mmLib.mmCIFBuilder.mmCIFStructureBuilder

Package mmLib :: Module mmCIFBuilder :: Class mmCIFStructureBuilder

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Type mmCIFStructureBuilder

      object --+    
               |    
StructureBuilder --+
                   |
                  mmCIFStructureBuilder

Builds a new Structure object by loading a mmCIF file.

Method Summary
	`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_sequence(self)` Read the sequence
	`read_start(self, filobj)`
	`read_struct_conf(self)` Reads the struct_conf table getting information on alpha helicies and turns in the structure.
	`read_struct_conn(self)` Read bond information form the struct_conn and struct_conn_type sections.
	`read_structure_id(self)` Read the PDB ID.
	`read_unit_cell(self)` Load unit cell and symmetry tables.
	`set_atom_site_auth(self)` Read atom_site.auth_ labels for atom definitions.
	`set_atom_site_data_columns(self)` Choose to use atom_site.auth_ labels, or atom_site.label_
	`set_atom_site_label(self)` Read atom_site.label_ items for atom definitions.
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_atom(self, atm_map)` Called repeatedly by the implementation of read_atoms to load all the data for a single atom.
	`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 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

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_sequence(self)

Read the sequence

read_struct_conf(self)

Reads the struct_conf table getting information on alpha helicies and turns in the structure.

read_struct_conn(self)

Read bond information form the struct_conn and struct_conn_type sections.

read_structure_id(self)

Read the PDB ID.

read_unit_cell(self)

Load unit cell and symmetry tables.

set_atom_site_auth(self)

Read atom_site.auth_ labels for atom definitions.

set_atom_site_data_columns(self)

Choose to use atom_site.auth_ labels, or atom_site.label_

set_atom_site_label(self)

Read atom_site.label_ items for atom definitions.

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