Package org.biojava.nbio.structure.io.mmcif.model
Datamodel objects used for processing mmcif files. This are beans that can represent the data from a category in mmcif.
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Class Summary Class Description AbstractBean a generic class that implements the toString method for a beanAtomSite 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_ordinalChemCompBond ChemCompDescriptor Container object for _pdbx_chem_comp_descriptorDatabasePDBremark DatabasePDBrev DatabasePdbrevRecord Entity A simple class to represent Entity records in mmCif filesEntityPoly Container for _entity_poly recordsEntityPolySeq Container for _entity_poly_seq recordsEntitySrcGen 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.identifierPdbxDatabaseStatus 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 categoryPdbxStructOperListXMLContainer Refine Struct a bean to contain the data of the _struct linesStructAsym Contains the data for _struct_asymStructConn A bean that stores data from the mmcif category _struct_connStructKeywords StructNcsOper A class containing the _struct_ncs_oper dataStructRef A class to containt the _struct_ref field dataStructRefSeq StructRefSeqDif A class to store sequence mismatch annotationsStructSite 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 labelIgnoreField Annotation indicating that a specific field of a bean should be ignored