Package mmLib :: Module PDBBuilder :: Class PDBStructureBuilder
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Class PDBStructureBuilder

source code

                       object --+    
                                |    
StructureBuilder.StructureBuilder --+
                                    |
                       object --+   |
                                |   |
              PDB.RecordProcessor --+
                                    |
                                   PDBStructureBuilder

Builds a new Structure object by loading a PDB file.

Instance Methods [hide private]
 
pdb_error(self, rec_name, text) source code
 
get_fragment_id(self, rec, res_seq='resSeq', icode='iCode') source code
 
read_start(self, fil, update_cb=None)
This methods needs to be reimplemented in a functional subclass.
source code
 
load_atom(self, atm_map)
Override load_atom to maintain a serial_num->atm map.
source code
 
read_atoms(self)
This method needs to be reimplemented in a functional subclass.
source code
 
read_metadata(self)
This method needs to be reimplemented in a functional subclass.
source code
 
process_ATOM(self, rec) source code
 
process_HETATM(self, rec) source code
 
process_SIGATM(self, rec) source code
 
process_ANISOU(self, rec) source code
 
process_SIGUIJ(self, rec) source code
 
process_MODEL(self, rec) source code
 
process_ENDMDL(self, rec) source code
 
process_HEADER(self, rec) source code
 
preprocess_TITLE(self, title) source code
 
preprocess_COMPND(self, compnd_list) source code
 
preprocess_SOURCE(self, source_list) source code
 
preprocess_KEYWDS(self, keywds_list) source code
 
preprocess_AUTHOR(self, author_list) source code
 
preprocess_EXPDTA(self, expdta_list) source code
 
preprocess_SEQRES(self, seqres) source code
 
process_CRYST1(self, rec) source code
 
process_HELIX(self, rec) source code
 
process_SHEET(self, rec) source code
 
process_SITE(self, rec) source code
 
bond_processor(self, **args)
Complicated method.
source code
 
process_SSBOND(self, rec) source code
 
process_LINK(self, rec) source code
 
process_HYDBND(self, rec) source code
 
process_SLTBRG(self, rec) source code
 
process_CONECT(self, rec) source code

Inherited from StructureBuilder.StructureBuilder: __init__, load_alpha_helicies, load_beta_sheets, load_bonds, load_sequence, load_sites, load_structure_id, load_unit_cell, name_service, read_atoms_finalize, read_end, read_end_finalize, read_metadata_finalize, read_start_finalize

Inherited from PDB.RecordProcessor: preprocess_default, process_default, process_pdb_records

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __repr__, __setattr__, __sizeof__, __str__, __subclasshook__

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

read_start(self, fil, update_cb=None)

source code 

This methods needs to be reimplemented in a functional subclass. This function is called with the file object (or any other object passed in to build a Structure from) to begin the reading process. This is usually used to open the source file.

Overrides: StructureBuilder.StructureBuilder.read_start
(inherited documentation)

load_atom(self, atm_map)

source code 

Override load_atom to maintain a serial_num->atm map.

Overrides: StructureBuilder.StructureBuilder.load_atom

read_atoms(self)

source code 

This method needs to be reimplemented in a functional subclass. The subclassed read_atoms method should call load_atom once for every atom in the structure, and should not call any other load_* methods.

Overrides: StructureBuilder.StructureBuilder.read_atoms
(inherited documentation)

read_metadata(self)

source code 

This method needs to be reimplemented in a functional subclass. The subclassed read_metadata method should call the various load_* methods to set non-atom coordinate data for the Structure.

Overrides: StructureBuilder.StructureBuilder.read_metadata
(inherited documentation)

process_ATOM(self, rec)

source code 
Overrides: PDB.RecordProcessor.process_ATOM

bond_processor(self, **args)

source code 

Complicated method. Required arguments are: rec = PDB record atm1/2 = Atom object, if you want to override the lookup chain_id_field1/2: PDB field name for the chain ID res_seq1/2_field: PDB field for the residue sequence num icode1/2_field: PDB field for the residue insertion code name1/2_field: PDB field for the atom name atl_loc1/2: PDB filed name for the atom alt_loc symop1/2_field: PDB field name for the atom symmetry operation

chain_id1/2: override the chain ID frag_id1/2: override the fragmetn ID name1/2: override the atom name alt_loc1/2: override the atom alt_loc