5.20. Extensions to Bio.PDB
— pdb.extensions
¶
Author: | Oliver Beckstein |
---|---|
Year: | 2009 |
License: | Biopython |
Extension to Bio.PDB
to handle large pdb files.
Partly published on http://biopython.org/wiki/Reading_large_PDB_files and more code at http://github.com/orbeckst/GromacsWrapper/tree/master/edPDB/
5.20.1. Classes¶
-
class
MDAnalysis.coordinates.pdb.extensions.
SloppyStructureBuilder
(verbose=False)[source]¶ 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
MDAnalysis.coordinates.pdb.extensions.
SloppyPDBIO
(use_model_flag=0)[source]¶ 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
Creat the PDBIO object.
@param use_model_flag: if 1, force use of the MODEL record in output. @type use_model_flag: int
5.20.2. Functions¶
-
MDAnalysis.coordinates.pdb.extensions.
get_structure
(pdbfile, pdbid='system')[source]¶ Read the pdbfilename and return a Bio.PDB structure.
This function ignores duplicate atom numbers and resids from the file and simply increments them.
Note
The call signature is reversed compared to the one of
Bio.PDB.PDBParser.get_structure()
.