mmLib.PDBBuilder.PDBStructureBuilder

Package mmLib :: Module PDBBuilder :: Class PDBStructureBuilder

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Type PDBStructureBuilder

      object --+    
               |    
 RecordProcessor --+
                   |
      object --+   |
               |   |
StructureBuilder --+
                   |
                  PDBStructureBuilder

Builds a new Structure object by loading a PDB file.

Method Summary
	`bond_processor(self, **args)` Complicated method.
	`get_fragment_id(self, rec, res_seq, icode)`
	`load_atom(self, atm_map)` Override load_atom to maintain a serial_num->atm map.
	`pdb_error(self, rec_name, text)`
	`preprocess_AUTHOR(self, author_list)`
	`preprocess_COMPND(self, compnd_list)`
	`preprocess_EXPDTA(self, expdta_list)`
	`preprocess_KEYWDS(self, keywds_list)`
	`preprocess_SEQRES(self, seqres)`
	`preprocess_SOURCE(self, source_list)`
	`preprocess_TITLE(self, title)`
	`process_ANISOU(self, rec)`
	`process_ATOM(self, rec)`
	`process_CONECT(self, rec)`
	`process_CRYST1(self, rec)`
	`process_ENDMDL(self, rec)`
	`process_HEADER(self, rec)`
	`process_HELIX(self, rec)`
	`process_HETATM(self, rec)`
	`process_HYDBND(self, rec)`
	`process_LINK(self, rec)`
	`process_MODEL(self, rec)`
	`process_SHEET(self, rec)`
	`process_SIGATM(self, rec)`
	`process_SIGUIJ(self, rec)`
	`process_SITE(self, rec)`
	`process_SLTBRG(self, rec)`
	`process_SSBOND(self, rec)`
	`read_atoms(self)` This method needs to be reimplemented in a fuctional subclass.
	`read_metadata(self)` This method needs to be reimplemented in a fuctional subclass.
	`read_start(self, fil)` This methods needs to be reimplemented in a functional subclass.
Inherited from StructureBuilder
	`__init__(self, sequence_from_structure, library_bonds, distance_bonds, **args)`
	`load_alpha_helicies(self, helix_list)` The argument helix_list is a list of Python dictionaries with information to build build AlphaHelix objects into the Structure.
	`load_beta_sheets(self, beta_sheet_list)` The argument beta_sheet_list is a list of Python dictionaries with information to build build BetaSheet objects into the Structure.
	`load_bonds(self, bond_map)` Call by the implementation of load_metadata to load bond information on the structure.
	`load_sequence(self, sequence_map)` The sequence map contains the following keys: chain_id: the chain ID fo the sequence; num_res: the number of residues in the sequence; sequence_list: a list of 3-letter codes of the residues in the sequence.
	`load_sites(self, site_list)` The argument site_list is a list of Python dictionaries with information to build build Site objects into the Structure.
	`load_structure_id(self, structure_id)`
	`load_unit_cell(self, ucell_map)` Called by the implementation of load_metadata to load the unit cell pararameters for the structure.
	`name_service(self)` Runs the name service on all atoms needing to be named.
	`read_atoms_finalize(self)` After loading all atom records, use the list of atom records to build the structure.
	`read_end(self)` This method needs to be reimplemented in a fuctional subclass.
	`read_end_finalize(self)` Called for final cleanup after structure source readinging is done.
	`read_metadata_finalize(self)` Called after the the metadata loading is complete.
	`read_start_finalize(self)` Called after the read_start method.
Inherited from RecordProcessor
	`preprocess_default(self, rec)`
	`process_default(self, rec)`
	`process_pdb_records(self, pdb_rec_iter, filter_func)` Iterates the PDB records in self, and searches for handling methods in the processor object for reading the objects.
Inherited from object
	`__delattr__(...)` x.__delattr__('name') <==> del x.name
	`__getattribute__(...)` x.__getattribute__('name') <==> x.name
	`__hash__(x)` x.__hash__() <==> hash(x)
	`__new__(T, S, ...)` T.__new__(S, ...) -> a new object with type S, a subtype of T
	`__reduce__(...)` helper for pickle
	`__reduce_ex__(...)` helper for pickle
	`__repr__(x)` x.__repr__() <==> repr(x)
	`__setattr__(...)` x.__setattr__('name', value) <==> x.name = value
	`__str__(x)` x.__str__() <==> str(x)

Method Details

bond_processor(self, **args)

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

load_atom(self, atm_map)

Override load_atom to maintain a serial_num->atm map.

Overrides:: mmLib.StructureBuilder.StructureBuilder.load_atom

read_atoms(self)

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

Overrides:: mmLib.StructureBuilder.StructureBuilder.read_atoms (inherited documentation)

read_metadata(self)

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

Overrides:: mmLib.StructureBuilder.StructureBuilder.read_metadata (inherited documentation)

read_start(self, fil, update_cb=None)

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:: mmLib.StructureBuilder.StructureBuilder.read_start (inherited documentation)

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