edPDB.xpdb – Extensions to Bio.PDB

Extensions to Bio.PDB, such as handling of large pdb files and some useful selections (see edPDB.selections).

Partly published on http://biopython.org/wiki/Reading_large_PDB_files

License: like Biopython

Module content

class edPDB.xpdb.SloppyStructureBuilder(verbose=False)

Cope with resSeq < 10,000 limitation by just incrementing internally.

Solves the follwing problem with Bio.PDB.StructureBuilder.StructureBuilder: Q: What’s wrong here??

Some atoms or residues will be missing in the data structure. WARNING: Residue (‘ ‘, 8954, ‘ ‘) redefined at line 74803. PDBConstructionException: Blank altlocs in duplicate residue SOL (‘ ‘, 8954, ‘ ‘) at line 74803.

A: resSeq only goes to 9999 –> goes back to 0 (PDB format is not really good here)

Warning

H and W records are probably not handled yet (don’t have examples to test)

class edPDB.xpdb.SloppyPDBIO(use_model_flag=0)

PDBIO class that can deal with large pdb files as used in MD simulations.

  • resSeq simply wrap and are printed modulo 10,000.
  • atom numbers wrap at 99,999 and are printed modulo 100,000

@param use_model_flag: if 1, force use of the MODEL record in output. @type use_model_flag: int

class edPDB.xpdb.AtomGroup(atoms=None)
edPDB.xpdb.get_structure(pdbfile, pdbid='system')
edPDB.xpdb.write_pdb(structure, filename, **kwargs)

Write Bio.PDB molecule structure to filename.

Arguments:
structure

Bio.PDB structure instance

filename

pdb file

selection

Bio.PDB.Selection

exclusions

list of residue instances that will not be included

inclusions

list of residue instances that will be included

chain

set the chain identifier for all atoms written; this can be useful to simply to erase all chain ids by setting it to ‘ ‘

Typical use is to supply a list of water molecules that should not be written or a ligand that should be include.

Note

Currently only one of selection, *exclusions or inclusions is supported.

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