- CDKConvention - Class in org.openscience.cdk.io.cml
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This is an implementation for the CDK convention.
- CDKConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CDKConvention
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- CDKConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.CDKConvention
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- CDKSourceCodeWriter - Class in org.openscience.cdk.io
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Converts a Molecule into CDK source code that would build the same
molecule.
- CDKSourceCodeWriter(Writer) - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter
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Constructs a new CDKSourceCodeWriter.
- CDKSourceCodeWriter(OutputStream) - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter
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- CDKSourceCodeWriter() - Constructor for class org.openscience.cdk.io.CDKSourceCodeWriter
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- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.CDKConvention
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- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.CMLCoreModule
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- characterData(CMLStack, char[], int, int) - Method in interface org.openscience.cdk.io.cml.ICMLModule
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- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.JMOLANIMATIONConvention
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- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.MDLMolConvention
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- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.PDBConvention
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- characterData(CMLStack, char[], int, int) - Method in class org.openscience.cdk.io.cml.PMPConvention
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- characters(char[], int, int) - Method in class org.openscience.cdk.io.cml.CMLHandler
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Implementation of the characters() procedure overwriting the DefaultHandler interface.
- CIFReader - Class in org.openscience.cdk.io
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This is not a reader for the CIF and mmCIF crystallographic formats.
- CIFReader(Reader) - Constructor for class org.openscience.cdk.io.CIFReader
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Create an CIF like file reader.
- CIFReader(InputStream) - Constructor for class org.openscience.cdk.io.CIFReader
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- CIFReader() - Constructor for class org.openscience.cdk.io.CIFReader
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- close() - Method in class org.openscience.cdk.io.CDKSourceCodeWriter
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Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.CIFReader
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- close() - Method in class org.openscience.cdk.io.CMLReader
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- close() - Method in class org.openscience.cdk.io.CTXReader
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- close() - Method in class org.openscience.cdk.io.Gaussian03Reader
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- close() - Method in class org.openscience.cdk.io.Gaussian98Reader
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- close() - Method in class org.openscience.cdk.io.GhemicalMMReader
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- close() - Method in class org.openscience.cdk.io.HINReader
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- close() - Method in class org.openscience.cdk.io.HINWriter
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Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
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- close() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundASNReader
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- close() - Method in class org.openscience.cdk.io.iterator.IteratingPCCompoundXMLReader
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- close() - Method in class org.openscience.cdk.io.iterator.IteratingPCSubstancesXMLReader
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- close() - Method in class org.openscience.cdk.io.Mol2Reader
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- close() - Method in class org.openscience.cdk.io.Mol2Writer
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Flushes the output and closes this object.
- close() - Method in class org.openscience.cdk.io.Mopac7Reader
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- close() - Method in class org.openscience.cdk.io.PCCompoundASNReader
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- close() - Method in class org.openscience.cdk.io.PCCompoundXMLReader
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- close() - Method in class org.openscience.cdk.io.PCSubstanceXMLReader
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- close() - Method in class org.openscience.cdk.io.PMPReader
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- close() - Method in class org.openscience.cdk.io.program.GaussianInputWriter
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- close() - Method in class org.openscience.cdk.io.program.Mopac7Writer
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- close() - Method in class org.openscience.cdk.io.ShelXReader
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- close() - Method in class org.openscience.cdk.io.XYZReader
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- close() - Method in class org.openscience.cdk.io.XYZWriter
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Flushes the output and closes this object.
- CMLCoreModule - Class in org.openscience.cdk.io.cml
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Core CML 1.x and 2.x elements are parsed by this class (see [Willighagen, E.L., Processing CML Conventions in Java, Internet Journal of Chemistry, 2001, 4:?-?]).
- CMLCoreModule(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CMLCoreModule
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- CMLCoreModule(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.CMLCoreModule
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- CMLErrorHandler - Class in org.openscience.cdk.io.cml
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CDK's SAX2 ErrorHandler for giving feedback on XML errors in the CML document.
- CMLErrorHandler() - Constructor for class org.openscience.cdk.io.cml.CMLErrorHandler
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Constructor a SAX2 ErrorHandler that uses the cdk.tools.LoggingTool
class to output errors and warnings to.
- CMLHandler - Class in org.openscience.cdk.io.cml
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SAX2 implementation for CML XML fragment reading.
- CMLHandler(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CMLHandler
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Constructor for the CMLHandler.
- CMLModuleStack - Class in org.openscience.cdk.io.cml
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Low weight alternative to Sun's Stack class.
- CMLModuleStack() - Constructor for class org.openscience.cdk.io.cml.CMLModuleStack
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- CMLReactionModule - Class in org.openscience.cdk.io.cml
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- CMLReactionModule(IChemFile) - Constructor for class org.openscience.cdk.io.cml.CMLReactionModule
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- CMLReactionModule(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.CMLReactionModule
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- CMLReader - Class in org.openscience.cdk.io
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Reads a molecule in CML 1.x and 2.0 format.
- CMLReader(InputStream) - Constructor for class org.openscience.cdk.io.CMLReader
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Reads CML from an java.io.InputStream, for example the FileInputStream.
- CMLReader() - Constructor for class org.openscience.cdk.io.CMLReader
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- CMLReader(String) - Constructor for class org.openscience.cdk.io.CMLReader
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Define this CMLReader to take the input from a java.io.Reader
class.
- CMLResolver - Class in org.openscience.cdk.io.cml
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This class resolves DOCTYPE declaration for Chemical Markup Language (CML)
files and uses a local version for validation.
- CMLResolver() - Constructor for class org.openscience.cdk.io.cml.CMLResolver
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- createReader(InputStream) - Method in class org.openscience.cdk.io.ReaderFactory
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Detects the format of the Reader input, and if known, it will return
a CDK Reader to read the format, or null when the reader is not
implemented.
- createReader(IChemFormat) - Method in class org.openscience.cdk.io.ReaderFactory
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Creates a new IChemObjectReader based on the given IChemFormat.
- createReader(Reader) - Method in class org.openscience.cdk.io.ReaderFactory
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Detects the format of the Reader input, and if known, it will return
a CDK Reader to read the format.
- createWriter(IChemFormat) - Method in class org.openscience.cdk.io.WriterFactory
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Creates a new IChemObjectWriter based on the given IChemFormat.
- crystalScalar - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- CTXReader - Class in org.openscience.cdk.io
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Reader that extracts information from the IDENT, NAME, ATOMS and BONDS
blocks in CTX files.
- CTXReader() - Constructor for class org.openscience.cdk.io.CTXReader
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- CTXReader(Reader) - Constructor for class org.openscience.cdk.io.CTXReader
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- CTXReader(InputStream) - Constructor for class org.openscience.cdk.io.CTXReader
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- curRef - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- current() - Method in class org.openscience.cdk.io.cml.CMLModuleStack
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Returns the last added entry.
- currentAtom - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- currentBond - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- currentChars - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- currentChemFile - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- currentChemModel - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- currentChemSequence - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- CurrentElement - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- currentMolecule - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- currentMoleculeSet - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- currentMonomer - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- currentReaction - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- currentReactionSet - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- currentStrand - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- parityARef1 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- parityARef2 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- parityARef3 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- parityARef4 - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- parityAtomsGiven - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- parityGiven - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- parseAtomCharges(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
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- parseAtomElements(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
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- parseCompoundsBlock(XMLStreamReader) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
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- parseMolecule(XMLStreamReader, IChemObjectBuilder) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
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- parserAtomBlock(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
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- parserBondBlock(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
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- parserCompoundInfoData(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
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- parserCoordBlock(XMLStreamReader, IAtomContainer) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
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- parseSubstance(XMLStreamReader) - Method in class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
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- partialCharges - Variable in class org.openscience.cdk.io.cml.CMLCoreModule
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- PCCompoundASNReader - Class in org.openscience.cdk.io
-
Reads an object from ASN formated input for PubChem Compound entries.
- PCCompoundASNReader(Reader) - Constructor for class org.openscience.cdk.io.PCCompoundASNReader
-
Construct a new reader from a Reader type object.
- PCCompoundASNReader(InputStream) - Constructor for class org.openscience.cdk.io.PCCompoundASNReader
-
- PCCompoundASNReader() - Constructor for class org.openscience.cdk.io.PCCompoundASNReader
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- PCCompoundXMLReader - Class in org.openscience.cdk.io
-
Reads an object from ASN.1 XML formated input for PubChem Compound entries.
- PCCompoundXMLReader(Reader) - Constructor for class org.openscience.cdk.io.PCCompoundXMLReader
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Construct a new reader from a Reader type object.
- PCCompoundXMLReader(InputStream) - Constructor for class org.openscience.cdk.io.PCCompoundXMLReader
-
- PCCompoundXMLReader() - Constructor for class org.openscience.cdk.io.PCCompoundXMLReader
-
- PCSubstanceXMLReader - Class in org.openscience.cdk.io
-
Reads an object from ASN formated input for PubChem Compound entries.
- PCSubstanceXMLReader(Reader) - Constructor for class org.openscience.cdk.io.PCSubstanceXMLReader
-
Construct a new reader from a Reader type object.
- PCSubstanceXMLReader(InputStream) - Constructor for class org.openscience.cdk.io.PCSubstanceXMLReader
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- PCSubstanceXMLReader() - Constructor for class org.openscience.cdk.io.PCSubstanceXMLReader
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- PDBConvention - Class in org.openscience.cdk.io.cml
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Implements the PDB convention used by PDB2CML.
- PDBConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.PDBConvention
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- PDBConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.PDBConvention
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- PMPConvention - Class in org.openscience.cdk.io.cml
-
Implementation of the PMPMol Covention for CML.
- PMPConvention(IChemFile) - Constructor for class org.openscience.cdk.io.cml.PMPConvention
-
- PMPConvention(ICMLModule) - Constructor for class org.openscience.cdk.io.cml.PMPConvention
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- PMPReader - Class in org.openscience.cdk.io
-
Reads an frames from a PMP formated input.
- PMPReader(Reader) - Constructor for class org.openscience.cdk.io.PMPReader
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- PMPReader(InputStream) - Constructor for class org.openscience.cdk.io.PMPReader
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- PMPReader() - Constructor for class org.openscience.cdk.io.PMPReader
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- pop() - Method in class org.openscience.cdk.io.cml.CMLModuleStack
-
Retrieves and deletes to last added entry.
- process() - Method in class org.openscience.cdk.io.iterator.event.EventCMLReader
-
Starts the reading of the CML file.
- processIOSettingQuestion(IOSetting) - Method in class org.openscience.cdk.io.listener.SwingGUIListener
-
Processes the IOSettings by listing the question, giving the options
and asking the user to provide their choice.
- processIOSettingQuestion(IOSetting) - Method in class org.openscience.cdk.io.listener.TextGUIListener
-
Processes the IOSettings by listing the question, giving the options
and asking the user to provide their choice.
- PubChemXMLHelper - Class in org.openscience.cdk.io.pubchemxml
-
Helper class to parse PubChem XML documents.
- PubChemXMLHelper(IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.pubchemxml.PubChemXMLHelper
-
- push(ICMLModule) - Method in class org.openscience.cdk.io.cml.CMLModuleStack
-
Adds an entry to the stack.