- MDLReader - Class in org.openscience.cdk.io
-
- MDLReader() - Constructor for class org.openscience.cdk.io.MDLReader
-
Deprecated.
- MDLReader(InputStream) - Constructor for class org.openscience.cdk.io.MDLReader
-
Deprecated.
Constructs a new MDLReader that can read Molecule from a given InputStream.
- MDLReader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLReader
-
Deprecated.
- MDLReader(Reader) - Constructor for class org.openscience.cdk.io.MDLReader
-
Deprecated.
Constructs a new MDLReader that can read Molecule from a given Reader.
- MDLReader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLReader
-
Deprecated.
- MDLRXNReader - Class in org.openscience.cdk.io
-
- MDLRXNReader(Reader) - Constructor for class org.openscience.cdk.io.MDLRXNReader
-
Deprecated.
Constructs a new MDLReader that can read Molecule from a given Reader.
- MDLRXNReader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNReader
-
Deprecated.
- MDLRXNReader(InputStream) - Constructor for class org.openscience.cdk.io.MDLRXNReader
-
Deprecated.
- MDLRXNReader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNReader
-
Deprecated.
- MDLRXNReader() - Constructor for class org.openscience.cdk.io.MDLRXNReader
-
Deprecated.
- MDLRXNV2000Reader - Class in org.openscience.cdk.io
-
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(Reader) - Constructor for class org.openscience.cdk.io.MDLRXNV2000Reader
-
Constructs a new MDLReader that can read Molecule from a given Reader.
- MDLRXNV2000Reader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNV2000Reader
-
- MDLRXNV2000Reader(InputStream) - Constructor for class org.openscience.cdk.io.MDLRXNV2000Reader
-
- MDLRXNV2000Reader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNV2000Reader
-
- MDLRXNV2000Reader() - Constructor for class org.openscience.cdk.io.MDLRXNV2000Reader
-
- MDLRXNV3000Reader - Class in org.openscience.cdk.io
-
Class that implements the new MDL mol format introduced in August 2002.
- MDLRXNV3000Reader(Reader) - Constructor for class org.openscience.cdk.io.MDLRXNV3000Reader
-
- MDLRXNV3000Reader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNV3000Reader
-
- MDLRXNV3000Reader(InputStream) - Constructor for class org.openscience.cdk.io.MDLRXNV3000Reader
-
- MDLRXNV3000Reader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLRXNV3000Reader
-
- MDLRXNV3000Reader() - Constructor for class org.openscience.cdk.io.MDLRXNV3000Reader
-
- MDLRXNWriter - Class in org.openscience.cdk.io
-
Writes a reaction to a MDL rxn or SDF file.
- MDLRXNWriter(Writer) - Constructor for class org.openscience.cdk.io.MDLRXNWriter
-
Constructs a new MDLWriter that can write an array of
Molecules to a Writer.
- MDLRXNWriter(OutputStream) - Constructor for class org.openscience.cdk.io.MDLRXNWriter
-
Constructs a new MDLWriter that can write an array of
Molecules to a given OutputStream.
- MDLRXNWriter() - Constructor for class org.openscience.cdk.io.MDLRXNWriter
-
- MDLV2000Reader - Class in org.openscience.cdk.io
-
Reads content from MDL molfiles and SD files.
- MDLV2000Reader() - Constructor for class org.openscience.cdk.io.MDLV2000Reader
-
- MDLV2000Reader(InputStream) - Constructor for class org.openscience.cdk.io.MDLV2000Reader
-
Constructs a new MDLReader that can read Molecule from a given
InputStream.
- MDLV2000Reader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLV2000Reader
-
- MDLV2000Reader(Reader) - Constructor for class org.openscience.cdk.io.MDLV2000Reader
-
Constructs a new MDLReader that can read Molecule from a given Reader.
- MDLV2000Reader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLV2000Reader
-
- MDLV2000Writer - Class in org.openscience.cdk.io
-
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]).
- MDLV2000Writer(Writer) - Constructor for class org.openscience.cdk.io.MDLV2000Writer
-
Constructs a new MDLWriter that can write an
IAtomContainer
to the MDL molfile format.
- MDLV2000Writer(OutputStream) - Constructor for class org.openscience.cdk.io.MDLV2000Writer
-
Constructs a new MDLWriter that can write an
IAtomContainer
to a given OutputStream.
- MDLV2000Writer() - Constructor for class org.openscience.cdk.io.MDLV2000Writer
-
- MDLV2000Writer.SPIN_MULTIPLICITY - Enum in org.openscience.cdk.io
-
Enumeration of all valid radical values.
- MDLV3000Reader - Class in org.openscience.cdk.io
-
Class that implements the MDL mol V3000 format.
- MDLV3000Reader(Reader) - Constructor for class org.openscience.cdk.io.MDLV3000Reader
-
- MDLV3000Reader(Reader, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLV3000Reader
-
- MDLV3000Reader(InputStream) - Constructor for class org.openscience.cdk.io.MDLV3000Reader
-
- MDLV3000Reader(InputStream, IChemObjectReader.Mode) - Constructor for class org.openscience.cdk.io.MDLV3000Reader
-
- MDLV3000Reader() - Constructor for class org.openscience.cdk.io.MDLV3000Reader
-
- MDLV3000Writer - Class in org.openscience.cdk.io
-
Ctab V3000 format output.
- MDLV3000Writer(Writer) - Constructor for class org.openscience.cdk.io.MDLV3000Writer
-
Create a new V3000 writer, output to the provided JDK writer.
- MDLV3000Writer(OutputStream) - Constructor for class org.openscience.cdk.io.MDLV3000Writer
-
Create a new V3000 writer, output to the provided JDK output stream.
- MDLV3000Writer() - Constructor for class org.openscience.cdk.io.MDLV3000Writer
-
Default empty constructor.
- RandomAccessSDFReader - Class in org.openscience.cdk.io.random
-
Random access of SDF file.
- RandomAccessSDFReader(File, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.random.RandomAccessSDFReader
-
- RandomAccessSDFReader(File, IChemObjectBuilder, IReaderListener) - Constructor for class org.openscience.cdk.io.random.RandomAccessSDFReader
-
- rdFields - Variable in class org.openscience.cdk.io.MDLRXNWriter
-
- read(T) - Method in class org.openscience.cdk.io.MDLReader
-
Deprecated.
Takes an object which subclasses IChemObject, e.g.
- read(T) - Method in class org.openscience.cdk.io.MDLRXNReader
-
Deprecated.
Takes an object which subclasses IChemObject, e.g.Molecule, and will read
this (from file, database, internet etc).
- read(T) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
-
Takes an object which subclasses IChemObject, e.g.Molecule, and will read
this (from file, database, internet etc).
- read(T) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
-
- read(T) - Method in class org.openscience.cdk.io.MDLV2000Reader
-
Takes an object which subclasses IChemObject, e.g.
- read(T) - Method in class org.openscience.cdk.io.MDLV3000Reader
-
- read(T) - Method in class org.openscience.cdk.io.RGroupQueryReader
-
Check input IChemObject and proceed to parse.
- readAtomBlock(IAtomContainer) - Method in class org.openscience.cdk.io.MDLV3000Reader
-
Reads the atoms, coordinates and charges.
- readBondBlock(IAtomContainer) - Method in class org.openscience.cdk.io.MDLV3000Reader
-
Reads the bond atoms, order and stereo configuration.
- readConnectionTable(IChemObjectBuilder) - Method in class org.openscience.cdk.io.MDLV3000Reader
-
- readHeader(IAtomContainer) - Method in class org.openscience.cdk.io.MDLV3000Reader
-
- readLine() - Method in class org.openscience.cdk.io.MDLV3000Reader
-
- readMolecule(IChemObjectBuilder) - Method in class org.openscience.cdk.io.MDLV3000Reader
-
- readSGroup(IAtomContainer) - Method in class org.openscience.cdk.io.MDLV3000Reader
-
Reads labels.
- remove() - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
-
- remove() - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
-
- RGroupQueryReader - Class in org.openscience.cdk.io
-
A reader for Symyx' Rgroup files (RGFiles).
- RGroupQueryReader() - Constructor for class org.openscience.cdk.io.RGroupQueryReader
-
Default constructor, input not set.
- RGroupQueryReader(InputStream) - Constructor for class org.openscience.cdk.io.RGroupQueryReader
-
Constructs a new RgroupQueryReader that can read RgroupAtomContainerSet
from a given InputStream.
- RGroupQueryReader(Reader) - Constructor for class org.openscience.cdk.io.RGroupQueryReader
-
Constructs a new RgroupQueryReader that can read RgroupAtomContainerSet
from a given Reader.
- RGroupQueryWriter - Class in org.openscience.cdk.io
-
A writer for Symyx' Rgroup files (RGFiles).
An RGfile describes a single molecular query with Rgroups.
- RGroupQueryWriter(Writer) - Constructor for class org.openscience.cdk.io.RGroupQueryWriter
-
Constructs a new writer that can write an
IRGroupQuery
to the Symx RGFile format.
- RGroupQueryWriter() - Constructor for class org.openscience.cdk.io.RGroupQueryWriter
-
Zero argument constructor.
- SDFWriter - Class in org.openscience.cdk.io
-
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]).
- SDFWriter(BufferedWriter) - Constructor for class org.openscience.cdk.io.SDFWriter
-
Create an SDfile writer that will output directly to the provided buffered writer.
- SDFWriter(Writer) - Constructor for class org.openscience.cdk.io.SDFWriter
-
Create an SDfile writer, the provided writer is buffered
if it's not an instance of BufferedWriter.
- SDFWriter(OutputStream) - Constructor for class org.openscience.cdk.io.SDFWriter
-
Create an SDfile writer, the provided output stream is wrapped
in a UTF-8 buffered writer.
- SDFWriter() - Constructor for class org.openscience.cdk.io.SDFWriter
-
- SDFWriter(Writer, Set<String>) - Constructor for class org.openscience.cdk.io.SDFWriter
-
Constructs a new SDFWriter that writes to the given
Writer.
- SDFWriter(OutputStream, Set<String>) - Constructor for class org.openscience.cdk.io.SDFWriter
-
Constructs a new SdfWriter that can write to a given
OutputStream.
- SDFWriter(Set<String>) - Constructor for class org.openscience.cdk.io.SDFWriter
-
Writes SD-File to a String including the given properties
- setAlwaysV3000(boolean) - Method in class org.openscience.cdk.io.SDFWriter
-
- setRdFields(Map<String, Object>) - Method in class org.openscience.cdk.io.MDLRXNWriter
-
Here you can set a map which will be used to build rd fields in the file.
- setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.MDLReader
-
Deprecated.
- setReader(InputStream) - Method in class org.openscience.cdk.io.MDLReader
-
Deprecated.
- setReader(Reader) - Method in class org.openscience.cdk.io.MDLRXNReader
-
Deprecated.
- setReader(InputStream) - Method in class org.openscience.cdk.io.MDLRXNReader
-
Deprecated.
- setReader(Reader) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.MDLRXNV2000Reader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.MDLRXNV3000Reader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.MDLV2000Reader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.MDLV2000Reader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.MDLV3000Reader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.MDLV3000Reader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
-
- setReader(InputStream) - Method in class org.openscience.cdk.io.random.RandomAccessSDFReader
-
- setReader(Reader) - Method in class org.openscience.cdk.io.RGroupQueryReader
-
Sets the input Reader.
- setReader(InputStream) - Method in class org.openscience.cdk.io.RGroupQueryReader
-
- setSkip(boolean) - Method in class org.openscience.cdk.io.iterator.IteratingSDFReader
-
Indicate whether the reader should skip over SDF records
that cause problems.
- setWriteAromaticBondTypes(boolean) - Method in class org.openscience.cdk.io.MDLV2000Writer
-
Convenience method to set the option for writing aromatic bond types.
- setWriter(Writer) - Method in class org.openscience.cdk.io.MDLRXNWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.MDLRXNWriter
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.MDLV2000Writer
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.MDLV2000Writer
-
- setWriter(Writer) - Method in class org.openscience.cdk.io.MDLV3000Writer
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.MDLV3000Writer
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.RGroupQueryWriter
-
Sets the writer to given output stream.
- setWriter(Writer) - Method in class org.openscience.cdk.io.RGroupQueryWriter
-
Sets the writer.
- setWriter(Writer) - Method in class org.openscience.cdk.io.SDFWriter
-
- setWriter(OutputStream) - Method in class org.openscience.cdk.io.SDFWriter
-