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A

addIBase(IChemObjectBase) - Method in class org.helm.chemtoolkit.cdk.CDKMolecule

atom - Variable in class org.helm.chemtoolkit.cdk.CDKAtom

B

bindAtoms(IAtomBase, IAtomBase) - Method in class org.helm.chemtoolkit.cdk.CDKManipulator

bond - Variable in class org.helm.chemtoolkit.cdk.CDKBond

bonds - Variable in class org.helm.chemtoolkit.cdk.CDKAtom

bonds - Variable in class org.helm.chemtoolkit.cdk.CDKBond

boundCount - Variable in class org.helm.chemtoolkit.cdk.CDKAtom

C

canonicalize(String) - Method in class org.helm.chemtoolkit.cdk.CDKManipulator

CDKAtom - Class in org.helm.chemtoolkit.cdk

CDKAtom(IAtom) - Constructor for class org.helm.chemtoolkit.cdk.CDKAtom

CDKAtom(IAtom, int) - Constructor for class org.helm.chemtoolkit.cdk.CDKAtom

CDKAtom(IAtom, int, List<IBond>) - Constructor for class org.helm.chemtoolkit.cdk.CDKAtom

CDKBond - Class in org.helm.chemtoolkit.cdk

CDKBond(IBond) - Constructor for class org.helm.chemtoolkit.cdk.CDKBond

CDKBond(IBond, IStereoElementBase) - Constructor for class org.helm.chemtoolkit.cdk.CDKBond

CDKManipulator - Class in org.helm.chemtoolkit.cdk

CDKManipulator() - Constructor for class org.helm.chemtoolkit.cdk.CDKManipulator

CDKMolecule - Class in org.helm.chemtoolkit.cdk

CDKMolecule(IAtomContainer) - Constructor for class org.helm.chemtoolkit.cdk.CDKMolecule

CDKMolecule(IAtomContainer, AttachmentList) - Constructor for class org.helm.chemtoolkit.cdk.CDKMolecule

CDKStereoElement - Class in org.helm.chemtoolkit.cdk

CDKStereoElement TODO comment me

CDKStereoElement(IStereoElement) - Constructor for class org.helm.chemtoolkit.cdk.CDKStereoElement

changeAtomLabel(int, int) - Method in class org.helm.chemtoolkit.cdk.CDKMolecule

cloneMolecule() - Method in class org.helm.chemtoolkit.cdk.CDKMolecule

compare(Object) - Method in class org.helm.chemtoolkit.cdk.CDKAtom

convert(String, AbstractChemistryManipulator.StType) - Method in class org.helm.chemtoolkit.cdk.CDKManipulator

convertMolecule(AbstractMolecule, AbstractChemistryManipulator.StType) - Method in class org.helm.chemtoolkit.cdk.CDKManipulator

convertMolIntoSmilesWithAtomMapping(String) - Method in class org.helm.chemtoolkit.cdk.CDKManipulator

D

dearomatize() - Method in class org.helm.chemtoolkit.cdk.CDKMolecule

G

generateCoordinates(int) - Method in class org.helm.chemtoolkit.cdk.CDKMolecule

getAtomBond() - Method in class org.helm.chemtoolkit.cdk.CDKBond

getBond() - Method in class org.helm.chemtoolkit.cdk.CDKStereoElement

getIAtno() - Method in class org.helm.chemtoolkit.cdk.CDKAtom

getIAtom1() - Method in class org.helm.chemtoolkit.cdk.CDKBond

getIAtom2() - Method in class org.helm.chemtoolkit.cdk.CDKBond

getIBond(int) - Method in class org.helm.chemtoolkit.cdk.CDKAtom

getIBondArray() - Method in class org.helm.chemtoolkit.cdk.CDKMolecule

getIBondCount() - Method in class org.helm.chemtoolkit.cdk.CDKAtom

getMolAtom() - Method in class org.helm.chemtoolkit.cdk.CDKAtom

getMolecule() - Method in class org.helm.chemtoolkit.cdk.CDKMolecule

getMolecule(String, AttachmentList) - Method in class org.helm.chemtoolkit.cdk.CDKManipulator

getMoleculeInfo(AbstractMolecule) - Method in class org.helm.chemtoolkit.cdk.CDKManipulator

getRgroup() - Method in class org.helm.chemtoolkit.cdk.CDKAtom

getRgroups() - Method in class org.helm.chemtoolkit.cdk.CDKMolecule

getStereoElement() - Method in class org.helm.chemtoolkit.cdk.CDKBond

getStereoElement() - Method in class org.helm.chemtoolkit.cdk.CDKStereoElement

getStereoInformation(AbstractMolecule, IAtomBase, IAtomBase, IAtomBase) - Method in class org.helm.chemtoolkit.cdk.CDKManipulator

getType() - Method in class org.helm.chemtoolkit.cdk.CDKBond

I

isConnected(String) - Method in class org.helm.chemtoolkit.cdk.CDKManipulator

isSingleStereo(IAtomBase) - Method in class org.helm.chemtoolkit.cdk.CDKMolecule

O

org.helm.chemtoolkit.cdk - package org.helm.chemtoolkit.cdk

R

removeIBase(IChemObjectBase) - Method in class org.helm.chemtoolkit.cdk.CDKMolecule

removeINode(IAtomBase) - Method in class org.helm.chemtoolkit.cdk.CDKMolecule

renderMol(String, AbstractChemistryManipulator.OutputType, int, int, int) - Method in class org.helm.chemtoolkit.cdk.CDKManipulator

renderSequence(String, AbstractChemistryManipulator.OutputType, int, int, int) - Method in class org.helm.chemtoolkit.cdk.CDKManipulator

rGroup - Variable in class org.helm.chemtoolkit.cdk.CDKAtom

S

setBond(IBond) - Method in class org.helm.chemtoolkit.cdk.CDKStereoElement

setRgroup(int) - Method in class org.helm.chemtoolkit.cdk.CDKAtom

setStereoInformation(AbstractMolecule, IAtomBase, AbstractMolecule, IAtomBase, IAtomBase, IAtomBase) - Method in class org.helm.chemtoolkit.cdk.CDKManipulator

stereoElement - Variable in class org.helm.chemtoolkit.cdk.CDKBond

V

validateSMILES(String) - Method in class org.helm.chemtoolkit.cdk.CDKManipulator

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