biopython v1.71.0 Bio.SCOP.Raf

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

Dictionary protein_letters_3to1 provides 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.

Link to this section Summary

Functions

normalize_letters()

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

parse()

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

Link to this section Functions

normalize_letters()

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

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

parse()

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

Arguments:

handle — file-like object.