CDKManager

[egonw]

• public ICDKMolecule newMolecule() {
• public ICDKMolecule newMolecule(IAtomContainer atomContainer) {
• public List asList( IAtomContainerSet set ) {
• public IAtomContainerSet asSet( List list ) {
• public MarkerErrorHandler(IFile file) {
• public void handleError(String message, int row, int colStart,
• public void handleError(String message, int row, int colStart,
• public void handleError(String message, Exception exception) {
• public void handleError(String message) {
• public ICDKMolecule loadMolecule(IFile file, IProgressMonitor monitor)
• public ICDKMolecule loadMolecule( InputStream instream,
• public List loadMolecules( IFile file,
• public List loadMolecules( InputStream contents,
• public List loadMolecules( IFile file,
• public void calculateSMILES(IMolecule molecule,IReturner returner,
• public void save(IChemModel model, String target, IChemFormat filetype,
• public void save( IAtomContainer model,
• public void save( IChemModel model,
• public void customize( IAtom atom, Object nodeToAdd )
• public void customize( IBond bond, Object nodeToAdd )
• public void customize( IAtomContainer molecule,
• public void saveMolecule(IMolecule mol)
• public void saveMolecule(IMolecule mol, String filename)
• public void saveMolecule(IMolecule mol, boolean overwrite)
• public void saveMolecule(IMolecule mol, String filename, boolean overwrite)
• public void saveMolecule(IMolecule mol, IFile file, boolean overwrite)
• public IChemFormat guessFormatFromExtension(String file) {
• public void saveMolecule( IMolecule mol_in,
• public void saveMolecule(IMolecule mol_in, IFile target, IChemFormat filetype)
• public void saveMolecule( IMolecule mol_in,
• public void saveMolecule( IMolecule mol_in,
• public void saveMolecule( IMolecule mol,
• public void saveMolecule( IMolecule mol,
• public void saveMolecules( List<? extends IMolecule> molecules,
• public void saveMolecules( List<? extends IMolecule> molecules,
• public void generateImage(IMolecule molecule, String path) throws Exception {
• public void generateImage(IMolecule molecule, String path, int width, int height) throws Exception {
• public ICDKMolecule fromSMILES(String smilesDescription)
• public ICDKMolecule fromCml(String molstring)
• public ICDKMolecule fromString(String molstring)
• public List moleculesFromString( String s )
• public Iterator
• public Iterator createConformerIterator(String path) {
• public Iterator
• public boolean fingerPrintMatches( ICDKMolecule molecule,
• public boolean subStructureMatches( ICDKMolecule molecule,
• public List subStructureMatches(
• public List getSubstructures(ICDKMolecule molecule,
• public boolean areIsomorphic( ICDKMolecule molecule,
• public ICDKMolecule asCDKMolecule(IMolecule imol) throws BioclipseException {
• public boolean smartsMatches(ICDKMolecule molecule, String smarts)
• public boolean isValidSmarts(String smarts){
• public boolean isValidCAS(String number){
• public List getSmartsMatches(ICDKMolecule molecule,
• public int numberOfEntriesInSDF(IFile file, IProgressMonitor monitor) {
• public Record(int s, int l) {
• public void createSDFileIndex( IFile file , IProgressMonitor monitor) {
• public List loadConformers( IFile file,
• public double calculateMass(IMolecule molecule) throws BioclipseException {
• public double calculateMajorIsotopeMass(IMolecule molecule) throws BioclipseException {
• public void generate2dCoordinates(IMolecule molecule,
• public void generate2dCoordinates(List molecules,
• public void saveMol2(ICDKMolecule mol, String filename)
• public List loadSMILESFile( IFile file,
• public List loadSMILESFile( InputStream contents,
• public int getNoMolecules(IFile file)
• public void generate3dCoordinates(IMolecule molecule,
• public void generate3dCoordinates(List molecules,
• public ICDKMolecule addExplicitHydrogens(IMolecule molecule)
• public ICDKMolecule addImplicitHydrogens(IMolecule molecule)
• public MoleculesInfo getInfo(IFile transform) {
• public boolean has2d(IMolecule mol) throws BioclipseException {
• public boolean has3d(IMolecule mol) throws BioclipseException {
• public void saveCML(ICDKMolecule cml, String filename)
• public void saveMDLMolfile(ICDKMolecule mol, String filename)
• public IChemFormat determineIChemFormatOfString(String fileContent)
• public IChemFormat determineIChemFormat(IFile file)
• public String determineFormat( String path ) throws IOException,
• public void appendToSDF( IFile sdFile, ICDKMolecule molecule ) throws BioclipseException {
• public void saveSDFile(final IFile file, List<? extends IMolecule> entries,
• public void run(IProgressMonitor monitor)
• public List extractFromSDFile( IFile file,
• public Map<Integer,String> createSDFPropertyMap( IFile file,
• public List extractFromSDFile( IFile file, int startenty,
• public IMolecularFormula molecularFormulaObject(ICDKMolecule m) {
• public String molecularFormula( ICDKMolecule m ) {
• public IChemFormat determineFormat(IContentType type) {
• public IChemFormat getFormat(String type) {
• public String getFormats() {
• public List createMoleculeList() throws BioclipseException,
• public ICDKMolecule perceiveAromaticity( IMolecule mol ) throws BioclipseException {
• public List perceiveAromaticity(List<? extends IMolecule> mols) throws BioclipseException{
• public List partition(IMolecule molecule)
• public int totalFormalCharge(IMolecule molecule)
• public float calculateTanimoto(BitSet fingerprint1, BitSet fingerprint2)
• public float calculateTanimoto(IMolecule calculateFor, BitSet reference )
• public float calculateTanimoto( IMolecule calculateFor,
• public void calculateTanimoto( List calculateFor,
• public IFile calculateTanimoto(List molecules,
• public IFile calculateRMSD(List molecules,
• public String getMDLMolfileString(IMolecule molecule_in) throws BioclipseException {
• public Object getProperty(ICDKMolecule molecule, Object propertyName) {
• public Object setProperty(ICDKMolecule molecule, Object propertyName,
• public ICDKMolecule removeExplicitHydrogens(ICDKMolecule molecule) {
• public ICDKMolecule removeImplicitHydrogens(ICDKMolecule molecule) {
• public boolean isConnected(IMolecule molecule) throws BioclipseException {
• public ICDKMolecule clone(ICDKMolecule molecule) throws BioclipseException {
• public ICDKMolecule mcss(List molecules,
• public List kabsch(List molecules,
• public List kabsch(List molecules,
• public List getTautomers(IMolecule molecule, IProgressMonitor monitor)
• public List<List> randomSplit(List mols_in, int parts){
• public List<List> randomSplit2parts(List mols_in, double firstRatio){
• public void convertSDFtoSMILESFile( IFile sdfFile,

[egonw]

New:

• public Set getAtomsWithUndefinedStereo(IMolecule molecule)
• public Set getAtomsWithDefinedStereo(IMolecule molecule)

[egonw]

New in 0.0.21:

• public String asSVG(IMolecule molecule)