Home | Trees | Indices | Help |
|
---|
|
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.
|
|||
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OBSLTE OBSLTE appears in entries which have been withdrawn from distribution.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The SPRSDE records contain a list of the ID codes of entries that were made obsolete by the given coordinate entry and withdrawn from the PDB release set.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 |
|
|||
|
|||
|
|||
|
|
|||
PDBRecordMap =
|
|||
PDBRecordOrder =
|
|||
__package__ =
|
|
PDBRecordMap
|
PDBRecordOrder
|
Home | Trees | Indices | Help |
|
---|
Generated by Epydoc 3.0.1 on Mon Jun 27 14:43:14 2011 | http://epydoc.sourceforge.net |