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
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)
PDBIO class that can deal with large pdb files as used in MD simulations.
@param use_model_flag: if 1, force use of the MODEL record in output. @type use_model_flag: int
Write Bio.PDB molecule structure to filename.
Arguments: |
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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.