| addAtom(string aSymbol) | KCFMolecule | [virtual] |
| Molecule::addAtom(string aSymbol, bool resetSSSR=true) | Molecule | [virtual] |
| Molecule::addAtom(Atom *, bool resetSSSR=true, bool resetMorganIndex=true) | Molecule | |
| addFloatDescriptor(string aLabel, float aValue, string aUnit, string aComment) | DataContainer | |
| addIntDescriptor(string aLabel, int aValue, string aUnit, string aComment) | DataContainer | |
| addKindFloatDescriptor(string aLabel, float aValue, string aUnit, string aComment) | DataContainer | |
| addKindFloatDescriptor(Descriptor< float > *aDescriptor) | DataContainer | |
| addKindIntDescriptor(string aLabel, int aValue, string aUnit, string aComment) | DataContainer | |
| addKindIntDescriptor(Descriptor< int > *aDescriptor) | DataContainer | |
| addKindStringDescriptor(string aLabel, string aValue, string aUnit, string aComment) | DataContainer | |
| addKindStringDescriptor(Descriptor< string > *aDescriptor) | DataContainer | |
| addStringDescriptor(string aLabel, string aValue, string aUnit, string aComment) | DataContainer | |
| addToSelfKernel(double) | Molecule | |
| addUnknownTypeDescriptor(string aName, string aValue) | DataContainer | |
| atomExists(Atom *anAtom) | Molecule | |
| atomicDistance(Atom *atom1, Atom *atom2) | Molecule | |
| atoms | Molecule | [protected] |
| atomsLabelsListing(vector< string > *) | Molecule | |
| atomsSymbolsListing(vector< string > *) | Molecule | |
| beginAtom() | Molecule | [inline] |
| beginBond(Atom *anAtom) | Molecule | [inline] |
| beginBond(int anId) | Molecule | [inline] |
| beginComponentSizes() | Molecule | [inline] |
| beginFloatDescriptor() | DataContainer | [inline] |
| beginIntDescriptor() | DataContainer | [inline] |
| beginStringDescriptor() | DataContainer | [inline] |
| binClassifyFromDescriptor(string descriptorName, float value, bool smallerOrEqual=true) | Molecule | |
| bondsListing(vector< int > *) | Molecule | |
| bondSum() | Molecule | |
| calculateSelfKernel(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 paramter1, int parameter2) | Molecule | |
| checkEdges(Atom *) | Molecule | |
| chiral | Molecule | [protected] |
| compute() | Molecule | |
| computeKernel(Molecule *anotherMolecule, double(*pt2GraphKernel)(Molecule *mol1, Molecule *mol2, double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(Bond *, Bond *), int parameter1, int parameter2), double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(Bond *, Bond *), int parameter1, int parameter2=1) | Molecule | |
| counter | Molecule | [protected, static] |
| DataContainer() | DataContainer | |
| DataContainer(DataContainer &aDataContainer) | DataContainer | |
| deleteAllDescriptors() | DataContainer | |
| deleteAllKindDescriptors() | DataContainer | [protected] |
| deleteBonds() | Molecule | |
| deleteDescriptor(string aString, bool found=false) | DataContainer | [virtual] |
| deleteHiddenAtoms() | Molecule | |
| describe() | Molecule | |
| describeEachAtom() | Molecule | |
| describeLong() | Molecule | |
| describeShort() | Molecule | |
| detectSSSR() | Molecule | |
| DFS(Atom *startAtom, string intDescriptorName, int markValue) | Molecule | |
| endAtom() | Molecule | [inline] |
| endBond(Atom *anAtom) | Molecule | [inline] |
| endBond(int anId) | Molecule | [inline] |
| endComponentSizes() | Molecule | [inline] |
| endFloatDescriptor() | DataContainer | [inline] |
| endIntDescriptor() | DataContainer | [inline] |
| endStringDescriptor() | DataContainer | [inline] |
| erase() | Molecule | |
| eraseAdjacency() | Molecule | |
| eraseAtom(Atom *anAtom) | Molecule | |
| eraseHiddenAtoms() | Molecule | |
| eraseRings() | Molecule | |
| eraseWalks() | Molecule | |
| flagActivity | Molecule | [protected] |
| flagElement | DataContainer | [protected] |
| flagHasSSSRDetected | Molecule | [protected] |
| floatDescriptors | DataContainer | [protected] |
| getActivity(bool silentMode=false) | Molecule | |
| getAdjacency(int i, int j) | Molecule | |
| getAtom(int anId) | Molecule | |
| getAtomByIndex(int ind) (defined in Molecule) | Molecule | |
| getAtoms() | Molecule | [inline] |
| getFloatDescriptor(string aLabel, bool silentError=true) | DataContainer | |
| getId() const | Molecule | [inline] |
| getIdString() | Molecule | |
| getIntDescriptor(string aLabel, bool silentError=true) | DataContainer | |
| getLocation() | Molecule | [inline] |
| getMaxMorganIteration() | Molecule | |
| getMW(bool silentError=false) | Molecule | |
| getName() | Molecule | [inline] |
| getNumAtoms() | Molecule | [inline] |
| getNumberOfDistinctMorganIndices(int anOrder) | Molecule | |
| getNumCarbonsOfComponent(string aDescriptorName, int aValue) | Molecule | |
| getNumNitrogensOfComponent(string aDescriptorName, int aValue) | Molecule | |
| getOriginalFormat() | Molecule | [inline] |
| getPossibleValuesInIntDescriptor(string aDescriptorName, vector< int > *) | DataContainer | |
| getRingWithID(int anID, bool createIfMissing) | Molecule | |
| getSelfKernel(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, int parameter2=1) | Molecule | [inline] |
| getSelfKernel() | Molecule | |
| getSortDescriptorName() | Molecule | [inline] |
| getSortDescriptorType() | Molecule | [inline] |
| getStringDescriptor(string aLabel, bool silentError=true) | DataContainer | |
| getWalks(int i, int j) | Molecule | |
| hasActivity() | Molecule | [inline] |
| hasFloatDescriptor(string aLabel) | DataContainer | |
| hasIntDescriptor(string aLabel) | DataContainer | |
| hasRing(Ring *newRing, bool detectingRing=false) | Molecule | |
| hasRing() | Molecule | |
| hasSSSRDetected() | Molecule | [inline] |
| hasStringDescriptor(string aLabel) | DataContainer | |
| hiddenAtoms | Molecule | [protected] |
| hideAllFragmentsBut(int aFragmentNumber) | Molecule | |
| hideAtom(vector< Atom * >::iterator anAtomI) | Molecule | |
| hideAtomAndToFromBonds(vector< Atom * >::iterator anAtomI) | Molecule | |
| hideAtomAndToFromBonds(Atom *anAtom) | Molecule | |
| hideAtomsByIntDescriptor(string aDescriptorName, int aValue, bool refreshBonds=true) | Molecule | |
| hideHydrogens() | Molecule | |
| hideSalts(stringstream *out) | Molecule | |
| id | Molecule | [protected] |
| intDescriptors | DataContainer | [protected] |
| isChiral() | Molecule | [inline] |
| isHiddenAtom(Atom *anAtom) | Molecule | |
| isSelected() | Molecule | [inline] |
| KCFMolecule() | KCFMolecule | |
| kindFloatDescriptors | DataContainer | [protected] |
| kindIntDescriptors | DataContainer | [protected] |
| kindStringDescriptors | DataContainer | [protected] |
| linkAtoms(Atom *aSource, Atom *aTarget, int aBondLabel, int aBondStereo=0, int aBondNotUsed=0, int aBondTopology=0, int aBondReactionCenter=0, bool resetSSSR=true) | Molecule | |
| linkAtoms(string aSource, string aTarget, int aBondLabel, int aBondStereo=0, int aBondNotUsed=0, int aBondTopology=0, int aBondReactionCenter=0, bool resetSSSR=true) | Molecule | |
| linkAtoms(int firstAtom, int secondAtom, int aBondLabel, int aBondStereo=0, int aBondNotUsed=0, int aBondTopology=0, int aBondReactionCenter=0, bool resetSSSR=true) | Molecule | |
| markFragments() | Molecule | |
| maxMorganIteration | Molecule | [protected] |
| Molecule() | Molecule | |
| Molecule(Molecule &aMolecule, bool bool_resetMorganIndex=true) | Molecule | |
| Molecule(Molecule &molecule1, Molecule &molecule2, double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(Bond *, Bond *)) | Molecule | |
| Molecule(Molecule &m1, Molecule &m2, double(*pt2AtomKernel)(Atom *, Atom *), double(*pt2BondKernel)(float, float, float), float edgeKernelParameter) | Molecule | |
| moleculeChanged(bool resetSSSR=true, bool resetMorganIndex=true) | Molecule | [protected] |
| noTottersTransform() | Molecule | |
| numAtoms() | Molecule | [inline] |
| numAtomsNonCSkeleton() | Molecule | |
| numBonds() | Molecule | |
| numHiddenAtoms() | Molecule | [inline] |
| numHiddenBonds() | Molecule | |
| numRings() | Molecule | [inline] |
| operator=(const Molecule &aMolecule) | Molecule | |
| raisePowerAdjacency() | Molecule | |
| raisePowerFast() | Molecule | |
| readKCF(string aFileName) | KCFMolecule | |
| readMOL(string aFilename, bool genericAtomType=false) | Molecule | |
| readMOLOld(string aFilename) | Molecule | |
| readPartialCharges(string charges) | Molecule | |
| refreshBonds() | Molecule | |
| resetMorganIndex() | Molecule | |
| resetSelfKernel() | Molecule | [inline] |
| resetSSSR() | Molecule | [inline] |
| restoreHiddenAtoms(bool flagRestoreBonds=true) | Molecule | |
| restoreHiddenBonds() | Molecule | |
| select() | Molecule | [inline] |
| selectedFlag | Molecule | [protected] |
| selfKernel | Molecule | [protected] |
| selfKernelCalculated | Molecule | [protected] |
| setActivity(float aNumber) | Molecule | [inline] |
| setActivity(string aNumber) | Molecule | [inline] |
| setAdjacency(int i, int j, double value) | Molecule | |
| setFloatDescriptor(string aLabel, float aValue, string aUnit, string aComment, bool addIfMissing, bool silentError) | DataContainer | |
| setHasSSSR() | Molecule | [inline] |
| setIntDescriptor(string aLabel, int aValue, string aUnit, string aComment, bool addIfMissing, bool silentError) | DataContainer | |
| setKashimaKernelProb(double aPq, bool skipSkeleton=false) | Molecule | |
| setMorganChargesLabels(double threshold) | Molecule | |
| setMorganLabels(int anOrder) | Molecule | |
| setName(string aName) | Molecule | [inline] |
| setOriginalFormat(int a) | Molecule | [inline] |
| setPerretLabels() | Molecule | |
| setSelfKernel(double value) | Molecule | |
| setSortDescriptor(string aName, int aType) | Molecule | |
| setStringDescriptor(string aLabel, string aValue, string aUnit, string aComment, bool addIfMissing, bool silentError) | DataContainer | |
| setUniqueMorganIndices() | Molecule | |
| setWalks(int i, int j, double value) | Molecule | |
| sortDescriptorName | Molecule | [protected] |
| sortDescriptorType | Molecule | [protected] |
| sssr | Molecule | [protected] |
| stringDescriptors | DataContainer | [protected] |
| substractToSelfKernel(double) | Molecule | |
| sumPQPS() | Molecule | |
| sumPQPSFast() | Molecule | |
| sumProbabilities() | Molecule | |
| sumProbabilitiesFast() | Molecule | |
| sumPT() | Molecule | |
| threeDtransform(int nBins, double distMin, double distMax) | Molecule | |
| toString() | Molecule | |
| toStringLong() | Molecule | |
| toStringShort() | Molecule | |
| traceDiagWalks() | Molecule | |
| traceWalks() | Molecule | |
| unmarkFragments() | Molecule | |
| unSelect() | Molecule | [inline] |
| unsetActivity() | Molecule | [inline] |
| unsetBondFlags() | Molecule | |
| unsetBondFlagsOriginal() | Molecule | |
| writeDOT(string aFilename, bool perretLabels=false) | Molecule | |
| writeFragments(ofstream *outStream) | Molecule | |
| writeKCF(string aFileName) | KCFMolecule | |
| writeMOL(string aFileName) | Molecule | |
| writeSD(string aFileName) | Molecule | |
| ~DataContainer() | DataContainer | [virtual] |
| ~KCFMolecule() | KCFMolecule | [virtual] |
| ~Molecule() | Molecule | [virtual] |
