Package org.biojava.nbio.structure.io.mmcif.model

Datamodel objects used for processing mmcif files.

See: Description

Class Summary

Class	Description
AbstractBean	a generic class that implements the toString method for a bean
AtomSite
AtomSites	A class containing the _atom_sites data.
AuditAuthor
Cell
ChemComp	A definition for a Chemical Component, as maintained by the wwPDB.
ChemCompAtom	stores these fields: _chem_comp_atom.comp_id _chem_comp_atom.atom_id _chem_comp_atom.alt_atom_id _chem_comp_atom.type_symbol _chem_comp_atom.charge _chem_comp_atom.pdbx_align _chem_comp_atom.pdbx_aromatic_flag _chem_comp_atom.pdbx_leaving_atom_flag _chem_comp_atom.pdbx_stereo_config _chem_comp_atom.model_Cartn_x _chem_comp_atom.model_Cartn_y _chem_comp_atom.model_Cartn_z _chem_comp_atom.pdbx_model_Cartn_x_ideal _chem_comp_atom.pdbx_model_Cartn_y_ideal _chem_comp_atom.pdbx_model_Cartn_z_ideal _chem_comp_atom.pdbx_component_comp_id _chem_comp_atom.pdbx_residue_numbering _chem_comp_atom.pdbx_component_atom_id _chem_comp_atom.pdbx_polymer_type _chem_comp_atom.pdbx_ref_id _chem_comp_atom.pdbx_component_id _chem_comp_atom.pdbx_ordinal
ChemCompBond
ChemCompDescriptor	Container object for _pdbx_chem_comp_descriptor
DatabasePDBremark
DatabasePDBrev
DatabasePdbrevRecord
Entity	A simple class to represent Entity records in mmCif files
EntityPoly	Container for _entity_poly records
EntityPolySeq	Container for _entity_poly_seq records Field Name mmCIF Data Item Section n.a.
EntitySrcGen	Data items in the ENTITY_SRC_GEN category record details of the source from which the entity was obtained in cases where the source was genetically manipulated.
EntitySrcNat	Data items in the ENTITY_SRC_NAT category record details of the source from which the entity was obtained in cases where the entity was isolated directly from a natural tissue.
EntitySrcSyn	PDBX_ENTITY_SRC_SYN records the details about each chemically synthesized molecule (entity) in the asymmetric unit.
Exptl
PdbxAuditRevisionHistory	Bean to hold data for _pdbx_audit_revision_history mmCIF category.
PdbxChemCompDescriptor
PdbxChemCompIdentifier	_pdbx_chem_comp_identifier.comp_id _pdbx_chem_comp_identifier.type _pdbx_chem_comp_identifier.program _pdbx_chem_comp_identifier.program_version _pdbx_chem_comp_identifier.identifier
PdbxDatabaseStatus	Bean to hold data for _pdbx_database_status mmCIF category.
PdbxEntityNonPoly	A bean for the Pdbx_entity_nonpoly category.
PdbxNonPolyScheme	A bean for the PDBX_NONPOLY_SCHEME category, which provides residue level nomenclature mapping for non-polymer entities.
PdbxPolySeqScheme	A bean for the PDBX_POLY_SEQ_SCHEME category, which provides residue level nomenclature mapping for polymer entities.
PdbxStructAssembly
PdbxStructAssemblyGen
PdbxStructAssemblyGenXMLContainer
PdbxStructAssemblyXMLContainer
PdbxStructOperList	The bean for pdbx_struct_oper_list category _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[3] _pdbx_struct_oper_list.name
PdbxStructOperListXMLContainer
Refine
Struct	a bean to contain the data of the _struct lines
StructAsym	Contains the data for _struct_asym
StructConn	A bean that stores data from the mmcif category _struct_conn
StructKeywords
StructNcsOper	A class containing the _struct_ncs_oper data _struct_ncs_oper.id _struct_ncs_oper.code _struct_ncs_oper.details _struct_ncs_oper.matrix[1][1] _struct_ncs_oper.matrix[1][2] _struct_ncs_oper.matrix[1][3] _struct_ncs_oper.matrix[2][1] _struct_ncs_oper.matrix[2][2] _struct_ncs_oper.matrix[2][3] _struct_ncs_oper.matrix[3][1] _struct_ncs_oper.matrix[3][2] _struct_ncs_oper.matrix[3][3] _struct_ncs_oper.vector[1] _struct_ncs_oper.vector[2] _struct_ncs_oper.vector[3]
StructRef	A class to containt the _struct_ref field data
StructRefSeq
StructRefSeqDif	A class to store sequence mismatch annotations
StructSite	Created by Matt on 11/1/2015.
StructSiteGen	Created by Matt on 10/31/2015.
Symmetry

Annotation Types Summary

Annotation Type	Description
CIFLabel	Annotation indicating that a specific field of a bean should be mapped to a different label
IgnoreField	Annotation indicating that a specific field of a bean should be ignored

Package org.biojava.nbio.structure.io.mmcif.model Description

Datamodel objects used for processing mmcif files. This are beans that can represent the data from a category in mmcif.