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

Packages that use org.biojava.nbio.structure.io.mmcif.model

Package	Description
org.biojava.nbio.structure	Interfaces and classes for protein structure (PDB).
org.biojava.nbio.structure.io	Input and Output of Structures
org.biojava.nbio.structure.io.mmcif	Input and Output of mmcif files.
org.biojava.nbio.structure.io.mmcif.chem
org.biojava.nbio.structure.io.mmcif.model	Datamodel objects used for processing mmcif files.
org.biojava.nbio.structure.quaternary
org.biojava.nbio.structure.quaternary.io

Classes in org.biojava.nbio.structure.io.mmcif.model used by org.biojava.nbio.structure

Class and Description
ChemComp A definition for a Chemical Component, as maintained by the wwPDB.
DatabasePdbrevRecord

Classes in org.biojava.nbio.structure.io.mmcif.model used by org.biojava.nbio.structure.io

Class and Description
StructConn A bean that stores data from the mmcif category _struct_conn

Classes in org.biojava.nbio.structure.io.mmcif.model used by org.biojava.nbio.structure.io.mmcif

Class and Description
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
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
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
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
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
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

Classes in org.biojava.nbio.structure.io.mmcif.model used by org.biojava.nbio.structure.io.mmcif.chem

Class and Description
ChemComp A definition for a Chemical Component, as maintained by the wwPDB.

Classes in org.biojava.nbio.structure.io.mmcif.model used by org.biojava.nbio.structure.io.mmcif.model

Class and Description
AbstractBean a generic class that implements the toString method for a bean
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
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

Classes in org.biojava.nbio.structure.io.mmcif.model used by org.biojava.nbio.structure.quaternary

Class and Description
PdbxStructAssembly
PdbxStructAssemblyGen
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

Classes in org.biojava.nbio.structure.io.mmcif.model used by org.biojava.nbio.structure.quaternary.io

Class and Description
PdbxStructAssembly
PdbxStructAssemblyGen
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