Uses of Class
org.openscience.cdk.io.ChemObjectIO

Packages that use ChemObjectIO

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 ChemObjectIO in org.openscience.cdk.io

Subclasses of ChemObjectIO in org.openscience.cdk.io

Modifier and Type	Class	Description
class	CDKSourceCodeWriter	Converts a Molecule into CDK source code that would build the same molecule.
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.
class	MDLRXNReader	Deprecated. Use V2000 or V3000
class	MDLRXNV2000Reader	Reads a molecule from an MDL RXN file [Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32].
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. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32]).
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. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32]).
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 ChemObjectIO in org.openscience.cdk.io.iterator

Subclasses of ChemObjectIO in org.openscience.cdk.io.iterator

Modifier and Type	Class	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 ChemObjectIO in org.openscience.cdk.io.iterator.event

Subclasses of ChemObjectIO in org.openscience.cdk.io.iterator.event

Modifier and Type	Class	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 ChemObjectIO in org.openscience.cdk.io.program

Subclasses of ChemObjectIO in org.openscience.cdk.io.program

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

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

Subclasses of ChemObjectIO in org.openscience.cdk.io.rdf

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