Search Java Classes and Packages
#Org.openscience.cdk.io Classes and Interfaces - 201 results found.
| Name | Description | Type | Package | Framework |
| ABINITFormat | Class | org.openscience.cdk.io.formats | CDK | |
| Aces2Format | Class | org.openscience.cdk.io.formats | CDK | |
| ADFFormat | Class | org.openscience.cdk.io.formats | CDK | |
| AlchemyFormat | Class | org.openscience.cdk.io.formats | CDK | |
| BGFFormat | Class | org.openscience.cdk.io.formats | CDK | |
| BooleanIOSetting | An class for a reader setting which must be of type String. | Class | org.openscience.cdk.io.setting | CDK |
| BSFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CacaoCartesianFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CacaoInternalFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CACheFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CDKConvention | This is an implementation for the CDK convention. | Class | org.openscience.cdk.io.cml | CDK |
| CDKOWLFormat | Serializes a CDK model into the Web Ontology Language using theBelongs to the set:io-formats | Class | org.openscience.cdk.io.formats | CDK |
| CDKOWLReader | Reads content from a CDK OWL serialization. | Class | org.openscience.cdk.io.rdf | CDK |
| CDKOWLWriter | Serializes the data model into CDK OWL. | Class | org.openscience.cdk.io.rdf | CDK |
| CDKSourceCodeFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CDKSourceCodeWriter | Converts a Molecule into CDK source code that would build the same molecule. | Class | org.openscience.cdk.io | CDK |
| Chem3D_Cartesian_1Format | Class | org.openscience.cdk.io.formats | CDK | |
| Chem3D_Cartesian_2Format | Class | org.openscience.cdk.io.formats | CDK | |
| ChemDrawFormat | Class | org.openscience.cdk.io.formats | CDK | |
| ChemtoolFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CIFFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CIFReader | This is not a reader for the CIF and mmCIF crystallographic formats. | Class | org.openscience.cdk.io | CDK |
| CMLCoreModule | Core CML 1. | Class | org.openscience.cdk.io.cml | CDK |
| CMLErrorHandler | CDK's SAX2 ErrorHandler for giving feedback on XML errors in the CML document. | Class | org.openscience.cdk.io.cml | CDK |
| CMLFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CMLHandler | SAX2 implementation for CML XML fragment reading. | Class | org.openscience.cdk.io.cml | CDK |
| CMLReactionModule | Class | org.openscience.cdk.io.cml | CDK | |
| CMLReader | Reads a molecule in CML 1. | Class | org.openscience.cdk.io | CDK |
| CMLResolver | This class resolves DOCTYPE declaration for Chemical Markup Language (CML) files and uses a local version for validation. | Class | org.openscience.cdk.io.cml | CDK |
| CMLRSSFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CMLStack | Low weigth alternative to Sun's Stack class. | Class | org.openscience.cdk.io.cml | CDK |
| CMLWriter | Serializes a IMoleculeSet or a IMolecule object to CML 2 code. | Class | org.openscience.cdk.io | CDK |
| CRK2DFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CRK3DFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CrystClustFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CrystClustReader | Class | org.openscience.cdk.io | CDK | |
| CrystClustWriter | Rather stupid file format used for storing crystal information. | Class | org.openscience.cdk.io | CDK |
| CTXFormat | Class | org.openscience.cdk.io.formats | CDK | |
| CTXReader | Reader that extracts information from the IDENT, NAME, ATOMS and BONDS blocks in CTX files. | Class | org.openscience.cdk.io | CDK |
| CustomSerializer | Custom Serializer with the sole purpose and functionality to not output the XML declaration. | Class | org.openscience.cdk.io.cml | CDK |
| DaltonFormat | Class | org.openscience.cdk.io.formats | CDK | |
| DefaultChemObjectReader | Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners. | Class | org.openscience.cdk.io | CDK |
| DefaultChemObjectWriter | Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners. | Class | org.openscience.cdk.io | CDK |
| DefaultEventChemObjectReader | Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners. | Class | org.openscience.cdk.io.iterator.event | CDK |
| DefaultIteratingChemObjectReader | Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners. | Class | org.openscience.cdk.io.iterator | CDK |
| DefaultRandomAccessChemObjectReader | Abstract class that IRandomAccessChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners. | Class | org.openscience.cdk.io.random | CDK |
| DMol3Format | Class | org.openscience.cdk.io.formats | CDK | |
| DOCK5Format | Class | org.openscience.cdk.io.formats | CDK | |
| EventCMLHandler | CDO object needed as interface with the JCFL library for reading CML in a event based manner. | Class | org.openscience.cdk.io.iterator.event | CDK |
| EventCMLReader | Reads a molecule in CML 1. | Class | org.openscience.cdk.io.iterator.event | CDK |
| FenskeHall_ZMatrixFormat | Class | org.openscience.cdk.io.formats | CDK | |
| FingerprintFormat | Class | org.openscience.cdk.io.formats | CDK | |
| FormatFactory | A factory for recognizing chemical file formats. | Class | org.openscience.cdk.io | CDK |
| GamessFormat | Class | org.openscience.cdk.io.formats | CDK | |
| GamessReader | A reader for GAMESS log file. | Class | org.openscience.cdk.io | CDK |
| Gaussian03Format | Class | org.openscience.cdk.io.formats | CDK | |
| Gaussian03Reader | A reader for Gaussian03 output. | Class | org.openscience.cdk.io | CDK |
| Gaussian90Format | Class | org.openscience.cdk.io.formats | CDK | |
| Gaussian92Format | Class | org.openscience.cdk.io.formats | CDK | |
| Gaussian94Format | Class | org.openscience.cdk.io.formats | CDK | |
| Gaussian95Format | Class | org.openscience.cdk.io.formats | CDK | |
| Gaussian98Format | Class | org.openscience.cdk.io.formats | CDK | |
| Gaussian98Reader | A reader for Gaussian98 output. | Class | org.openscience.cdk.io | CDK |
| GaussianInputFormat | Class | org.openscience.cdk.io.formats | CDK | |
| GaussianInputWriter | File writer thats generates input files for Gaussian calculation jobs. | Class | org.openscience.cdk.io.program | CDK |
| GhemicalMMFormat | Class | org.openscience.cdk.io.formats | CDK | |
| GhemicalMMReader | http://www. | Class | org.openscience.cdk.io | CDK |
| GhemicalSPMFormat | Class | org.openscience.cdk.io.formats | CDK | |
| GROMOS96Format | Class | org.openscience.cdk.io.formats | CDK | |
| HINFormat | Class | org.openscience.cdk.io.formats | CDK | |
| HINReader | Reads an object from HIN formated input. | Class | org.openscience.cdk.io | CDK |
| HINWriter | Writer that outputs in the HIN format. | Class | org.openscience.cdk.io | CDK |
| IChemFormat | This class is the interface that all ChemFormat's should implement. | Interface | org.openscience.cdk.io.formats | CDK |
| IChemFormatMatcher | This interface is used for classes that are able to match a certain chemical file format. | Interface | org.openscience.cdk.io.formats | CDK |
| IChemObjectIO | This class is the interface that all IO readers should implement. | Interface | org.openscience.cdk.io | CDK |
| IChemObjectIOListener | Allows monitoring of progress of file reader activities. | Interface | org.openscience.cdk.io.listener | CDK |
| IChemObjectReader | This interface specifies the common functionality all IO readers should provide. | Interface | org.openscience.cdk.io | CDK |
| IChemObjectReader .Mode | Only fail on serious format problemsFail on any format problem | Class | org.openscience.cdk.io | CDK |
| IChemObjectReaderErrorHandler | Interface for classes aimed to handle IChemObjectReader errors. | Interface | org.openscience.cdk.io | CDK |
| IChemObjectWriter | This class is the interface that all IO writers should implement. | Interface | org.openscience.cdk.io | CDK |
| ICMLConvention | This interface describes the procedures classes must implement to be plugable into the CMLHandler. | Interface | org.openscience.cdk.io.cml | CDK |
| ICMLModule | This interface describes the procedures classes must implement to be plugable into the CMLHandler. | Interface | org.openscience.cdk.io.cml | CDK |
| IEventChemObjectReader | Interface for an iterating molecule reader. | Interface | org.openscience.cdk.io.iterator.event | CDK |
| IIteratingChemObjectReader | Interface for an iterating molecule reader. | Interface | org.openscience.cdk.io.iterator | CDK |
| INChIContentProcessorTool | Tool to help process INChI 1. | Class | org.openscience.cdk.io.inchi | CDK |
| INChIFormat | Class | org.openscience.cdk.io.formats | CDK | |
| INChIHandler | SAX2 implementation for INChI XML fragment parsing. | Class | org.openscience.cdk.io.inchi | CDK |
| INChIPlainTextFormat | Class | org.openscience.cdk.io.formats | CDK | |
| INChIPlainTextReader | Reads the content of a IUPAC/NIST Chemical Identifier (INChI) plain text document. | Class | org.openscience.cdk.io | CDK |
| INChIReader | Reads the content of a IUPAC/NIST Chemical Identifier (INChI) document. | Class | org.openscience.cdk.io | CDK |
| IntegerIOSetting | An class for a reader setting which must be of type String. | Class | org.openscience.cdk.io.setting | CDK |
| IOSetting | An interface for reader settings. | Class | org.openscience.cdk.io.setting | CDK |
| IRandomAccessChemObjectReader | Extension of ListIterator. | Interface | org.openscience.cdk.io.random | CDK |
| IReaderListener | Allows monitoring of progress of file reader activities. | Interface | org.openscience.cdk.io.listener | CDK |
| IResourceFormat | This class is the interface that all ResourceFormat's should implement. | Interface | org.openscience.cdk.io.formats | CDK |
| ISimpleChemObjectReader | This class is the interface that all IO readers should implement. | Interface | org.openscience.cdk.io | CDK |
| IteratingMDLConformerReader | Iterate over conformers of a collection of molecules stored in SDF format. | Class | org.openscience.cdk.io.iterator | CDK |
| IteratingMDLReader | Iterating MDL SDF reader. | Class | org.openscience.cdk.io.iterator | CDK |
| IteratingPCCompoundASNReader | Iterating PubChem PCCompound ASN reader. | Class | org.openscience.cdk.io.iterator | CDK |
| IteratingPCCompoundXMLReader | Iterating PubChem PCCompound ASN. | Class | org.openscience.cdk.io.iterator | CDK |
| IteratingPCSubstancesXMLReader | Iterating PubChem PC-Substances ASN. | Class | org.openscience.cdk.io.iterator | CDK |
| IteratingSMILESReader | Iterating SMILES file reader. | Class | org.openscience.cdk.io.iterator | CDK |
| IWriterListener | Interface | org.openscience.cdk.io.listener | CDK | |
| JaguarFormat | Class | org.openscience.cdk.io.formats | CDK | |
| JMEFormat | Class | org.openscience.cdk.io.formats | CDK | |
| JMOLANIMATIONConvention | Class | org.openscience.cdk.io.cml | CDK | |
| MacroModelFormat | Class | org.openscience.cdk.io.formats | CDK | |
| MDLFormat | Class | org.openscience.cdk.io.formats | CDK | |
| MDLMolConvention | Class | org.openscience.cdk.io.cml | CDK | |
| MDLReader | Reads a molecule from the original MDL MOL or SDF file . | Class | org.openscience.cdk.io | CDK |
| MDLRXNFormat | Class | org.openscience.cdk.io.formats | CDK | |
| MDLRXNReader | Reads a molecule from an MDL RXN file . | Class | org.openscience.cdk.io | CDK |
| MDLRXNV2000Reader | Reads a molecule from an MDL RXN file . | Class | org.openscience.cdk.io | CDK |
| MDLRXNV3000Format | Class | org.openscience.cdk.io.formats | CDK | |
| MDLRXNV3000Reader | Class that implements the new MDL mol format introduced in August 2002. | Class | org.openscience.cdk.io | CDK |
| MDLRXNWriter | Writes a reaction to a MDL rxn or SDF file. | Class | org.openscience.cdk.io | CDK |
| MDLV2000Format | Class | org.openscience.cdk.io.formats | CDK | |
| MDLV2000Reader | Reads content from MDL molfiles and SD files. | Class | org.openscience.cdk.io | CDK |
| MDLV2000Writer | Writes MDL molfiles, which contains a single molecule (see ). | Class | org.openscience.cdk.io | CDK |
| MDLV3000Format | Class | org.openscience.cdk.io.formats | CDK | |
| MDLV3000Reader | Class that implements the MDL mol V3000 format. | Class | org.openscience.cdk.io | CDK |
| MDMoleculeConvention | Class | org.openscience.cdk.io.cml | CDK | |
| MMODFormat | Class | org.openscience.cdk.io.formats | CDK | |
| Mol2Format | Class | org.openscience.cdk.io.formats | CDK | |
| Mol2Reader | Reads a molecule from an Mol2 file, such as written by Sybyl. | Class | org.openscience.cdk.io | CDK |
| Mol2Writer | An output Writer that writes molecular data into the Tripos Mol2 format. | Class | org.openscience.cdk.io | CDK |
| MOPAC2002Format | Class | org.openscience.cdk.io.formats | CDK | |
| MOPAC7Format | Class | org.openscience.cdk.io.formats | CDK | |
| MOPAC93Format | Class | org.openscience.cdk.io.formats | CDK | |
| MOPAC97Format | Class | org.openscience.cdk.io.formats | CDK | |
| MoSSOutputFormat | Class | org.openscience.cdk.io.formats | CDK | |
| MoSSOutputReader | Reader for MoSS output files which present the results of a substructure mining study. | Class | org.openscience.cdk.io | CDK |
| MPQCFormat | Class | org.openscience.cdk.io.formats | CDK | |
| NWChemFormat | Class | org.openscience.cdk.io.formats | CDK | |
| OptionIOSetting | An class for a reader setting which must be found in the list of possible settings. | Class | org.openscience.cdk.io.setting | CDK |
| PCCompoundASNReader | Reads an object from ASN formated input for PubChem Compound entries. | Class | org.openscience.cdk.io | CDK |
| PCCompoundXMLReader | Reads an object from ASN. | Class | org.openscience.cdk.io | CDK |
| PCModelFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PCSubstanceXMLReader | Reads an object from ASN formated input for PubChem Compound entries. | Class | org.openscience.cdk.io | CDK |
| PDBConvention | This is a lousy implementation, though. | Class | org.openscience.cdk.io.cml | CDK |
| PDBFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PDBMLFormat | XML version of the PDB format. | Class | org.openscience.cdk.io.formats | CDK |
| PDBReader | Reads the contents of a PDBFile. | Class | org.openscience.cdk.io | CDK |
| PDBWriter | Saves small molecules in a rudimentary PDB format. | Class | org.openscience.cdk.io | CDK |
| PMPConvention | Class | org.openscience.cdk.io.cml | CDK | |
| PMPFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PMPReader | Reads an frames from a PMP formated input. | Class | org.openscience.cdk.io | CDK |
| POVRayFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PQSChemFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PropertiesListener | Answers the questions by looking up the values in a Properties object. | Class | org.openscience.cdk.io.listener | CDK |
| PubChemASNFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PubChemCompoundsXMLFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PubChemCompoundXMLFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PubChemFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PubChemSubstancesASNFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PubChemSubstancesXMLFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PubChemSubstanceXMLFormat | Class | org.openscience.cdk.io.formats | CDK | |
| PubChemXMLHelper | Helper class to parse PubChem XML documents. | Class | org.openscience.cdk.io.pubchemxml | CDK |
| QChemFormat | Class | org.openscience.cdk.io.formats | CDK | |
| QSARConvention | This is an implementation for the CDK convention. | Class | org.openscience.cdk.io.cml | CDK |
| RandomAccessReader | Random access to text files of compounds. | Class | org.openscience.cdk.io.random | CDK |
| RandomAccessSDFReader | Random access of SDF file. | Class | org.openscience.cdk.io.random | CDK |
| RawCopyFormat | Class | org.openscience.cdk.io.formats | CDK | |
| ReaderEvent | Signals that something has happened in a file reader. | Class | org.openscience.cdk.io | CDK |
| ReaderFactory | A factory for creating ChemObjectReaders. | Class | org.openscience.cdk.io | CDK |
| RGroupQueryFormat | Format for Symyx RGfiles (Rgroup query files). | Class | org.openscience.cdk.io.formats | CDK |
| RGroupQueryReader | A reader for Symyx' Rgroup files (RGFiles). | Class | org.openscience.cdk.io | CDK |
| RGroupQueryWriter | A writer for Symyx' Rgroup files (RGFiles). | Class | org.openscience.cdk.io | CDK |
| RssWriter | Generates an RSS feed. | Class | org.openscience.cdk.io | CDK |
| SDFFormat | Class | org.openscience.cdk.io.formats | CDK | |
| SDFWriter | Writes MDL SD files (). | Class | org.openscience.cdk.io | CDK |
| ShelXFormat | Class | org.openscience.cdk.io.formats | CDK | |
| ShelXReader | A reader for ShelX output (RES) files. | Class | org.openscience.cdk.io | CDK |
| ShelXWriter | Serializes a MoleculeSet or a Molecule object to ShelX code. | Class | org.openscience.cdk.io | CDK |
| SMARTSFormat | Class | org.openscience.cdk.io.formats | CDK | |
| SMILESFIXFormat | Class | org.openscience.cdk.io.formats | CDK | |
| SMILESFormat | Class | org.openscience.cdk.io.formats | CDK | |
| SMILESReader | This Reader reads files which has one SMILES string on each line, where the format is given as below: | Class | org.openscience.cdk.io | CDK |
| SMILESWriter | Writes the SMILES strings to a plain text file. | Class | org.openscience.cdk.io | CDK |
| SpartanFormat | Class | org.openscience.cdk.io.formats | CDK | |
| StringIOSetting | An class for a reader setting which must be of type String. | Class | org.openscience.cdk.io.setting | CDK |
| SVGFormat | Class | org.openscience.cdk.io.formats | CDK | |
| SwingGUIListener | Allows processing of IOSetting quesions which are passed to the user by using Swing dialogs. | Class | org.openscience.cdk.io.listener | CDK |
| SybylDescriptorFormat | Class | org.openscience.cdk.io.formats | CDK | |
| TextGUIListener | Allows processing of IOSetting quesions which are passed to the user by using the System. | Class | org.openscience.cdk.io.listener | CDK |
| TinkerMM2Format | Class | org.openscience.cdk.io.formats | CDK | |
| TinkerXYZFormat | Class | org.openscience.cdk.io.formats | CDK | |
| TurboMoleFormat | Class | org.openscience.cdk.io.formats | CDK | |
| UniChemXYZFormat | Class | org.openscience.cdk.io.formats | CDK | |
| VASPFormat | Class | org.openscience.cdk.io.formats | CDK | |
| VASPReader | Read output files generated with the VASP software. | Class | org.openscience.cdk.io | CDK |
| ViewmolFormat | Class | org.openscience.cdk.io.formats | CDK | |
| WriterFactory | Helper tool to create IChemObjectWriters. | Class | org.openscience.cdk.io | CDK |
| XEDFormat | Class | org.openscience.cdk.io.formats | CDK | |
| XYZFormat | Class | org.openscience.cdk.io.formats | CDK | |
| XYZReader | Reads an object from XYZ formated input. | Class | org.openscience.cdk.io | CDK |
| XYZWriter | Class | org.openscience.cdk.io | CDK | |
| YasaraFormat | Class | org.openscience.cdk.io.formats | CDK | |
| ZindoFormat | Class | org.openscience.cdk.io.formats | CDK | |
| ZMatrixFormat | Class | org.openscience.cdk.io.formats | CDK | |
| ZMatrixReader | It reads Z matrices like in Gaussian input files. | Class | org.openscience.cdk.io | CDK |