denoptim.utils.MoleculeUtils Member List

This is the complete list of members for denoptim.utils.MoleculeUtils, including all inherited members.

builder	denoptim.utils.MoleculeUtils	privatestatic
calculateCentroid(IAtomContainer mol)	denoptim.utils.MoleculeUtils	static
countAtomsOfElement(IAtomContainer mol, String symbol)	denoptim.utils.MoleculeUtils	static
ensureNoUnsetBondOrders(IAtomContainer iac)	denoptim.utils.MoleculeUtils	static
ensureNoUnsetBondOrdersSilent(IAtomContainer iac)	denoptim.utils.MoleculeUtils	static
explicitHydrogens(IAtomContainer mol)	denoptim.utils.MoleculeUtils	static
extractIACForSubgraph(IAtomContainer wholeIAC, DGraph subGraph, DGraph wholeGraph, Logger logger, Randomizer randomizer)	denoptim.utils.MoleculeUtils	static
generate2DCoordinates(IAtomContainer ac, Logger logger)	denoptim.utils.MoleculeUtils	static
getAtomRef(IAtom atm, IAtomContainer mol)	denoptim.utils.MoleculeUtils	static
getDimensions(IAtomContainer mol)	denoptim.utils.MoleculeUtils	static
getHeavyAtomCount(IAtomContainer mol)	denoptim.utils.MoleculeUtils	static
getInChIKeyForMolecule(IAtomContainer mol, Logger logger)	denoptim.utils.MoleculeUtils	static
getInChIKeyForMolecule(IAtomContainer mol, InchiOptions options, Logger logger)	denoptim.utils.MoleculeUtils	static
getMolecularWeight(IAtomContainer mol)	denoptim.utils.MoleculeUtils	static
getNumberOfRotatableBonds(IAtomContainer mol)	denoptim.utils.MoleculeUtils	static
getPoint3d(IAtom atm)	denoptim.utils.MoleculeUtils	static
getSMILESForMolecule(IAtomContainer mol, Logger logger)	denoptim.utils.MoleculeUtils	static
getSymbolOrLabel(IAtom atm)	denoptim.utils.MoleculeUtils	static
getVertexToAtomIdMap(ArrayList< Vertex > vertLst, IAtomContainer mol)	denoptim.utils.MoleculeUtils	static
isDummy(IAtom atm)	denoptim.utils.MoleculeUtils	static
isElement(IAtom atom)	denoptim.utils.MoleculeUtils	static
isElement(String symbol)	denoptim.utils.MoleculeUtils	static
makeSameAs(IAtomContainer mol)	denoptim.utils.MoleculeUtils	static
makeSameAtomAs(IAtom oAtm)	denoptim.utils.MoleculeUtils	static
makeSameAtomAs(IAtom oAtm, boolean ignoreValence, boolean ignoreImplicitH)	denoptim.utils.MoleculeUtils	static
missmatchingAromaticity(IAtomContainer mol)	denoptim.utils.MoleculeUtils	static
moleculeToPNG(IAtomContainer mol, String filename, Logger logger)	denoptim.utils.MoleculeUtils	static
numOfBondsWithBO(IAtom atm, IAtomContainer mol, IBond.Order order)	denoptim.utils.MoleculeUtils	static
removeRCA(IAtomContainer mol)	denoptim.utils.MoleculeUtils	static
removeUsedRCA(IAtomContainer mol, DGraph graph, Logger logger)	denoptim.utils.MoleculeUtils	static
SDG	denoptim.utils.MoleculeUtils	privatestatic
setZeroImplicitHydrogensToAllAtoms(IAtomContainer iac)	denoptim.utils.MoleculeUtils	static
SMGEN	denoptim.utils.MoleculeUtils	privatestatic