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
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Methods
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__add__
__getslice__
__iadd__
__init__
append
extend
getAtoms
index
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__add__
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__add__ ( self, other )
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__getslice__
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__getslice__ (
self,
i,
j,
)
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__iadd__
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__iadd__ ( self, other )
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__init__
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__init__ ( self )
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append
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append ( self, res )
Append another Res object onto the list of residue mappings.
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extend
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extend ( self, other )
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.
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Exceptions
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TypeError, "Can only extend a SeqMap with a SeqMap."
TypeError, "Cannot add fragments from different proteins"
TypeError, "Different pdb dates!"
TypeError, "Incompatible rafs"
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getAtoms
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getAtoms (
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_handle
- A handle to the relevant PDB file.
- out_handle
- All output is written to this file like object.
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Exceptions
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RuntimeError, 'I could not find at least one ATOM or ' + 'HETATM record for each and every residue in this sequence map.'
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index
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index (
self,
resid,
chainid="_",
)
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Exceptions
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KeyError, "No such residue " + chainid + resid
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