| addCappingGroups(FragmentSpace fragSpace) | denoptim.graph.DGraph | |
| addCappingGroups(List< Vertex > vertexAddedToThis, FragmentSpace fragSpace) | denoptim.graph.DGraph | |
| addEdge(Edge edge) | denoptim.graph.DGraph | |
| addRing(Ring ring) | denoptim.graph.DGraph | |
| addRing(Vertex vI, Vertex vJ) | denoptim.graph.DGraph | |
| addRing(Vertex vI, Vertex vJ, BondType bndTyp) | denoptim.graph.DGraph | |
| addSymmetricSetOfVertices(SymmetricVertexes symSet) | denoptim.graph.DGraph | |
| addVertex(Vertex vertex) | denoptim.graph.DGraph | |
| apCounter | denoptim.graph.DGraph | private |
| appendGraphOnAP(AttachmentPoint apOnThisGraph, AttachmentPoint apOnIncomingGraph, BondType bndType) | denoptim.graph.DGraph | |
| appendGraphOnAP(Vertex parentVertex, int parentAPIdx, DGraph subGraph, Vertex childVertex, int childAPIdx, BondType bndType, Map< Vertex, SymmetricVertexes > newSymSets) | denoptim.graph.DGraph | |
| appendGraphOnGraph(List< Vertex > parentVertices, List< Integer > parentAPIdx, DGraph subGraph, Vertex childVertex, int childAPIdx, BondType bndType, boolean onAllSymmAPs) | denoptim.graph.DGraph | |
| appendGraphOnGraph(Vertex parentVertex, int parentAPIdx, DGraph subGraph, Vertex childVertex, int childAPIdx, BondType bndType, Map< Vertex, SymmetricVertexes > newSymSets, boolean onAllSymmAPs) | denoptim.graph.DGraph | |
| appendVertexOnAP(AttachmentPoint srcAP, AttachmentPoint trgAP) | denoptim.graph.DGraph | |
| candidate | denoptim.graph.DGraph | package |
| changeSignOfVertexID() | denoptim.graph.DGraph | |
| checkConsistency(RunTimeParameters settings) | denoptim.graph.DGraph | |
| checkConsistency(RunTimeParameters settings, boolean permissive) | denoptim.graph.DGraph | |
| cleanup() | denoptim.graph.DGraph | |
| clone() | denoptim.graph.DGraph | |
| closableChains | denoptim.graph.DGraph | package |
| compareGraphNodes(Vertex thisV, DGraph thisG, Vertex otherV, DGraph otherG) | denoptim.graph.DGraph | static |
| compareGraphNodes(Vertex seedOnA, DGraph gA, Vertex seedOnB, DGraph gB, Map< Vertex, Vertex > vertexMap, StringBuilder reason) | denoptim.graph.DGraph | privatestatic |
| containsAtoms() | denoptim.graph.DGraph | |
| containsOrEmbedsVertex(Vertex v) | denoptim.graph.DGraph | |
| containsVertex(Vertex v) | denoptim.graph.DGraph | |
| containsVertexID(long l) | denoptim.graph.DGraph | |
| convertSymmetricLabelsToSymmetricSets() | denoptim.graph.DGraph | protected |
| detectSymVertexSets() | denoptim.graph.DGraph | |
| dfsEncodePaths(Vertex current, String currentPath, Set< Vertex > visited, Map< String, List< Vertex > > pathMap) | denoptim.graph.DGraph | private |
| DGraph(List< Vertex > gVertices, List< Edge > gEdges) | denoptim.graph.DGraph | |
| DGraph(List< Vertex > gVertices, List< Edge > gEdges, List< Ring > gRings) | denoptim.graph.DGraph | |
| DGraph(List< Vertex > gVertices, List< Edge > gEdges, List< Ring > gRings, List< SymmetricVertexes > symSets) | denoptim.graph.DGraph | |
| DGraph(List< Vertex > gVertices, List< Edge > gEdges, List< Ring > gRings, List< ClosableChain > closableChains, List< SymmetricVertexes > symVertices) | denoptim.graph.DGraph | |
| DGraph() | denoptim.graph.DGraph | |
| directedPathExists(Vertex src, Vertex trg) | denoptim.graph.DGraph | |
| editGraph(ArrayList< GraphEdit > edits, boolean symmetry, FragmentSpace fragSpace, Logger logger) | denoptim.graph.DGraph | |
| embedPatternsInTemplates(GraphPattern pattern, FragmentSpace fragSpace) | denoptim.graph.DGraph | |
| embedPatternsInTemplates(GraphPattern pattern, FragmentSpace fragSpace, ContractLevel contract) | denoptim.graph.DGraph | |
| ensureUniqueApIDs() | denoptim.graph.DGraph | protected |
| extractPattern(GraphPattern pattern) | denoptim.graph.DGraph | |
| extractPattern(GraphPattern pattern, boolean recordConnectivity) | denoptim.graph.DGraph | |
| extractSubgraph(int index) | denoptim.graph.DGraph | |
| extractSubgraph(Vertex seed) | denoptim.graph.DGraph | |
| extractSubgraph(Vertex seed, int numLayers, boolean stopBeforeRCVs) | denoptim.graph.DGraph | |
| extractSubgraph(Vertex seed, List< Vertex > limits, boolean stopBeforeRCVs) | denoptim.graph.DGraph | |
| extractSubgraph(Vertex seed, boolean stopBeforeRCVs) | denoptim.graph.DGraph | |
| extractSubgraph(Collection< Vertex > definedOn) | denoptim.graph.DGraph | |
| extractSubgraph(Collection< Vertex > definedOn, Set< Edge > connectionToSubgraph, Set< Edge > connectionFromSubgraph) | denoptim.graph.DGraph | |
| findVertices(VertexQuery vrtxQuery, Logger logger) | denoptim.graph.DGraph | |
| findVertices(VertexQuery vrtxQuery, boolean purgeSym, Logger logger) | denoptim.graph.DGraph | |
| findVerticesIds(VertexQuery query, Logger logger) | denoptim.graph.DGraph | |
| fixEdgeDirections(DGraph graph) | denoptim.graph.DGraph | privatestatic |
| fixEdgeDirections(Vertex v, Set< Long > visited) | denoptim.graph.DGraph | privatestatic |
| fromJson(String json) | denoptim.graph.DGraph | static |
| fromJson(Reader reader) | denoptim.graph.DGraph | static |
| gEdges | denoptim.graph.DGraph | package |
| getAPOnLeftVertexID(long nbrVid, long vid) | denoptim.graph.DGraph | |
| getAPWithId(int id) | denoptim.graph.DGraph | |
| getAttachmentPoints() | denoptim.graph.DGraph | |
| getAvailableAPs() | denoptim.graph.DGraph | |
| getAvailableAPsThroughout() | denoptim.graph.DGraph | |
| getBondingAPIndex(Vertex srcVert, int dapidx, Vertex dstVert) | denoptim.graph.DGraph | |
| getBranchIdOfVertex(Vertex v) | denoptim.graph.DGraph | |
| getBranchIdOfVertexAsStr(Vertex v) | denoptim.graph.DGraph | |
| getBranchIdOfVertexAtPosition(int i) | denoptim.graph.DGraph | |
| getCandidateOwner() | denoptim.graph.DGraph | |
| getChildrenTree(Vertex vertex, List< Vertex > children) | denoptim.graph.DGraph | |
| getChildrenTree(Vertex vertex, List< Vertex > children, boolean markBranches) | denoptim.graph.DGraph | |
| getChildrenTree(Vertex vertex, List< Vertex > children, AtomicInteger branchIdGenerator, List< Integer > prevBranchId) | denoptim.graph.DGraph | |
| getChildrenTree(Vertex vertex, List< Vertex > children, int numLayers, boolean stopBeforeRCVs) | denoptim.graph.DGraph | |
| getChildTreeLimited(Vertex vertex, List< Vertex > children, boolean stopBeforeRCVs) | denoptim.graph.DGraph | |
| getChildTreeLimited(Vertex vertex, List< Vertex > children, Set< Vertex > limits) | denoptim.graph.DGraph | |
| getChildTreeLimited(Vertex vertex, List< Vertex > children, List< Vertex > limitsInClone, boolean stopBeforeRCVs) | denoptim.graph.DGraph | |
| getChildVertices(Vertex vertex) | denoptim.graph.DGraph | |
| getClosableChains() | denoptim.graph.DGraph | |
| getDeepestAmongThese(List< Vertex > list) | denoptim.graph.DGraph | |
| getEdgeAtPosition(int pos) | denoptim.graph.DGraph | |
| getEdgeCount() | denoptim.graph.DGraph | |
| getEdgeList() | denoptim.graph.DGraph | |
| getEdgesWithChild(int vid) | denoptim.graph.DGraph | |
| getEdgesWithSrc(Vertex v) | denoptim.graph.DGraph | |
| getEdgesWithTrg(Vertex v) | denoptim.graph.DGraph | |
| getEdgeWithParent(long l) | denoptim.graph.DGraph | |
| getEmbeddedGraphInClone(DGraph graphY, DGraph graphB, List< Template > path) | denoptim.graph.DGraph | static |
| getEmbeddingPath() | denoptim.graph.DGraph | |
| getFreeRCVertices() | denoptim.graph.DGraph | |
| getGraphId() | denoptim.graph.DGraph | |
| getHeavyAtomsCount() | denoptim.graph.DGraph | |
| getIndexOfEdgesWithChild(int vid) | denoptim.graph.DGraph | |
| getInterfaceAPs(List< Vertex > subGraphB) | denoptim.graph.DGraph | |
| getLevel(Vertex v) | denoptim.graph.DGraph | |
| getLocalMsg() | denoptim.graph.DGraph | |
| getMaxVertexId() | denoptim.graph.DGraph | |
| getMutableSites() | denoptim.graph.DGraph | |
| getMutableSites(List< MutationType > ignoredTypes) | denoptim.graph.DGraph | |
| getOutermostGraphOwner() | denoptim.graph.DGraph | |
| getParent(Vertex v) | denoptim.graph.DGraph | |
| getParentTree(Vertex vertex, List< Vertex > parentTree) | denoptim.graph.DGraph | |
| getRCVertices() | denoptim.graph.DGraph | |
| getRingCount() | denoptim.graph.DGraph | |
| getRings() | denoptim.graph.DGraph | |
| getRingsInvolvingVertex(Vertex v) | denoptim.graph.DGraph | |
| getRingsInvolvingVertex(Vertex[] vs) | denoptim.graph.DGraph | |
| getRingsInvolvingVertexID(int vid) | denoptim.graph.DGraph | |
| getSelectedMutableSites(MutationType requestedType) | denoptim.graph.DGraph | |
| getSourceVertex() | denoptim.graph.DGraph | |
| getSubgraphAPs(List< Vertex > subGraphB) | denoptim.graph.DGraph | |
| getSymmetricSetCount() | denoptim.graph.DGraph | |
| getSymmetricSubGraphs(List< Vertex > subGrpVrtxs) | denoptim.graph.DGraph | |
| getSymSetForVertex(Vertex v) | denoptim.graph.DGraph | |
| getSymSetsIterator() | denoptim.graph.DGraph | |
| getSymVerticesForVertex(Vertex v) | denoptim.graph.DGraph | |
| getTemplateJacket() | denoptim.graph.DGraph | |
| getUniqueAPIndex() | denoptim.graph.DGraph | protected |
| getUsedRCVertices() | denoptim.graph.DGraph | |
| getVertexAtPosition(int pos) | denoptim.graph.DGraph | |
| getVertexCount() | denoptim.graph.DGraph | |
| getVertexList() | denoptim.graph.DGraph | |
| getVertexWithId(long vid) | denoptim.graph.DGraph | |
| graphId | denoptim.graph.DGraph | package |
| graphNeedsCappingGroups(FragmentSpace fragSpace) | denoptim.graph.DGraph | |
| gRings | denoptim.graph.DGraph | package |
| gVertices | denoptim.graph.DGraph | package |
| hasForbiddenEnd(FragmentSpaceParameters fsSettings) | denoptim.graph.DGraph | |
| hasOrEmbedsRings() | denoptim.graph.DGraph | |
| hasRings() | denoptim.graph.DGraph | |
| hasScaffoldTypeVertex() | denoptim.graph.DGraph | |
| hasSymmetricAP() | denoptim.graph.DGraph | |
| hasSymmetryInvolvingVertex(Vertex v) | denoptim.graph.DGraph | |
| indexOf(Vertex v) | denoptim.graph.DGraph | |
| indexOfVertexWithID(long vid) | denoptim.graph.DGraph | |
| insertSingleVertex(Edge edge, Vertex newLink, LinkedHashMap< AttachmentPoint, AttachmentPoint > apMap) | denoptim.graph.DGraph | |
| insertVertex(Edge edge, int bbId, BBType bbt, LinkedHashMap< AttachmentPoint, Integer > apMap, FragmentSpace fragSpace) | denoptim.graph.DGraph | |
| isIsomorphicTo(DGraph other) | denoptim.graph.DGraph | |
| isIsostructuralTo(DGraph other) | denoptim.graph.DGraph | |
| isReversible(FragmentSpace fragSpace) | denoptim.graph.DGraph | |
| isVertexIDInRing(int vid) | denoptim.graph.DGraph | |
| isVertexInRing(Vertex v) | denoptim.graph.DGraph | |
| jGraph | denoptim.graph.DGraph | private |
| jGraphKernel | denoptim.graph.DGraph | private |
| localMsg | denoptim.graph.DGraph | package |
| makeAllGraphsWithDifferentRingSets(RunTimeParameters settings) | denoptim.graph.DGraph | |
| reassignSymmetricLabels() | denoptim.graph.DGraph | protected |
| removeBranchStartingAt(Vertex v, boolean symmetry) | denoptim.graph.DGraph | |
| removeBranchStartingAt(Vertex v) | denoptim.graph.DGraph | |
| removeCappingGroups(List< Vertex > lstVerts) | denoptim.graph.DGraph | |
| removeCappingGroups() | denoptim.graph.DGraph | |
| removeCappingGroupsFromChilds(List< Vertex > lstVerts) | denoptim.graph.DGraph | |
| removeCappingGroupsOn(Vertex vertex) | denoptim.graph.DGraph | |
| removeChainUpToBranching(Vertex v, FragmentSpace fragSpace) | denoptim.graph.DGraph | |
| removeEdge(Edge edge) | denoptim.graph.DGraph | |
| removeOrphanBranchStartingAt(Vertex v) | denoptim.graph.DGraph | |
| removeRing(Ring ring) | denoptim.graph.DGraph | |
| removeSingleVertexAndWeld(Vertex vertex, FragmentSpace fragSpace) | denoptim.graph.DGraph | |
| removeSymmetryRedundance(List< Vertex > list) | denoptim.graph.DGraph | |
| removeSymmetryRedundantIds(ArrayList< Long > list) | denoptim.graph.DGraph | |
| removeSymmetrySet(SymmetricVertexes ss) | denoptim.graph.DGraph | |
| removeVertex(Vertex vertex) | denoptim.graph.DGraph | |
| removeVertexAndWeld(Vertex vertex, FragmentSpace fragSpace) | denoptim.graph.DGraph | |
| renumberGraphVertices() | denoptim.graph.DGraph | |
| renumberVerticesGetMap() | denoptim.graph.DGraph | |
| reorderVertexList(DGraph g) | denoptim.graph.DGraph | privatestatic |
| replaceSingleSubGraph(List< Vertex > subGrpVrtxs, DGraph newSubGraph, LinkedHashMap< AttachmentPoint, AttachmentPoint > apMap) | denoptim.graph.DGraph | |
| replaceSubGraph(List< Vertex > subGrpVrtxs, DGraph incomingGraph, LinkedHashMap< AttachmentPoint, AttachmentPoint > apMap, FragmentSpace fragSpace) | denoptim.graph.DGraph | |
| replaceUnusedRCVsWithCapps(FragmentSpace fragSpace) | denoptim.graph.DGraph | |
| replaceVertex(Vertex vertex, int bbId, BBType bbt, LinkedHashMap< Integer, Integer > apIdMap, FragmentSpace fragSpace) | denoptim.graph.DGraph | |
| replaceVertex(Vertex vertex, int bbId, BBType bbt, LinkedHashMap< Integer, Integer > apIdMap, boolean symmetry, FragmentSpace fragSpace) | denoptim.graph.DGraph | |
| sameAs(DGraph other, StringBuilder reason) | denoptim.graph.DGraph | |
| sameAsRings(StringBuilder reason, Map< Vertex, Vertex > vertexMap, Ring rT, Vertex vhT, Vertex vtT, Ring rO) | denoptim.graph.DGraph | private |
| setCandidateClosableChains(ArrayList< ClosableChain > closableChains) | denoptim.graph.DGraph | |
| setCandidateOwner(Candidate candidate) | denoptim.graph.DGraph | |
| setEdgeList(ArrayList< Edge > edges) | denoptim.graph.DGraph | |
| setGraphId(int id) | denoptim.graph.DGraph | |
| setLocalMsg(String msg) | denoptim.graph.DGraph | |
| setRings(ArrayList< Ring > rings) | denoptim.graph.DGraph | |
| setScaffold(Vertex v) | denoptim.graph.DGraph | static |
| setSymmetricVertexSets(List< SymmetricVertexes > symVertices) | denoptim.graph.DGraph | |
| setTemplateJacket(Template template) | denoptim.graph.DGraph | |
| setVertexList(ArrayList< Vertex > vertices) | denoptim.graph.DGraph | |
| storeCurrentVertexIDs() | denoptim.graph.DGraph | |
| SYM_ID | denoptim.graph.DGraph | privatestatic |
| symVertices | denoptim.graph.DGraph | private |
| templateJacket | denoptim.graph.DGraph | package |
| toJson() | denoptim.graph.DGraph | |
| toString() | denoptim.graph.DGraph | |
1.9.4