Package Bio :: Package SCOP :: Module Raf :: Class SeqMap
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Class SeqMap

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object --+
         |
        SeqMap

An ASTRAL RAF (Rapid Access Format) Sequence Map.

This is a list like object; You can find the location of particular residues with index(), slice this SeqMap 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

Instance Methods [hide private]
 
__init__(self, line=None)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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_process(self, line)
Parses a RAF record into a SeqMap object.
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index(self, resid, chainid='_') source code
 
__getitem__(self, index) source code
 
append(self, res)
Append another Res object onto the list of residue mappings.
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extend(self, other)
Append another SeqMap onto the end of self.
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__iadd__(self, other) source code
 
__add__(self, other) source code
 
getAtoms(self, pdb_handle, out_handle)
Extract all relevant ATOM and HETATOM records from a PDB file.
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Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, line=None)
(Constructor)

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x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Overrides: object.__init__
(inherited documentation)

extend(self, other)

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Append another SeqMap onto the end of self.

Both SeqMaps 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.

getAtoms(self, pdb_handle, out_handle)

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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_handle -- A handle to the relevant PDB file.

out_handle -- All output is written to this file like object.