| activitySet | MoleculeSet | [protected] |
| add(MoleculeSet *aSet) | MoleculeSet | |
| addFragmentsToSet(Molecule *aMol, int minAtoms=1) | MoleculeSet | |
| addKCF(string aFileName, long beginMolecule=-1, long endMolecule=-1) | MoleculeSet | |
| addMolecule(Molecule *aMolecule) | MoleculeSet | |
| addMoleculeCopy(Molecule *aMolecule) | MoleculeSet | |
| addMutag(string aFileName, string rFileName="", uint numMolToRead=500) | MoleculeSet | |
| addSD(string aFileName, bool genericAtomType=false, long beginMolecule=-1, long endMolecule=-1) | MoleculeSet | |
| addSingleKCF(string aMolFile) | MoleculeSet | |
| addSingleMOL(string aMolFile, bool genericAtomType=false) | MoleculeSet | |
| addToGram(int row, int col, double value) | MoleculeSet | |
| addToGramNormal(int row, int col, double value) | MoleculeSet | |
| atomsLabelsListing() | MoleculeSet | |
| atomsSymbolsListing() | MoleculeSet | |
| binClassifyFromDescriptor(string descriptorName, float value, bool smallerOrEqual=true) | MoleculeSet | |
| bondsListing() | MoleculeSet | |
| comparisonSet | MoleculeSet | [protected] |
| convergenceCondition | MoleculeSet | [protected] |
| deleteAll() | MoleculeSet | |
| deleteHiddenAtoms() | MoleculeSet | |
| describe(bool selectedOnly=false) | MoleculeSet | |
| describeLong() | MoleculeSet | |
| describeShort() | MoleculeSet | |
| diversityBaryMean() | MoleculeSet | |
| findFirstMoleculeWithName(string aName) | MoleculeSet | |
| getConvergenceCondition() | MoleculeSet | [inline] |
| getGramValue(int row, int col) | MoleculeSet | |
| getMolByIndex(int anInd) | MoleculeSet | |
| getMolByName(string aName) | MoleculeSet | |
| getPossibleValuesInIntDescriptor(string aDescriptorName, vector< int > *p) | MoleculeSet | |
| getPq() | MoleculeSet | [inline] |
| getSortDescriptorName() | MoleculeSet | [protected] |
| gram | MoleculeSet | [protected] |
| gramCalculated | MoleculeSet | [protected] |
| gramCompute(double aPq, double(*pt2GraphKernel)(Molecule *mol1, Molecule *mol2, double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(Bond *, Bond *), int, int), double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(Bond *, Bond *), int aParameter=1000, string aReportFileName="", int nbThreadsWanted=1, bool silentMode=false, bool filterTotters=false) | MoleculeSet | |
| gramCompute(MoleculeSet *anotherSet, double aPq, double(*pt2GraphKernel)(Molecule *mol1, Molecule *mol2, double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(Bond *, Bond *), int, int), double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(Bond *, Bond *), int aParameter=1000, string aReportFileName="", int nbThreadsWanted=1, bool silentMode=false, bool filterTotters=false) | MoleculeSet | |
| gramCompute(double aPq, double(*pt2GraphKernel)(Molecule *mol1, Molecule *mol2, double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(Bond *, Bond *), int, int), double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(Bond *, Bond *), int parameter1=1000, int parameter2=1, string aReportFileName="", int nbThreadsWanted=1, bool silentMode=false, bool filterTotters=false) | MoleculeSet | |
| gramCompute(MoleculeSet *anotherSet, double aPq, double(*pt2GraphKernel)(Molecule *mol1, Molecule *mol2, double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(Bond *, Bond *), int, int), double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(Bond *, Bond *), int parameter1=1000, int parameter2=1, string aReportFileName="", int nbThreadsWanted=1, bool silentMode=false, bool filterTotters=false) | MoleculeSet | |
| gramCompute3D(double(*pt2GraphKernel)(Molecule *mol1, Molecule *mol2, double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(float, float, float), float), double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(float, float, float), float edgeKernelparameter, bool silentMode) | MoleculeSet | |
| gramCompute3D(MoleculeSet *anotherSet, double(*pt2GraphKernel)(Molecule *mol1, Molecule *mol2, double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(float, float, float), float), double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(float, float, float), float edgeKernelparameter, bool silentMode) | MoleculeSet | |
| gramNormal | MoleculeSet | [protected] |
| hasActivity() | MoleculeSet | [inline] |
| hideHydrogens() | MoleculeSet | |
| hideSalts(string aReportFileName="") | MoleculeSet | |
| initializeGram(double value) | MoleculeSet | |
| initializeSelfKernel(double value) | MoleculeSet | |
| kernelCompute(Molecule *aMol, double(*pt2GraphKernel)(Molecule *mol1, Molecule *mol2, double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(Bond *, Bond *), int, int), double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(Bond *, Bond *), vector< double > *resultsRaw, vector< double > *resultsNormal, int convergenceCondition=1000, int parameter2=1, bool silentMode=false) | MoleculeSet | |
| minMaxDistances(double *distMin, double *distMax) | MoleculeSet | |
| MoleculeSet() | MoleculeSet | |
| MoleculeSet(const MoleculeSet &aSet) (defined in MoleculeSet) | MoleculeSet | |
| nameExists(string aName) | MoleculeSet | |
| normalizeGram() | MoleculeSet | |
| normalizeGram_raw() | MoleculeSet | |
| normalizeTanimoto() | MoleculeSet | |
| normalizeTanimoto_raw() | MoleculeSet | |
| normalizeTanimotoMinMax() | MoleculeSet | |
| noTottersTransform() | MoleculeSet | |
| numMolecules() | MoleculeSet | [inline] |
| operator[](string aName) | MoleculeSet | |
| operator[](int anInd) | MoleculeSet | |
| pq | MoleculeSet | [protected] |
| pushFragments(Molecule *aMol, int minAtoms=1) | MoleculeSet | |
| readActivityFile(string aFileName) | MoleculeSet | |
| readDescriptorFile(string aFileName, string separator=";") | MoleculeSet | |
| readGistActivityFile(string aFileName, string aDescriptor) | MoleculeSet | |
| readGistClassifyFile(string aFileName) | MoleculeSet | |
| readGram(string aFileName, vector< vector< double > > *gram) | MoleculeSet | |
| readGramNormal(string aFileName) | MoleculeSet | |
| readGramRaw(string aFileName) | MoleculeSet | |
| readKcfDirectory(string dataDir, long beginMolecule=-1, long endMolecule=-1) | MoleculeSet | |
| readMolDirectory(string aPath, bool genericAtomType=false, long beginMolecule=-1, long endMolecule=-1) | MoleculeSet | |
| readPartialCharges(string fileName) | MoleculeSet | |
| removeDuplicates() | MoleculeSet | |
| resetGramMatrix() | MoleculeSet | |
| resetSelfKernels() | MoleculeSet | |
| restoreHiddenAtoms() | MoleculeSet | |
| select(vector< string > *aSubset) | MoleculeSet | |
| selectAll() | MoleculeSet | |
| selectByActivity(float aValue) | MoleculeSet | |
| selectByFloatDescriptor(string aName, float aValue) | MoleculeSet | |
| selectByIntDescriptor(string aName, int aValue) | MoleculeSet | |
| selectByMW(float minmw, float maxmw=-1, bool addMolecularDescriptor=false) | MoleculeSet | |
| selectByNumAtoms(float minNumAtoms, float maxNumAtoms=-1, bool addMolecularDescriptor=false) | MoleculeSet | |
| selectHasActivity() | MoleculeSet | |
| setActivity(string aMolecule, float aValue) | MoleculeSet | |
| setComparisonSet(MoleculeSet *) | MoleculeSet | |
| setIntDescriptor(string aName, int aValue) | MoleculeSet | |
| setIntDescriptor(string aLabel, string aMolecule, int aValue) | MoleculeSet | |
| setKashimaKernelParam(double aPq, int aConvergenceCondition, bool skipSkeleton=false) | MoleculeSet | |
| setMorganChargesLabels(double threshold) | MoleculeSet | |
| setMorganLabels(int anOrder) | MoleculeSet | |
| setSortDescriptor(string aName, int aType, bool reverse=false) | MoleculeSet | [protected] |
| setUniqueMorganIndices() | MoleculeSet | |
| sortByDescriptor(string aDescriptorName, int aDescriptorType, bool reverse=false) | MoleculeSet | |
| sortByDescriptor(string aDescriptorName, bool reverse=false) | MoleculeSet | |
| sortByMW() | MoleculeSet | |
| sortByNumAtoms() | MoleculeSet | |
| subsetSize | MoleculeSet | [protected] |
| subsetStart | MoleculeSet | [protected] |
| substractToGram(int row, int col, double value) | MoleculeSet | |
| threeDtransform(int nBins, double distMin, double distMax) | MoleculeSet | |
| toString(bool selectedOnly=false) | MoleculeSet | |
| toStringLong() | MoleculeSet | |
| toStringShort() | MoleculeSet | |
| unSelect(vector< string > *aSubset) | MoleculeSet | |
| unSelectAll() | MoleculeSet | |
| writeActivityFile(string aFilename, bool addActivityExtension=true, string activityDescriptor=ACTIVITY) | MoleculeSet | |
| writeDescriptors(string aFileName, bool selectedOnly=false) | MoleculeSet | |
| writeDotsToDir(string aDirectory, bool selectedOnly=false, bool perretLabels=false) | MoleculeSet | |
| writeGramMatrix(string aFileName, bool normal=false, bool self=false, bool silentMode=false) | MoleculeSet | |
| writeKCF(string aFileName, bool selectedOnly=false) | MoleculeSet | |
| writeMolToDir(string aDirName, bool selectedOnly=false) | MoleculeSet | |
| writeSD(string aFileName, bool selectedOnly=false) | MoleculeSet | |
| writeSelfKernelList(string aFilename, bool silentMode=false) | MoleculeSet | |
| writeSubsetKCF(string aFileName, vector< string > *anOrder) | MoleculeSet | |
| writeSubsetSD(string aFileName, vector< string > *anOrder) | MoleculeSet | |
| ~MoleculeSet() | MoleculeSet | |
