A B C D G H I K L M N O P R S U W

A

Absolute - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output canonical SMILES with stereochemistry, atomic masses.

absolute() - Static method in class org.openscience.cdk.smiles.SmilesGenerator

Create a absolute SMILES generator.

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.MoSSOutputReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.SMILESReader

accepts(Class<? extends IChemObject>) - Method in class org.openscience.cdk.io.SMILESWriter

aromatic() - Method in class org.openscience.cdk.smiles.SmilesGenerator

Deprecated.

configure with SmiFlavor

AtomAtomMap - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output atom-atom mapping for reactions and atom classes for molecules.

AtomicMass - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output atomic mass on atoms.

AtomicMassStrict - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Deprecated.

no longer needed, default CDK behaviour is now to pass through mass numbers if non-null

B

BAD_SMILES_INPUT - Static variable in class org.openscience.cdk.io.iterator.IteratingSMILESReader

Store the problem input as a property.

C

Canonical - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output SMILES in a canonical order.

close() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader

Close the reader.

close() - Method in class org.openscience.cdk.io.MoSSOutputReader

close() - Method in class org.openscience.cdk.io.SMILESReader

close() - Method in class org.openscience.cdk.io.SMILESWriter

Flushes the output and closes this object.

create(IAtomContainer) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Generate SMILES for the provided molecule.

create(IAtomContainer, int[]) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Creates a SMILES string of the flavour specified in the constructor and write the output order to the provided array.

create(IAtomContainer, int, int[]) - Static method in class org.openscience.cdk.smiles.SmilesGenerator

Creates a SMILES string of the flavour specified as a parameter and write the output order to the provided array.

create(IReaction) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Create a SMILES for a reaction of the flavour specified in the constructor.

create(IReaction, int[]) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Create a SMILES for a reaction of the flavour specified in the constructor and write the output order to the provided array.

createReactionSMILES(IReaction) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Deprecated.

use SmilesGenerator.create(IAtomContainer)

createSMILES(IAtomContainer) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Deprecated.

use #create

createSMILES(IReaction) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Deprecated.

use #createReactionSMILES

customizeJob() - Method in class org.openscience.cdk.io.SMILESWriter

Cx2dCoordinates - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output 2D coordinates.

Cx3dCoordinates - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output 3D coordinates.

CxAtomLabel - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output atom labels, atom labels are specified by IPseudoAtom.getLabel().

CxAtomValue - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output atom values, atom values are specified by IPseudoAtom.getLabel().

CxCoordinates - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output either 2D/3D coordinates.

CxFragmentGroup - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output fragment grouping for reactions.

CxMulticenter - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output multicenter bonds, positional variation is specified with Sgroups of the type SgroupType.ExtMulticenter.

CxPolymer - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output polymer repeat units is specified with Sgroups.

CxRadical - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output radicals, radicals are specified by IAtomContainer.getConnectedSingleElectronsCount(IAtom)

CxSmiles - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output CXSMILES layers.

CxSmilesGenerator - Class in org.openscience.cdk.smiles

CxSmilesGenerator() - Constructor for class org.openscience.cdk.smiles.CxSmilesGenerator

CxSmilesWithCoords - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output CXSMILES layers and coordinates.

D

Default - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Default SMILES output write Stereochemistry, Atomic Mass, and CXSMILES layers.

G

Generic - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output non-canonical SMILES without stereochemistry, atomic masses.

generic() - Static method in class org.openscience.cdk.smiles.SmilesGenerator

Create a generator for generic SMILES.

getBitFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter

getCountFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter

getFormat() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader

Get the format for this reader.

getFormat() - Method in class org.openscience.cdk.io.MoSSOutputReader

getFormat() - Method in class org.openscience.cdk.io.SMILESReader

getFormat() - Method in class org.openscience.cdk.io.SMILESWriter

getParameters() - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter

getRawFingerprint(IAtomContainer) - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter

getSize() - Method in class org.openscience.cdk.fingerprint.LingoFingerprinter

H

hasNext() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader

Checks whether there is another molecule to read.

I

InChILabelling - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output SMILES in a canonical order using the InChI labelling algorithm.

Isomeric - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output non-canonical SMILES with stereochemistry, atomic masses.

isomeric() - Static method in class org.openscience.cdk.smiles.SmilesGenerator

Convenience method for creating an isomeric generator.

isPreservingAromaticity() - Method in class org.openscience.cdk.smiles.SmilesParser

Deprecated.

IteratingSMILESReader - Class in org.openscience.cdk.io.iterator

Iterating SMILES file reader.

IteratingSMILESReader(Reader, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingSMILESReader

Constructs a new IteratingSMILESReader that can read Molecule from a given Reader.

IteratingSMILESReader(InputStream, IChemObjectBuilder) - Constructor for class org.openscience.cdk.io.iterator.IteratingSMILESReader

Constructs a new IteratingSMILESReader that can read Molecule from a given InputStream and IChemObjectBuilder.

K

kekulise(boolean) - Method in class org.openscience.cdk.smiles.SmilesParser

Indicated whether structures should be automatically kekulised if they are provided as aromatic.

L

LingoFingerprinter - Class in org.openscience.cdk.fingerprint

An implementation of the LINGO fingerprint [Vidal, D. and Thormann, M. and Pons, M., LINGO, an Efficient Holographic Text Based Method To Calculate Biophysical Properties and Intermolecular Similarities, J. Chem. Inf. Model., 2005, 45:386-393, doi:10.1021/ci0496797].

LingoFingerprinter() - Constructor for class org.openscience.cdk.fingerprint.LingoFingerprinter

Initialize the fingerprinter with a default substring length of 4.

LingoFingerprinter(int) - Constructor for class org.openscience.cdk.fingerprint.LingoFingerprinter

Initialize the fingerprinter.

M

MoSSOutputReader - Class in org.openscience.cdk.io

Reader for MoSS output files [Unknown BibTeXML type: BOR2002] which present the results of a substructure mining study.

MoSSOutputReader(Reader) - Constructor for class org.openscience.cdk.io.MoSSOutputReader

Create a reader for MoSS output files from a Reader.

MoSSOutputReader(InputStream) - Constructor for class org.openscience.cdk.io.MoSSOutputReader

Create a reader for MoSS output files from an InputStream.

MoSSOutputReader() - Constructor for class org.openscience.cdk.io.MoSSOutputReader

Create a reader for MoSS output files from an empty string.

N

next() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader

Get the next molecule from the stream.

O

org.openscience.cdk.fingerprint - package org.openscience.cdk.fingerprint

org.openscience.cdk.io - package org.openscience.cdk.io

org.openscience.cdk.io.iterator - package org.openscience.cdk.io.iterator

org.openscience.cdk.smiles - package org.openscience.cdk.smiles

P

parseReactionSmiles(String) - Method in class org.openscience.cdk.smiles.SmilesParser

Parse a reaction SMILES.

parseSmiles(String) - Method in class org.openscience.cdk.smiles.SmilesParser

Parses a SMILES string and returns a structure (IAtomContainer).

R

read(T) - Method in class org.openscience.cdk.io.MoSSOutputReader

Read a IAtomContainerSet from the input source.

read(T) - Method in class org.openscience.cdk.io.SMILESReader

Reads the content from a XYZ input.

remove() - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader

S

setPreservingAromaticity(boolean) - Method in class org.openscience.cdk.smiles.SmilesParser

Deprecated.

setReader(Reader) - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader

setReader(InputStream) - Method in class org.openscience.cdk.io.iterator.IteratingSMILESReader

setReader(Reader) - Method in class org.openscience.cdk.io.MoSSOutputReader

setReader(InputStream) - Method in class org.openscience.cdk.io.MoSSOutputReader

setReader(Reader) - Method in class org.openscience.cdk.io.SMILESReader

setReader(InputStream) - Method in class org.openscience.cdk.io.SMILESReader

setUseAromaticityFlag(boolean) - Method in class org.openscience.cdk.smiles.SmilesGenerator

Deprecated.

since 1.5.6, use SmilesGenerator.aromatic() - invoking this method does nothing

setWriter(Writer) - Method in class org.openscience.cdk.io.SMILESWriter

setWriter(OutputStream) - Method in class org.openscience.cdk.io.SMILESWriter

SmiFlavor - Class in org.openscience.cdk.smiles

Flags for customising SMILES generation.

SmilesGenerator - Class in org.openscience.cdk.smiles

SMILES [Weininger, David, SMILES, a Chemical Language and Information System. 1. Introduction to Methodology and Encoding Rules, Journal of Chemical Information and Computer Sciences, 1988, 28:31-36, Weininger, David and Weininger, Arthur and Weininger, Joseph L., SMILES 2. Algorithm for Generation of Unique SMILES Notation, Journal of Chemical Information and Computer Sciences, 1989, 29:97-101] provides a compact representation of chemical structures and reactions.

SmilesGenerator() - Constructor for class org.openscience.cdk.smiles.SmilesGenerator

Deprecated.

use SmilesGenerator.SmilesGenerator(int) configuring with SmiFlavor.

SmilesGenerator(int) - Constructor for class org.openscience.cdk.smiles.SmilesGenerator

Create a SMILES generator with the specified SmiFlavor.

SmilesParser - Class in org.openscience.cdk.smiles

Read molecules and reactions from a SMILES [?Authors?, SMILES Tutorial] string.

SmilesParser(IChemObjectBuilder) - Constructor for class org.openscience.cdk.smiles.SmilesParser

Create a new SMILES parser which will create IAtomContainers with the specified builder.

SMILESReader - Class in org.openscience.cdk.io

This Reader reads files which has one SMILES string on each line, where the format is given as below:

SMILESReader(Reader) - Constructor for class org.openscience.cdk.io.SMILESReader

Construct a new reader from a Reader and a specified builder object.

SMILESReader(InputStream) - Constructor for class org.openscience.cdk.io.SMILESReader

SMILESReader() - Constructor for class org.openscience.cdk.io.SMILESReader

SMILESWriter - Class in org.openscience.cdk.io

Writes the SMILES strings to a plain text file.

SMILESWriter(Writer) - Constructor for class org.openscience.cdk.io.SMILESWriter

Constructs a new SMILESWriter that can write a list of SMILES to a Writer

SMILESWriter(OutputStream) - Constructor for class org.openscience.cdk.io.SMILESWriter

SMILESWriter() - Constructor for class org.openscience.cdk.io.SMILESWriter

SMILESWriter(FileOutputStream) - Constructor for class org.openscience.cdk.io.SMILESWriter

Constructs a new SMILESWriter that can write an list of SMILES to a given OutputStream

Stereo - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output supported stereochemistry types.

StereoCisTrans - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output cis-trans stereochemistry specified by directional \ of / bonds.

StereoExTetrahedral - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output extended tetrahedral stereochemistry on atoms as @ and @@.

StereoTetrahedral - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output tetrahedral stereochemistry on atoms as @ and @@.

U

Unique - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output canonical SMILES without stereochemistry, atomic masses.

unique() - Static method in class org.openscience.cdk.smiles.SmilesGenerator

Create a unique SMILES generator.

UniversalSmiles - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Output canonical SMILES with stereochemistry and atomic masses, This output uses the InChI labelling algorithm to generate a 'Universal SMILES' [O'Boyle, Noel, Towards a Universal SMILES representation - A standard method to generate canonical SMILES based on the InChI, Journal of Cheminformatics, 2012, 4:?-?, doi:10.1186/1758-2946-4-22].

UseAromaticSymbols - Static variable in class org.openscience.cdk.smiles.SmiFlavor

Writes aromatic atoms as lower case letters.

W

withAtomClasses() - Method in class org.openscience.cdk.smiles.SmilesGenerator

Deprecated.

configure with SmiFlavor

write(IChemObject) - Method in class org.openscience.cdk.io.SMILESWriter

Writes the content from object to output.

writeAtomContainer(IAtomContainer) - Method in class org.openscience.cdk.io.SMILESWriter

Writes the content from molecule to output.

writeAtomContainerSet(IAtomContainerSet) - Method in class org.openscience.cdk.io.SMILESWriter

Writes a list of molecules to an OutputStream.

A B C D G H I K L M N O P R S U W