Uses of Interface
org.openscience.cdk.io.IChemObjectIO

Packages that use IChemObjectIO

Package	Description
org.openscience.cdk.io
org.openscience.cdk.io.iterator
org.openscience.cdk.io.iterator.event
org.openscience.cdk.io.program
org.openscience.cdk.io.rdf

Uses of IChemObjectIO in org.openscience.cdk.io

Subinterfaces of IChemObjectIO in org.openscience.cdk.io

Modifier and Type	Interface and Description
interface	IChemObjectReader This interface specifies the common functionality all IO readers should provide.
interface	IChemObjectWriter This class is the interface that all IO writers should implement.
interface	ISimpleChemObjectReader This class is the interface that all IO readers should implement.

Classes in org.openscience.cdk.io that implement IChemObjectIO

Modifier and Type	Class and Description
class	CDKSourceCodeWriter Converts a Molecule into CDK source code that would build the same molecule.
class	ChemObjectIO Provides some basic functionality for readers and writers.
class	CIFReader This is not a reader for the CIF and mmCIF crystallographic formats.
class	CMLReader Reads a molecule in CML 1.x and 2.0 format.
class	CMLWriter Serializes a IAtomContainerSet or a IAtomContainer object to CML 2 code.
class	CrystClustReader
class	CrystClustWriter Rather stupid file format used for storing crystal information.
class	CTXReader Reader that extracts information from the IDENT, NAME, ATOMS and BONDS blocks in CTX files.
class	DefaultChemObjectReader Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
class	DefaultChemObjectWriter Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
class	GamessReader A reader for GAMESS log file.
class	Gaussian03Reader A reader for Gaussian03 output.
class	Gaussian98Reader A reader for Gaussian98 output.
class	GhemicalMMReader Reads Ghemical ( http://www.uku.fi/~thassine/ghemical/) molecular mechanics (*.mm1gp) files.
class	HINReader Reads an object from HIN formated input.
class	HINWriter Writer that outputs in the HIN format.
class	INChIPlainTextReader Reads the content of a IUPAC/NIST Chemical Identifier (INChI) plain text document.
class	INChIReader Reads the content of a IUPAC/NIST Chemical Identifier (INChI) document.
class	MDLReader Deprecated. This reader is only for molfiles without a version tag, typically the most common molfile now encountered is V2000 and the MDLV2000Reader should be used instead. The V2000 reader can actually read files missing the version tag when in relaxed mode.
class	MDLRXNReader Reads a molecule from an MDL RXN file [Dalby, A. and Nourse, J. G. and Hounshell, W. D. and Gushurst, A. K. and Grier, D. L. and Leland, B. A. and Laufer, J., Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255].
class	MDLRXNV2000Reader Reads a molecule from an MDL RXN file [Dalby, A. and Nourse, J. G. and Hounshell, W. D. and Gushurst, A. K. and Grier, D. L. and Leland, B. A. and Laufer, J., Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255].
class	MDLRXNV3000Reader Class that implements the new MDL mol format introduced in August 2002.
class	MDLRXNWriter Writes a reaction to a MDL rxn or SDF file.
class	MDLV2000Reader Reads content from MDL molfiles and SD files.
class	MDLV2000Writer Writes MDL molfiles, which contains a single molecule (see [Dalby, A. and Nourse, J. G. and Hounshell, W. D. and Gushurst, A. K. and Grier, D. L. and Leland, B. A. and Laufer, J., Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255]).
class	MDLV3000Reader Class that implements the MDL mol V3000 format.
class	MDLV3000Writer Ctab V3000 format output.
class	Mol2Reader Reads a molecule from an Mol2 file, such as written by Sybyl.
class	Mol2Writer An output Writer that writes molecular data into the Tripos Mol2 format.
class	Mopac7Reader Reads MOPAC output, extracts several electronic parameters and assigns them as a molecule properties.
class	MoSSOutputReader Reader for MoSS output files [Unknown BibTeXML type: BOR2002] which present the results of a substructure mining study.
class	PCCompoundASNReader Reads an object from ASN formated input for PubChem Compound entries.
class	PCCompoundXMLReader Reads an object from ASN.1 XML formated input for PubChem Compound entries.
class	PCSubstanceXMLReader Reads an object from ASN formated input for PubChem Compound entries.
class	PDBReader Reads the contents of a PDBFile.
class	PDBWriter Saves small molecules in a rudimentary PDB format.
class	PMPReader Reads an frames from a PMP formated input.
class	RGroupQueryReader A reader for Symyx' Rgroup files (RGFiles).
class	RGroupQueryWriter A writer for Symyx' Rgroup files (RGFiles). An RGfile describes a single molecular query with Rgroups.
class	RssWriter Generates an RSS feed.
class	SDFWriter Writes MDL SD files ([Dalby, A. and Nourse, J. G. and Hounshell, W. D. and Gushurst, A. K. and Grier, D. L. and Leland, B. A. and Laufer, J., Description of Several Chemical Structure File Formats Used by Computer Programs Developed at Molecular Design Limited, Journal of Chemical Information and Computer Sciences, 1992, 32:244-255]).
class	ShelXReader A reader for ShelX output (RES) files.
class	ShelXWriter Serializes a MoleculeSet or a Molecule object to ShelX code.
class	SMILESReader This Reader reads files which has one SMILES string on each line, where the format is given as below:
class	SMILESWriter Writes the SMILES strings to a plain text file.
class	VASPReader Read output files generated with the VASP software.
class	XYZReader Reads an object from XYZ formated input.
class	XYZWriter
class	ZMatrixReader It reads Z matrices like in Gaussian input files.

Uses of IChemObjectIO in org.openscience.cdk.io.iterator

Subinterfaces of IChemObjectIO in org.openscience.cdk.io.iterator

Modifier and Type	Interface and Description
interface	IIteratingChemObjectReader<T extends IChemObject> Interface for an iterating molecule reader.

Classes in org.openscience.cdk.io.iterator that implement IChemObjectIO

Modifier and Type	Class and Description
class	DefaultIteratingChemObjectReader<T extends IChemObject> Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
class	IteratingPCCompoundASNReader Iterating PubChem PCCompound ASN reader.
class	IteratingPCCompoundXMLReader Iterating PubChem PCCompound ASN.1 XML reader.
class	IteratingPCSubstancesXMLReader Iterating PubChem PC-Substances ASN.1 XML reader.
class	IteratingSDFReader Iterating MDL SDF reader.
class	IteratingSMILESReader Iterating SMILES file reader.

Uses of IChemObjectIO in org.openscience.cdk.io.iterator.event

Subinterfaces of IChemObjectIO in org.openscience.cdk.io.iterator.event

Modifier and Type	Interface and Description
interface	IEventChemObjectReader Interface for an iterating molecule reader.

Classes in org.openscience.cdk.io.iterator.event that implement IChemObjectIO

Modifier and Type	Class and Description
class	DefaultEventChemObjectReader Abstract class that IteratingChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
class	EventCMLReader Reads a molecule in CML 1.x and 2.0 format.

Uses of IChemObjectIO in org.openscience.cdk.io.program

Classes in org.openscience.cdk.io.program that implement IChemObjectIO

Modifier and Type	Class and Description
class	GaussianInputWriter File writer thats generates input files for Gaussian calculation jobs.
class	Mopac7Writer Prepares input file for running MOPAC.

Uses of IChemObjectIO in org.openscience.cdk.io.rdf

Classes in org.openscience.cdk.io.rdf that implement IChemObjectIO

Modifier and Type	Class and Description
class	CDKOWLReader Reads content from a CDK OWL serialization.
class	CDKOWLWriter Serializes the data model into CDK OWL.