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CoreBio

Package corebio :: Package resource :: Module astral :: Class RafSeqMap
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Type RafSeqMap

object --+
         |
        RafSeqMap


ASTRAL RAF (Rapid Access Format) Sequence Maps.

RafSeqMap is a list like object; You can find the location of particular
residues with index(), slice this RafSeqMap into fragments, and glue 
fragments back together with extend().

- pdbid -- The PDB 4 character ID
- pdb_datestamp -- From the PDB file
- version -- The RAF format version. e.g. 0.01
- flags -- RAF flags. (See release notes for more information.)
- res -- A list of Res objects, one for each residue in this sequence map
Method Summary
  __init__(self, raf_record)
Parses a RAF record into a RafSeqMap object.
  __add__(self, other)
  __getslice__(self, i, j)
  __iadd__(self, other)
  append(self, res)
Append another Res object onto the list of residue mappings.
  extend(self, other)
Append another RafSeqMap onto the end of self.
  extract_atoms(self, pdb_handle, out_handle)
Extract all relevant ATOM and HETATOM records from a PDB file.
  index(self, resid, chainid)
  records(raf_file)
Iterates over a Raf file, generating RafSeqMaps... (Static method)
    Inherited from object
  __delattr__(...)
x.__delattr__('name') <==> del x.name...
  __getattribute__(...)
x.__getattribute__('name') <==> x.name...
  __hash__(x)
x.__hash__() <==> hash(x)...
  __new__(T, S, ...)
T.__new__(S, ...) -> a new object with type S, a subtype of T...
  __reduce__(...)
helper for pickle...
  __reduce_ex__(...)
helper for pickle...
  __repr__(x)
x.__repr__() <==> repr(x)...
  __setattr__(...)
x.__setattr__('name', value) <==> x.name = value...
  __str__(x)
x.__str__() <==> str(x)...

Instance Method Details

__init__(self, raf_record=None)
(Constructor) 

Parses a RAF record into a RafSeqMap object.
Overrides:
__builtin__.object.__init__

append(self, res) 

Append another Res object onto the list of residue mappings.

extend(self, other) 

Append another RafSeqMap onto the end of self.

Both RafSeqMaps must have the same PDB ID, PDB datestamp and
RAF version.  The RAF flags are erased if they are inconsistent. This
may happen when fragments are taken from different chains.

extract_atoms(self, pdb_handle, out_handle) 

Extract all relevant ATOM and HETATOM records from a PDB file.

The PDB file is scanned for ATOM and HETATOM records. If the
chain ID, residue ID (seqNum and iCode), and residue type match
a residue in this sequence map, then the record is echoed to the
output handle.

This is typically used to find the coordinates of a domain, or other
residue subset.

pdb_file -- A handle to the relevant PDB file.
out_file -- All output is written to this stream.

Static Method Details

records(raf_file) 

Iterates over a Raf file, generating RafSeqMaps

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