| addFusedRingsToFragmentLibrary(DGraph graph) | denoptim.fragspace.FragmentSpace | |
| addFusedRingsToFragmentLibrary(DGraph graph, boolean addIfScaffold, boolean addIfFragment) | denoptim.fragspace.FragmentSpace | |
| addFusedRingsToFragmentLibrary(DGraph graph, boolean addIfScaffold, boolean addIfFragment, IAtomContainer wholeMol) | denoptim.fragspace.FragmentSpace | |
| apClassBasedApproch | denoptim.fragspace.FragmentSpace | private |
| apClassCompatibilityMatrix | denoptim.fragspace.FragmentSpace | private |
| apClassesPerFrag | denoptim.fragspace.FragmentSpace | private |
| appendVertexToLibrary(Vertex v, Vertex.BBType bbt, ArrayList< Vertex > library) | denoptim.fragspace.FragmentSpace | |
| appendVerticesToLibrary(ArrayList< Vertex > list, Vertex.BBType bbt, ArrayList< Vertex > library) | denoptim.fragspace.FragmentSpace | |
| cappingLib | denoptim.fragspace.FragmentSpace | private |
| cappingMap | denoptim.fragspace.FragmentSpace | private |
| classifyFragment(Vertex frg, int fragId) | denoptim.fragspace.FragmentSpace | |
| clearAll() | denoptim.fragspace.FragmentSpace | |
| define(FragmentSpaceParameters settings, ArrayList< Vertex > scaffLib, ArrayList< Vertex > fragLib, ArrayList< Vertex > cappLib, HashMap< APClass, ArrayList< APClass > > cpMap, HashMap< APClass, APClass > capMap, HashSet< APClass > forbEnds, HashMap< APClass, ArrayList< APClass > > rcCpMap, HashMap< APClass, Double > symCntrMap) | denoptim.fragspace.FragmentSpace | private |
| forbiddenEndList | denoptim.fragspace.FragmentSpace | private |
| fragmentLib | denoptim.fragspace.FragmentSpace | private |
| FragmentSpace() | denoptim.fragspace.FragmentSpace | |
| FragmentSpace(FragmentSpaceParameters settings, String scaffFile, String fragFile, String capFile, String cpmFile) | denoptim.fragspace.FragmentSpace | |
| FragmentSpace(FragmentSpaceParameters settings, ArrayList< Vertex > scaffLib, ArrayList< Vertex > fragLib, ArrayList< Vertex > cappLib, HashMap< APClass, ArrayList< APClass > > cpMap, HashMap< APClass, APClass > capMap, HashSet< APClass > forbEnds, HashMap< APClass, ArrayList< APClass > > rcCpMap) | denoptim.fragspace.FragmentSpace | |
| FragmentSpace(FragmentSpaceParameters settings, ArrayList< Vertex > scaffLib, ArrayList< Vertex > fragLib, ArrayList< Vertex > cappLib, HashMap< APClass, ArrayList< APClass > > cpMap, HashMap< APClass, APClass > capMap, HashSet< APClass > forbEnds, HashMap< APClass, ArrayList< APClass > > rcCpMap, HashMap< APClass, Double > symCntrMap) | denoptim.fragspace.FragmentSpace | |
| FragmentSpace(FragmentSpaceParameters settings, String scaffFile, String fragFile, String capFile, String cpmFile, String rcpmFile, HashMap< APClass, Double > symCntrMap) | denoptim.fragspace.FragmentSpace | |
| fragPoolPerNumAP | denoptim.fragspace.FragmentSpace | private |
| fragsApsPerApClass | denoptim.fragspace.FragmentSpace | private |
| getAllAPClassesFromCPMap() | denoptim.fragspace.FragmentSpace | |
| getAPClassesPerFragment(int fragId) | denoptim.fragspace.FragmentSpace | |
| getAPClassForFragment(IdFragmentAndAP apId) | denoptim.fragspace.FragmentSpace | |
| getAPClassOfCappingVertex(APClass srcApClass) | denoptim.fragspace.FragmentSpace | |
| getAPsCompatibleWithClass(APClass aPC1) | denoptim.fragspace.FragmentSpace | |
| getAPsCompatibleWithThese(ArrayList< AttachmentPoint > srcAPs) | denoptim.fragspace.FragmentSpace | |
| getCappingFragment(APClass rcnCap) | denoptim.fragspace.FragmentSpace | |
| getCappingGroupsWithAPClass(APClass capApCls) | denoptim.fragspace.FragmentSpace | |
| getCappingLibrary() | denoptim.fragspace.FragmentSpace | |
| getCappingMap() | denoptim.fragspace.FragmentSpace | |
| getCappingVertexWithAPClass(APClass capApCls) | denoptim.fragspace.FragmentSpace | |
| getCompatibilityMatrix() | denoptim.fragspace.FragmentSpace | |
| getCompatibleAPClasses(APClass apc) | denoptim.fragspace.FragmentSpace | |
| getCompatibleCappingFragments(APClass cmpReac) | denoptim.fragspace.FragmentSpace | |
| getForbiddenEndList() | denoptim.fragspace.FragmentSpace | |
| getFragAPsCompatibleWithClass(APClass aPC1) | denoptim.fragspace.FragmentSpace | |
| getFragAPsCompatibleWithTheseAPs(ArrayList< IdFragmentAndAP > srcAPs) | denoptim.fragspace.FragmentSpace | |
| getFragmentLibrary() | denoptim.fragspace.FragmentSpace | |
| getFragmentsCompatibleWithTheseAPs(ArrayList< IdFragmentAndAP > srcAPs) | denoptim.fragspace.FragmentSpace | |
| getFragsWithAPClass(APClass apc) | denoptim.fragspace.FragmentSpace | |
| getFragsWithNumAps(int nAps) | denoptim.fragspace.FragmentSpace | |
| getMapOfFragsPerNumAps() | denoptim.fragspace.FragmentSpace | |
| getPolarizedRCV(boolean polarity) | denoptim.fragspace.FragmentSpace | static |
| getRandomizer() | denoptim.fragspace.FragmentSpace | |
| getRCCompatibilityMatrix() | denoptim.fragspace.FragmentSpace | |
| getRCVs() | denoptim.fragspace.FragmentSpace | |
| getRCVsForAPClass(APClass apc) | denoptim.fragspace.FragmentSpace | |
| getRCVsWithAPClass(APClass apc) | denoptim.fragspace.FragmentSpace | |
| getScaffoldLibrary() | denoptim.fragspace.FragmentSpace | |
| getSymmetryConstrain(APClass apClass) | denoptim.fragspace.FragmentSpace | |
| getVertexFromLibrary(Vertex.BBType bbType, int bbIdx) | denoptim.fragspace.FragmentSpace | |
| getVerticesWithAPClass(APClass apc) | denoptim.fragspace.FragmentSpace | |
| getVerticesWithAPClasses(Set< APClass > apcs) | denoptim.fragspace.FragmentSpace | |
| getVerticesWithAPClassStartingWith(String root) | denoptim.fragspace.FragmentSpace | |
| getVerticesWithAPFingerprint(Map< APClass, Integer > apcCounts) | denoptim.fragspace.FragmentSpace | |
| groupAndClassifyFragments(boolean apClassBasedApproch) | denoptim.fragspace.FragmentSpace | |
| hasIsomorph(DGraph graph, BBType type) | denoptim.fragspace.FragmentSpace | |
| hasSymmetryConstrain(APClass apClass) | denoptim.fragspace.FragmentSpace | |
| importCompatibilityMatrixFromFile(String inFile) | denoptim.fragspace.FragmentSpace | |
| importRCCompatibilityMatrixFromFile(String inFile) | denoptim.fragspace.FragmentSpace | |
| imposeSymmetryOnAPsOfClass(APClass apClass) | denoptim.fragspace.FragmentSpace | |
| isDefined() | denoptim.fragspace.FragmentSpace | |
| isValid | denoptim.fragspace.FragmentSpace | private |
| LOCK | denoptim.fragspace.FragmentSpace | private |
| makeRandomScaffold() | denoptim.fragspace.FragmentSpace | |
| mapAPClassCompatibilities(List< AttachmentPoint > listA, List< AttachmentPoint > listB, int maxCombinations) | denoptim.fragspace.FragmentSpace | |
| rcCompatMap | denoptim.fragspace.FragmentSpace | private |
| rcvs | denoptim.fragspace.FragmentSpace | private |
| registerRCV(Vertex v) | denoptim.fragspace.FragmentSpace | |
| scaffoldLib | denoptim.fragspace.FragmentSpace | private |
| setAPclassBasedApproach(boolean useAPC) | denoptim.fragspace.FragmentSpace | |
| setCappingLibrary(ArrayList< Vertex > lib) | denoptim.fragspace.FragmentSpace | |
| setCappingMap(HashMap< APClass, APClass > map) | denoptim.fragspace.FragmentSpace | |
| setCompatibilityMatrix(HashMap< APClass, ArrayList< APClass > > map) | denoptim.fragspace.FragmentSpace | |
| setForbiddenEndList(Set< APClass > lst) | denoptim.fragspace.FragmentSpace | |
| setFragmentLibrary(ArrayList< Vertex > lib) | denoptim.fragspace.FragmentSpace | |
| setRCCompatibilityMatrix(HashMap< APClass, ArrayList< APClass > > map) | denoptim.fragspace.FragmentSpace | |
| setScaffoldLibrary(ArrayList< Vertex > lib) | denoptim.fragspace.FragmentSpace | |
| setSymmConstraints(HashMap< APClass, Double > map) | denoptim.fragspace.FragmentSpace | |
| settings | denoptim.fragspace.FragmentSpace | private |
| symmConstraints | denoptim.fragspace.FragmentSpace | private |
| useAPclassBasedApproach() | denoptim.fragspace.FragmentSpace | |
1.9.4