate(reference.residues, start=1):
if residue in mapping:
aligned.append(mapping[residue])
else:
aligned.append(self.create_gap(sparse.alphabet))
assert len(aligned) == reference.length
return self._build(sparse, aligned)
def _build_pattern(self, residues):
"""
Build and return a sparse regular rexpression for C{residues}.
"""
fragments = []
for rn, r in enumerate(residues):
res_name = self._encode(r)
if rn == 0:
# First residue, start a new fragment:
fragments.append([res_name])
elif r.insertion_code: # and not residues[rn - 1].insertion_code:
# If residue i has an insertion code, initiate a new fragment:
fragments.append([res_name])
elif r.sequence_number - residues[rn - 1].sequence_number in (0, 1, -1):
# If the seq numbers of residues [i-1, i] are consecutive, extend the last fragment:
fragments[-1].append(res_name)
else:
# They are not consecutive, so we better start a new fragment:
fragments.append([res_name])
for i, frag in enumerate(fragments):
fragments[i] = ''.join(frag)
if len(fragments) > FastResidueMapper.MAX_FRAGMENTS:
# Wow, that's a lot of fragments. Better use a different mapper
raise ResidueMappingError("Can't map chain with large number of fragments")
blocks = FastResidueMapper.DELIMITER.join(fragments)
pattern = FastResidueMapper.PATTERN.format(blocks)
return pattern
def _encode(self, r):
"""
Return a unique single-letter representation of C{r.type}.
"""
if not r.is_modified:
return str(r.type)
else:
return self._register_label(r.label)
def _encode_sequence(self, s):
return ''.join(map(self._encode, s.residues))
def _register_label(self, label):
"""
Assign a new unicode character to C{label} and cache it.
@return: cached single-letter representation of label.
@rtype: unicode char
"""
if label not in self._cache:
if set(label).intersection(FastResidueMapper.FORBIDDEN_CHARS):
raise ResidueMappingError("Invalid residue label")
self._charcode += 1
code = self._charcode
self._cache[label] = csb.io.unichr(code)
return self._cache[label]
class RobustResidueMapper(AbstractResidueMapper):
"""
Exhaustive residue mapper, which uses Needleman-Wunsch global alignment.
Much slower (quadratic), but fail-proof even with incompatible sequences
(can insert gaps in both the C{sparse} and the C{reference} sequence).
@param match: score for a match
@type match: float
@param mismatch: score for a mismatch (by default mismatches are heavily
penalized, while gaps are allowed)
@type mismatch: float
@param gap: gap penalty
@type gap: float
"""
class GlobalAligner(alignment.GlobalAlignmentAlgorithm):
def _sequence(self, s):
return [r.label for r in s.residues]
def __init__(self, match=1, mismatch=-10, gap=0):
scoring = alignment.IdentityMatrix(match=match, mismatch=mismatch)
aligner = RobustResidueMapper.GlobalAligner(scoring=scoring, gap=gap)
self._aligner = aligner
def map(self, sparse, reference):
aligned = []
ali = self._aligner.align(sparse, reference)
if ali.is_empty:
raise ResidueMappingError("Global alignment failed")
for mapped, residue in zip(ali.query, ali.subject):
if residue.type == reference.alphabet.GAP:
continue
elif mapped.type == sparse.alphabet.GAP:
aligned.append(self.create_gap(sparse.alphabet))
else:
aligned.append(mapped)
return self._build(sparse, aligned)
class CombinedResidueMapper(AbstractResidueMapper):
"""
The best of both worlds: attempts to map the residues using
L{FastResidueMapper}, but upon failure secures success by switching to
L{RobustResidueMapper}.
"""
FAST = FastResidueMapper()
ROBUST = RobustResidueMapper()
def map(self, sparse, reference):
try:
return CombinedResidueMapper.FAST.map(sparse, reference)
except ResidueMappingError:
return CombinedResidueMapper.ROBUST.map(sparse, reference)
class FileBuilder(object):
"""
Base abstract files for all structure file formatters.
Defines a common step-wise interface according to the Builder pattern.
@param output: output stream (this is where the product is constructed)
@type output: stream
"""
__metaclass__ = ABCMeta
def __init__(self, output):
if not hasattr(output, 'write'):
raise TypeError(output)
def isnull(this, that, null=None):
if this is null:
return that
else:
return this
self._out = output
self._isnull = isnull
@property
def output(self):
"""
Destination stream
@rtype: stream
"""
return self._out
@property
def isnull(self):
"""
ISNULL(X, Y) function
@rtype: callable
"""
return self._isnull
def write(self, text):
"""
Write a chunk of text
"""
self._out.write(text)
def writeline(self, text):
"""
Write a chunk of text and append a new line terminator
"""
self._out.write(text)
self._out.write('\n')
@abstractmethod
def add_header(self, master_structure):
pass
@abstractmethod
def add_structure(self, structure):
pass
def finalize(self):
pass
class PDBFileBuilder(FileBuilder):
"""
PDB file format builder.
"""
def writeline(self, text):
self.write('{0:80}\n'.format(text))
def add_header(self, master):
"""
Write the HEADER of the file using C{master}
@type master: L{Structure}
"""
isnull = self.isnull
header = 'HEADER {0:40}{1:%d-%b-%y} {2:4}'
self.writeline(header.format('.', datetime.datetime.now(), master.accession.upper()))
molecules = { }
for chain_id in master.chains:
chain = master.chains[chain_id]
if chain.molecule_id not in molecules:
molecules[chain.molecule_id] = [ ]
molecules[chain.molecule_id].append(chain_id)
k = 0
for mol_id in sorted(molecules):
chains = molecules[mol_id]
first_chain = master.chains[ chains[0] ]
self.writeline('COMPND {0:3} MOL_ID: {1};'.format(k + 1, isnull(mol_id, '0')))
self.writeline('COMPND {0:3} MOLECULE: {1};'.format(k + 2, isnull(first_chain.name, '')))
self.writeline('COMPND {0:3} CHAIN: {1};'.format(k + 3, ', '.join(chains)))
k += 3
for chain_id in master.chains:
chain = master.chains[chain_id]
res = [ r.label for r in chain.residues ]
rn = 0
for j in range(0, chain.length, 13):
rn += 1
residues = [ '{0:>3}'.format(r) for r in res[j : j + 13] ]
self.writeline('SEQRES {0:>3} {1} {2:>4} {3}'.format(
rn, chain.id, chain.length, ' '.join(residues) ))
def add_structure(self, structure):
"""
Append a new model to the file
@type structure: L{Structure}
"""
isnull = self.isnull
for chain_id in structure.chains:
chain = structure.chains[chain_id]
for residue in chain.residues:
atoms = [ ]
for an in residue.atoms:
atom = residue.atoms[an]
if isinstance(atom, csb.bio.structure.DisorderedAtom):
for dis_atom in atom: atoms.append(dis_atom)
else:
atoms.append(atom)
atoms.sort()
for atom in atoms:
alt = atom.alternate
if alt is True:
alt = 'A'
elif alt is False:
alt = ' '
if atom.element:
element = repr(atom.element)
else:
element = ' '
self.writeline('ATOM {0:>5} {1:>4}{2}{3:>3} {4}{5:>4}{6} {7:>8.3f}{8:>8.3f}{9:>8.3f}{10:>6.2f}{11:>6.2f}{12:>12}{13:2}'.format(
atom.serial_number, atom._full_name, isnull(alt, ' '),
residue.label, chain.id,
isnull(residue.sequence_number, residue.rank), isnull(residue.insertion_code, ' '),
atom.vector[0], atom.vector[1], atom.vector[2], isnull(atom.occupancy, 0.0), isnull(atom.bfactor, 0.0),
element, isnull(atom.charge, ' ') ))
self.writeline('TER')
def finalize(self):
"""
Add the END marker
"""
self.writeline('END')
self._out.flush()
class PDBEnsembleFileBuilder(PDBFileBuilder):
"""
Supports serialization of NMR ensembles.
Functions as a simple decorator, which wraps C{add_structure} with
MODEL/ENDMDL records.
"""
def add_structure(self, structure):
model_id = self.isnull(structure.model_id, 1)
self.writeline('MODEL {0:>4}'.format(model_id))
super(PDBEnsembleFileBuilder, self).add_structure(structure)
self.writeline('ENDMDL')
class StructureProvider(object):
"""
Base class for all PDB data source providers.
Concrete classes need to implement the C{find} method, which abstracts the
retrieval of a PDB structure file by a structure identifier. This is a hook
method called internally by C{get}, but subclasses can safely override both
C{find} and {get} to in order to achieve completely custom behavior.
"""
__metaclass__ = ABCMeta
def __getitem__(self, id):
return self.get(id)
@abstractmethod
def find(self, id):
"""
Attempt to discover a PDB file, given a specific PDB C{id}.
@param id: structure identifier (e.g. 1x80)
@type id: str
@return: path and file name on success, None otherwise
@rtype: str or None
"""
pass
def get(self, id, model=None):
"""
Discover, parse and return the PDB structure, corresponding to the
specified C{id}.
@param id: structure identifier (e.g. 1x80)
@type id: str
@param model: optional model identifier
@type model: str
@rtype: L{csb.bio.Structure}
@raise StructureNotFoundError: when C{id} could not be found
"""
pdb = self.find(id)
if pdb is None:
raise StructureNotFoundError(id)
else:
return StructureParser(pdb).parse_structure(model=model)
class FileSystemStructureProvider(StructureProvider):
"""
Simple file system based PDB data source. Scans a list of local directories
using pre-defined file name templates.
@param paths: a list of paths
@type paths: iterable or str
"""
def __init__(self, paths=None):
self._templates = ['pdb{id}.ent', 'pdb{id}.pdb', '{id}.pdb', '{id}.ent']
self._paths = csb.core.OrderedDict()
if paths is not None:
if isinstance(paths, csb.core.string):
paths = [paths]
for path in paths:
self.add(path)
@property
def paths(self):
"""
Current search paths
@rtype: tuple
"""
return tuple(self._paths)
@property
def templates(self):
"""
Current file name match templates
@rtype: tuple
"""
return tuple(self._templates)
def add(self, path):
"""
Register a new local C{path}.
@param path: directory name
@type path: str
@raise IOError: if C{path} is not a valid directory
"""
if os.path.isdir(path):
self._paths[path] = path
else:
raise IOError(path)
def add_template(self, template):
"""
Register a custom file name name C{template}. The template must contain
an E{lb}idE{rb} macro, e.g. pdbE{lb}idE{rb}.ent
@param template: pattern
@type template: str
"""
if '{id}' not in template:
raise ValueError('Template does not contain an "{id}" macro')
if template not in self._templates:
self._templates.append(template)
def remove(self, path):
"""
Unregister an existing local C{path}.
@param path: directory name
@type path: str
@raise ValueError: if C{path} had not been registered
"""
if path not in self._paths:
raise ValueError('path not found: {0}'.format(path))
del self._paths[path]
def find(self, id):
for path in self._paths:
for token in self.templates:
fn = os.path.join(path, token.format(id=id))
if os.path.exists(fn):
return fn
return None
class RemoteStructureProvider(StructureProvider):
"""
Retrieves PDB structures from a specified remote URL.
The URL requested from remote server takes the form: <prefix>/<ID><suffix>
@param prefix: URL prefix, including protocol
@type prefix: str
@param suffix: optional URL suffix (.ent by default)
@type suffix: str
"""
def __init__(self, prefix='http://www.rcsb.org/pdb/files/pdb', suffix='.ent'):
self._prefix = None
self._suffix = None
self.prefix = prefix
self.suffix = suffix
@property
def prefix(self):
"""
Current URL prefix
@rtype: str
"""
return self._prefix
@prefix.setter
def prefix(self, value):
self._prefix = value
@property
def suffix(self):
"""
Current URL suffix
@rtype: str
"""
return self._suffix
@suffix.setter
def suffix(self, value):
self._suffix = value
def _find(self, id):
try:
return csb.io.urllib.urlopen(self.prefix + id + self.suffix)
except:
raise StructureNotFoundError(id)
def find(self, id):
stream = self._find(id)
try:
tmp = csb.io.TempFile(dispose=False)
tmp.write(stream.read().decode('utf-8'))
tmp.flush()
return tmp.name
except StructureNotFoundError:
return None
finally:
stream.close()
def get(self, id, model=None):
stream = self._find(id)
try:
with csb.io.TempFile() as tmp:
tmp.write(stream.read().decode('utf-8'))
tmp.flush()
return StructureParser(tmp.name).parse_structure(model=model)
finally:
stream.close()
class CustomStructureProvider(StructureProvider):
"""
A custom PDB data source. Functions as a user-defined map of structure
identifiers and their corresponding local file names.
@param files: initialization dictionary of id:file pairs
@type files: dict-like
"""
def __init__(self, files={}):
self._files = {}
for id in files:
self.add(id, files[id])
@property
def paths(self):
"""
List of currently registered file names
@rtype: tuple
"""
return tuple(self._files.values())
@property
def identifiers(self):
"""
List of currently registered structure identifiers
@rtype: tuple
"""
return tuple(self._files)
def add(self, id, path):
"""
Register a new local C{id}:C{path} pair.
@param id: structure identifier
@type id: str
@param path: path and file name
@type path: str
@raise IOError: if C{path} is not a valid file name
"""
if os.path.isfile(path):
self._files[id] = path
else:
raise IOError(path)
def remove(self, id):
"""
Unregister an existing structure C{id}.
@param id: structure identifier
@type id: str
@raise ValueError: if C{id} had not been registered
"""
if id not in self._files:
raise ValueError(id)
else:
del self._files[id]
def find(self, id):
if id in self._files:
return self._files[id]
else:
return None
def get(accession, model=None, prefix='http://www.rcsb.org/pdb/files/pdb'):
"""
Download and parse a PDB entry.
@param accession: accession number of the entry
@type accession: str
@param model: model identifier
@type model: str
@param prefix: download URL prefix
@type prefix: str
@return: object representation of the selected model
@rtype: L{Structure}
"""
return RemoteStructureProvider(prefix).get(accession, model=model)
def find(id, paths):
"""
Try to discover a PDB file for PDB C{id} in C{paths}.
@param id: PDB ID of the entry
@type id: str
@param paths: a list of directories to scan
@type paths: list of str
@return: path and file name on success, None otherwise
@rtype: str
"""
return FileSystemStructureProvider(paths).find(id)
class AsyncParseResult(object):
def __init__(self, result, exception):
self.result = result
self.exception = exception
def __repr__(self):
return '<AsyncParseResult: result={0.result}, error={0.exception.__class__.__name__}>'.format(self)
def _parse_async(parser, file, model):
p = parser(file)
return p.parse_structure(model)
class AsyncStructureParser(object):
"""
Wraps StructureParser in an asynchronous call. Since a new process is
started by Python internally (as opposed to only starting a new thread),
this makes the parser slower, but provides a way to set a parse timeout
limit.
If initialized with more than one worker, supports parallel parsing
through the C{self.parse_async} method.
@param workers: number of worker threads (1 by default)
@type workers: int
"""
def __init__(self, workers=1):
self._pool = None
self._workers = 1
if int(workers) > 0:
self._workers = int(workers)
else:
raise ValueError(workers)
self._recycle()
def _recycle(self):
if self._pool:
self._pool.terminate()
self._pool = multiprocessing.Pool(processes=self._workers)
def parse_structure(self, structure_file, timeout, model=None,
parser=RegularStructureParser):
"""
Call StructureParser.parse_structure() in a separate process and return
the output. Raise TimeoutError if the parser does not respond within
C{timeout} seconds.
@param structure_file: structure file to parse
@type structure_file: str
@param timeout: raise multiprocessing.TimeoutError if C{timeout} seconds
elapse before the parser completes its job
@type timeout: int
@param parser: any implementing L{AbstractStructureParser} class
@type parser: type
@return: parsed structure
@rtype: L{csb.structure.Structure}
"""
r = self.parse_async([structure_file], timeout, model, parser)
if len(r) > 0:
if r[0].exception is not None:
raise r[0].exception
else:
return r[0].result
return None
def parse_async(self, structure_files, timeout, model=None,
parser=RegularStructureParser):
"""
Call C{self.parse_structure} for a list of structure files
simultaneously. The actual degree of parallelism will depend on the
number of workers specified while constructing the parser object.
@note: Don't be tempted to pass a large list of structures to this
method. Every time a C{TimeoutError} is encountered, the
corresponding worker process in the pool will hang until the
process terminates on its own. During that time, this worker is
unusable. If a sufficiently high number of timeouts occur, the
whole pool of workers will be unsable. At the end of the method
however a pool cleanup is performed and any unusable workers
are 'reactivated'. However, that only happens at B{the end} of
C{parse_async}.
@param structure_files: a list of structure files
@type structure_files: tuple of str
@param timeout: raise multiprocessing.TimeoutError if C{timeout} seconds
elapse before the parser completes its job
@type timeout: int
@param parser: any implementing L{AbstractStructureParser} class
@type parser: type
@return: a list of L{AsyncParseResult} objects
@rtype: list
"""
pool = self._pool
workers = []
results = []
for file in list(structure_files):
result = pool.apply_async(_parse_async, [parser, file, model])
workers.append(result)
hanging = False
for w in workers:
result = AsyncParseResult(None, None)
try:
result.result = w.get(timeout=timeout)
except KeyboardInterrupt as ki:
pool.terminate()
raise ki
except Exception as ex:
result.exception = ex
if isinstance(ex, multiprocessing.TimeoutError):
hanging = True
results.append(result)
if hanging:
self._recycle()
return results
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