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 |
Modifier and Type | Class and 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. The V2000 reader can actually read files missing the version tag when
in relaxed mode. |
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.
|
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.
|
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.
|
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.
|
Modifier and Type | Class and Description |
---|---|
class |
CDKOWLReader
Reads content from a CDK OWL serialization.
|
class |
CDKOWLWriter
Serializes the data model into CDK OWL.
|
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