csb.bio.io

Package io

I/O for various biological file formats.

Submodules

csb.bio.io.clans: Classes for parsing/manipulating/writing CLANS (by Tancred Frickey) files
csb.bio.io.cs: Simple NMR STAR chemical shift readers.
csb.bio.io.dssp: DSSP Parser
csb.bio.io.fasta: FASTA format sequence I/O.
csb.bio.io.hhpred: HHpred-related format parsers.
csb.bio.io.mrc: Cryo-EM density map I/O
csb.bio.io.noe: Simple XEASY and Sparky peak list parsers.
csb.bio.io.procheck: Procheck parser
csb.bio.io.psipred: PSIPRED Parser
csb.bio.io.svg: Build SVG diagrams from various csb objects.
csb.bio.io.vasco: VASCO Chemical Shift format parser.
csb.bio.io.whatif: Simple WhatIf/WhatCheck Summary parser
csb.bio.io.wwpdb: PDB structure parsers, format builders and database providers.

Classes

AsyncStructureParser
Wraps StructureParser in an asynchronous call.

ClansParser
CLANS file format aware parser.

DSSPParser
Simple DSSP Secondary Structure Parser.

HHOutputParser
Parser for HHsearch result (*.hhr) files.

HHProfileParser
A class that is HHpred HMM format aware.

HHpredOutputParser
Parser for HHsearch result (*.hhr) files.

HHpredProfileParser
A class that is HHpred HMM format aware.

PDBHeaderParser
Ultra fast PDB HEADER parser.

PDBSequenceParser
PDB FASTA parser.

SequenceParser
Standard FASTA parser.

StrideParser
Simple STRIDE Secondary Structure Parser.

Functions

AbstractStructureParser

StructureParser(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.

source code

Function Details

StructureParser(structure_file, check_ss=False, mapper=None)

source code

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, RegularStructureParser is returned, otherwise LegacyStructureParser is instantiated. In the latter case LegacyStructureParser will read the sequence data directly from the ATOMs.

Parameters:

structure_file (str) - the PDB file to parse
check_ss (bool) - if True, secondary structure errors in the file will cause SecStructureFormatError exceptions
mapper (AbstractResidueMapper) - residue mapper, used to align ATOM records to SEQRES. If None, use the default (CombinedResidueMapper)

Returns: AbstractStructureParser