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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 AbstractStructureParser. This class has several implementations:
Unless you have a special reason, you should use the StructureParser factory, which returns a proper AbstractStructureParser implementation, depending on the input PDB file. If the input file looks like a regular PDB file, the factory returns a RegularStructureParser, otherwise it instantiates RegularStructureParser. StructureParser is in fact an alias for AbstractStructureParser.create_parser.
Another important abstraction in this module is StructureProvider. It has several implementations which can be used to retrieve PDB Structures from various sources: file system directories, remote URLs, etc. You can easily create your own provider as well. See StructureProvider for details.
Finally, this module gives you some FileBuilders, used for text serialization of Structures and Ensembles:
>>> 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 Ensemble and Structure from csb.bio.structure for details on these objects.
Classes | |
AbstractStructureParser A base PDB structure format-aware parser. |
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AsyncParseResult | |
AsyncStructureParser Wraps StructureParser in an asynchronous call. |
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CustomStructureProvider A custom PDB data source. |
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DegenerateID Looks like a StandardID, except that the accession number may have arbitrary length. |
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EntryID Represents a PDB Chain identifier. |
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FileBuilder Base abstract files for all structure file formatters. |
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FileSystemStructureProvider Simple file system based PDB data source. |
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HeaderFormatError | |
InvalidEntryIDError | |
LegacyStructureParser This is a customized PDB parser, which is designed to read both sequence and atom data from the ATOM section. |
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PDBEnsembleFileBuilder Supports serialization of NMR ensembles. |
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PDBFileBuilder PDB file format builder. |
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PDBHeaderParser Ultra fast PDB HEADER parser. |
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PDBParseError | |
RegularStructureParser This is the de facto PDB parser, which is designed to read SEQRES and ATOM sections separately, and them map them. |
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RemoteStructureProvider Retrieves PDB structures from a specified remote URL. |
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SecStructureFormatError | |
SeqResID Same as a StandardID, but contains an additional underscore between te accession number and the chain identifier. |
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StandardID Standard PDB ID in the following form: xxxxY, where xxxx is the accession number (lower case) and Y is an optional chain identifier. |
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StructureFormatError | |
StructureNotFoundError | |
StructureProvider Base class for all PDB data source providers. |
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UnknownPDBResidueError |
Functions | |||
AbstractStructureParser |
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str |
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Structure |
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Variables | |
PDB_AMINOACIDS =
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PDB_NUCLEOTIDES =
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__package__ =
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Function Details |
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.
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Try to discover a PDB file for PDB
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Download and parse a PDB entry.
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Variables Details |
PDB_AMINOACIDS
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PDB_NUCLEOTIDES
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