| Modifier and Type | Class and Description |
|---|---|
class |
CTKSmilesException |
| 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
|
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