*/
public enum PDBDocField
{
- PDB_ID("PDB Id", "pdb_id"), TITLE("Title", "title"), MOLECULE_NAME(
- "Molecule", "molecule_name"), MOLECULE_TYPE("Molecule Type",
- "molecule_type"), MOLECULE_SEQUENCE("Sequence",
- "molecule_sequence"), PFAM_ACCESSION("PFAM Accession",
- "pfam_accession"), PFAM_NAME("PFAM Name", "pfam_name"), INTERPRO_NAME(
- "InterPro Name", "interpro_name"), INTERPRO_ACCESSION(
- "InterPro Accession", "interpro_accession"), UNIPROT_ID(
- "UniProt Id", "uniprot_id"), UNIPROT_ACCESSION(
- "UniProt Accession", "uniprot_accession"), UNIPROT_COVERAGE(
- "UniProt Coverage", "uniprot_coverage"), UNIPROT_FEATURES(
- "Uniprot Features", "uniprot_features"), R_FACTOR("R Factor",
- "r_factor"), RESOLUTION("Resolution", "resolution"), DATA_QUALITY(
- "Data Quality", "data_quality"), OVERALL_QUALITY(
- "Overall Quality", "overall_quality"), POLYMER_COUNT(
- "Number of Polymers", "number_of_polymers"), PROTEIN_CHAIN_COUNT(
- "Number of Protein Chains", "number_of_protein_chains"), BOUND_MOLECULE_COUNT(
- "Number of Bound Molecule", "number_of_bound_molecules"), POLYMER_RESIDUE_COUNT(
- "Number of Polymer Residue", "number_of_polymer_residues"), GENUS(
- "GENUS", "genus"), GENE_NAME("Gene Name", "gene_name"), EXPERIMENTAL_METHOD(
- "Experimental Method", "experimental_method"), GO_ID("GO Id",
- "go_id"), ASSEMBLY_ID("Assembly Id", "assembly_form"), ASSEMBLY_FORM(
- "Assembly Form", "assembly_id"), ASSEMBLY_TYPE("Assembly Type",
- "assembly_type"), SPACE_GROUP("Space Group", "spacegroup"), CATH_CODE(
- "Cath Code", "cath_code"), TAX_ID("Tax Id", "tax_id"), TAX_QUERY(
- "Tax Query", "tax_query"), INTERACTING_ENTRY_ID(
- "Interacting Entry Id", "interacting_entry_id"), INTERACTING_ENTITY_ID(
- "Interacting Entity Id", "interacting_entity_id"), INTERACTING_MOLECULES(
- "Interacting Molecules", "interacting_molecules"), PUBMED_ID(
- "Pubmed Id", "pubmed_id"), STATUS("Status", "status"), MODEL_QUALITY(
- "Model Quality", "model_quality"), PIVOT_RESOLUTION(
- "Pivot Resolution", "pivot_resolution"), DATA_REDUCTION_SOFTWARE(
- "Data reduction software", "data_reduction_software"), MAX_OBSERVED_RES(
- "Max observed residues", "max_observed_residues"), ORG_SCI_NAME(
- "Organism scientific name", "organism_scientific_name"), SUPER_KINGDOM(
- "Super kingdom", "superkingdom"), RANK("Rank", "rank"), CRYSTALLISATION_PH(
- "Crystallisation Ph", "crystallisation_ph"), BIOLOGICAL_FUNCTION(
- "Biological Function", "biological_function"), BIOLOGICAL_PROCESS(
- "Biological Process", "biological_process"), BIOLOGICAL_CELL_COMPONENT(
- "Biological Cell Component", "biological_cell_component"), COMPOUND_NAME(
- "Compound Name", "compound_name"), COMPOUND_ID("Compound Id",
- "compound_id"), COMPOUND_WEIGHT("Compound Weight",
- "compound_weight"), COMPOUND_SYSTEMATIC_NAME(
- "Compound Systematic Name", "compound_systematic_name"), INTERACTING_LIG(
- "Interacting Ligands", "interacting_ligands"), JOURNAL(
- "Journal", "journal"), ALL_AUTHORS("All Authors", "all_authors"), EXPERIMENTAL_DATA_AVAILABLE(
- "Experiment Data Available", "experiment_data_available"), DIFFRACTION_PROTOCOL(
- "Diffraction Protocol", "diffraction_protocol"), REFINEMENT_SOFTWARE(
- "Refinement Software", "refinement_software"), STRUCTURE_DETERMINATION_METHOD(
+ PDB_ID("PDB Id", "pdb_id", Group.CROSS_REFS), TITLE(
+ "Title",
+ "title", Group.MISCELLENOUS), MOLECULE_NAME("Molecule",
+ "molecule_name",
+ Group.NAMES_AND_TAXONOMY), MOLECULE_TYPE(
+ "Molecule Type", "molecule_type", Group.NAMES_AND_TAXONOMY), MOLECULE_SEQUENCE(
+ "Sequence", "molecule_sequence", Group.MISCELLENOUS), PFAM_ACCESSION(
+ "PFAM Accession", "pfam_accession",
+ Group.CROSS_REFS), PFAM_NAME(
+ "PFAM Name", "pfam_name", Group.NAMES_AND_TAXONOMY), INTERPRO_NAME(
+ "InterPro Name", "interpro_name", Group.NAMES_AND_TAXONOMY), INTERPRO_ACCESSION(
+ "InterPro Accession", "interpro_accession",
+ Group.CROSS_REFS), UNIPROT_ID("UniProt Id",
+ "uniprot_id", Group.CROSS_REFS), UNIPROT_ACCESSION(
+ "UniProt Accession", "uniprot_accession",
+ Group.CROSS_REFS),
+
+ UNIPROT_COVERAGE(
+ "UniProt Coverage", "uniprot_coverage", Group.MISCELLENOUS), UNIPROT_FEATURES(
+ "Uniprot Features", "uniprot_features", Group.MISCELLENOUS), R_FACTOR(
+"R Factor",
+ "r_factor", Group.QUALITY_MEASURES), RESOLUTION("Resolution",
+ "resolution", Group.QUALITY_MEASURES), DATA_QUALITY(
+ "Data Quality", "data_quality", Group.QUALITY_MEASURES), OVERALL_QUALITY(
+ "Overall Quality", "overall_quality", Group.QUALITY_MEASURES), POLYMER_COUNT(
+ "Number of Polymers", "number_of_polymers", Group.MISCELLENOUS), PROTEIN_CHAIN_COUNT(
+ "Number of Protein Chains", "number_of_protein_chains",
+ Group.MISCELLENOUS), BOUND_MOLECULE_COUNT(
+ "Number of Bound Molecule", "number_of_bound_molecules",
+ Group.MISCELLENOUS), POLYMER_RESIDUE_COUNT(
+ "Number of Polymer Residue", "number_of_polymer_residues",
+ Group.MISCELLENOUS), GENUS("GENUS", "genus",
+ Group.NAMES_AND_TAXONOMY), GENE_NAME("Gene Name", "gene_name",
+ Group.NAMES_AND_TAXONOMY), EXPERIMENTAL_METHOD(
+ "Experimental Method", "experimental_method",
+ Group.PROCEDURE_AND_SOFTWARE), GO_ID("GO Id", "go_id",
+ Group.CROSS_REFS), ASSEMBLY_ID("Assembly Id",
+ "assembly_id", Group.CROSS_REFS), ASSEMBLY_FORM(
+ "Assembly Form", "assembly_form", Group.MISCELLENOUS), ASSEMBLY_TYPE(
+ "Assembly Type", "assembly_type", Group.MISCELLENOUS), SPACE_GROUP(
+ "Space Group", "spacegroup", Group.MISCELLENOUS), CATH_CODE(
+ "Cath Code", "cath_code", Group.CROSS_REFS), TAX_ID(
+ "Tax Id", "tax_id", Group.CROSS_REFS), TAX_QUERY(
+ "Tax Query", "tax_query", Group.CROSS_REFS), INTERACTING_ENTITY_ID(
+ "Interacting Entity Id", "interacting_entity_id",
+ Group.CROSS_REFS), INTERACTING_MOLECULES(
+ "Interacting Molecules", "interacting_molecules",
+ Group.MISCELLENOUS), PUBMED_ID("Pubmed Id", "pubmed_id",
+ Group.CROSS_REFS), STATUS("Status", "status",
+ Group.MISCELLENOUS), MODEL_QUALITY("Model Quality",
+ "model_quality", Group.QUALITY_MEASURES), PIVOT_RESOLUTION(
+ "Pivot Resolution", "pivot_resolution", Group.QUALITY_MEASURES), DATA_REDUCTION_SOFTWARE(
+ "Data reduction software", "data_reduction_software",
+ Group.PROCEDURE_AND_SOFTWARE), MAX_OBSERVED_RES(
+ "Max observed residues",
+ "max_observed_residues", Group.MISCELLENOUS), ORG_SCI_NAME(
+ "Organism scientific name", "organism_scientific_name",
+ Group.NAMES_AND_TAXONOMY), SUPER_KINGDOM("Super kingdom",
+ "superkingdom", Group.NAMES_AND_TAXONOMY), RANK("Rank", "rank",
+ Group.NAMES_AND_TAXONOMY), CRYSTALLISATION_PH(
+ "Crystallisation Ph",
+ "crystallisation_ph", Group.MISCELLENOUS), BIOLOGICAL_FUNCTION(
+ "Biological Function", "biological_function",
+ Group.MISCELLENOUS), BIOLOGICAL_PROCESS("Biological Process",
+ "biological_process", Group.MISCELLENOUS), BIOLOGICAL_CELL_COMPONENT(
+ "Biological Cell Component", "biological_cell_component",
+ Group.MISCELLENOUS), COMPOUND_NAME("Compound Name",
+ "compound_name", Group.NAMES_AND_TAXONOMY), COMPOUND_ID(
+ "Compound Id", "compound_id", Group.CROSS_REFS), COMPOUND_WEIGHT(
+ "Compound Weight", "compound_weight", Group.MISCELLENOUS), COMPOUND_SYSTEMATIC_NAME(
+ "Compound Systematic Name", "compound_systematic_name",
+ Group.NAMES_AND_TAXONOMY), INTERACTING_LIG(
+ "Interacting Ligands",
+ "interacting_ligands", Group.MISCELLENOUS), JOURNAL("Journal",
+ "journal", Group.MISCELLENOUS), ALL_AUTHORS("All Authors",
+ "all_authors", Group.MISCELLENOUS), EXPERIMENTAL_DATA_AVAILABLE(
+ "Experiment Data Available", "experiment_data_available",
+ Group.MISCELLENOUS), DIFFRACTION_PROTOCOL(
+ "Diffraction Protocol", "diffraction_protocol",
+ Group.PROCEDURE_AND_SOFTWARE), REFINEMENT_SOFTWARE(
+ "Refinement Software", "refinement_software",
+ Group.PROCEDURE_AND_SOFTWARE), STRUCTURE_DETERMINATION_METHOD(
"Structure Determination Method",
- "structure_determination_method"), SYNCHROTON_SITE(
- "Synchrotron Site", "synchrotron_site"), SAMPLE_PREP_METHOD(
- "Sample Preparation Method", "sample_preparation_method"), ENTRY_AUTHORS(
- "Entry Authors", "entry_authors"), CITATION_TITLE(
- "Citation Title", "citation_title"), STRUCTURE_SOLUTION_SOFTWARE(
- "Structure Solution Software", "structure_solution_software"), ENTRY_ENTITY(
- "Entry Entity", "entry_entity"), R_FREE("R Free", "r_free"), NO_OF_POLYMER_ENTITIES(
- "Number of Polymer Entities", "number_of_polymer_entities"), NO_OF_BOUND_ENTITIES(
- "Number of Bound Entities", "number_of_bound_entities"), CRYSTALLISATION_RESERVOIR(
- "Crystallisation Reservoir", "crystallisation_reservoir"), DATA_SCALING_SW(
- "Data Scalling Software", "data_scaling_software"), DETECTOR(
- "Detector", "detector"), DETECTOR_TYPE("Detector Type",
- "detector_type"), MODIFIED_RESIDUE_FLAG(
- "Modified Residue Flag", "modified_residue_flag"), NUMBER_OF_COPIES(
- "Number of Copies", "number_of_copies"), STRUCT_ASYM_ID(
- "Struc Asym Id", "struct_asym_id"), HOMOLOGUS_PDB_ENTITY_ID(
- "Homologus PDB Entity Id", "homologus_pdb_entity_id"), MOLECULE_SYNONYM(
- "Molecule Synonym", "molecule_synonym"), DEPOSITION_SITE(
- "Deposition Site", "deposition_site"), SYNCHROTRON_BEAMLINE(
- "Synchrotron Beamline", "synchrotron_beamline"), ENTITY_ID(
- "Entity Id", "entity_id"), BEAM_SOURCE_NAME("Beam Source Name",
- "beam_source_name"), PROCESSING_SITE("Processing Site",
- "processing_site"), ENTITY_WEIGHT("Entity Weight",
- "entity_weight"), VERSION("Version", "_version_"), ALL("ALL",
- "text");
+ "structure_determination_method", Group.PROCEDURE_AND_SOFTWARE), SYNCHROTON_SITE(
+ "Synchrotron Site", "synchrotron_site", Group.MISCELLENOUS), SAMPLE_PREP_METHOD(
+ "Sample Preparation Method", "sample_preparation_method",
+ Group.PROCEDURE_AND_SOFTWARE), ENTRY_AUTHORS("Entry Authors",
+ "entry_authors", Group.MISCELLENOUS), CITATION_TITLE(
+ "Citation Title", "citation_title", Group.MISCELLENOUS), STRUCTURE_SOLUTION_SOFTWARE(
+ "Structure Solution Software", "structure_solution_software",
+ Group.PROCEDURE_AND_SOFTWARE), ENTRY_ENTITY("Entry Entity",
+ "entry_entity", Group.MISCELLENOUS), R_FREE("R Free", "r_free",
+ Group.QUALITY_MEASURES), NO_OF_POLYMER_ENTITIES(
+ "Number of Polymer Entities", "number_of_polymer_entities",
+ Group.MISCELLENOUS), NO_OF_BOUND_ENTITIES(
+ "Number of Bound Entities", "number_of_bound_entities",
+ Group.MISCELLENOUS), CRYSTALLISATION_RESERVOIR(
+ "Crystallisation Reservoir", "crystallisation_reservoir",
+ Group.MISCELLENOUS), DATA_SCALING_SW("Data Scalling Software",
+ "data_scaling_software", Group.PROCEDURE_AND_SOFTWARE), DETECTOR(
+ "Detector", "detector", Group.MISCELLENOUS), DETECTOR_TYPE(
+ "Detector Type", "detector_type", Group.MISCELLENOUS), MODIFIED_RESIDUE_FLAG(
+ "Modified Residue Flag", "modified_residue_flag",
+ Group.MISCELLENOUS), NUMBER_OF_COPIES("Number of Copies",
+ "number_of_copies", Group.MISCELLENOUS), STRUCT_ASYM_ID(
+ "Struc Asym Id", "struct_asym_id",
+ Group.CROSS_REFS), HOMOLOGUS_PDB_ENTITY_ID(
+ "Homologus PDB Entity Id", "homologus_pdb_entity_id",
+ Group.CROSS_REFS), MOLECULE_SYNONYM(
+ "Molecule Synonym",
+ "molecule_synonym", Group.MISCELLENOUS), DEPOSITION_SITE(
+ "Deposition Site", "deposition_site", Group.MISCELLENOUS), SYNCHROTRON_BEAMLINE(
+ "Synchrotron Beamline", "synchrotron_beamline",
+ Group.MISCELLENOUS), ENTITY_ID("Entity Id", "entity_id",
+ Group.CROSS_REFS), BEAM_SOURCE_NAME(
+ "Beam Source Name",
+ "beam_source_name",
+ Group.NAMES_AND_TAXONOMY), PROCESSING_SITE(
+ "Processing Site", "processing_site", Group.MISCELLENOUS), ENTITY_WEIGHT(
+ "Entity Weight", "entity_weight", Group.MISCELLENOUS), VERSION(
+ "Version", "_version_", Group.MISCELLENOUS), ALL("ALL", "text",
+ Group.MISCELLENOUS);
+
+ private enum Group
+ {
+ DATE_OF("Date Of"), NAMES_AND_TAXONOMY("Names & Taxonomy"), MISCELLENOUS(
+ "Miscellenous"), QUALITY_MEASURES("Quality Measures"), CROSS_REFS(
+ "Cross References"), PROCEDURE_AND_SOFTWARE(
+ "Procedures & Softwares");
+
+ Group(String name)
+ {
+ this.name = name;
+ }
+
+ private String name;
+ public String getName()
+ {
+ return this.name;
+ }
+ };
private String name;
private String code;
- PDBDocField(String name, String code)
+ private Group group;
+
+ PDBDocField(String name, String code, Group group)
{
this.name = name;
this.code = code;
+ this.group = group;
}
public String getName()
return code;
}
+ public String getGroup()
+ {
+ return group.getName();
+ }
+
@Override
public String toString()
{
git://source.jalview.org / jalview.git / blobdiff