| addAP(int atomPositionNumber) | denoptim.graph.Fragment | |
| addAP(int atomPositionNumber, APClass apClass) | denoptim.graph.Fragment | |
| addAP(int atomPositionNumber, Point3d dirVec, APClass apClass) | denoptim.graph.Fragment | |
| addAP(int srcAtmId, APClass apc, Point3d vector) | denoptim.graph.Fragment | |
| addAPOnAtom(IAtom srcAtm, APClass apc, Point3d vector) | denoptim.graph.Fragment | |
| addAtom(IAtom atom) | denoptim.graph.Fragment | |
| addBond(IBond bond) | denoptim.graph.Fragment | |
| addSymmetricAPSet(SymmetricAPs symAPs) | denoptim.graph.Fragment | protected |
| allowedMutationTypes | denoptim.graph.Vertex | private |
| atoms() | denoptim.graph.Fragment | |
| atomsAreCompatible(IAtomContainer mol, int a1, int a2) | denoptim.graph.Fragment | privatestatic |
| bonds() | denoptim.graph.Fragment | |
| buildingBlockId | denoptim.graph.Vertex | protected |
| buildingBlockType | denoptim.graph.Vertex | protected |
| cleanup() | denoptim.graph.Vertex | |
| clone() | denoptim.graph.Fragment | |
| connectedTo(Vertex other) | denoptim.graph.Vertex | |
| containsAtoms() | denoptim.graph.Fragment | |
| convertIACToVertex(IAtomContainer iac, Vertex.BBType bbt) | denoptim.graph.Vertex | static |
| copyStringBasedProperties() | denoptim.graph.Vertex | protected |
| Fragment() | denoptim.graph.Fragment | |
| Fragment(long vertexId) | denoptim.graph.Fragment | |
| Fragment(long l, IAtomContainer mol, BBType bbt) | denoptim.graph.Fragment | |
| Fragment(long vertexId, IAtomContainer mol, BBType bbt, boolean isRCV) | denoptim.graph.Fragment | |
| Fragment(IAtomContainer mol, BBType bbt) | denoptim.graph.Fragment | |
| fromJson(String json) | denoptim.graph.Fragment | static |
| getAllAPClasses() | denoptim.graph.Vertex | |
| getAllAvailableAPClasses() | denoptim.graph.Vertex | |
| getAP(int i) | denoptim.graph.Vertex | |
| getAPCountOnAtom(int srcAtmId) | denoptim.graph.Fragment | |
| getAPCountOnAtom(IAtom srcAtm) | denoptim.graph.Fragment | |
| getAPsFromAtom(IAtom srcAtm) | denoptim.graph.Fragment | |
| getAPsFromChildren() | denoptim.graph.Vertex | |
| getAPWithId(int i) | denoptim.graph.Vertex | |
| getAtom(int number) | denoptim.graph.Fragment | |
| getAtomCount() | denoptim.graph.Fragment | |
| getAtomHoldingAP(AttachmentPoint ap) | denoptim.graph.Fragment | |
| getAttachmentPoints() | denoptim.graph.Fragment | |
| getBondCount() | denoptim.graph.Fragment | |
| 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 | |
| getConnectedAtomsCount(IAtom atom) | denoptim.graph.Fragment | |
| getConnectedAtomsList(IAtom atom) | denoptim.graph.Fragment | |
| getCurrentAPs() | denoptim.graph.Fragment | |
| 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.Fragment | |
| getIAtomContainer() | denoptim.graph.Fragment | |
| getIAtomContainer(Logger logger, Randomizer rng, boolean removeUsedRCAs, boolean rebuild) | denoptim.graph.Fragment | |
| getIndexOfAP(AttachmentPoint ap) | denoptim.graph.Vertex | |
| getJGraphFragIsomorphism() | denoptim.graph.Fragment | |
| getMutationSites(List< MutationType > ignoredTypes) | denoptim.graph.Fragment | |
| denoptim::graph::Vertex.getMutationSites() | denoptim.graph.Vertex | |
| getMutationTypes() | denoptim.graph.Vertex | |
| getMutationTypes(List< MutationType > excludedTypes) | denoptim.graph.Vertex | |
| getNumberOfAPs() | denoptim.graph.Vertex | |
| getParent() | denoptim.graph.Vertex | |
| getPathIDs(AttachmentPoint apA, AttachmentPoint apB) | denoptim.graph.Vertex | |
| getProperties() | denoptim.graph.Vertex | |
| getProperty(Object property) | denoptim.graph.Vertex | |
| getSymmetricAPs(AttachmentPoint ap) | denoptim.graph.Vertex | |
| getSymmetricAPSets() | denoptim.graph.Fragment | |
| 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 | |
| identifySymmetryRelatedAPSets(IAtomContainer mol, List< AttachmentPoint > daps) | denoptim.graph.Fragment | privatestatic |
| indexOf(IAtom atom) | denoptim.graph.Fragment | |
| is3D() | denoptim.graph.Fragment | |
| isIsomorphicTo(Vertex other) | denoptim.graph.Fragment | |
| isRCV | denoptim.graph.Vertex | private |
| isRCV() | denoptim.graph.Vertex | |
| jGraphFragIsomorphism | denoptim.graph.Fragment | private |
| lstAPs | denoptim.graph.Fragment | private |
| lstSymAPs | denoptim.graph.Fragment | private |
| mol | denoptim.graph.Fragment | 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 |
| projectAPsToProperties() | denoptim.graph.Fragment | |
| projectListAPToAtomProperties() | denoptim.graph.Fragment | |
| projectPropertyToAP() | denoptim.graph.Fragment | |
| projectPropertyToAP(String allAtomsProp) | denoptim.graph.Fragment | |
| properties | denoptim.graph.Vertex | protected |
| removeAP(AttachmentPoint ap) | denoptim.graph.Fragment | |
| removeAtom(IAtom atom) | denoptim.graph.Fragment | |
| removeAtoms(Collection< IAtom > atoms) | denoptim.graph.Fragment | |
| removeBond(int position) | denoptim.graph.Fragment | |
| removeBond(IAtom atom1, IAtom atom2) | denoptim.graph.Fragment | |
| removeBond(IBond bond) | denoptim.graph.Fragment | |
| removeMutationType(MutationType mt) | denoptim.graph.Vertex | |
| removeProperty(Object key) | denoptim.graph.Vertex | |
| resetGraphOwner() | denoptim.graph.Vertex | |
| sameAs(Fragment other, StringBuilder reason) | denoptim.graph.Fragment | |
| 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 | |
| setGraphOwner(DGraph owner) | denoptim.graph.Vertex | |
| 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.Fragment | protected |
| setUniquefyingProperty(String key) | denoptim.graph.Vertex | |
| setVertexId(long vertexId2) | denoptim.graph.Vertex | |
| toJson() | denoptim.graph.Fragment | |
| toString() | denoptim.graph.Fragment | |
| uniquefyingPropertyKeys | denoptim.graph.Vertex | protected |
| updateAPs() | denoptim.graph.Fragment | |
| updateSymmetryRelations() | denoptim.graph.Fragment | 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