Package mmLib :: Module mmCIFBuilder :: Class mmCIFStructureBuilder
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Class mmCIFStructureBuilder

source code

                       object --+    
                                |    
StructureBuilder.StructureBuilder --+
                                    |
                                   mmCIFStructureBuilder

Builds a new Structure object by loading an mmCIF file.

Instance Methods [hide private]
 
read_start(self, filobj)
This methods needs to be reimplemented in a functional subclass.
source code
 
set_atom_site_auth(self)
Read atom_site.auth_ labels for atom definitions.
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set_atom_site_label(self)
Read atom_site.label_ items for atom definitions.
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set_atom_site_data_columns(self)
Choose to use atom_site.auth_ labels, or atom_site.label_
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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.
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read_sequence(self)
Read the sequence.
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read_structure_id(self)
Read the PDB ID.
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read_unit_cell(self)
Load unit cell and symmetry tables.
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read_struct_conn(self)
Read bond information form the struct_conn and struct_conn_type sections.
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read_struct_conf(self)
Reads the struct_conf table getting information on alpha helicies and turns in the structure.
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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 

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)