Package org.openscience.cdk.io

Interface Summary

Interface	Description
IChemObjectIO	This class is the interface that all IO readers should implement.
IChemObjectReader	This interface specifies the common functionality all IO readers should provide.
IChemObjectReaderErrorHandler	Interface for classes aimed to handle IChemObjectReader errors.
IChemObjectWriter	This class is the interface that all IO writers should implement.
ISimpleChemObjectReader	This class is the interface that all IO readers should implement.

Class Summary

Class	Description
CDKSourceCodeWriter	Converts a Molecule into CDK source code that would build the same molecule.
ChemObjectIO	Provides some basic functionality for readers and writers.
CIFReader	This is not a reader for the CIF and mmCIF crystallographic formats.
CMLReader	Reads a molecule in CML 1.x and 2.0 format.
CMLWriter	Serializes a IAtomContainerSet or a IAtomContainer object to CML 2 code.
CrystClustReader
CrystClustWriter	Rather stupid file format used for storing crystal information.
CTXReader	Reader that extracts information from the IDENT, NAME, ATOMS and BONDS blocks in CTX files.
DefaultChemObjectReader	Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
DefaultChemObjectWriter	Abstract class that ChemObjectReader's can implement to have it take care of basic stuff, like managing the ReaderListeners.
FormatFactory	A factory for recognizing chemical file formats.
GamessReader	A reader for GAMESS log file.
Gaussian03Reader	A reader for Gaussian03 output.
Gaussian98Reader	A reader for Gaussian98 output.
GhemicalMMReader	Reads Ghemical ( http://www.uku.fi/~thassine/ghemical/) molecular mechanics (*.mm1gp) files.
HINReader	Reads an object from HIN formated input.
HINWriter	Writer that outputs in the HIN format.
INChIPlainTextReader	Reads the content of a IUPAC/NIST Chemical Identifier (INChI) plain text document.
INChIReader	Reads the content of a IUPAC/NIST Chemical Identifier (INChI) document.
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.
MDLRXNReader	Deprecated Use V2000 or V3000
MDLRXNV2000Reader	Reads a molecule from an MDL RXN file (Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32).
MDLRXNV3000Reader	Class that implements the new MDL mol format introduced in August 2002.
MDLRXNWriter	Writes a reaction to a MDL rxn or SDF file.
MDLV2000Reader	Reads content from MDL molfiles and SD files.
MDLV2000Writer	Writes MDL molfiles, which contains a single molecule (see (Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32)).
MDLV3000Reader	Class that implements the MDL mol V3000 format.
MDLV3000Writer	Ctab V3000 format output.
Mol2Reader	Reads a molecule from an Mol2 file, such as written by Sybyl.
Mol2Writer	An output Writer that writes molecular data into the Tripos Mol2 format.
Mopac7Reader	Reads MOPAC output, extracts several electronic parameters and assigns them as a molecule properties.
MoSSOutputReader	Reader for MoSS output files (Unknown BibTeXML type: BOR2002) which present the results of a substructure mining study.
PCCompoundASNReader	Reads an object from ASN formated input for PubChem Compound entries.
PCCompoundXMLReader	Reads an object from ASN.1 XML formated input for PubChem Compound entries.
PCSubstanceXMLReader	Reads an object from ASN formated input for PubChem Compound entries.
PDBReader	Reads the contents of a PDBFile.
PDBWriter	Saves small molecules in a rudimentary PDB format.
PMPReader	Reads an frames from a PMP formated input.
ReaderEvent	Signals that something has happened in a file reader.
ReaderFactory	A factory for creating ChemObjectReaders.
RGroupQueryReader	A reader for Symyx' Rgroup files (RGFiles).
RGroupQueryWriter	A writer for Symyx' Rgroup files (RGFiles). An RGfile describes a single molecular query with Rgroups.
RssWriter	Generates an RSS feed.
SDFWriter	Writes MDL SD files ((Dalby, A. et. al.. Journal of Chemical Information and Computer Sciences. 1992. 32)).
ShelXReader	A reader for ShelX output (RES) files.
ShelXWriter	Serializes a MoleculeSet or a Molecule object to ShelX code.
SMILESReader	This Reader reads files which has one SMILES string on each line, where the format is given as below:
SMILESWriter	Writes the SMILES strings to a plain text file.
VASPReader	Read output files generated with the VASP software.
WriterFactory	Helper tool to create IChemObjectWriters.
XYZReader	Reads an object from XYZ formated input.
XYZWriter
ZMatrixReader	It reads Z matrices like in Gaussian input files.

Enum Summary

Enum	Description
IChemObjectReader.Mode
MDLV2000Writer.SPIN_MULTIPLICITY	Enumeration of all valid radical values.