Package diffpy :: Package Structure :: Package Parsers :: Module P_pdb :: Class P_pdb

Class P_pdb

structureparser.StructureParser --+
                                  |
                                 P_pdb

Simple parser for PDB format.
The parser understands following PDB records: TITLE, CRYST1, SCALE1,
SCALE2, SCALE3, ATOM, SIGATM, ANISOU, SIGUIJ, TER, HETATM, END

Static data members:

orderOfRecords -- order of PDB record labels
validRecords   -- dictionary of valid PDB records

Instance Methods

[hide private]

__init__(self)

source code

parseLines(self, lines)
Parse list of lines in PDB format.

source code

titleLines(self, stru)
build lines corresponding to TITLE record

source code

cryst1Lines(self, stru)
build lines corresponding to CRYST1 record

source code

atomLines(self, stru, idx)
build ATOM records and possibly SIGATM, ANISOU or SIGUIJ records...

source code

toLines(self, stru)
Convert Structure stru to a list of lines in PDFFit format.

source code

Inherited from structureparser.StructureParser: parse, parseFile, tostring

Class Variables

[hide private]

orderOfRecords = ['HEADER', 'OBSLTE', 'TITLE', 'CAVEAT', 'COMP...

validRecords = {'ANISOU': None, 'ATOM': None, 'AUTHOR': None, ...

Method Details

[hide private]

init(self)
(Constructor)

source code

Overrides: structureparser.StructureParser.__init__

parseLines(self, lines)

source code

Parse list of lines in PDB format.

Return Structure instance or raise StructureFormatError.

Overrides: structureparser.StructureParser.parseLines

atomLines(self, stru, idx)

source code

build ATOM records and possibly SIGATM, ANISOU or SIGUIJ records
for structure stru atom number aidx

toLines(self, stru)

source code

Convert Structure stru to a list of lines in PDFFit format.

Return list of strings.

Overrides: structureparser.StructureParser.toLines

Class Variable Details

[hide private]

orderOfRecords

Value:

['HEADER',
 'OBSLTE',
 'TITLE',
 'CAVEAT',
 'COMPND',
 'SOURCE',
 'KEYWDS',
 'EXPDTA',
...

validRecords

Value:

{'ANISOU': None,
 'ATOM': None,
 'AUTHOR': None,
 'CAVEAT': None,
 'CISPEP': None,
 'COMPND': None,
 'CONECT': None,
 'CRYST1': None,
...

Class P_pdb

__init__(self) (Constructor)

parseLines(self, lines)

atomLines(self, stru, idx)

toLines(self, stru)

orderOfRecords

validRecords

init(self)
(Constructor)