Module xpdb

source code

:mod:`edPDB.xpdb` -- Extensions to :mod:`Bio.PDB`

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

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

License: like Biopython

Module content

.. autoclass:: SloppyStructureBuilder .. autoclass:: SloppyPDBIO .. autoclass:: AtomGroup

.. autofunction:: get_structure .. autofunction:: write_pdb

Classes

[hide private]

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

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

AtomGroup

Functions

[hide private]

get_structure(pdbfile, pdbid='system') source code

write_pdb(structure, filename, **kwargs)
Write Bio.PDB molecule *structure* to *filename*.

source code

Variables

[hide private]

logger = logging.getLogger('edPDB.xpdb')

sloppyparser = Bio.PDB.PDBParser(PERMISSIVE= True, structure_b...

writelogger = logging.getLogger('edPDB.write_pdb')

Function Details

[hide private]

write_pdb(structure, filename, **kwargs)

source code

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.

Variables Details

[hide private]

sloppyparser

Value:

Bio.PDB.PDBParser(PERMISSIVE= True, structure_builder= SloppyStructure
Builder())