Author: | Oliver Beckstein |
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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/
Cope with resSeq < 10,000 limitation by just incrementing internally.
Solves the follwing problem with Bio.PDB.StructureBuilder.StructureBuilder:
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
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().
Write Bio.PDB molecule structure to filename.
Arguments : |
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