Uses of Class
org.helm.chemtoolkit.CTKException

Uses of CTKException in org.helm.chemtoolkit

Subclasses of CTKException in org.helm.chemtoolkit

Modifier and Type	Class and Description
class	CTKSmilesException

Methods in org.helm.chemtoolkit that throw CTKException

Modifier and Type	Method and Description
protected abstract IBondBase	AbstractChemistryManipulator.bindAtoms(IAtomBase atom1, IAtomBase atom2)
abstract String	AbstractChemistryManipulator.canonicalize(String data) returns canonical smiles
abstract void	AbstractMolecule.changeAtomLabel(int index, int toIndex)
abstract AbstractMolecule	AbstractMolecule.cloneMolecule()
abstract String	AbstractChemistryManipulator.convert(String data, AbstractChemistryManipulator.StType type) convert input notation to another
abstract String	AbstractChemistryManipulator.convertMolecule(AbstractMolecule container, AbstractChemistryManipulator.StType type) produces chemical notation for input molecule
abstract void	AbstractMolecule.dearomatize()
abstract void	AbstractMolecule.generateCoordinates(int dem)
abstract IBondBase	IAtomBase.getIBond(int arg0)
abstract AbstractMolecule	AbstractChemistryManipulator.getMolecule(String smiles, AttachmentList attachments) returns a molecule i)nstance of AbstractMolecule
abstract MoleculeInfo	AbstractChemistryManipulator.getMoleculeInfo(AbstractMolecule container) returns molecule info like molecular formula,exact mass and molecular weight
protected IAtomBase	AbstractChemistryManipulator.getNeighborAtom(IAtomBase rgroup)
IAtomBase	AbstractMolecule.getRGroupAtom(int groupId, boolean rgatom)
Map<String,IAtomBase>	AbstractMolecule.getRgroups()
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
protected AttachmentList	AbstractChemistryManipulator.mergeAttachments(AbstractMolecule container, AbstractMolecule secondContainer)
void	AbstractMolecule.removeAttachment(IAtomBase toRemove) removes a given attachment from molecule
abstract void	AbstractMolecule.removeINode(IAtomBase node)
abstract byte[]	AbstractChemistryManipulator.renderMol(String molFile, AbstractChemistryManipulator.OutputType outputType, int width, int height, int rgb) renders a image of given molecule
abstract byte[]	AbstractChemistryManipulator.renderSequence(String sequence, AbstractChemistryManipulator.OutputType outputType, int width, int height, int rgb) renders a image of molecule
abstract void	IAtomBase.setRgroup(int rGroup)
protected boolean	AbstractChemistryManipulator.setStereoInformation(AbstractMolecule firstContainer, IAtomBase firstRgroup, AbstractMolecule secondContainer, IAtomBase secondRgroup, IAtomBase atom1, IAtomBase atom2) recycles and set stereo information on firstContaner