|
Class Summary |
| 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 |
Reads a molecule from the original MDL MOL or SDF 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]. |
| 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]. |
| 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]. |
| 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. 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]). |
| MDLV3000Reader |
Class that implements the MDL mol V3000 format. |
| 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. 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]). |
| 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. |