CDKManager - Githubissues

[ ] 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) {
[x] public ICDKMolecule loadMolecule(IFile file, IProgressMonitor monitor)
[x] public ICDKMolecule loadMolecule( InputStream instream,
[ ] public List loadMolecules( IFile file,
[ ] public List loadMolecules( InputStream contents,
[ ] public List loadMolecules( IFile file,
[x] 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 {
[x] public ICDKMolecule fromSMILES(String smilesDescription)
[x] public ICDKMolecule fromCml(String molstring)
[x] 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,
[x] public ICDKMolecule asCDKMolecule(IMolecule imol) throws BioclipseException {
[ ] public boolean smartsMatches(ICDKMolecule molecule, String smarts)
[ ] public boolean isValidSmarts(String smarts){
[x] 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,
[x] public double calculateMass(IMolecule molecule) throws BioclipseException {
[x] 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)
[x] public IChemFormat determineIChemFormatOfString(String fileContent)
[x] public IChemFormat determineIChemFormat(IFile file)
[ ] public String determineFormat( String path ) throws IOException,
[x] 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,
[x] public IMolecularFormula molecularFormulaObject(ICDKMolecule m) {
[x] public String molecularFormula( ICDKMolecule m ) {
[ ] public IChemFormat determineFormat(IContentType type) {
[x] public IChemFormat getFormat(String type) {
[x] public String getFormats() {
[x] public List createMoleculeList() throws BioclipseException,
[ ] public ICDKMolecule perceiveAromaticity( IMolecule mol ) throws BioclipseException {
[ ] public List perceiveAromaticity(List<? extends IMolecule> mols) throws BioclipseException{
[x] public List partition(IMolecule molecule)
[x] 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 {
[x] public Object getProperty(ICDKMolecule molecule, Object propertyName) {
[x] 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 / bacting

CDKManager #35