Uses of Class
org.helm.chemtoolkit.IAtomBase

Uses of IAtomBase in org.helm.chemtoolkit

Fields in org.helm.chemtoolkit with type parameters of type IAtomBase

Modifier and Type	Field and Description
protected List<IAtomBase>	AbstractMolecule.atoms

Methods in org.helm.chemtoolkit that return IAtomBase

Modifier and Type	Method and Description
IAtomBase	IBondBase.getIAtom1()
IAtomBase	IBondBase.getIAtom2()
protected IAtomBase	AbstractChemistryManipulator.getNeighborAtom(IAtomBase rgroup)
IAtomBase	AbstractMolecule.getRGroupAtom(int groupId, boolean rgatom)

Methods in org.helm.chemtoolkit that return types with arguments of type IAtomBase

Modifier and Type	Method and Description
List<IAtomBase>	AbstractMolecule.getIAtomArray()
Map<String,IAtomBase>	AbstractMolecule.getRgroups()

Methods in org.helm.chemtoolkit with parameters of type IAtomBase

Modifier and Type	Method and Description
protected abstract IBondBase	AbstractChemistryManipulator.bindAtoms(IAtomBase atom1, IAtomBase atom2)
protected IAtomBase	AbstractChemistryManipulator.getNeighborAtom(IAtomBase rgroup)
protected abstract IStereoElementBase	AbstractChemistryManipulator.getStereoInformation(AbstractMolecule container, IAtomBase rGroup, IAtomBase atom1, IAtomBase atom2)
abstract boolean	AbstractMolecule.isSingleStereo(IAtomBase atom) check a given atom connections
AbstractMolecule	AbstractChemistryManipulator.merge(AbstractMolecule firstContainer, IAtomBase firstRgroup, AbstractMolecule secondContainer, IAtomBase secondRgroup) merges second molecule to first using given rGroups
void	AbstractMolecule.removeAttachment(IAtomBase toRemove) removes a given attachment from molecule
abstract void	AbstractMolecule.removeINode(IAtomBase node)
protected boolean	AbstractChemistryManipulator.setStereoInformation(AbstractMolecule firstContainer, IAtomBase firstRgroup, AbstractMolecule secondContainer, IAtomBase secondRgroup, IAtomBase atom1, IAtomBase atom2) recycles and set stereo information on firstContaner