+ /**
+ * Takes a collection of PDBDocField and converts its 'code' Field values into
+ * a comma delimited string.
+ *
+ * @param pdbDocfields
+ * the collection of PDBDocField to process
+ * @return the comma delimited string from the pdbDocFields collection
+ */
+ public static String getPDBDocFieldsAsCommaDelimitedString(
+ Collection<PDBDocField> pdbDocfields)
+ {
+ String result = "";
+ if (pdbDocfields != null && !pdbDocfields.isEmpty())
+ {
+ StringBuilder returnedFields = new StringBuilder();
+ for (PDBDocField field : pdbDocfields)
+ {
+ returnedFields.append(",").append(field.getCode());
+ }
+ returnedFields.deleteCharAt(0);
+ result = returnedFields.toString();
+ }
+ return result;
+ }
+
+ /**
+ * Determines the column index for 'PDB Id' Fields in the dynamic summary
+ * table. The PDB Id serves as a unique identifier for a given row in the
+ * summary table
+ *
+ * @param wantedFields
+ * the available table columns in no particular order
+ * @return the pdb id field column index
+ */
+ public static int getPDBIdColumIndex(
+ Collection<PDBDocField> wantedFields, boolean hasRefSeq)
+ {
+
+ // If a reference sequence is attached then start counting from 1 else
+ // start from zero
+ int pdbFieldIndexCounter = hasRefSeq ? 1 : 0;
+
+ for (PDBDocField field : wantedFields)
+ {
+ if (field.equals(PDBDocField.PDB_ID))
+ {
+ break; // Once PDB Id index is determined exit iteration
+ }
+ ++pdbFieldIndexCounter;
+ }
+ return pdbFieldIndexCounter;
+ }
+
+ /**
+ * This enum represents the fields available in the PDB JSON response
+ *
+ */
+ 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(
+ "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");
+
+ private String name;
+
+ private String code;
+
+ PDBDocField(String name, String code)
+ {
+ this.name = name;
+ this.code = code;
+ }
+
+ public String getName()
+ {
+ return name;
+ }
+
+ public String getCode()
+ {
+ return code;
+ }
+
+ public String toString()
+ {
+ return name;
+ }
+ }
+}
\ No newline at end of file