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 | Interface and 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.
|
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
IMoleculeSet or a IMolecule 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
Reads a molecule from the original MDL MOL or SDF file .
|
class |
MDLRXNReader
Reads a molecule from an MDL RXN file .
|
class |
MDLRXNV2000Reader
Reads a molecule from an MDL RXN file .
|
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 ).
|
class |
MDLV3000Reader
Class that implements the MDL mol V3000 format.
|
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 |
MoSSOutputReader
Reader for MoSS output files 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 ().
|
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 | Interface and Description |
---|---|
interface |
IIteratingChemObjectReader<T extends IChemObject>
Interface for an iterating molecule reader.
|
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 |
IteratingMDLReader
Iterating MDL SDF reader.
|
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 |
IteratingSMILESReader
Iterating SMILES file reader.
|
Modifier and Type | Interface and Description |
---|---|
interface |
IEventChemObjectReader
Interface for an iterating molecule 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.
|
Modifier and Type | Class and Description |
---|---|
class |
CDKOWLReader
Reads content from a CDK OWL serialization.
|
class |
CDKOWLWriter
Serializes the data model into CDK OWL.
|