Index (Unnamed - com.dumontierlab:pdb2rdf-parser:jar:0.0.8 0.0.8 API)

Overview

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Class

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Deprecated

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A B C D E F G H I J L M N O P Q R S T U V W Y

A

abort() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
ABSORT_COEFFICIENT_MU - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ABSORT_CORRECTION_T_MAX - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ABSORT_CORRECTION_T_MIN - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ABSORT_CORRECTION_TYPE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ABSORT_PROCESS_DETAILS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
AbsortCorrectionTypes - Class in com.dumontierlab.pdb2rdf.parser.vocabulary
AbsortCorrectionTypes() - Constructor for class com.dumontierlab.pdb2rdf.parser.vocabulary.AbsortCorrectionTypes
ABSTRACT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
AbstractPdbXmlParser - Class in com.dumontierlab.pdb2rdf.parser
AbstractPdbXmlParser() - Constructor for class com.dumontierlab.pdb2rdf.parser.AbstractPdbXmlParser
add(List<Statement>) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
add(Model, boolean) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
add(Model) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
add(Resource, Property, RDFNode) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
add(Resource, Property, String, boolean) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
add(Resource, Property, String, RDFDatatype) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
add(Resource, Property, String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
add(Resource, Property, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
add(Statement) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
add(Statement[]) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
add(StmtIterator) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
addLiteral(Resource, Property, boolean) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
addLiteral(Resource, Property, char) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
addLiteral(Resource, Property, double) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
addLiteral(Resource, Property, float) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
addLiteral(Resource, Property, int) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
addLiteral(Resource, Property, long) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
addLiteral(Resource, Property, Object) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
addLiteral(Resource, Property, Literal) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
ANGLE_ALPHA - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANGLE_ALPHA_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANGLE_BETA - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANGLE_BETA_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANGLE_GAMMA - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANGLE_GAMMA_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_B11 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
Aniso_B11 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_B11_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_B12 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
Aniso_B12 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_B12_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_B13 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
Aniso_B13 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_B13_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_B22 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
Aniso_B22 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_B22_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_B23 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
Aniso_B23 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_B23_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_B33 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
Aniso_B33 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_B33_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_RATIO - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_U11 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_U11_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_U12 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_U12_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_U13 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_U13_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_U22 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_U22_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_U23 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_U23_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_U33 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ANISO_U33_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
anonUri(String, String) - Static method in class com.dumontierlab.pdb2rdf.util.UriUtil
asRDFNode(Node) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
asStatement(Triple) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
ATCC - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ATOM_SITE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ATOM_SITE_CATEGORY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
AtomSiteCategoryHandler - Class in com.dumontierlab.pdb2rdf.parser
AtomSiteCategoryHandler(PdbRdfModel, UriBuilder, String, Map<String, Collection<Resource>>) - Constructor for class com.dumontierlab.pdb2rdf.parser.AtomSiteCategoryHandler
ATTACHED_HYDROGENS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
AUTH_ASYM_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
AUTH_ATOM_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
AUTH_COMP_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
AUTH_SEQ_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
AVERAGE_CONSTRAINT_VIOLATIONS_PER_RESIDUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
AVERAGE_CONSTRAINTS_PER_RESIDUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
AVERAGE_DISTANCE_CONSTRAINT_VIOLATION - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary

B

B_EQUIVALENT_GEOMETRIC_MEAN - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
B_EQUIVALENT_GEOMETRIC_MEAN_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
B_ISO_MAX - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
B_ISO_MEAN - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
B_ISO_MIN - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
B_ISO_OR_EQUIVALENT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
B_ISO_OR_EQUIVALENT_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
BEG_AUTH_ASYM_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
BEG_AUTH_COMP_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
BEG_AUTH_SEQ_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
begin() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
Bio2RdfPdbUriPattern - Enum in com.dumontierlab.pdb2rdf.parser.vocabulary.uri
BOOK_ISBN - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
BOOK_PUBLISHER - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
BOOK_TITLE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
BUCKLE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
buffer - Variable in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
buildUri(UriPattern, String...) - Method in class com.dumontierlab.pdb2rdf.parser.vocabulary.uri.UriBuilder

C

CALC_ATTACHED_ATOM - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CARTN_X - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CARTN_X_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CARTN_Y - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CARTN_Y_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CARTN_Z - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CARTN_Z_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CELL_CATEGORY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CELL_LINE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CELL_TYPE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CellCategoryHandler - Class in com.dumontierlab.pdb2rdf.parser
CellCategoryHandler(PdbRdfModel, UriBuilder, String) - Constructor for class com.dumontierlab.pdb2rdf.parser.CellCategoryHandler
characters(char[], int, int) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
ChemCompCategory - Class in com.dumontierlab.pdb2rdf.parser
ChemCompCategory(PdbRdfModel, UriBuilder, String, Map<String, Collection<Resource>>) - Constructor for class com.dumontierlab.pdb2rdf.parser.ChemCompCategory
CHEMICAL_AMOUNT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CHEMICAL_COMPONENT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CHEMICAL_COMPONENT_CATEGORY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CHEMICAL_CONN_NUMBER - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CITATION - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CITATION_AUTHOR - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CITATION_AUTHOR_CATEGORY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CITATION_CATEGORY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CITATION_ID_ATT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CitationAuthorCategoryHandler - Class in com.dumontierlab.pdb2rdf.parser
CitationAuthorCategoryHandler(PdbRdfModel, UriBuilder, String) - Constructor for class com.dumontierlab.pdb2rdf.parser.CitationAuthorCategoryHandler
CitationCategoryHandler - Class in com.dumontierlab.pdb2rdf.parser
CitationCategoryHandler(PdbRdfModel, UriBuilder, String) - Constructor for class com.dumontierlab.pdb2rdf.parser.CitationCategoryHandler
clear() - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
close() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
com.dumontierlab.pdb2rdf.model - package com.dumontierlab.pdb2rdf.model
com.dumontierlab.pdb2rdf.parser - package com.dumontierlab.pdb2rdf.parser
com.dumontierlab.pdb2rdf.parser.rna - package com.dumontierlab.pdb2rdf.parser.rna
com.dumontierlab.pdb2rdf.parser.rna.vocabulary - package com.dumontierlab.pdb2rdf.parser.rna.vocabulary
com.dumontierlab.pdb2rdf.parser.rna.vocabulary.uri - package com.dumontierlab.pdb2rdf.parser.rna.vocabulary.uri
com.dumontierlab.pdb2rdf.parser.vocabulary - package com.dumontierlab.pdb2rdf.parser.vocabulary
com.dumontierlab.pdb2rdf.parser.vocabulary.uri - package com.dumontierlab.pdb2rdf.parser.vocabulary.uri
com.dumontierlab.pdb2rdf.util - package com.dumontierlab.pdb2rdf.util
commit() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
CONF_TYPE_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CONFORMER_SELECTION_CRITERIA - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CONSTRAINTS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
contains(Resource, Property, RDFNode) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
contains(Resource, Property, String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
contains(Resource, Property, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
contains(Resource, Property) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
contains(Statement) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
containsAll(Model) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
containsAll(StmtIterator) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
containsAny(Model) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
containsAny(StmtIterator) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
containsLiteral(Resource, Property, boolean) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
containsLiteral(Resource, Property, char) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
containsLiteral(Resource, Property, double) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
containsLiteral(Resource, Property, float) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
containsLiteral(Resource, Property, int) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
containsLiteral(Resource, Property, long) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
containsLiteral(Resource, Property, Object) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
containsResource(RDFNode) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
ContentHandlerState - Class in com.dumontierlab.pdb2rdf.parser
ContentHandlerState(PdbRdfModel, UriBuilder) - Constructor for class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
CORRELATION_COEFF_FO_TO_FC - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
CORRELATION_COEFF_FO_TO_FC_FREE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
COUNTRY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
createAlt() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createAlt(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createBag() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createBag(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createDecimalLiteral(String) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
createList() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createList(Iterator<? extends RDFNode>) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createList(RDFNode[]) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createLiteral(String, boolean) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createLiteral(String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createLiteral(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createLiteral(String, String) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
createLiteralStatement(Resource, Property, boolean) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createLiteralStatement(Resource, Property, char) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createLiteralStatement(Resource, Property, double) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createLiteralStatement(Resource, Property, float) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createLiteralStatement(Resource, Property, int) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createLiteralStatement(Resource, Property, long) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createLiteralStatement(Resource, Property, Object) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createProperty(String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createProperty(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createReifiedStatement(Statement) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createReifiedStatement(String, Statement) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createResource() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createResource(AnonId) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createResource(Resource) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createResource(ResourceF) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createResource(String, Resource) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createResource(String, ResourceF) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createResource(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createResource(UriPattern, String...) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
createSeq() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createSeq(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createStatement(Resource, Property, RDFNode) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createStatement(Resource, Property, String, boolean) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createStatement(Resource, Property, String, String, boolean) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createStatement(Resource, Property, String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createStatement(Resource, Property, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createTypedLiteral(boolean) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createTypedLiteral(Calendar) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createTypedLiteral(char) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createTypedLiteral(double) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createTypedLiteral(float) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createTypedLiteral(int) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createTypedLiteral(long) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createTypedLiteral(Object, RDFDatatype) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createTypedLiteral(Object, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createTypedLiteral(Object) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createTypedLiteral(String, RDFDatatype) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createTypedLiteral(String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
createTypedLiteral(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
CSD_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary

D

DATABLOCK - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
DATABLOCK_NAME_ATT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
DataBlockHandler - Class in com.dumontierlab.pdb2rdf.parser
DataBlockHandler(PdbRdfModel, UriBuilder) - Constructor for class com.dumontierlab.pdb2rdf.parser.DataBlockHandler
DEFAULT_NAMESPACE - Static variable in class com.dumontierlab.pdb2rdf.parser.rna.vocabulary.RnaKbOwlVocabulary
DEFAULT_NAMESPACE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary
DESCRIPTION - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
DETAILS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
difference(Model) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
DISORDER_ASSEMBLY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
DISORDER_GROUP - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
DOI_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary

E

END_AUTH_ASYM_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
END_AUTH_COMP_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
END_AUTH_SEQ_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
endDocument() - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.AtomSiteCategoryHandler
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.CellCategoryHandler
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.ChemCompCategory
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.CitationCategoryHandler
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.DataBlockHandler
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.EntityCategoryHandler
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.EntityPolyCategoryHandler
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.EntitySourceGeneticallyManipulatedHandler
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.EntitySourceNaturalCategoryHandler
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.ExptlCategoryHandler
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.NmrEnsembleCategoryHandler
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.NmrRefineCategoryHandler
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.PdbXmlContentHandler
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.RefineCategoryHandler
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.rna.RnaPdbXmlContentHandler
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.rna.StructNucleicAcidBasePairCategoryHandler
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.StructCategoryHandler
endElement(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.StructConfigCategoryHandler
endPrefixMapping(String) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
enterCriticalSection(boolean) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
ENTITY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ENTITY_CATEGORY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ENTITY_ID_ATT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ENTITY_POLY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ENTITY_POLY_CATEGORY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ENTITY_SOURCE_GEN - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ENTITY_SOURCE_GEN_CATEGORY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ENTITY_SOURCE_METHOD_MAN_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ENTITY_SOURCE_METHOD_NAT_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ENTITY_SOURCE_METHOD_SYN_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ENTITY_SOURCE_NATURAL - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ENTITY_SOURCE_NATURAL_CATEGORY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ENTITY_TYPE_MACROLIDE_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ENTITY_TYPE_NON_POLYMER_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ENTITY_TYPE_POLYMER_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ENTITY_TYPE_WATER_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
EntityCategoryHandler - Class in com.dumontierlab.pdb2rdf.parser
EntityCategoryHandler(PdbRdfModel, UriBuilder, String) - Constructor for class com.dumontierlab.pdb2rdf.parser.EntityCategoryHandler
EntityPolyCategoryHandler - Class in com.dumontierlab.pdb2rdf.parser
EntityPolyCategoryHandler(PdbRdfModel, UriBuilder, String) - Constructor for class com.dumontierlab.pdb2rdf.parser.EntityPolyCategoryHandler
EntitySourceGeneticallyManipulatedHandler - Class in com.dumontierlab.pdb2rdf.parser
EntitySourceGeneticallyManipulatedHandler(PdbRdfModel, UriBuilder, String) - Constructor for class com.dumontierlab.pdb2rdf.parser.EntitySourceGeneticallyManipulatedHandler
EntitySourceNaturalCategoryHandler - Class in com.dumontierlab.pdb2rdf.parser
EntitySourceNaturalCategoryHandler(PdbRdfModel, UriBuilder, String) - Constructor for class com.dumontierlab.pdb2rdf.parser.EntitySourceNaturalCategoryHandler
equals(Object) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
error(SAXParseException) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
executeInTransaction(Command) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
expandPrefix(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
EXPERIMENTAL_FORMULA_WEIGHT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
EXPERIMENTAL_FORMULA_WEIGHT_METHOD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ExperimentalMethods - Class in com.dumontierlab.pdb2rdf.parser.vocabulary
ExperimentalMethods() - Constructor for class com.dumontierlab.pdb2rdf.parser.vocabulary.ExperimentalMethods
EXPTL - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
EXPTL_CATEGORY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ExptlCategoryHandler - Class in com.dumontierlab.pdb2rdf.parser
ExptlCategoryHandler(PdbRdfModel, UriBuilder, String) - Constructor for class com.dumontierlab.pdb2rdf.parser.ExptlCategoryHandler

F

fatalError(SAXParseException) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
FIRST_PAGE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
FOOTNOTE_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
FORMULA - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
FORMULA_WEIGHT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
FRACTION_X - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
FRACTION_X_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
FRACTION_Y - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
FRACTION_Y_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
FRACTION_Z - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
FRACTION_Z_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary

G

GENE_SOURCE_ATCC - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
GENE_SOURCE_CELL - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
GENE_SOURCE_CELL_LINE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
GENE_SOURCE_CELLULAR_LOCATION - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
GENE_SOURCE_GENE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
GENE_SOURCE_ORGAN - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
GENE_SOURCE_ORGANELLE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
GENE_SOURCE_ORGANISM_SCIENTIFIC_NAME - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
GENE_SOURCE_ORGANISM_TAXONOMY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
GENE_SOURCE_PLASMID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
GENE_SOURCE_PLASMID_NAME - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
GENE_SRC_DETAILS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
GENE_SRC_DEVELOMENT_STAGE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
GENE_SRC_TISSUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
GENE_SRC_TISSUE_FRACTION - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
get(int) - Static method in class com.dumontierlab.pdb2rdf.parser.rna.vocabulary.LeontisWesthofClassification
get(int) - Static method in class com.dumontierlab.pdb2rdf.parser.rna.vocabulary.SangerClassification
get(String) - Static method in class com.dumontierlab.pdb2rdf.parser.vocabulary.AbsortCorrectionTypes
get(String) - Static method in class com.dumontierlab.pdb2rdf.parser.vocabulary.ExperimentalMethods
get(String) - Static method in class com.dumontierlab.pdb2rdf.parser.vocabulary.PeriodicTable
get(String) - Static method in class com.dumontierlab.pdb2rdf.parser.vocabulary.SecondaryStructures
get(String) - Static method in class com.dumontierlab.pdb2rdf.parser.vocabulary.Vectors
getAbsorptCorrectionResource() - Method in class com.dumontierlab.pdb2rdf.parser.ExptlCategoryHandler
getAlt(Resource) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getAlt(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getAnyReifiedStatement(Statement) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getBag(Resource) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getBag(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getBufferContent() - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
getContentHandler(PdbRdfModel) - Method in class com.dumontierlab.pdb2rdf.parser.AbstractPdbXmlParser
getContentHandler(PdbRdfModel) - Method in class com.dumontierlab.pdb2rdf.parser.PdbXmlParser
getContentHandler(PdbRdfModel) - Method in class com.dumontierlab.pdb2rdf.parser.rna.RnaPdbXmlParser
getGraph() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getLock() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getNsPrefixMap() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getNsPrefixURI(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getNsURIPrefix(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getOntology() - Static method in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary
getPattern() - Method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.uri.RnaKbUriPattern
getPattern() - Method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.uri.Bio2RdfPdbUriPattern
getPattern() - Method in interface com.dumontierlab.pdb2rdf.parser.vocabulary.uri.UriPattern
getPdbId() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getPdbXml(String) - Method in class com.dumontierlab.pdb2rdf.util.PdbHttpClient
getProperty(Resource, Property) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getProperty(String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getProperty(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getRdfModel() - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
getRDFNode(Node) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getReader() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getReader(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getReificationStyle() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getRequiredProperty(Resource, Property) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getResource(String, ResourceF) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getResource(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getSeq(Resource) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getSeq(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getSymbol(String) - Static method in class com.dumontierlab.pdb2rdf.parser.vocabulary.PeriodicTable
getUriBuilder() - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
getWriter() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
getWriter(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
GROUP_PDB - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary

H

hash(String) - Static method in class com.dumontierlab.pdb2rdf.util.UriUtil
HBOND_TYPE_12 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
HBOND_TYPE_28 - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
HOST_CELL - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
HOST_CELL_LINE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
HOST_CELLULAR_LOCATION - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
HOST_GENE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
HOST_ORGAN - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
HOST_ORGANELLE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
HOST_ORGANISM_DETAILS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
HOST_ORGANISM_TAXONOMY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
HOST_SCIENTIFIC_NAME - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
HOST_TISSUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
HOST_TISSUE_FRACTION - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
HOST_VECTOR_TYPE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary

I

I_AUTH_ASYM_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
I_AUTH_SEQ_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ID_ATT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ignorableWhitespace(char[], int, int) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
independent() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
intersection(Model) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
isBuffering() - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
isClosed() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
isEmpty() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
isIsomorphicWith(Model) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
isNil(Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
isReified(Statement) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel

J

J_AUTH_ASYM_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
J_AUTH_SEQ_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
JOURNAL_ABBREVIATION - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
JOURNAL_CSD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
JOURNAL_FULL - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
JOURNAL_ISSN - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
JOURNAL_VOLUME - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary

L

LABEL_COMP_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LABEL_ENTITY_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LANGUAGE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LAST_PAGE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
leaveCriticalSection() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
LENGTH_A - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LENGTH_A_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LENGTH_B - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LENGTH_B_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LENGTH_C - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LENGTH_C_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LeontisWesthofClassification - Class in com.dumontierlab.pdb2rdf.parser.rna.vocabulary
LeontisWesthofClassification() - Constructor for class com.dumontierlab.pdb2rdf.parser.rna.vocabulary.LeontisWesthofClassification
listLiteralStatements(Resource, Property, boolean) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listLiteralStatements(Resource, Property, char) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listLiteralStatements(Resource, Property, double) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listLiteralStatements(Resource, Property, long) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listLiteralStatements(Resource, Property, float) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listNameSpaces() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listObjects() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listObjectsOfProperty(Property) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listObjectsOfProperty(Resource, Property) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listReifiedStatements() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listReifiedStatements(Statement) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listResourcesWithProperty(Property, boolean) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listResourcesWithProperty(Property, char) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listResourcesWithProperty(Property, double) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listResourcesWithProperty(Property, float) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listResourcesWithProperty(Property, long) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listResourcesWithProperty(Property, Object) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listResourcesWithProperty(Property, RDFNode) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listResourcesWithProperty(Property) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listStatements() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listStatements(Resource, Property, RDFNode) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listStatements(Resource, Property, String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listStatements(Resource, Property, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listStatements(Selector) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listSubjects() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listSubjectsWithProperty(Property, RDFNode) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listSubjectsWithProperty(Property, String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listSubjectsWithProperty(Property, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
listSubjectsWithProperty(Property) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
lock() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
LS_D_RES_HIGH - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LS_D_RES_LOW - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LS_NUMBER_PARAMETERS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LS_NUMBER_REFLNS_ALL - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LS_NUMBER_REFLNS_OBS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LS_NUMBER_REFLNS_R_FREE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LS_NUMBER_RESTRAINTS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LS_PERCENT_REFLNS_OBS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LS_PERCENT_REFLNS_R_FREE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LS_R_FACTOR_ALL - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LS_R_FACTOR_OBS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LS_R_FACTOR_R_FREE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LS_R_FACTOR_R_FREE_ERROR - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LS_R_FACTOR_R_FREE_ERROR_DETAILS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LS_R_FACTOR_R_WORK - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LS_REDUNDANCY_REFLNS_OBS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LS_WR_FACTOR_R_FREE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
LS_WR_FACTOR_R_WORK - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary

M

main(String[]) - Static method in class com.dumontierlab.pdb2rdf.parser.PdbOwlOntologyGenerator
main(String[]) - Static method in class com.dumontierlab.pdb2rdf.parser.PdbXmlParser
main(String[]) - Static method in class com.dumontierlab.pdb2rdf.parser.rna.RnaPdbXmlParser
main(String[]) - Static method in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary
MEDLINE_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
METHOD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
METHOD_ATT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
MODEL_NUMBER - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
MODEL_NUMBER_ATT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
MODIFICATION - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
MUTATION - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary

N

NAME - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
NAME_ATT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
NCBI_TAXONOMY_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
NDB_STRUCT_NUCLIC_ACID_BASE_PAIR - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
NDB_STRUCT_NUCLIC_ACID_BASE_PAIR_CATEGORY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
NIL_ATT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
NmrEnsembleCategoryHandler - Class in com.dumontierlab.pdb2rdf.parser
NmrEnsembleCategoryHandler(PdbRdfModel, UriBuilder, String) - Constructor for class com.dumontierlab.pdb2rdf.parser.NmrEnsembleCategoryHandler
NmrRefineCategoryHandler - Class in com.dumontierlab.pdb2rdf.parser
NmrRefineCategoryHandler(PdbRdfModel, UriBuilder, String) - Constructor for class com.dumontierlab.pdb2rdf.parser.NmrRefineCategoryHandler
notationDecl(String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
notifyEvent(Object) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
NUMBER_OF_ATOMS_ALL - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
NUMBER_OF_MONOMERS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
NUMBER_OF_NON_HYDROGEN_ATOMS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary

O

OCCUPANCY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
OCCUPANCY_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
OCCUPANCY_MAX - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
OCCUPANCY_MIN - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ONE_LETTER_SEQUENCE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ONE_LETTER_SEQUENCE_CANONICAL - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
OPENING - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ORDINAL_ATT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ORGAN - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ORGANELLE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
ORGANISM_SCIENTIFIC_NAME - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
OVERALL_FOM_FREE_R_SET - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
OVERALL_FOM_WORK_R_SET - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
OVERALL_SU_B - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
OVERALL_SU_ML - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
OVERALL_SU_R_CRUICKSHANK_DPI - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
OVERALL_SU_R_FREE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary

P

parse(String) - Method in class com.dumontierlab.pdb2rdf.parser.AbstractPdbXmlParser
parse(String, PdbRdfModel) - Method in class com.dumontierlab.pdb2rdf.parser.AbstractPdbXmlParser
parse(InputSource) - Method in class com.dumontierlab.pdb2rdf.parser.AbstractPdbXmlParser
parse(InputSource, PdbRdfModel) - Method in class com.dumontierlab.pdb2rdf.parser.AbstractPdbXmlParser
PDB_GROUP_ATOM_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PdbHttpClient - Class in com.dumontierlab.pdb2rdf.util
PdbHttpClient() - Constructor for class com.dumontierlab.pdb2rdf.util.PdbHttpClient
PdbOwlOntologyGenerator - Class in com.dumontierlab.pdb2rdf.parser
PdbOwlOntologyGenerator() - Constructor for class com.dumontierlab.pdb2rdf.parser.PdbOwlOntologyGenerator
PdbOwlVocabulary - Class in com.dumontierlab.pdb2rdf.parser.vocabulary
PdbOwlVocabulary() - Constructor for class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary
PdbOwlVocabulary.Annotation - Enum in com.dumontierlab.pdb2rdf.parser.vocabulary
PdbOwlVocabulary.Class - Enum in com.dumontierlab.pdb2rdf.parser.vocabulary
PdbOwlVocabulary.DataProperty - Enum in com.dumontierlab.pdb2rdf.parser.vocabulary
PdbOwlVocabulary.Indivudual - Enum in com.dumontierlab.pdb2rdf.parser.vocabulary
PdbOwlVocabulary.ObjectProperty - Enum in com.dumontierlab.pdb2rdf.parser.vocabulary
PdbRdfModel - Class in com.dumontierlab.pdb2rdf.model
PdbRdfModel() - Constructor for class com.dumontierlab.pdb2rdf.model.PdbRdfModel
PdbRdfModel(Model) - Constructor for class com.dumontierlab.pdb2rdf.model.PdbRdfModel
PDBX_DATA_CUTOFF_HIGH_ABSF - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_DATA_CUTOFF_HIGH_RMS_ABSF - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_DATA_CUTOFF_LOW_ABSF - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_FORMAL_CHARGE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_ISOTROPIC_THERMAL_MODEL - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_LS_CROSS_VALID_METHOD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_LS_SIGMA_F - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_LS_SIGMA_I - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_METHOD_TO_DETERMINE_STRUCT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_NCS_DOM_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_NMR_ENSEMBLE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_NMR_ENSEMBLECATEGORY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_NMR_REFINE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_NMR_REFINECATEGORY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_OVERALL_ESU_R - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_OVERALL_ESU_R_FREE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_OVERALL_PHASE_ERROR - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_PDB_HELIX_LENGTH - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_PLASMID_DETAILS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_PLASMID_NAME - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_R_FREE_SELECTION_DETAILS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_SOLVENT_ION_PROBE_RADII - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_SOLVENT_SHRINKAGE_RADII - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_SOLVENT_VDW_PROBE_RADII - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_STARTING_MODEL - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_STEREOCHEM_TARGET_VAL_SPEC_CASE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_STEREOCHEMISTRY_TARGET_VALUES - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PDBX_TLS_GROUP_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PdbXmlContentHandler - Class in com.dumontierlab.pdb2rdf.parser
PdbXmlContentHandler(PdbRdfModel) - Constructor for class com.dumontierlab.pdb2rdf.parser.PdbXmlContentHandler
PdbXmlParser - Class in com.dumontierlab.pdb2rdf.parser
PdbXmlParser() - Constructor for class com.dumontierlab.pdb2rdf.parser.PdbXmlParser
PdbXmlVocabulary - Class in com.dumontierlab.pdb2rdf.parser.vocabulary
PdbXmlVocabulary() - Constructor for class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PeriodicTable - Class in com.dumontierlab.pdb2rdf.parser.vocabulary: A one to one mapping between symbols from the periodic table and atom classes.
PeriodicTable() - Constructor for class com.dumontierlab.pdb2rdf.parser.vocabulary.PeriodicTable
PLASMID_DETAILS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
PLASMID_NAME - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
POLYMER_TYPE_CYCLIC_PSEUDO_PEPTIDE_L_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
POLYMER_TYPE_HYBRID_L_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
POLYMER_TYPE_POLYDEOXYRIBONUCLEOTIDE_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
POLYMER_TYPE_POLYPEPTIDE_D_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
POLYMER_TYPE_POLYPEPTIDE_L_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
POLYMER_TYPE_POLYRIBONUCLEOTIDE_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
POLYMER_TYPE_POLYSACCHARIDE_D_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
POLYMER_TYPE_POLYSACCHARIDE_L_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
processingInstruction(String, String) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
PROPELLER - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
property() - Method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.RnaKbOwlVocabulary.DataProperty
property() - Method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.RnaKbOwlVocabulary.ObjectProperty
property() - Method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.Annotation
property() - Method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.DataProperty
property() - Method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.ObjectProperty
PUBMED_ID - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary

Q

qnameFor(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
query(Selector) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
queryHandler() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel

R

read(InputStream, String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
read(InputStream, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
read(Reader, String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
read(Reader, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
read(String, String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
read(String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
read(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
RECIPROCAL_ANGLE_ALPHA - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
RECIPROCAL_ANGLE_ALPHA_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
RECIPROCAL_ANGLE_BETA - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
RECIPROCAL_ANGLE_BETA_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
RECIPROCAL_ANGLE_GAMMA - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
RECIPROCAL_ANGLE_GAMMA_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
RECIPROCAL_LENGTH_A - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
RECIPROCAL_LENGTH_A_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
RECIPROCAL_LENGTH_B - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
RECIPROCAL_LENGTH_B_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
RECIPROCAL_LENGTH_C - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
RECIPROCAL_LENGTH_C_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
REFINE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
REFINE_CATEGORY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
RefineCategoryHandler - Class in com.dumontierlab.pdb2rdf.parser
RefineCategoryHandler(PdbRdfModel, UriBuilder, String) - Constructor for class com.dumontierlab.pdb2rdf.parser.RefineCategoryHandler
register(ModelChangedListener) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
remove(List<Statement>) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
remove(Model, boolean) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
remove(Model) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
remove(Resource, Property, RDFNode) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
remove(Statement) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
remove(Statement[]) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
remove(StmtIterator) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
removeAll() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
removeAll(Resource, Property, RDFNode) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
removeAllReifications(Statement) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
removeNsPrefix(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
removeReification(ReifiedStatement) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
removeSpaces(String) - Static method in class com.dumontierlab.pdb2rdf.util.UriUtil
replacePrimes(String) - Static method in class com.dumontierlab.pdb2rdf.util.UriUtil
replaceSpacesByUnderscore(String) - Static method in class com.dumontierlab.pdb2rdf.util.UriUtil
resolveEntity(String, String) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
resource() - Method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.RnaKbOwlVocabulary.Class
resource() - Method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.Class
RESTRAINTS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
RnaKbOwlVocabulary - Class in com.dumontierlab.pdb2rdf.parser.rna.vocabulary
RnaKbOwlVocabulary() - Constructor for class com.dumontierlab.pdb2rdf.parser.rna.vocabulary.RnaKbOwlVocabulary
RnaKbOwlVocabulary.Class - Enum in com.dumontierlab.pdb2rdf.parser.rna.vocabulary
RnaKbOwlVocabulary.DataProperty - Enum in com.dumontierlab.pdb2rdf.parser.rna.vocabulary
RnaKbOwlVocabulary.ObjectProperty - Enum in com.dumontierlab.pdb2rdf.parser.rna.vocabulary
RnaKbUriPattern - Enum in com.dumontierlab.pdb2rdf.parser.rna.vocabulary.uri
RnaPdbXmlContentHandler - Class in com.dumontierlab.pdb2rdf.parser.rna
RnaPdbXmlContentHandler(PdbRdfModel) - Constructor for class com.dumontierlab.pdb2rdf.parser.rna.RnaPdbXmlContentHandler
RnaPdbXmlParser - Class in com.dumontierlab.pdb2rdf.parser.rna
RnaPdbXmlParser() - Constructor for class com.dumontierlab.pdb2rdf.parser.rna.RnaPdbXmlParser

S

samePrefixMappingAs(PrefixMapping) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
SangerClassification - Class in com.dumontierlab.pdb2rdf.parser.rna.vocabulary
SangerClassification() - Constructor for class com.dumontierlab.pdb2rdf.parser.rna.vocabulary.SangerClassification
SecondaryStructures - Class in com.dumontierlab.pdb2rdf.parser.vocabulary
SecondaryStructures() - Constructor for class com.dumontierlab.pdb2rdf.parser.vocabulary.SecondaryStructures
SECRETION - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
setDocumentLocator(Locator) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
setModel(Model) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
setNsPrefix(String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
setNsPrefixes(Map<String, String>) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
setNsPrefixes(PrefixMapping) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
setPdbId(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
setReaderClassName(String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
setState(ContentHandlerState) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
setWriterClassName(String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
SHEAR - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
shortForm(String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
size() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
skippedEntity(String) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
SOLVENT_MODEL_DETAILS - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
SOLVENT_MODEL_PARAM_BSOL - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
SOLVENT_MODEL_PARAM_KSOL - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
SOURCE_METHOD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
SpaceGroupCategoryHandler - Class in com.dumontierlab.pdb2rdf.parser
SpaceGroupCategoryHandler() - Constructor for class com.dumontierlab.pdb2rdf.parser.SpaceGroupCategoryHandler
STAGGER - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
startBuffering() - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
startDocument() - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.AtomSiteCategoryHandler
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.CellCategoryHandler
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.ChemCompCategory
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.CitationAuthorCategoryHandler
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.CitationCategoryHandler
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.DataBlockHandler
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.EntityCategoryHandler
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.EntityPolyCategoryHandler
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.EntitySourceGeneticallyManipulatedHandler
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.EntitySourceNaturalCategoryHandler
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.ExptlCategoryHandler
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.NmrEnsembleCategoryHandler
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.NmrRefineCategoryHandler
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.PdbXmlContentHandler
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.RefineCategoryHandler
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.rna.RnaPdbXmlContentHandler
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.rna.StructNucleicAcidBasePairCategoryHandler
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.StructCategoryHandler
startElement(String, String, String, Attributes) - Method in class com.dumontierlab.pdb2rdf.parser.StructConfigCategoryHandler
startPrefixMapping(String, String) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
stopBuffering() - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
STRETCH - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
STRUCT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
STRUCT_CATEGORY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
STRUCT_CONF - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
STRUCT_CONFIG_CATEGORY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
StructCategoryHandler - Class in com.dumontierlab.pdb2rdf.parser
StructCategoryHandler(PdbRdfModel, UriBuilder, String) - Constructor for class com.dumontierlab.pdb2rdf.parser.StructCategoryHandler
StructConfigCategoryHandler - Class in com.dumontierlab.pdb2rdf.parser
StructConfigCategoryHandler(PdbRdfModel, UriBuilder, String) - Constructor for class com.dumontierlab.pdb2rdf.parser.StructConfigCategoryHandler
StructNucleicAcidBasePairCategoryHandler - Class in com.dumontierlab.pdb2rdf.parser.rna
StructNucleicAcidBasePairCategoryHandler(PdbRdfModel, UriBuilder, String) - Constructor for class com.dumontierlab.pdb2rdf.parser.rna.StructNucleicAcidBasePairCategoryHandler
supportsSetOperations() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
supportsTransactions() - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
SYMMETRY_MULTIPLICITY - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary

T

TARGET_IDENTIFIER - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
TISSUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
TISSUE_FRACTION - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
TITLE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
toCamelCase(String) - Static method in class com.dumontierlab.pdb2rdf.util.UriUtil
toString() - Method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.RnaKbOwlVocabulary.Class
toString() - Method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.RnaKbOwlVocabulary.DataProperty
toString() - Method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.RnaKbOwlVocabulary.ObjectProperty
toString() - Method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.Annotation
toString() - Method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.Class
toString() - Method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.DataProperty
toString() - Method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.ObjectProperty
TYPE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
TYPE_SYMBOL - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary

U

U_EQUIVALENT_GEOMETRIC_MEAN - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
U_EQUIVALENT_GEOMETRIC_MEAN_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
U_ISO_OR_EQUIVALENT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
U_ISO_OR_EQUIVALENT_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
union(Model) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
UNITS_ATT - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
unparsedEntityDecl(String, String, String, String) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
unregister(ModelChangedListener) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
uri() - Method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.RnaKbOwlVocabulary.Class
uri() - Method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.RnaKbOwlVocabulary.DataProperty
uri() - Method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.RnaKbOwlVocabulary.ObjectProperty
uri() - Method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.Annotation
uri() - Method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.Class
uri() - Method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.DataProperty
uri() - Method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.ObjectProperty
UriBuilder - Class in com.dumontierlab.pdb2rdf.parser.vocabulary.uri
UriBuilder() - Constructor for class com.dumontierlab.pdb2rdf.parser.vocabulary.uri.UriBuilder
UriPattern - Interface in com.dumontierlab.pdb2rdf.parser.vocabulary.uri
UriUtil - Class in com.dumontierlab.pdb2rdf.util
UriUtil() - Constructor for class com.dumontierlab.pdb2rdf.util.UriUtil
urlEncode(String) - Static method in class com.dumontierlab.pdb2rdf.util.UriUtil

V

valueOf(String) - Static method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.RnaKbOwlVocabulary.Class: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.RnaKbOwlVocabulary.DataProperty: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.RnaKbOwlVocabulary.ObjectProperty: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.uri.RnaKbUriPattern: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.Annotation: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.Class: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.DataProperty: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.Indivudual: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.ObjectProperty: Returns the enum constant of this type with the specified name.
valueOf(String) - Static method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.uri.Bio2RdfPdbUriPattern: Returns the enum constant of this type with the specified name.
values() - Static method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.RnaKbOwlVocabulary.Class: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.RnaKbOwlVocabulary.DataProperty: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.RnaKbOwlVocabulary.ObjectProperty: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.dumontierlab.pdb2rdf.parser.rna.vocabulary.uri.RnaKbUriPattern: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.Annotation: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.Class: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.DataProperty: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.Indivudual: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.PdbOwlVocabulary.ObjectProperty: Returns an array containing the constants of this enum type, in the order they are declared.
values() - Static method in enum com.dumontierlab.pdb2rdf.parser.vocabulary.uri.Bio2RdfPdbUriPattern: Returns an array containing the constants of this enum type, in the order they are declared.
VECTOR_TYPE_BACTERIAL_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
VECTOR_TYPE_BACTERIUM_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
VECTOR_TYPE_BACULOVIRUS_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
VECTOR_TYPE_COSMID_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
VECTOR_TYPE_MACROPHAGE_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
VECTOR_TYPE_PLASMID_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
VECTOR_TYPE_VIRUS_VALUE - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
Vectors - Class in com.dumontierlab.pdb2rdf.parser.vocabulary
Vectors() - Constructor for class com.dumontierlab.pdb2rdf.parser.vocabulary.Vectors
VOLUME - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary
VOLUME_ESD - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary

W

warning(SAXParseException) - Method in class com.dumontierlab.pdb2rdf.parser.ContentHandlerState
withDefaultMappings(PrefixMapping) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
write(OutputStream, String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
write(OutputStream, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
write(OutputStream) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
write(Writer, String, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
write(Writer, String) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
write(Writer) - Method in class com.dumontierlab.pdb2rdf.model.PdbRdfModel
WYCKOFF_SYMBOL - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary

Y

YEAR - Static variable in class com.dumontierlab.pdb2rdf.parser.vocabulary.PdbXmlVocabulary

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