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GromacsWrapper
Package edPDB :: Module xpdb :: Class SloppyPDBIO
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Class SloppyPDBIO

source code

??.PDBIO --+
           |
          SloppyPDBIO

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
Instance Methods [hide private]
 
_get_atom_line(self, atom, hetfield, segid, atom_number, resname, resseq, icode, chain_id, element=' ', charge=' ')
Returns an ATOM PDB string that is guaranteed to fit into the ATOM format.		 source code

Inherited from unreachable.PDBIO: __init__, save, set_structure

Class Variables [hide private]
  _ATOM_FORMAT_STRING = '%s%5i %-4s%c%3s %c%4i%c %8.3f%8.3f%8....
Method Details [hide private]

_get_atom_line(self, atom, hetfield, segid, atom_number, resname, resseq, icode, chain_id, element=' ', charge=' ')

source code  

Returns an ATOM PDB string that is guaranteed to fit into the ATOM format.

- Resid (resseq) is wrapped (modulo 10,000) to fit into %4i (4I) format
- Atom number (atom_number) is wrapped (modulo 100,000) to fit into %4i (4I) format
Overrides: unreachable.PDBIO._get_atom_line

Class Variable Details [hide private]

_ATOM_FORMAT_STRING

Value:
'''%s%5i %-4s%c%3s %c%4i%c   %8.3f%8.3f%8.3f%6.2f%6.2f      %4s%2s%2s
'''

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