Type Raf

object --+    
         |    
 FileIndex --+
             |
            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) 
and 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

The RAF file itself is about 50 MB. Each line consists of a sequence map of
a different protein chain. This index provides rapid, random
access of RAF records without having to load the entire file into memory.

This class does not load the entire RAF file into memory. Instead, it
reads the file once, noting the location and content of each RafSeqMap.
The index key is a concatenation of the  PDB ID and chain ID. e.g
"2drcA", "155c_". RAF uses an underscore to indicate blank
chain IDs. Custom maps of subsequences or spanning multiple chains, can
be constructed with the get_seqmap method.

Get the sequence map for a collection of residues.

residues -- A SCOP style description of a collection of residues from a
            PDB strucure, (e.g. '(1bba A:10-20,B:)'), as a string or a
            scop.Residues instance.