Uses of Interface
org.openscience.cdk.io.IChemObjectIO
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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 -
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Uses of IChemObjectIO in org.openscience.cdk.io
Subinterfaces of IChemObjectIO in org.openscience.cdk.io Modifier and Type Interface 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 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 aIAtomContainerSet
or aIAtomContainer
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 theMDLV2000Reader
should be used instead.class
MDLRXNReader
Deprecated.Use V2000 or V3000class
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 IChemObjectIO in org.openscience.cdk.io.iterator
Subinterfaces of IChemObjectIO in org.openscience.cdk.io.iterator Modifier and Type Interface 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 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 Description interface
IEventChemObjectReader
Interface for an iterating molecule reader.Classes in org.openscience.cdk.io.iterator.event that implement IChemObjectIO 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 IChemObjectIO in org.openscience.cdk.io.program
Classes in org.openscience.cdk.io.program that implement IChemObjectIO 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 IChemObjectIO in org.openscience.cdk.io.rdf
Classes in org.openscience.cdk.io.rdf that implement IChemObjectIO Modifier and Type Class Description class
CDKOWLReader
Reads content from a CDK OWL serialization.class
CDKOWLWriter
Serializes the data model into CDK OWL.
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