Package Bio :: Package SCOP :: Module Raf
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Module Raf

source code

ASTRAL RAF (Rapid Access Format) Sequence Maps.

The ASTRAL RAF Sequence Maps record the relationship between the PDB SEQRES records (representing the sequence of the molecule used in an experiment) to the ATOM records (representing the atoms experimentally observed).

This data is derived from the Protein Data Bank CIF files. Known errors in the CIF files are corrected manually, with the original PDB file serving as the final arbiter in case of discrepancies.

Residues are referenced by residue ID. This consists of a the PDB residue sequence number (up to 4 digits) and an optional PDB insertion code (an ascii alphabetic character, a-z, A-Z). e.g. "1", "10A", "1010b", "-1"

See "ASTRAL RAF Sequence Maps":http://astral.stanford.edu/raf.html

protein_letters_3to1 -- A mapping from the 3-letter amino acid codes found
in PDB files to 1-letter codes. The 3-letter codes include chemically modified residues.
Classes [hide private]
  SeqMapIndex
An RAF file index.
  SeqMap
An ASTRAL RAF (Rapid Access Format) Sequence Map.
  Res
A single residue mapping from a RAF record.
Functions [hide private]
 
normalize_letters(one_letter_code)
Convert RAF one-letter amino acid codes into IUPAC standard codes.
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parse(handle)
Iterates over a RAF file, returning a SeqMap object for each line in the file.
source code
Variables [hide private]
  __package__ = 'Bio.SCOP'
Function Details [hide private]

normalize_letters(one_letter_code)

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Convert RAF one-letter amino acid codes into IUPAC standard codes.

Letters are uppercased, and "." ("Unknown") is converted to "X".

parse(handle)

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Iterates over a RAF file, returning a SeqMap object for each line in the file.

Arguments:

handle -- file-like object.