Module: Raf

Bio/SCOP/Raf.py

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 (upto 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

to_one_letter_code: 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.

Imported modules

from FileIndex import FileIndex
from Residues import Residues
from copy import copy
from types import *

Functions

normalize_letters

normalize_letters ( one_letter_code )

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

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

Classes

Iterator	Iterates over a RAF file.
Parser	Parses a RAF record into a SeqMap object.
Res	A single residue mapping from a RAF record.
SeqMap	An ASTRAL RAF (Rapid Access Format) Sequence Map.
SeqMapIndex	An RAF file index.

Table of Contents

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