biopython v1.71.0 Bio.SCOP.Raf.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().
Attributes:
- 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
Link to this section Summary
Functions
Initialize the class
Parses a RAF record into a SeqMap object
Append another Res object onto the list of residue mappings
Append another SeqMap onto the end of self
Extract all relevant ATOM and HETATOM records from a PDB file
Link to this section Functions
Initialize the class.
Parses a RAF record into a SeqMap object.
Append another Res object onto the list of residue mappings.
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.
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.
Arguments:
- pdb_handle — A handle to the relevant PDB file.
- out_handle — All output is written to this file like object.