Package Bio :: Package SeqIO :: Module PdbIO
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Module PdbIO

source code

Functions [hide private]
 
PdbSeqresIterator(handle)
Returns SeqRecord objects for each chain in a PDB file.
source code
 
PdbAtomIterator(handle)
Returns SeqRecord objects for each chain in a PDB file
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Variables [hide private]
  __package__ = 'Bio.SeqIO'
Function Details [hide private]

PdbSeqresIterator(handle)

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Returns SeqRecord objects for each chain in a PDB file.

The sequences are derived from the SEQRES lines in the PDB file header, not the atoms of the 3D structure.

Specifically, these PDB records are handled: DBREF, SEQADV, SEQRES, MODRES

See: http://www.wwpdb.org/documentation/format23/sect3.html

PdbAtomIterator(handle)

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Returns SeqRecord objects for each chain in a PDB file

The sequences are derived from the 3D structure (ATOM records), not the SEQRES lines in the PDB file header.

Unrecognised three letter amino acid codes (e.g. "CSD") from HETATM entries are converted to "X" in the sequence.

In addition to information from the PDB header (which is the same for all records), the following chain specific information is placed in the annotation:

record.annotations["residues"] = List of residue ID strings record.annotations["chain"] = Chain ID (typically A, B ,...) record.annotations["model"] = Model ID (typically zero)

Where amino acids are missing from the structure, as indicated by residue numbering, the sequence is filled in with 'X' characters to match the size of the missing region, and None is included as the corresponding entry in the list record.annotations["residues"].

This function uses the Bio.PDB module to do most of the hard work. The annotation information could be improved but this extra parsing should be done in parse_pdb_header, not this module.