| addBond(Bond *aBond) | Atom | |
| 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 | |
| addRing(Ring *aRing) | Atom | [inline] |
| addStringDescriptor(string aLabel, string aValue, string aUnit, string aComment) | DataContainer | |
| addUnknownTypeDescriptor(string aName, string aValue) | DataContainer | |
| an | Atom | [private] |
| Atom() | Atom | |
| Atom(const Atom &anAtom) | Atom | |
| Atom(string aLabel) | Atom | |
| beginBond() | Atom | [inline] |
| beginFloatDescriptor() | DataContainer | [inline] |
| beginIntDescriptor() | DataContainer | [inline] |
| beginRing() | Atom | [inline] |
| beginStringDescriptor() | DataContainer | [inline] |
| BFSBondVector | Atom | [protected] |
| BFSVector | Atom | [protected] |
| Bond (defined in Atom) | Atom | [friend] |
| bondExists(Bond *aBond) | Atom | |
| bonds | Atom | [private] |
| bondSum() | Atom | |
| counter | Atom | [private, static] |
| DataContainer() | DataContainer | |
| DataContainer(DataContainer &aDataContainer) | DataContainer | |
| degree() | Atom | [inline] |
| deleteAllDescriptors() | DataContainer | |
| deleteAllKindDescriptors() | DataContainer | [protected] |
| deleteBonds() | Atom | |
| deleteDescriptor(string aString, bool found=false) | DataContainer | [virtual] |
| deleteHiddenBonds() | Atom | |
| describe() | Atom | |
| describeShort() | Atom | |
| Elements (defined in Atom) | Atom | [friend] |
| endBond() | Atom | [inline] |
| endFloatDescriptor() | DataContainer | [inline] |
| endIntDescriptor() | DataContainer | [inline] |
| endRing() | Atom | [inline] |
| endStringDescriptor() | DataContainer | [inline] |
| eraseCoordinates() | Atom | |
| flagElement | DataContainer | [protected] |
| flagHasCoordinates | Atom | [private] |
| flagHasPq | Node | [protected] |
| flagHasPs | Node | [protected] |
| floatDescriptors | DataContainer | [protected] |
| genericAtomType | Atom | [private] |
| getAN() const | Atom | [inline] |
| getBFSBondVector() | Atom | [inline] |
| getBFSVector() | Atom | [inline] |
| getBFSVectorSize() | Atom | [inline] |
| getBondIteratorWithTarget(Atom *otherAtom) | Atom | |
| getBonds() | Atom | [inline] |
| getBondWithTarget(Atom *otherAtom) | Atom | |
| getElementSymbol() | Atom | [inline] |
| getFloatDescriptor(string aLabel, bool silentError=true) | DataContainer | |
| getId() const | Atom | [inline] |
| getIdInMolecule() const | Atom | [inline] |
| getIdString() | Atom | |
| getIntDescriptor(string aLabel, bool silentError=true) | DataContainer | |
| getKashimaPQ(bool silentError=false) | Node | |
| getKashimaPS(bool silentError=false) | Node | |
| getKashimaPT(Atom *anAtom) | Atom | |
| getLabel() | Node | [inline] |
| getMorganIndex(int order) | Atom | |
| getMorganLabel(bool silentError=false) | Atom | |
| getName() | Atom | [inline] |
| getNumAromaticBonds() | Atom | |
| getPerretLabel(bool silentError=false) | Atom | |
| getPossibleValuesInIntDescriptor(string aDescriptorName, vector< int > *) | DataContainer | |
| getRingBFS(vector< Atom * > *toVisit, vector< Bond * > *toVisitBond) | Atom | |
| getRPosition() | Node | [inline] |
| getStringDescriptor(string aLabel, bool silentError=true) | DataContainer | |
| getSumOfNeighboorMorganIndex(int anOrder) | Atom | |
| getSymbol() | Atom | [inline] |
| getType() const | Atom | [inline] |
| getUniqueMorganIndex(bool silentError=false) | Atom | |
| getVectorIntersect(vector< Atom * > *v1, vector< Atom * > *v2, vector< Atom * > *result) | Atom | [static] |
| getX() | Atom | [inline] |
| getY() | Atom | [inline] |
| getZ() | Atom | [inline] |
| hasCoordinates() | Atom | |
| hasFloatDescriptor(string aLabel) | DataContainer | |
| hasIntDescriptor(string aLabel) | DataContainer | |
| hasRing(Ring *aRing) | Atom | |
| hasRing() | Atom | [inline] |
| hasStringDescriptor(string aLabel) | DataContainer | |
| hiddenBonds | Atom | [private] |
| hideAllToFromBonds() | Atom | |
| hideBond(map< Atom *, Bond * >::iterator aBondI) | Atom | |
| hideBond(Bond *aBond) | Atom | |
| hideBond(Atom *aTarget) | Atom | |
| hideHydrogenBonds() | Atom | |
| hideToFromBonds(Atom *aTarget) | Atom | |
| hideToFromFirstBond() | Atom | |
| id | Atom | [private] |
| idInMolecule | Atom | [private] |
| intDescriptors | DataContainer | [protected] |
| isCSkeleton() | Atom | |
| isGeneric() | Atom | [inline] |
| kindFloatDescriptors | DataContainer | [protected] |
| kindIntDescriptors | DataContainer | [protected] |
| kindStringDescriptors | DataContainer | [protected] |
| label | Node | [protected] |
| Molecule (defined in Atom) | Atom | [friend] |
| morganIndex | Atom | [protected] |
| morganLabel | Atom | [protected] |
| nextUnvisitedAtom() | Atom | |
| Node() | Node | |
| Node(const DataContainer &aDataContainer) | Node | |
| numBonds() | Atom | [inline] |
| numHiddenBonds() | Atom | [inline] |
| numRings() | Atom | [inline] |
| operator<<(ostream &os, const Atom &anAtom) | Atom | [friend] |
| operator=(const Atom &anAtom) | Atom | |
| partialCharge | Atom | [protected] |
| perretLabel | Atom | [protected] |
| pq | Node | [protected] |
| ps | Node | [protected] |
| pushBFSVector(vector< Atom * > *aPath, vector< Bond * > *aBondPath) | Atom | |
| resetBFSVector() | Atom | [inline] |
| resetCounter() | Atom | [inline, protected, static] |
| resetMorganIndex() | Atom | |
| restoreHiddenBond(Bond *aBond) | Atom | |
| restoreHiddenBond(Atom *aTarget) | Atom | |
| restoreHiddenBonds() | Atom | |
| rings | Atom | [private] |
| rPosition | Node | [protected] |
| setAN(int a) | Atom | [inline, protected] |
| setCoordinates(float aX, float aY, float aZ) | Atom | |
| setElementSymbol(string anElement) | Atom | |
| setFloatDescriptor(string aLabel, float aValue, string aUnit, string aComment, bool addIfMissing, bool silentError) | DataContainer | |
| setIdInMolecule(int anId) | Atom | |
| setIntDescriptor(string aLabel, int aValue, string aUnit, string aComment, bool addIfMissing, bool silentError) | DataContainer | |
| setKashimaPQ(double aPq) | Node | [inline] |
| setKashimaPS(double aPs) | Node | [inline] |
| setLabel(string aString) | Node | |
| setMorganChargeLabel(double threshold) | Atom | |
| setMorganLabel(string aLabel) | Atom | |
| setMorganLabel(int anOrder) | Atom | |
| setPartialCharge(double aValue) | Atom | |
| setPerretLabel() | Atom | |
| setRPosition(int aR) | Node | [inline] |
| setStringDescriptor(string aLabel, string aValue, string aUnit, string aComment, bool addIfMissing, bool silentError) | DataContainer | |
| setType(int aType) | Atom | [inline, protected] |
| setUniqueMorganIndex(int anOrder) | Atom | |
| setVisited() | Atom | [inline] |
| stringDescriptors | DataContainer | [protected] |
| toString() | Atom | |
| toStringBFSVector() | Atom | |
| toStringShort() | Atom | |
| type | Atom | [private] |
| uniqueMorganIndex | Atom | [protected] |
| unsetBondFlags() | Atom | |
| unsetBondFlagsOriginal() | Atom | |
| unsetVisited() | Atom | [inline] |
| visited | Atom | [private] |
| wasVisited() | Atom | [inline] |
| x | Atom | [private] |
| y | Atom | [private] |
| z | Atom | [private] |
| ~Atom() | Atom | |
| ~DataContainer() | DataContainer | [virtual] |
| ~Node() | Node | |
