Package mmLib :: Module PDB
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Module PDB

source code

Brookhaven PDB v2.2 file parser. All records in the PDB v2.2 specification have corresponding 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 [hide private]
  PDBError
  PDBValueError
  PDBRecord
Base class for all PDB file records.
  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.
  OBSLTE
OBSLTE appears in entries which have been withdrawn from distribution.
  TITLE
The TITLE record contains a title for the experiment or analysis that is represented in the entry.
  CAVEAT
CAVEAT warns of severe errors in an entry.
  COMPND
The COMPND record describes the macromolecular contents of an entry.
  SOURCE
The SOURCE record specifies the biological and/or chemical source of each biological molecule in the entry.
  KEYWDS
The KEYWDS record contains a set of terms relevant to the entry.
  EXPDTA
The EXPDTA record presents information about the experiment.
  AUTHOR
The AUTHOR record contains the names of the people responsible for the contents of the entry.
  REVDAT
REVDAT records contain a history of the modifications made to an entry since its release.
  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The SPRSDE records contain a list of the ID codes of entries that were made obsolete by the given coordinate entry and withdrawn from the PDB release set.
  JRNL
The JRNL record contains the primary literature citation that describes the experiment which resulted in the deposited coordinate set.
  REMARK
REMARK records present experimental details, annotations, comments, and information not included in other records.
  DBREF
The DBREF record provides cross-reference links between PDB sequences and the corresponding database entry or entries.
  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.
  MODRES
The MODRES record provides descriptions of modifications (e.g., chemical or post-translational) to protein and nucleic acid residues.
  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.
  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.
  FORMUL
The FORMUL record presents the chemical formula and charge of a non-standard group.
  HELIX
HELIX records are used to identify the position of helices in the molecule.
  SHEET
SHEET records are used to identify the position of sheets in the molecule.
  TURN
The TURN records identify turns and other short loop turns which normally connect other secondary structure segments.
  SSBOND
The SSBOND record identifies each disulfide bond in protein and polypeptide structures by identifying the two residues involved in the bond.
  LINK
The LINK records specify connectivity between residues that is not implied by the primary structure.
  HYDBND
The HYDBND records specify hydrogen bonds in the entry.
  SLTBRG
The SLTBRG records specify salt bridges in the entry.
  CISPEP
CISPEP records specify the prolines and other peptides found to be in the cis conformation.
  SITE
The SITE records supply the identification of groups comprising important sites in the macromolecule.
  CRYSTn
The CRYSTn (n=1,2,3) record presents the unit cell parameters, space group, and Z value.
  CRYST1
  CRYST2
  CRYST3
  ORIGXn
The ORIGXn (n = 1, 2, or 3) records present the transformation from the orthogonal coordinates contained in the entry to the submitted coordinates.
  ORIGX1
  ORIGX2
  ORIGX3
  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.
  SCALE1
  SCALE2
  SCALE3
  MTRIXn
The MTRIXn (n = 1, 2, or 3) records present transformations expressing non-crystallographic symmetry.
  MTRIX1
  MTRIX2
  MTRIX3
  TVECT
The TVECT records present the translation vector for infinite covalently connected structures.
  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.
  ATOM
The ATOM records present the atomic coordinates for standard residues.
  ANISOU
The ANISOU records present the anisotropic temperature factors.
  HETATM
The HETATM records present the atomic coordinate records for atoms within "non-standard" groups.
  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 10**4 (Angstroms**2).
  TER
The TER record indicates the end of a list of ATOM/HETATM records for a chain.
  ENDMDL
The ENDMDL records are paired with MODEL records to group individual structures found in a coordinate entry.
  CONECT
The CONECT records specify connectivity between atoms for which coordinates are supplied.
  MASTER
The MASTER record is a control record for bookkeeping.
  END
The END record marks the end of the PDB file.
  PDBFile
Class for managing a PDB file.
  RecordProcessor
Functions [hide private]
 
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, an alpha-carbon (CA)
source code
 
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.
source code
 
test_module() source code
Variables [hide private]
  PDBRecordMap = {'ANISOU': <class 'mmLib.PDB.ANISOU'>, 'ATOM '...
  PDBRecordOrder = [('HEADER', <class 'mmLib.PDB.HEADER'>, 'mand...
  __package__ = 'mmLib'
Variables Details [hide private]

PDBRecordMap

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

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'),
...