Package Bio :: Package FSSP
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Package FSSP

source code

Parser for FSSP files, used in a database of protein fold classifications.

This is a module to handle FSSP files. For now it parses only the header,
summary and alignment sections.

See: Holm and Sander (1996) The FSSP database: fold classification based on
structure-structure alignment of proteins.

functions: read_fssp(file_handle): reads an fssp file into the records. Returns a
tuple of two instances.
mult_align: returns a Biopython alignment object

Submodules [hide private]

Classes [hide private]
  FSSPHeader
  PosAlign
  FSSPSumRec
Contains info from an FSSP summary record
  FSSPAlignRec
  FSSPAlignDict
  FSSPSumDict
Functions [hide private]
 
read_fssp(fssp_handle) source code
Variables [hide private]
  header_records = {'author': re.compile(r'^AUTHOR'), 'compnd': ...
  summary_title = re.compile(r'## +SUMMARY')
  summary_rec = re.compile(r' *[0-9]+: +[1-9][0-9a-z]{3}')
  alignments_title = re.compile(r'## +ALIGNMENTS')
  alignments_rec = re.compile(r' *[0-9]+ +-?[0-9]+')
  equiv_title = re.compile(r'## +EQUIVALENCES')
  __package__ = 'Bio.FSSP'
Variables Details [hide private]

header_records

Value:
{'author': re.compile(r'^AUTHOR'),
 'compnd': re.compile(r'^COMPND'),
 'database': re.compile(r'^DATABASE'),
 'header': re.compile(r'^HEADER'),
 'nalign': re.compile(r'^NALIGN'),
 'pdbid': re.compile(r'^PDBID'),
 'seqlength': re.compile(r'^SEQLENGTH'),
 'source': re.compile(r'^SOURCE')}