__init__ (
        self,
        PERMISSIVE=0,
        structure_builder=None,
        )

The PDB parser call a number of standard methods in an aggregated StructureBuilder object. Normally this object is instanciated by the PDBParser object itself, but if the user provides his own StructureBuilder object, the latter is used instead.

Arguments: o PERMISSIVE - int, if this is 0 (default) exceptions in constructing the SMCRA data structure are fatal. If 1, the exceptions are caught, but some residues or atoms will be missing. o structure_builder - an optional user implemented StructureBuilder class.

_get_header ( self,  header_coords_trailer )

Get the header of the PDB file, return the rest.

_handle_PDB_exception (
        self,
        message,
        line_counter,
        )

This method catches an exception that occurs in the StructureBuilder object (if PERMISSIVE==1), or raises it again, this time adding the PDB line number to the error message.

_parse ( self,  header_coords_trailer )

Parse the PDB file.

_parse_coordinates ( self,  coords_trailer )

Parse the atomic data in the PDB file.

get_header ( self )

Return the header.

get_structure (
        self,
        id,
        filename,
        )

Return the structure.

Arguments: o id - string, the id that will be used for the structure o filename - name of the PDB file

get_trailer ( self )

Return the trailer.