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 10**4 (Angstroms**2).
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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