| addInnerToOuterAPMapping(AttachmentPoint newInnerAP) | denoptim.graph.Template | |
| addRequiredAP(Point3d pt, APClass apClass) | denoptim.graph.Template | |
| addSymmetricAPSet(SymmetricAPs symAPs) | denoptim.graph.Template | protected |
| allowedMutationTypes | denoptim.graph.Vertex | private |
| buildingBlockId | denoptim.graph.Vertex | protected |
| buildingBlockType | denoptim.graph.Vertex | protected |
| cleanup() | denoptim.graph.Vertex | |
| clearIAtomContainer() | denoptim.graph.Template | |
| clone() | denoptim.graph.Template | |
| connectedTo(Vertex other) | denoptim.graph.Vertex | |
| containsAtoms() | denoptim.graph.Template | |
| contractLevel | denoptim.graph.Template | private |
| convertIACToVertex(IAtomContainer iac, Vertex.BBType bbt) | denoptim.graph.Vertex | static |
| copyStringBasedProperties() | denoptim.graph.Vertex | protected |
| freezeTemplate() | denoptim.graph.Template | |
| fromJson(String json) | denoptim.graph.Template | static |
| getAllAPClasses() | denoptim.graph.Vertex | |
| getAllAvailableAPClasses() | denoptim.graph.Vertex | |
| getAP(int i) | denoptim.graph.Vertex | |
| getAPsFromChildren() | denoptim.graph.Vertex | |
| getAPWithId(int i) | denoptim.graph.Vertex | |
| getAttachmentPoints() | denoptim.graph.Template | |
| getBuildingBlockId() | denoptim.graph.Vertex | |
| getBuildingBlockType() | denoptim.graph.Vertex | |
| getCappedAPCountThroughout() | denoptim.graph.Vertex | |
| getCappedAPs() | denoptim.graph.Vertex | |
| getCappedAPsThroughout() | denoptim.graph.Vertex | |
| getChilddren() | denoptim.graph.Vertex | |
| getChildrenThroughout() | denoptim.graph.Vertex | |
| getContractLevel() | denoptim.graph.Template | |
| getEdgeToParent() | denoptim.graph.Vertex | |
| getEdgeWith(Vertex other) | denoptim.graph.Vertex | |
| getFreeAPCount() | denoptim.graph.Vertex | |
| getFreeAPCountThroughout() | denoptim.graph.Vertex | |
| getFreeAPThroughout() | denoptim.graph.Vertex | |
| getGraphOwner() | denoptim.graph.Vertex | |
| getHeavyAtomsCount() | denoptim.graph.Template | |
| getIAtomContainer() | denoptim.graph.Template | |
| getIAtomContainer(Logger logger, Randomizer rng, boolean removeUsedRCAs, boolean rebuild) | denoptim.graph.Template | |
| getIndexOfAP(AttachmentPoint ap) | denoptim.graph.Vertex | |
| getInnerAPFromOuterAP(AttachmentPoint outerAP) | denoptim.graph.Template | |
| getInnerGraph() | denoptim.graph.Template | |
| getMutationSites(List< MutationType > ignoredTypes) | denoptim.graph.Template | |
| denoptim::graph::Vertex.getMutationSites() | denoptim.graph.Vertex | |
| getMutationTypes(List< MutationType > ignoredTypes) | denoptim.graph.Template | |
| denoptim::graph::Vertex.getMutationTypes() | denoptim.graph.Vertex | |
| getNumberOfAPs() | denoptim.graph.Vertex | |
| getOuterAPFromInnerAP(AttachmentPoint innerAP) | denoptim.graph.Template | |
| getParent() | denoptim.graph.Vertex | |
| getPathIDs(AttachmentPoint apA, AttachmentPoint apB) | denoptim.graph.Template | |
| getProperties() | denoptim.graph.Vertex | |
| getProperty(Object property) | denoptim.graph.Vertex | |
| getRequiredAPs() | denoptim.graph.Template | private |
| getSymmetricAPs(AttachmentPoint ap) | denoptim.graph.Vertex | |
| getSymmetricAPSets() | denoptim.graph.Template | |
| getTestTemplate(ContractLevel contractLevel) | denoptim.graph.Template | static |
| getUnfilteredMutationTypes() | denoptim.graph.Vertex | protected |
| getUniqueAPIndex() | denoptim.graph.Vertex | protected |
| getVertexId() | denoptim.graph.Vertex | |
| getVertexType() | denoptim.graph.Vertex | |
| hasFreeAP() | denoptim.graph.Vertex | |
| hasProperty(Object property) | denoptim.graph.Vertex | |
| hasSymmetricAP() | denoptim.graph.Vertex | |
| innerGraph | denoptim.graph.Template | private |
| innerToOuterAPs | denoptim.graph.Template | private |
| isRCV | denoptim.graph.Vertex | private |
| isRCV() | denoptim.graph.Vertex | |
| isValidInnerGraph(DGraph g) | denoptim.graph.Template | private |
| mol | denoptim.graph.Template | private |
| newVertexFromLibrary(int bbId, Vertex.BBType bbt, FragmentSpace fragSpace) | denoptim.graph.Vertex | static |
| newVertexFromLibrary(long vertexId, int bbId, Vertex.BBType bbt, FragmentSpace fragSpace) | denoptim.graph.Vertex | static |
| owner | denoptim.graph.Vertex | private |
| parseVertexFromSDFFormat(IAtomContainer mol, Gson reader, BBType bbt) | denoptim.graph.Vertex | static |
| properties | denoptim.graph.Vertex | protected |
| removeMutationType(MutationType mt) | denoptim.graph.Vertex | |
| removeProjectionOfInnerAP(AttachmentPoint oldInnerAP) | denoptim.graph.Template | |
| removeProperty(Object key) | denoptim.graph.Vertex | |
| requiredAPs | denoptim.graph.Template | private |
| resetGraphOwner() | denoptim.graph.Vertex | |
| sameAs(Template other, StringBuilder reason) | denoptim.graph.Template | |
| denoptim::graph::Vertex.sameAs(Vertex other) | denoptim.graph.Vertex | |
| denoptim::graph::Vertex.sameAs(Vertex other, StringBuilder reason) | denoptim.graph.Vertex | |
| sameVertexFeatures(Vertex other, StringBuilder reason) | denoptim.graph.Vertex | |
| setAsRCV(boolean isRCV) | denoptim.graph.Vertex | |
| setBuildingBlockId(int buildingBlockId) | denoptim.graph.Vertex | |
| setBuildingBlockType(Vertex.BBType buildingBlockType) | denoptim.graph.Vertex | |
| setContractLevel(ContractLevel contract) | denoptim.graph.Template | |
| setGraphOwner(DGraph owner) | denoptim.graph.Vertex | |
| setIAtomContainer(IAtomContainer mol, boolean updateAPsAccordingToIAC) | denoptim.graph.Template | |
| setInnerGraph(DGraph innerGraph) | denoptim.graph.Template | |
| setMutationTypes(List< MutationType > lst) | denoptim.graph.Vertex | |
| setProperties(Map< Object, Object > properties) | denoptim.graph.Vertex | |
| setProperty(Object key, Object property) | denoptim.graph.Vertex | |
| setSymmetricAPSets(List< SymmetricAPs > sAPs) | denoptim.graph.Template | protected |
| setUniquefyingProperty(String key) | denoptim.graph.Vertex | |
| setVertexId(long vertexId2) | denoptim.graph.Vertex | |
| Template(Vertex.BBType bbType) | denoptim.graph.Template | |
| toJson() | denoptim.graph.Template | |
| toString() | denoptim.graph.Vertex | |
| uniquefyingPropertyKeys | denoptim.graph.Vertex | protected |
| updateInnerApID(AttachmentPoint oldInnerAP, AttachmentPoint newInnerAP) | denoptim.graph.Template | |
| updateInnerToOuter(TreeMap< Integer, AttachmentPoint > map) | denoptim.graph.Template | private |
| updateMutTypeToFixedSTructure() | denoptim.graph.Template | private |
| Vertex(VertexType vertexType) | denoptim.graph.Vertex | |
| Vertex(VertexType vertexType, long id) | denoptim.graph.Vertex | |
| vertexId | denoptim.graph.Vertex | private |
| vertexType | denoptim.graph.Vertex | protected |
1.9.4