Package edPDB :: Module xpdb :: Class SloppyStructureBuilder
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Class SloppyStructureBuilder

source code

Bio.PDB.StructureBuilder.StructureBuilder --+
                                            |
                                           SloppyStructureBuilder

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

Solves the follwing problem with :class:`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)

Instance Methods [hide private]
 
__init__(self, verbose=False) source code
 
init_residue(self, resname, field, resseq, icode)
Initiate a new Residue object.
source code

Inherited from Bio.PDB.StructureBuilder.StructureBuilder: get_structure, init_atom, init_chain, init_model, init_seg, init_structure, set_anisou, set_header, set_line_counter, set_sigatm, set_siguij, set_symmetry

Inherited from Bio.PDB.StructureBuilder.StructureBuilder (private): _is_completely_disordered

Method Details [hide private]

__init__(self, verbose=False)
(Constructor)

source code 
Overrides: Bio.PDB.StructureBuilder.StructureBuilder.__init__

init_residue(self, resname, field, resseq, icode)

source code 

Initiate a new Residue object.

Arguments:
o resname - string, e.g. "ASN"
o field - hetero flag, "W" for waters, "H" for 
    hetero residues, otherwise blanc.
o resseq - int, sequence identifier
o icode - string, insertion code

Overrides: Bio.PDB.StructureBuilder.StructureBuilder.init_residue