mmLib.PDB

Package mmLib :: Module PDB

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Module mmLib.PDB

Brookhaven PDB v2.2 file parser. All records in the PDB v2.2 specification have coorasponding classes defined here. PDB files are loaded into a list of these cassed, and also can be constrcted/modified and written back out as PDB files.

Classes
`ANISOU`	The ANISOU records present the anisotropic temperature factors.
`ATOM`	The ATOM records present the atomic coordinates for standard residues.
`AUTHOR`	The AUTHOR record contains the names of the people responsible for the contents of the entry.
`CAVEAT`	CAVEAT warns of severe errors in an entry.
`CISPEP`	CISPEP records specify the prolines and other peptides found to be in the cis conformation.
`COMPND`	The COMPND record describes the macromolecular contents of an entry.
`CONECT`	The CONECT records specify connectivity between atoms for which coordinates are supplied.
`CRYST1`
`CRYST2`
`CRYST3`
`CRYSTn`	The CRYSTn (n=1,2,3) record presents the unit cell parameters, space group, and Z value.
`DBREF`	The DBREF record provides cross-reference links between PDB sequences and the corresponding database entry or entries.
`END`	The END record marks the end of the PDB file.
`ENDMDL`	The ENDMDL records are paired with MODEL records to group individual structures found in a coordinate entry.
`EXPDTA`	The EXPDTA record presents information about the experiment.
`FORMUL`	The FORMUL record presents the chemical formula and charge of a non-standard group.
`HEADER`	This section contains records used to describe the experiment and the biological macromolecules present in the entry: HEADER, OBSLTE, TITLE, CAVEAT, COMPND, SOURCE, KEYWDS, EXPDTA, AUTHOR, REVDAT, SPRSDE, JRNL, and REMARK records.
`HELIX`	HELIX records are used to identify the position of helices in the molecule.
`HET`	The HET records are used to describe non-standard residues, such as prosthetic groups, inhibitors, solvent molecules, and ions for which coordinates are supplied.
`HETATM`	The HETATM records present the atomic coordinate records for atoms within "non-standard" groups.
`HETNAM`	This record gives the chemical name of the compound with the given hetID.
`HETSYN`	This record provides synonyms, if any, for the compound in the corresponding (i.e., same hetID) HETNAM record.
`HYDBND`	The HYDBND records specify hydrogen bonds in the entry.
`JRNL`	The JRNL record contains the primary literature citation that describes the experiment which resulted in the deposited coordinate set.
`KEYWDS`	The KEYWDS record contains a set of terms relevant to the entry.
`LINK`	The LINK records specify connectivity between residues that is not implied by the primary structure.
`MASTER`	The MASTER record is a control record for bookkeeping.
`MODEL`	The MODEL record specifies the model serial number when multiple structures are presented in a single coordinate entry, as is often the case with structures determined by NMR.
`MODRES`	The MODRES record provides descriptions of modifications (e.g., chemical or post-translational) to protein and nucleic acid residues.
`MTRIX1`
`MTRIX2`
`MTRIX3`
`MTRIXn`	The MTRIXn (n = 1, 2, or 3) records present transformations expressing non-crystallographic symmetry.
`OBSLTE`	OBSLTE appears in entries which have been withdrawn from distribution.
`ORIGX1`
`ORIGX2`
`ORIGX3`
`ORIGXn`	The ORIGXn (n = 1, 2, or 3) records present the transformation from the orthogonal coordinates contained in the entry to the submitted coordinates.
`PDBFile`	Class for managing a PDB file.
`PDBRecord`	Base class for all PDB file records.
`RecordProcessor`
`REMARK`	REMARK records present experimental details, annotations, comments, and information not included in other records.
`REVDAT`	REVDAT records contain a history of the modifications made to an entry since its release.
`SCALE1`
`SCALE2`
`SCALE3`
`SCALEn`	The SCALEn (n = 1, 2, or 3) records present the transformation from the orthogonal coordinates as contained in the entry to fractional crystallographic coordinates.
`SEQADV`	The SEQADV record identifies conflicts between sequence information in the ATOM records of the PDB entry and the sequence database entry given on DBREF.
`SEQRES`	The SEQRES records contain the amino acid or nucleic acid sequence of residues in each chain of the macromolecule that was studied.
`SHEET`	SHEET records are used to identify the position of sheets in the molecule.
`SIGATM`	The SIGATM records present the standard deviation of atomic parameters as they appear in ATOM and HETATM records.
`SIGUIJ`	The SIGUIJ records present the standard deviations of anisotropic temperature factors scaled by a factor of 104 (Angstroms2).
`SITE`	The SITE records supply the identification of groups comprising important sites in the macromolecule.
`SLTBRG`	The SLTBRG records specify salt bridges in the entry.
`SOURCE`	The SOURCE record specifies the biological and/or chemical source of each biological molecule in the entry.
`SPRSDE`	The SPRSDE records contain a list of the ID codes of entries that were made obsolete by the given coordinate entry and withdrawn from the PDB release set.
`SSBOND`	The SSBOND record identifies each disulfide bond in protein and polypeptide structures by identifying the two residues involved in the bond.
`TER`	The TER record indicates the end of a list of ATOM/HETATM records for a chain.
`TITLE`	The TITLE record contains a title for the experiment or analysis that is represented in the entry.
`TURN`	The TURN records identify turns and other short loop turns which normally connect other secondary structure segments.
`TVECT`	The TVECT records present the translation vector for infinite covalently connected structures.

Exceptions
`PDBError`
`PDBValueError`

Function Summary
	`ATOM_get_name(rec)` This should help older applications which do not use the element field of the ATOM record, these applications used column alignment to distinguish calcium (CA) from, say, a alpha-carbon (CA)
	`iter_pdb_records(iterable)` Reads a sequence of PDB lines from iterable sequence and converts them to the correct PDB record objects, then yields them.
	`test_module()`

Variable Summary
`dict`	`PDBRecordMap` = `{'KEYWDS': <class 'mmLib.PDB.KEYWDS'>, 'S...`
`list`	`PDBRecordOrder` = `[('HEADER', <class 'mmLib.PDB.HEADER'>,...`

Function Details

ATOM_get_name(rec)

This should help older applications which do not use the element field of the ATOM record, these applications used column alignment to distinguish calcium (CA) from, say, a alpha-carbon (CA)

iter_pdb_records(iterable)

Reads a sequence of PDB lines from iterable sequence and converts them to the correct PDB record objects, then yields them.

Variable Details

PDBRecordMap

Type:: dict
Value:: {'ANISOU': <class 'mmLib.PDB.ANISOU'>, 'ATOM ': <class 'mmLib.PDB.ATOM'>, 'AUTHOR': <class 'mmLib.PDB.AUTHOR'>, 'CAVEAT': <class 'mmLib.PDB.CAVEAT'>, 'CISPEP': <class 'mmLib.PDB.CISPEP'>, 'COMPND': <class 'mmLib.PDB.COMPND'>, 'CONECT': <class 'mmLib.PDB.CONECT'>, 'CRYST1': <class 'mmLib.PDB.CRYST1'>, ...

PDBRecordOrder

Type:: list
Value:: [('HEADER', <class 'mmLib.PDB.HEADER'>, 'mandatory'), ('OBSLTE', <class 'mmLib.PDB.OBSLTE'>, 'optional'), ('TITLE ', <class 'mmLib.PDB.TITLE'>, 'mandatory'), ('CAVEAT', <class 'mmLib.PDB.CAVEAT'>, 'optional'), ('COMPND', <class 'mmLib.PDB.COMPND'>, 'mandatory'), ('SOURCE', <class 'mmLib.PDB.SOURCE'>, 'mandatory'), ('KEYWDS', <class 'mmLib.PDB.KEYWDS'>, 'mandatory'), ('EXPDTA', <class 'mmLib.PDB.EXPDTA'>, 'mandatory'), ...

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