Package mmLib :: Module CIFBuilder :: Class CIFStructureBuilder
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Class CIFStructureBuilder

source code

                       object --+    
                                |    
StructureBuilder.StructureBuilder --+
                                    |
                                   CIFStructureBuilder

Builds a new Structure object by loading a CIF file.

Instance Methods [hide private]
 
read_start(self, filobj)
This methods needs to be reimplemented in a functional subclass.
source code
 
get_cell_parameters(self)
Read unit information form various tags and compute the fractional-to-Cartesian conversion matrix.
source code
 
read_atoms(self)
Read atom information form the atom_site section.
source code
 
read_geom_bond(self, bond_map)
Read bond information form the geom_bond section.
source code
 
read_geom_angle(self, bond_map)
Read bond information form the geom_angle section.
source code
 
read_metadata(self)
This method needs to be reimplemented in a functional subclass.
source code
 
read_structure_id(self)
Read the PDB ID.
source code

Inherited from StructureBuilder.StructureBuilder: __init__, load_alpha_helicies, load_atom, 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 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, filobj)

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)

read_atoms(self)

source code 

Read atom information form the atom_site section.

Overrides: StructureBuilder.StructureBuilder.read_atoms

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)