A B C D E F G H I L M N O P Q R S T U V W

A

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

Returns whether the given IChemObject can be read or written.

add(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds all atoms and electronContainers of a given atomcontainer to this container.

add(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Adds all atomContainers in the AtomContainerSet to this container.

add(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.ICrystal

Adds the atoms in the AtomContainer as cell content.

add(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Adds an molecularFormula to this MolecularFormula.

add(IMolecularFormulaSet) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet

Adds all molecularFormulas in the MolecularFormulaSet to this chemObject.

add(IReactionScheme) - Method in interface org.openscience.cdk.interfaces.IReactionScheme

Add a scheme of reactions.

add(IRingSet) - Method in interface org.openscience.cdk.interfaces.IRingSet

Adds all rings of another RingSet if they are not allready part of this ring set.

addAgent(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction

Adds an agent to this reaction.

addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds an atom to this container.

addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Adds the atom oAtom without specifying a Monomer or a Strand.

addAtom(IAtom, IStrand) - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Adds the atom oAtom to a specified Strand, whereas the Monomer is unspecified.

addAtom(IAtom, IMonomer, IStrand) - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Adds the atom to a specified Strand and a specified Monomer.

addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.ICrystal

Adds the atom to the crystal.

addAtom(IPDBAtom) - Method in interface org.openscience.cdk.interfaces.IPDBPolymer

Adds the atom oAtom without specifying a Monomer or a Strand.

addAtom(IPDBAtom, IMonomer, IStrand) - Method in interface org.openscience.cdk.interfaces.IPDBPolymer

Adds the atom to a specified Strand and a specified Monomer.

addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IPolymer

Adds the atom oAtom without specifying a Monomer.

addAtom(IAtom, IMonomer) - Method in interface org.openscience.cdk.interfaces.IPolymer

Adds the atom oAtom to a specified Monomer.

addAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IStrand

Adds the atom oAtom without specifying a Monomer or a Strand.

addAtom(IAtom, IMonomer) - Method in interface org.openscience.cdk.interfaces.IStrand

Adds the atom oAtom to a specific Monomer.

addAtomContainer(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Adds an atomContainer to this container.

addAtomContainer(IAtomContainer, double) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Adds an atomContainer to this container with the given multiplier.

addBond(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds a Bond to this AtomContainer.

addBond(int, int, IBond.Order, IBond.Stereo) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds a bond to this container.

addBond(int, int, IBond.Order) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds a bond to this container.

addChemModel(IChemModel) - Method in interface org.openscience.cdk.interfaces.IChemSequence

Adds an chemModel to this container.

addChemObjectIOListener(IChemObjectIOListener) - Method in interface org.openscience.cdk.io.IChemObjectIO

Adds a IChemObjectIOListener to this IChemObjectIO.

addChemSequence(IChemSequence) - Method in interface org.openscience.cdk.interfaces.IChemFile

Adds an IChemSequence to this container.

addCTerminus(IAtom) - Method in interface org.openscience.cdk.interfaces.IAminoAcid

Add an Atom and makes it the C-terminus atom.

addElectronContainer(IElectronContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds a ElectronContainer to this AtomContainer.

addIsotope(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Adds an Isotope to this MolecularFormula one time.

addIsotope(IIsotope, int) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Adds an Isotope to this MolecularFormula in a number of occurrences.

addListener(IChemObjectListener) - Method in interface org.openscience.cdk.interfaces.IChemObject

Use this to add yourself to this IChemObject as a listener.

addLonePair(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds a lone pair to this AtomContainer.

addLonePair(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds a LonePair to this Atom.

addMapping(IMapping) - Method in interface org.openscience.cdk.interfaces.IReaction

Adds a mapping between the reactant and product side to this Reaction.

addMolecularFormula(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet

Adds an IMolecularFormula to this chemObject.

addNTerminus(IAtom) - Method in interface org.openscience.cdk.interfaces.IAminoAcid

Add an Atom and makes it the N-terminus atom.

addProduct(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction

Adds a product to this reaction.

addProduct(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction

Adds a product to this reaction.

addProperties(Map<Object, Object>) - Method in interface org.openscience.cdk.interfaces.IChemObject

Add properties to this object, duplicate keys will replace any existing value.

addReactant(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction

Adds a reactant to this reaction.

addReactant(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction

Adds a reactant to this reaction with a stoichiometry coefficient.

addReaction(IReaction) - Method in interface org.openscience.cdk.interfaces.IReactionSet

Adds an reaction to this container.

addSetting(IOSetting) - Method in interface org.openscience.cdk.io.IChemObjectIO

Add an IOSetting to the reader/writer.

addSettings(Collection<IOSetting>) - Method in interface org.openscience.cdk.io.IChemObjectIO

Adds a collection of IOSettings to the reader/writer.

addSingleElectron(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds a single electron to this AtomContainer.

addSingleElectron(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds a SingleElectron to this Atom.

addStereoElement(IStereoElement) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Adds a stereo element to this container.

addStructure(IPDBStructure) - Method in interface org.openscience.cdk.interfaces.IPDBPolymer

Adds the PDBStructure structure a this PDBPolymer.

AL - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

ExtendedTetrahedral (e.g.

Allenal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

ExtendedTetrahedral (e.g.

AT - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Atropisomeric (e.g.

atomContainers() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Get an Iterable for this AtomContainerSet.

AtomEncoder - Interface in org.openscience.cdk.hash

An encoder for invariant atom properties.

AtomHashGenerator - Interface in org.openscience.cdk.hash

A hash function which generates 64-bit hash codes for the atoms of a molecule.

atoms() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns an Iterable for looping over all atoms in this container.

atoms() - Method in interface org.openscience.cdk.interfaces.IBond

Returns the Iterable to atoms making up this bond.

Atropisomeric - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Atropisomeric (e.g.

B

bonds() - Method in interface org.openscience.cdk.interfaces.IAtom

Returns the bonds connected to this atom.

bonds() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns an Iterable for looping over all bonds in this container.

C

CDKException - Exception in org.openscience.cdk.exception

Exception that is thrown by CDK classes when some problem has occurred.

CDKException(String) - Constructor for exception org.openscience.cdk.exception.CDKException

Constructs a new CDKException with the given message.

CDKException(String, Throwable) - Constructor for exception org.openscience.cdk.exception.CDKException

Constructs a new CDKException with the given message and the Exception as cause.

CFG_MASK - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

chemModels() - Method in interface org.openscience.cdk.interfaces.IChemSequence

Returns an Iterable to ChemModels in this container.

chemSequences() - Method in interface org.openscience.cdk.interfaces.IChemFile

Returns the Iterable to ChemSequences of this container.

CisTrans - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Geometric CisTrans (e.g.

clone() - Method in interface org.openscience.cdk.interfaces.IAdductFormula

Clones this IAdductFormula object and its content.

clone() - Method in interface org.openscience.cdk.interfaces.IAminoAcid

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IAtom

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IBond

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.ICrystal

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Clones this MolecularFormula object and its content.

clone() - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet

Clones this IMolecularFormulaSet object and its content.

clone() - Method in interface org.openscience.cdk.interfaces.IMonomer

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IPDBPolymer

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IPolymer

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IPseudoAtom

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IReactionScheme

Clones this IReactionScheme object and its content.

clone() - Method in interface org.openscience.cdk.interfaces.IRing

Returns a deep clone of this IChemObject.

clone() - Method in interface org.openscience.cdk.interfaces.IStrand

Returns a deep clone of this IChemObject.

close() - Method in interface org.openscience.cdk.io.IChemObjectIO

Closes this IChemObjectIO's resources.

CLS_MASK - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

compare(Object) - Method in interface org.openscience.cdk.interfaces.IBond

Compares a bond with this bond.

compareTo(IChemFormatMatcher.MatchResult) - Method in class org.openscience.cdk.io.formats.IChemFormatMatcher.MatchResult

Compares the match result with another, results with lower position are ordered before those with higher position.

contains(IIsotope) - Method in interface org.openscience.cdk.interfaces.IAdductFormula

True, if the AdductFormula contains the given IIsotope object.

contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

True, if the AtomContainer contains the given atom object.

contains(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

True, if the AtomContainer contains the given bond object.

contains(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

True, if the AtomContainer contains the given LonePair object.

contains(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

True, if the AtomContainer contains the given SingleElectron object.

contains(IElectronContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

True, if the AtomContainer contains the given ElectronContainer object.

contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond

Returns true if the given atom participates in this bond.

contains(IAtom) - Method in interface org.openscience.cdk.interfaces.ILonePair

Returns true if the given atom participates in this lone pair.

contains(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

True, if the MolecularFormula contains the given IIsotope object.

contains(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet

True, if the IMolecularFormulaSet contains the given IMolecularFormula object.

contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IRingSet

True, if at least one of the rings in the ringset contains the given atom.

contains(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IRingSet

True, if this set contains the IAtomContainer.

contains(IAtom) - Method in interface org.openscience.cdk.interfaces.ISingleElectron

Returns true if the given atom participates in this SingleElectron.

contains(IAtom) - Method in interface org.openscience.cdk.interfaces.IStereoElement

Does the stereo element contain the provided atom.

createLoggingTool(Class<?>) - Static method in class org.openscience.cdk.tools.LoggingToolFactory

Dynamically create a ILoggingTool for the given sourceClass.

CT - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Geometric CisTrans (e.g.

customize(IAtom, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer

Customized the nodeToAdd for the given Atom.

customize(IBond, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer

Customized the nodeToAdd for the given IBond.

customize(IAtomContainer, Object) - Method in interface org.openscience.cdk.libio.cml.ICMLCustomizer

Customized the nodeToAdd for the given Molecule.

D

debug(Object) - Method in interface org.openscience.cdk.tools.ILoggingTool

Shows DEBUG output for the Object.

debug(Object, Object...) - Method in interface org.openscience.cdk.tools.ILoggingTool

Shows DEBUG output for the given Object's.

DEFAULT_LOGGING_TOOL_CLASS - Static variable in class org.openscience.cdk.tools.LoggingToolFactory

Default logging tool.

DEFAULT_STACK_LENGTH - Static variable in interface org.openscience.cdk.tools.ILoggingTool

Default number of StackTraceElements to be printed by debug(Exception).

dumpClasspath() - Method in interface org.openscience.cdk.tools.ILoggingTool

Outputs the system property for java.class.path.

dumpSystemProperties() - Method in interface org.openscience.cdk.tools.ILoggingTool

Outputs system properties for the operating system and the java version.

E

electronContainers() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns an Iterable for looping over all electron containers in this container.

encode(IAtom, IAtomContainer) - Method in interface org.openscience.cdk.hash.AtomEncoder

Encode an invariant attribute of the given atom.

EnsembleHashGenerator - Interface in org.openscience.cdk.hash

A hash function which generates a single 64-bit hash code for a set of molecules (ensemble).

error(Object) - Method in interface org.openscience.cdk.tools.ILoggingTool

Shows ERROR output for the Object.

error(Object, Object...) - Method in interface org.openscience.cdk.tools.ILoggingTool

Shows ERROR output for the given Object's.

F

fatal(Object) - Method in interface org.openscience.cdk.tools.ILoggingTool

Shows FATAL output for the Object.

first() - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader

format() - Method in class org.openscience.cdk.io.formats.IChemFormatMatcher.MatchResult

What was the format which matched if there was a match (IChemFormatMatcher.MatchResult.matched()).

frameRead(ReaderEvent) - Method in interface org.openscience.cdk.io.listener.IReaderListener

Indicates that a new frame has been read.

frameRead(ReaderEvent) - Method in class org.openscience.cdk.io.listener.PropertiesListener

G

generate(IAtomContainer) - Method in interface org.openscience.cdk.hash.AtomHashGenerator

Generate invariant 64-bit hash codes for the atoms of the molecule.

generate(Set<IAtomContainer>) - Method in interface org.openscience.cdk.hash.EnsembleHashGenerator

Generate invariant 64-bit hash code for an ensemble of molecules.

generate(IAtomContainer) - Method in interface org.openscience.cdk.hash.MoleculeHashGenerator

Generate invariant 64-bit hash code for a molecule.

get2DCenter() - Method in interface org.openscience.cdk.interfaces.IBond

Returns the geometric 2D center of the bond.

get3DCenter() - Method in interface org.openscience.cdk.interfaces.IBond

Returns the geometric 3D center of the bond.

getA() - Method in interface org.openscience.cdk.interfaces.ICrystal

Gets the A unit cell axes in carthesian coordinates as a three element double array.

getAgents() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns a IAtomContaineSet containing the agents in this reaction.

getAltLoc() - Method in interface org.openscience.cdk.interfaces.IPDBAtom

get the Alternate location indicator of this atom.

getAtom(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Get the atom at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getAtomCount().

getAtom(int) - Method in interface org.openscience.cdk.interfaces.IBond

Returns an Atom from this bond.

getAtom() - Method in interface org.openscience.cdk.interfaces.ILonePair

Returns the associated Atom.

getAtom() - Method in interface org.openscience.cdk.interfaces.ISingleElectron

Returns the associated Atom.

getAtomContainer(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Returns the AtomContainer at position number in the container.

getAtomContainer() - Method in interface org.openscience.cdk.io.iterator.event.IEventChemObjectReader

getAtomContainerCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Returns the number of AtomContainers in this Container.

getAtomCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the number of Atoms in this Container.

getAtomCount() - Method in interface org.openscience.cdk.interfaces.IBond

Returns the number of Atoms in this Bond.

getAtomicNumber() - Method in interface org.openscience.cdk.interfaces.IElement

Returns the atomic number of this element.

getAtomNumber(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Deprecated.

use IAtomContainer.indexOf(IAtom)

getAtomTypeName() - Method in interface org.openscience.cdk.interfaces.IAtomType

Gets the id attribute of the AtomType object.

getAttachPointNum() - Method in interface org.openscience.cdk.interfaces.IPseudoAtom

Access the attachment point number.

getB() - Method in interface org.openscience.cdk.interfaces.ICrystal

Gets the B unit cell axes in carthesian coordinates as a three element double array.

getBegin() - Method in interface org.openscience.cdk.interfaces.IBond

Access the begin (or first) atom of the bond.

getBond(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Get the bond at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getBondCount().

getBond(IAtom, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the bond that connects the two given atoms.

getBondCount() - Method in interface org.openscience.cdk.interfaces.IAtom

getBondCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the number of Bonds in this Container.

getBondNumber(IAtom, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Deprecated.

use IAtomContainer.indexOf(IBond)

getBondNumber(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Deprecated.

use IAtomContainer.indexOf(IBond)

getBondOrderSum(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the sum of the bond orders for a given Atom.

getBondOrderSum() - Method in interface org.openscience.cdk.interfaces.IAtomType

Gets the bondOrderSum attribute of the AtomType object.

getBondOrderSum() - Method in interface org.openscience.cdk.interfaces.IRing

Returns the sum of all bond orders in the ring.

getBonds() - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry

Returns an array of ligand bonds around the double bond.

getBuilder() - Method in interface org.openscience.cdk.interfaces.ICDKObject

Returns a IChemObjectBuilder for the data classes that extend this class.

getC() - Method in interface org.openscience.cdk.interfaces.ICrystal

Gets the C unit cell axes in carthesian coordinates as a three element double array.

getCarriers() - Method in interface org.openscience.cdk.interfaces.IStereoElement

The carriers of the stereochemistry

getChainID() - Method in interface org.openscience.cdk.interfaces.IPDBAtom

get the Chain identifier of this atom.

getChainID() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer

Gets the Chain ID of this monomer.

getCharge() - Method in interface org.openscience.cdk.interfaces.IAdductFormula

Returns the partial charge of this Adduct.

getCharge() - Method in interface org.openscience.cdk.interfaces.IAtom

Returns the partial charge of this atom.

getCharge() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Access the charge of this IMolecularFormula.

getChemModel(int) - Method in interface org.openscience.cdk.interfaces.IChemSequence

Returns the ChemModel at position number in the container.

getChemModelCount() - Method in interface org.openscience.cdk.interfaces.IChemSequence

Returns the number of ChemModels in this Container.

getChemObject(int) - Method in interface org.openscience.cdk.interfaces.IMapping

Retrieve the first or second of the related IChemObjects.

getChemSequence(int) - Method in interface org.openscience.cdk.interfaces.IChemFile

Returns the ChemSequence at position number in the container.

getChemSequenceCount() - Method in interface org.openscience.cdk.interfaces.IChemFile

Returns the number of ChemSequences in this Container.

getChiralAtom() - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality

Atom that is the chirality center.

getConfig() - Method in interface org.openscience.cdk.interfaces.IStereoElement

Access the configuration order and class of the stereochemistry.

getConfigClass() - Method in interface org.openscience.cdk.interfaces.IStereoElement

The configuration class of the stereochemistry.

getConfigOrder() - Method in interface org.openscience.cdk.interfaces.IStereoElement

The configuration order of the stereochemistry.

getConnectedAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond

Deprecated.

use the method IBond.getOther(IAtom)

getConnectedAtoms(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond

Returns all the atoms in the bond connected to the given atom.

getConnectedAtomsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Deprecated.

use IAtomContainer.getConnectedBondsCount(IAtom)

getConnectedAtomsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the atoms connected connected to the specified atom by a bond.

getConnectedBondsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the number of connected bonds (explicit degree) to the specified atom.

getConnectedBondsCount(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the number of connected bonds (explicit degree) to atom at the specified index.

getConnectedBondsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the bonds connected connected to the specified atom.

getConnectedElectronContainersList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the electron containers (bonds, radicals, and lone pairs ) connected connected to the specified atom.

getConnectedLonePairsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the number of lone pairs connected to the specified atom.

getConnectedLonePairsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the lone pairs connected connected to the specified atom.

getConnectedRings(IRing) - Method in interface org.openscience.cdk.interfaces.IRingSet

Returns all the rings in the RingSet that share one or more atoms with a given ring.

getConnectedSingleElectronsCount(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the number of single electrons connected to the specified atom.

getConnectedSingleElectronsList(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the single electrons connected connected to the specified atom.

getContainer() - Method in interface org.openscience.cdk.interfaces.IAtom

Access the IAtomContainer of which this atom is a member of.

getContainer() - Method in interface org.openscience.cdk.interfaces.IBond

getCovalentRadius() - Method in interface org.openscience.cdk.interfaces.IAtomType

Returns the covalent radius for this AtomType.

getCrystal() - Method in interface org.openscience.cdk.interfaces.IChemModel

Gets the Crystal contained in this ChemModel.

getCTerminus() - Method in interface org.openscience.cdk.interfaces.IAminoAcid

Retrieves the C-terminus atom.

getDefaultSetting() - Method in class org.openscience.cdk.io.setting.IOSetting

getDirection() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns the IReaction.Direction of the reaction.

getElectronContainer(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the ElectronContainer at position number in the container.

getElectronContainerCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the number of ElectronContainers in this Container.

getElectronCount() - Method in interface org.openscience.cdk.interfaces.IElectronContainer

Returns the number of electrons in this electron container.

getEnd() - Method in interface org.openscience.cdk.interfaces.IBond

Access the end (or second) atom of the bond.

getEndChainID() - Method in interface org.openscience.cdk.interfaces.IPDBStructure

get the ending Chain identifier of this structure.

getEndInsertionCode() - Method in interface org.openscience.cdk.interfaces.IPDBStructure

get the ending Code for insertion of residues of this structure.

getEndSequenceNumber() - Method in interface org.openscience.cdk.interfaces.IPDBStructure

get the ending sequence number of this structure.

getExactMass() - Method in interface org.openscience.cdk.interfaces.IIsotope

Gets the ExactMass attribute of the Isotope object.

getFirstAtom() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Deprecated.

use IAtomContainer.getAtom(int)

getFlag(int) - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns the value of a given flag.

getFlags() - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns the whole set of flags.

getFlagValue() - Method in interface org.openscience.cdk.interfaces.IChemObject

Access the internal value used to store the flags.

getFocus() - Method in interface org.openscience.cdk.interfaces.IStereoElement

The focus atom or bond at the 'centre' of the stereo-configuration.

getFormalCharge() - Method in interface org.openscience.cdk.interfaces.IAtomType

Returns the formal charge of this atom.

getFormalNeighbourCount() - Method in interface org.openscience.cdk.interfaces.IAtomType

Returns the formal neighbour count of this atom.

getFormat() - Method in interface org.openscience.cdk.io.IChemObjectIO

Returns the IResourceFormat class for this IO class.

getFormatName() - Method in interface org.openscience.cdk.io.formats.IResourceFormat

Returns a one-lined format name of the format.

getFractionalPoint3d() - Method in interface org.openscience.cdk.interfaces.IAtom

Returns a point specifying the location of this atom in a Crystal unit cell.

getFragment() - Method in interface org.openscience.cdk.interfaces.IFragmentAtom

Returns the fully expended form of the IFragmentAtom.

getHetAtom() - Method in interface org.openscience.cdk.interfaces.IPDBAtom

Determine whether this is a heteroatom or not.

getHybridization() - Method in interface org.openscience.cdk.interfaces.IAtomType

Returns the hybridization of this atom.

getICode() - Method in interface org.openscience.cdk.interfaces.IPDBAtom

get Code for insertion of residues of this atom.

getICode() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer

Gets the ICode of this monomer.

getID() - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns the identifier (ID) of this object.

getImplicitHydrogenCount() - Method in interface org.openscience.cdk.interfaces.IAtom

Returns the implicit hydrogen count of this atom.

getIndex() - Method in interface org.openscience.cdk.interfaces.IAtom

Acces the index of an atom in the context of an IAtomContainer.

getIndex() - Method in interface org.openscience.cdk.interfaces.IBond

getIOSettings() - Method in interface org.openscience.cdk.io.IChemObjectIO

Returns an array of IOSettings defined by this IChemObjectIO class.

getIsotopeCount(IIsotope) - Method in interface org.openscience.cdk.interfaces.IAdductFormula

Checks a set of Nodes for the occurrence of the isotope in the adduct formula from a particular isotope.

getIsotopeCount() - Method in interface org.openscience.cdk.interfaces.IAdductFormula

Checks a set of Nodes for the number of different isotopes in the adduct formula.

getIsotopeCount(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Checks a set of Nodes for the occurrence of the isotope in the IMolecularFormula from a particular isotope.

getIsotopeCount() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Checks a set of Nodes for the number of different isotopes in the IMolecularFormula.

getLabel() - Method in interface org.openscience.cdk.interfaces.IPseudoAtom

Returns the label of this PseudoAtom.

getLastAtom() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Deprecated.

use IAtomContainer.getAtom(int)

getLevel() - Method in class org.openscience.cdk.io.setting.IOSetting

getLigands() - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality

Returns an array of ligand atoms around the chiral atom.

getListenerCount() - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns the number of ChemObjectListeners registered with this object.

getListeners() - Method in interface org.openscience.cdk.io.IChemObjectIO

Access all the listeners for this ChemObject Reader or Writer.

getLoggingToolClass() - Static method in class org.openscience.cdk.tools.LoggingToolFactory

Gets the currently used ILoggingTool implementation.

getLonePair(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Get the lone pair at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getLonePairCount().

getLonePairCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the number of LonePairs in this Container.

getLonePairNumber(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Deprecated.

use IAtomContainer.indexOf(ILonePair)

getMapping(int) - Method in interface org.openscience.cdk.interfaces.IReaction

Retrieves a mapping between the reactant and product side to this Reaction.

getMappingCount() - Method in interface org.openscience.cdk.interfaces.IReaction

Get the number of mappings between the reactant and product side to this Reaction.

getMassNumber() - Method in interface org.openscience.cdk.interfaces.IIsotope

Returns the atomic mass of this element.

getMaxBondOrder() - Method in interface org.openscience.cdk.interfaces.IAtomType

Gets the MaxBondOrder attribute of the AtomType object.

getMaximumBondOrder(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the maximum bond order that this atom currently has in the context of this AtomContainer.

getMIMEType() - Method in interface org.openscience.cdk.io.formats.IResourceFormat

Returns the accepted MIME type for this format.

getMinimumBondOrder(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the minimum bond order that this atom currently has in the context of this AtomContainer.

getMolecularFormula(int) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet

Returns the IMolecularFormula at position number in the chemObject.

getMoleculeSet() - Method in interface org.openscience.cdk.interfaces.IChemModel

Returns the IAtomContainerSet of this ChemModel.

getMonomer(String, String) - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Retrieve a Monomer object by specifying its name.

getMonomer(String) - Method in interface org.openscience.cdk.interfaces.IPolymer

Retrieve a Monomer object by specifying its name.

getMonomer(String) - Method in interface org.openscience.cdk.interfaces.IStrand

Retrieve a Monomer object by specifying its name.

getMonomerCount() - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Return the number of monomers present in BioPolymer.

getMonomerCount() - Method in interface org.openscience.cdk.interfaces.IPolymer

Return the number of monomers present in the Polymer.

getMonomerCount() - Method in interface org.openscience.cdk.interfaces.IStrand

Return the number of monomers present in the Strand.

getMonomerName() - Method in interface org.openscience.cdk.interfaces.IMonomer

Retrieve the monomer name.

getMonomerNames() - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Returns a collection of the names of all Monomers in this BioPolymer.

getMonomerNames() - Method in interface org.openscience.cdk.interfaces.IPolymer

Returns a collection of the names of all Monomers in this polymer.

getMonomerNames() - Method in interface org.openscience.cdk.interfaces.IStrand

Returns a collection of the names of all Monomers in this polymer.

getMonomers() - Method in interface org.openscience.cdk.interfaces.IStrand

Returns the monomers in this strand.

getMonomerType() - Method in interface org.openscience.cdk.interfaces.IMonomer

Retrieve the monomer type.

getMultiplier(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Returns the multiplier for the AtomContainer at position number in the container.

getMultiplier(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Returns the multiplier of the given AtomContainer.

getMultipliers() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Returns an array of double with the stoichiometric coefficients of the products.

getName() - Method in interface org.openscience.cdk.interfaces.IPDBAtom

get the Atom name of this atom.

getName() - Method in interface org.openscience.cdk.interfaces.ISetting

Access the name of the setting.

getName() - Method in class org.openscience.cdk.io.setting.IOSetting

getNameExtensions() - Method in interface org.openscience.cdk.io.formats.IResourceFormat

Returns an array of common resource name extensions.

getNaturalAbundance() - Method in interface org.openscience.cdk.interfaces.IIsotope

Gets the NaturalAbundance attribute of the Isotope object.

getNextBond(IBond, IAtom) - Method in interface org.openscience.cdk.interfaces.IRing

Returns the next bond in order, relative to a given bond and atom.

getNotification() - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns the flag that indicates whether notification messages are sent around.

getNTerminus() - Method in interface org.openscience.cdk.interfaces.IAminoAcid

Retrieves the N-terminus atom.

getOccupancy() - Method in interface org.openscience.cdk.interfaces.IPDBAtom

get the Occupancy of this atom.

getOrder() - Method in interface org.openscience.cdk.interfaces.IBond

Returns the bond order of this bond.

getOther(IAtom) - Method in interface org.openscience.cdk.interfaces.IBond

Returns the other atom in the bond, the atom is connected to the given atom.This method is only correct for two-centre bonds, for n-centre bonds the behaviour is undefined and the more correct IBond.getConnectedAtoms(IAtom) should be used.

getOxt() - Method in interface org.openscience.cdk.interfaces.IPDBAtom

Returns true of this atom is a PDB OXT atom.

getPoint2d() - Method in interface org.openscience.cdk.interfaces.IAtom

Returns a point specifying the location of this atom in a 2D space.

getPoint3d() - Method in interface org.openscience.cdk.interfaces.IAtom

Returns a point specifying the location of this atom in a 3D space.

getPreferredNameExtension() - Method in interface org.openscience.cdk.io.formats.IResourceFormat

Returns the preferred resource name extension.

getProductCoefficient(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction

Returns the stoichiometry coefficient of the given product.

getProductCoefficients() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns an array of double with the stoichiometric coefficients of the products.

getProductCount() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns the number of products in this reaction.

getProducts() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns a IAtomContaineSet containing the products of this reaction.

getProperties() - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns a Map with the IChemObject's properties.

getProperties() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Returns a Map with the IChemObject's properties.I should integrate into ChemObject.

getProperty(Object) - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns a property for the IChemObject - the object is automatically cast to the required type.

getProperty(Object, Class<T>) - Method in interface org.openscience.cdk.interfaces.IChemObject

Access a property of the given description and cast the specified class.

getProperty(Object) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Returns a property for the IChemObject - the object is automatically cast to the required type.

getProperty(Object, Class<T>) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Access a property of the given description and cast the specified class.

getQuestion() - Method in class org.openscience.cdk.io.setting.IOSetting

getReactantCoefficient(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IReaction

Returns the stoichiometry coefficient of the given reactant.

getReactantCoefficients() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns an array of double with the stoichiometric coefficients of the reactants.

getReactantCount() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns the number of reactants in this reaction.

getReactants() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns a IAtomContaineSet containing the reactants in this reaction.

getReaction(int) - Method in interface org.openscience.cdk.interfaces.IReactionSet

Returns the Reaction at position number in the container.

getReactionCount() - Method in interface org.openscience.cdk.interfaces.IReactionSet

Returns the number of Reactions in this Container.

getReactionSchemeCount() - Method in interface org.openscience.cdk.interfaces.IReactionScheme

Returns the number of ReactionScheme in this Scheme.

getReactionSet() - Method in interface org.openscience.cdk.interfaces.IChemModel

Gets the ReactionSet contained in this ChemModel.

getReaderClassName() - Method in interface org.openscience.cdk.io.formats.IChemFormat

Returns the class name of the CDK Reader for this format.

getRecord() - Method in interface org.openscience.cdk.interfaces.IPDBAtom

Get one entire line from the PDB entry file which describe the IPDBAtom.

getRequiredDataFeatures() - Method in interface org.openscience.cdk.io.formats.IChemFormat

Returns an integer indicating the data features that this format requires.

getResName() - Method in interface org.openscience.cdk.interfaces.IPDBAtom

get the Residue name of this atom.

getResSeq() - Method in interface org.openscience.cdk.interfaces.IPDBAtom

get the Residue sequence number of this atom.

getResSeq() - Method in interface org.openscience.cdk.interfaces.IPDBMonomer

Gets the sequence identifier of this monomer.

getRings(IBond) - Method in interface org.openscience.cdk.interfaces.IRingSet

Returns a vector of all rings that this bond is part of.

getRings(IAtom) - Method in interface org.openscience.cdk.interfaces.IRingSet

Returns a vector of all rings that this atom is part of.

getRingSet() - Method in interface org.openscience.cdk.interfaces.IChemModel

Returns the RingSet of this ChemModel.

getRingSize() - Method in interface org.openscience.cdk.interfaces.IRing

Returns the number of atoms/bonds in this ring.

getSegID() - Method in interface org.openscience.cdk.interfaces.IPDBAtom

get the Segment identifier, left-justified of this atom.

getSerial() - Method in interface org.openscience.cdk.interfaces.IPDBAtom

get the Atom serial number of this atom.

getSetting(String) - Method in interface org.openscience.cdk.io.IChemObjectIO

Access a named setting managed by this reader/writer.

getSetting(String, Class<S>) - Method in interface org.openscience.cdk.io.IChemObjectIO

Access a named setting managed by this reader/writer.

getSetting() - Method in class org.openscience.cdk.io.setting.IOSetting

Sets the setting for a certain question.

getSettings() - Method in interface org.openscience.cdk.io.IChemObjectIO

Access a collection of IOSettings for this reader/writer.

getSingleElectron(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Get the single electron at the specified idx, the index should be in the range 0 ≤ idx < IAtomContainer.getSingleElectronCount().

getSingleElectronCount() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the number of the single electrons in this container.

getSingleElectronNumber(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Deprecated.

use IAtomContainer.indexOf(ISingleElectron)

getSource() - Method in interface org.openscience.cdk.interfaces.IChemObjectChangeEvent

IChemObject that fired the event.

getSpaceGroup() - Method in interface org.openscience.cdk.interfaces.ICrystal

Gets the space group of this crystal.

getStartChainID() - Method in interface org.openscience.cdk.interfaces.IPDBStructure

get start Chain identifier of this structure.

getStartInsertionCode() - Method in interface org.openscience.cdk.interfaces.IPDBStructure

get start Code for insertion of residues of this structure.

getStartSequenceNumber() - Method in interface org.openscience.cdk.interfaces.IPDBStructure

get the start sequence number of this structure.

getStereo() - Method in interface org.openscience.cdk.interfaces.IBond

Returns the stereo descriptor for this bond.

getStereo() - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry

Defines the stereochemistry around the double bond.

getStereo() - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality

Defines the stereochemistry around the chiral atom.

getStereoBond() - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry

IBond that is the stereo center.

getStereoParity() - Method in interface org.openscience.cdk.interfaces.IAtom

Deprecated.

use IStereoElements for storing stereochemistry

getStrand(String) - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Retrieve a Monomer object by specifying its name.

getStrandCount() - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Return the number of strands present in the BioPolymer.

getStrandName() - Method in interface org.openscience.cdk.interfaces.IStrand

Retrieve the strand name.

getStrandNames() - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Returns a collection of the names of all Strands in this BioPolymer.

getStrands() - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Returns a Map containing the strands in the Polymer.

getStrandType() - Method in interface org.openscience.cdk.interfaces.IStrand

Retrieve the strand type.

getStructures() - Method in interface org.openscience.cdk.interfaces.IPDBPolymer

Returns a Collection containing the PDBStructure in the PDBPolymer.

getStructureType() - Method in interface org.openscience.cdk.interfaces.IPDBStructure

get Structure Type of this structure.

getSupportedDataFeatures() - Method in interface org.openscience.cdk.io.formats.IChemFormat

Returns an integer indicating the data features that this format supports.

getSymbol() - Method in interface org.openscience.cdk.interfaces.IElement

Returns the element symbol of this element.

getTempFactor() - Method in interface org.openscience.cdk.interfaces.IPDBAtom

get the Temperature factor of this atom.

getTitle() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Access the title of the record.

getValency() - Method in interface org.openscience.cdk.interfaces.IAtomType

Gets the the exact electron valency of the AtomType object.

getWriterClassName() - Method in interface org.openscience.cdk.io.formats.IChemFormat

Returns the class name of the CDK Writer for this format.

getZ() - Method in interface org.openscience.cdk.interfaces.ICrystal

Gets the number of asymmetric parts in the unit cell.

H

handleError(String) - Method in interface org.openscience.cdk.io.IChemObjectReader

Redirects an error message to the IChemObjectReaderErrorHandler.

handleError(String, Exception) - Method in interface org.openscience.cdk.io.IChemObjectReader

Redirects an error message to the IChemObjectReaderErrorHandler.

handleError(String, int, int, int) - Method in interface org.openscience.cdk.io.IChemObjectReader

Redirects an error message to the IChemObjectReaderErrorHandler.

handleError(String, int, int, int, Exception) - Method in interface org.openscience.cdk.io.IChemObjectReader

Redirects an error message to the IChemObjectReaderErrorHandler.

handleError(String) - Method in interface org.openscience.cdk.io.IChemObjectReaderErrorHandler

Method that should react on an error message send by an IChemObjectReader.

handleError(String, Exception) - Method in interface org.openscience.cdk.io.IChemObjectReaderErrorHandler

Method that should react on an error message send by an IChemObjectReader.

handleError(String, int, int, int) - Method in interface org.openscience.cdk.io.IChemObjectReaderErrorHandler

Method that should react on an error message send by an IChemObjectReader.

handleError(String, int, int, int, Exception) - Method in interface org.openscience.cdk.io.IChemObjectReaderErrorHandler

Method that should react on an error message send by an IChemObjectReader.

hasSetting(String) - Method in interface org.openscience.cdk.io.IChemObjectIO

Determine whether this reader/writer has a setting of the provided name.

HBPY8 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Hexagonal Bipyramidal (HBPY-8)

HBPY9 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Heptagonal Bipyramidal (HBPY-9)

HeptagonalBipyramidal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Heptagonal Bipyramidal (HBPY-9)

HexagonalBipyramidal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Hexagonal Bipyramidal (HBPY-8)

I

IAdductFormula - Interface in org.openscience.cdk.interfaces

Class defining an adduct object in a MolecularFormula.

IAminoAcid - Interface in org.openscience.cdk.interfaces

A AminoAcid is Monomer which stores additional amino acid specific informations, like the N-terminus atom.

IAtom - Interface in org.openscience.cdk.interfaces

Represents the idea of an chemical atom.

IAtomContainer - Interface in org.openscience.cdk.interfaces

Base class for all chemical objects that maintain a list of Atoms and ElectronContainers.

IAtomContainerSet - Interface in org.openscience.cdk.interfaces

A set of AtomContainers.

IAtomType - Interface in org.openscience.cdk.interfaces

The base class for atom types.

IAtomType.Hybridization - Enum in org.openscience.cdk.interfaces

An enum for the different hybridization states.

IBioPolymer - Interface in org.openscience.cdk.interfaces

A BioPolymer is a subclass of a Polymer which is supposed to store additional informations about the Polymer which are connected to BioPolymers.

IBond - Interface in org.openscience.cdk.interfaces

Implements the concept of a covalent bond between two or more atoms.

IBond.Order - Enum in org.openscience.cdk.interfaces

A list of permissible bond orders.

IBond.Stereo - Enum in org.openscience.cdk.interfaces

Enumeration of possible stereo types of two-atom bonds.

ICDKChangeListener - Interface in org.openscience.cdk.event

A ChangeListener for the CDK, to be independent from the Swing package.

ICDKObject - Interface in org.openscience.cdk.interfaces

The base class for all data objects in this CDK.

IChemFile - Interface in org.openscience.cdk.interfaces

An IChemObject containing a number of ChemSequences.

IChemFormat - Interface in org.openscience.cdk.io.formats

This class is the interface that all ChemFormat's should implement.

IChemFormatMatcher - Interface in org.openscience.cdk.io.formats

This interface is used for classes that are able to match a certain chemical file format.

IChemFormatMatcher.MatchResult - Class in org.openscience.cdk.io.formats

Simple class holds whether a format matcher matched, when it matched and what the format was.

IChemModel - Interface in org.openscience.cdk.interfaces

An object containing multiple MoleculeSet and the other lower level concepts like rings, sequences, fragments, etc.

IChemObject - Interface in org.openscience.cdk.interfaces

The base class for all chemical objects in this cdk.

IChemObjectBuilder - Interface in org.openscience.cdk.interfaces

A helper class to instantiate a ICDKObject instance for a specific implementation.

IChemObjectChangeEvent - Interface in org.openscience.cdk.interfaces

Event fired by CDK IChemObject classes to their registered listeners in case something changed within them.

IChemObjectIO - Interface in org.openscience.cdk.io

This class is the interface that all IO readers should implement.

IChemObjectIOListener - Interface in org.openscience.cdk.io.listener

Allows monitoring of progress of file reader activities.

IChemObjectListener - Interface in org.openscience.cdk.interfaces

Classes implementing this interface must implement this method such that they react appropriately to changes in the object they are interested in.

IChemObjectReader - Interface in org.openscience.cdk.io

This interface specifies the common functionality all IO readers should provide.

IChemObjectReader.Mode - Enum in org.openscience.cdk.io

IChemObjectReaderErrorHandler - Interface in org.openscience.cdk.io

Interface for classes aimed to handle IChemObjectReader errors.

IChemObjectWriter - Interface in org.openscience.cdk.io

This class is the interface that all IO writers should implement.

IChemSequence - Interface in org.openscience.cdk.interfaces

A sequence of ChemModels, which can, for example, be used to store the course of a reaction.

ICMLCustomizer - Interface in org.openscience.cdk.libio.cml

Interface for classes that allow the Convertor to be customized for certain features.

ICrystal - Interface in org.openscience.cdk.interfaces

Class representing a molecular crystal.

IDoubleBondStereochemistry - Interface in org.openscience.cdk.interfaces

Stereochemistry specification for double bond stereochemistry.

IDoubleBondStereochemistry.Conformation - Enum in org.openscience.cdk.interfaces

Enumeration that defines the two possible values for this stereochemistry type.

IElectronContainer - Interface in org.openscience.cdk.interfaces

Base class for entities containing electrons, like bonds, orbitals, lone-pairs.

IElement - Interface in org.openscience.cdk.interfaces

Implements the idea of an element in the periodic table.

IEventChemObjectReader - Interface in org.openscience.cdk.io.iterator.event

Interface for an iterating molecule reader.

IFragmentAtom - Interface in org.openscience.cdk.interfaces

Class to represent an IPseudoAtom which embeds an IAtomContainer.

IGraphMatrix - Interface in org.openscience.cdk.graph.matrix

Interface describing a molecular graph matrix calculator.

IIsotope - Interface in org.openscience.cdk.interfaces

Used to store and retrieve data of a particular isotope.

IIteratingChemObjectReader<T extends IChemObject> - Interface in org.openscience.cdk.io.iterator

Interface for an iterating molecule reader.

ILoggingTool - Interface in org.openscience.cdk.tools

Useful for logging messages.

ILonePair - Interface in org.openscience.cdk.interfaces

A LonePair is an orbital primarily located with one Atom, containing two electrons.

IMapping - Interface in org.openscience.cdk.interfaces

Represents a mapping of two atoms.

IMolecularFormula - Interface in org.openscience.cdk.interfaces

Class defining a molecular formula object.

IMolecularFormulaSet - Interface in org.openscience.cdk.interfaces

Class defining a molecular formula object.

IMonomer - Interface in org.openscience.cdk.interfaces

A Monomer is an AtomContainer which stores additional monomer specific informations for a group of Atoms.

indexOf(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Access the storage index of an atom.

indexOf(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Access the storage index of a bond.

indexOf(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Access the storage index of a single electron (radical).

indexOf(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Access the storage index of a long pair.

info(Object) - Method in interface org.openscience.cdk.tools.ILoggingTool

Shows INFO output for the Object.

info(Object, Object...) - Method in interface org.openscience.cdk.tools.ILoggingTool

Shows INFO output for the given Object's.

Intractable - Exception in org.openscience.cdk.exception

Indicates a computation did not complete within some predefined bound.

Intractable(String) - Constructor for exception org.openscience.cdk.exception.Intractable

Create a new exception with the specified message.

InvalidSmilesException - Exception in org.openscience.cdk.exception

Exception thrown when an error is occurred during SMILES parsing.

InvalidSmilesException(String) - Constructor for exception org.openscience.cdk.exception.InvalidSmilesException

Constructs a new exception with a custom message.

InvalidSmilesException(String, Exception) - Constructor for exception org.openscience.cdk.exception.InvalidSmilesException

Constructs a new exception with a custom message and a stacktrace.

invert() - Method in enum org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation

Invert this conformation, inv(together) = opposite, inv(opposite) = together.

invert() - Method in enum org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo

Invert this conformation, inv(clockwise) = anti_clockwise, inv(anti_clockwise) = clockwise.

IOSetting - Class in org.openscience.cdk.io.setting

An interface for reader settings.

IOSetting(String, IOSetting.Importance, String, String) - Constructor for class org.openscience.cdk.io.setting.IOSetting

The default constructor that sets this field.

IOSetting.Importance - Enum in org.openscience.cdk.io.setting

IPDBAtom - Interface in org.openscience.cdk.interfaces

A PDBAtom is a subclass of a Atom which is supposed to store additional informations about the Atom.

IPDBMonomer - Interface in org.openscience.cdk.interfaces

Represents the idea of an protein monomer as found in PDB files.

IPDBPolymer - Interface in org.openscience.cdk.interfaces

A PDBPolymer is a subclass of a BioPolymer which is supposed to store additional informations about the BioPolymer which are connected to BioPolymers.

IPDBStructure - Interface in org.openscience.cdk.interfaces

Represents the idea of an chemical structure.

IPolymer - Interface in org.openscience.cdk.interfaces

Subclass of Molecule to store Polymer specific attributes that a Polymer has.

IPseudoAtom - Interface in org.openscience.cdk.interfaces

Represents the idea of a non-chemical atom-like entity, like Me, R, X, Phe, His, etc.

IQueryAtom - Interface in org.openscience.cdk.isomorphism.matchers

Defines the ability to be matched against IAtom's.

IQueryAtomContainer - Interface in org.openscience.cdk.isomorphism.matchers

General concept of a IAtomContainer aimed at doing molecular subgraph queries using the UniversalIsomorphismTester.

IQueryBond - Interface in org.openscience.cdk.isomorphism.matchers

Defines the abililty to be matched against IBond's.

IRandomAccessChemObjectReader<T> - Interface in org.openscience.cdk.io.random

Extension of ListIterator.

IReaction - Interface in org.openscience.cdk.interfaces

Represents the idea of a chemical reaction.

IReaction.Direction - Enum in org.openscience.cdk.interfaces

Permissible reaction directions.

IReactionScheme - Interface in org.openscience.cdk.interfaces

Classes that implement this interface of a scheme.

IReactionSet - Interface in org.openscience.cdk.interfaces

A set of reactions, for example those taking part in a reaction.

IReaderListener - Interface in org.openscience.cdk.io.listener

Allows monitoring of progress of file reader activities.

IResourceFormat - Interface in org.openscience.cdk.io.formats

This class is the interface that all ResourceFormat's should implement.

IRing - Interface in org.openscience.cdk.interfaces

Class representing a ring structure in a molecule.

IRingSet - Interface in org.openscience.cdk.interfaces

Maintains a set of Ring objects.

isAromatic() - Method in interface org.openscience.cdk.interfaces.IAtom

Access whether this atom has been marked as aromatic.

isAromatic() - Method in interface org.openscience.cdk.interfaces.IBond

Access whether this bond has been marked as aromatic.

isConnectedTo(IBond) - Method in interface org.openscience.cdk.interfaces.IBond

Checks whether a bond is connected to another one.

isDebugEnabled() - Method in interface org.openscience.cdk.tools.ILoggingTool

Use this method for computational demanding debug info.

isEmpty() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Indicates whether this container is empty.

isEmpty() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Returns true if this IAtomContainerSet is empty.

isEmpty() - Method in interface org.openscience.cdk.interfaces.IChemModel

Returns true if this ChemModel is empty.

isEmpty() - Method in interface org.openscience.cdk.interfaces.IReactionSet

Returns true if this IReactionSet is empty.

isEmpty() - Method in interface org.openscience.cdk.interfaces.IRingSet

Returns true if this IRingSet has no atoms.

ISetting - Interface in org.openscience.cdk.interfaces

A simple setting that can be managed by the SettingManager.

isExpanded() - Method in interface org.openscience.cdk.interfaces.IFragmentAtom

Helper method to indicate that the method should be drawn fully, and not just the abbreviated form.

ISimpleChemObjectReader - Interface in org.openscience.cdk.io

This class is the interface that all IO readers should implement.

ISingleElectron - Interface in org.openscience.cdk.interfaces

A Single Electron is an orbital which is occupied by only one electron.

isInRing() - Method in interface org.openscience.cdk.interfaces.IAtom

Access whether this atom has been flagged as in a ring.

isInRing() - Method in interface org.openscience.cdk.interfaces.IBond

Access whether this bond has been flagged as in a ring.

isotopes() - Method in interface org.openscience.cdk.interfaces.IAdductFormula

Returns an Iterator for looping over all isotopes in this adduct formula.

isotopes() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Returns an Iterable for looping over all isotopes in this IMolecularFormula.

IStereoElement<F extends IChemObject,C extends IChemObject> - Interface in org.openscience.cdk.interfaces

Representation of stereochemical configuration.

IStrand - Interface in org.openscience.cdk.interfaces

A Strand is an AtomContainer which stores additional strand specific informations for a group of Atoms.

ISubstance - Interface in org.openscience.cdk.interfaces

A chemical substance that consists of one or more chemical structures.

isXMLBased() - Method in interface org.openscience.cdk.io.formats.IResourceFormat

Indicates if the format is an XML-based language.

ITetrahedralChirality - Interface in org.openscience.cdk.interfaces

Stereochemistry specification for quadrivalent atoms.

ITetrahedralChirality.Stereo - Enum in org.openscience.cdk.interfaces

Enumeration that defines the two possible chiralities for this stereochemistry type.

IWriterListener - Interface in org.openscience.cdk.io.listener

Allows monitoring of progress of writing activities.

L

last() - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader

LEFT - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

level - Variable in class org.openscience.cdk.io.setting.IOSetting

LoggingToolFactory - Class in org.openscience.cdk.tools

Factory used to instantiate a ILoggingTool.

LoggingToolFactory() - Constructor for class org.openscience.cdk.tools.LoggingToolFactory

lonePairs() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns an Iterable for looping over all lone pairs in this container.

M

map(Map<IAtom, IAtom>, Map<IBond, IBond>) - Method in interface org.openscience.cdk.interfaces.IDoubleBondStereochemistry

Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.

map(Map<IChemObject, IChemObject>) - Method in interface org.openscience.cdk.interfaces.IStereoElement

map(Map<IAtom, IAtom>, Map<IBond, IBond>) - Method in interface org.openscience.cdk.interfaces.IStereoElement

Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.

map(Map<IAtom, IAtom>, Map<IBond, IBond>) - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality

Map the atoms/bonds in this instance to a new stereo element using the provided atom/bond mapping.

mappings() - Method in interface org.openscience.cdk.interfaces.IReaction

Returns the mappings between the reactant and the product side.

matched() - Method in class org.openscience.cdk.io.formats.IChemFormatMatcher.MatchResult

Did the chem format match.

matches(List<String>) - Method in interface org.openscience.cdk.io.formats.IChemFormatMatcher

Method that checks whether the given lines are part of the format read by this reader.

matches(IAtom) - Method in interface org.openscience.cdk.isomorphism.matchers.IQueryAtom

Returns true of the given atom matches this IQueryAtom.

matches(IBond) - Method in interface org.openscience.cdk.isomorphism.matchers.IQueryBond

Returns true of the given bond matches this IQueryBond.

MatchResult(boolean, IChemFormat, int) - Constructor for class org.openscience.cdk.io.formats.IChemFormatMatcher.MatchResult

molecularFormulas() - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet

Returns the array of IMolecularFormula of this chemObject.

MoleculeHashGenerator - Interface in org.openscience.cdk.hash

A hash function which generates a single 64-bit hash code for a molecule.

N

name - Variable in class org.openscience.cdk.io.setting.IOSetting

newAtom() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Create a new atom using the default constructor.

newAtomContainer() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Create a new atom container using the default constructor.

newBond() - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Create a new bond using the default constructor.

newInstance(Class<T>, Object...) - Method in interface org.openscience.cdk.interfaces.IChemObjectBuilder

Creates a new instance of an ICDKObject, using the constructor defined by the given parameters.

NO_MATCH - Static variable in interface org.openscience.cdk.io.formats.IChemFormatMatcher

Convenience method for indicating a format did not match.

NoSuchAtomException - Exception in org.openscience.cdk.exception

Exception that is thrown when an Atom is requested or required that does not exist in the relevant environment.

NoSuchAtomException(String) - Constructor for exception org.openscience.cdk.exception.NoSuchAtomException

Constructs a new NoSuchAtomException with the given message.

NoSuchAtomTypeException - Exception in org.openscience.cdk.exception

Exception that may be thrown when an atom type is looked up or perceived but no such atom type was found.

NoSuchAtomTypeException(String) - Constructor for exception org.openscience.cdk.exception.NoSuchAtomTypeException

Constructs a new NoSuchAtomTypeException.

notifyChanged() - Method in interface org.openscience.cdk.interfaces.IChemObject

This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.

notifyChanged(IChemObjectChangeEvent) - Method in interface org.openscience.cdk.interfaces.IChemObject

This should be triggered by an method that changes the content of an object to that the registered listeners can react to it.

numeric() - Method in enum org.openscience.cdk.interfaces.IBond.Order

Access a numeric value for the number of bonded electron pairs.

O

OC - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Octahedral (OC-6)

Octahedral - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Octahedral (OC-6)

OPPOSITE - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

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

org.openscience.cdk.event - package org.openscience.cdk.event

org.openscience.cdk.exception - package org.openscience.cdk.exception

org.openscience.cdk.graph.matrix - package org.openscience.cdk.graph.matrix

org.openscience.cdk.hash - package org.openscience.cdk.hash

org.openscience.cdk.interfaces - package org.openscience.cdk.interfaces

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

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

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

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

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

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

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

org.openscience.cdk.isomorphism.matchers - package org.openscience.cdk.isomorphism.matchers

org.openscience.cdk.libio.cml - package org.openscience.cdk.libio.cml

org.openscience.cdk.tools - package org.openscience.cdk.tools

P

PBPY - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Pentagonal Bipyramidal (PBPY-7)

PentagonalBipyramidal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Pentagonal Bipyramidal (PBPY-7)

processIOSettingQuestion(IOSetting) - Method in interface org.openscience.cdk.io.listener.IChemObjectIOListener

Prompted when the IO filter needs information to process the file.

processIOSettingQuestion(IOSetting) - Method in class org.openscience.cdk.io.listener.PropertiesListener

Processes the IOSettings by listing the question, giving the options and asking the user to provide their choice.

PropertiesListener - Class in org.openscience.cdk.io.listener

Answers the questions by looking up the values in a Properties object.

PropertiesListener(Properties) - Constructor for class org.openscience.cdk.io.listener.PropertiesListener

Q

question - Variable in class org.openscience.cdk.io.setting.IOSetting

R

ReactionRole - Enum in org.openscience.cdk

reactions() - Method in interface org.openscience.cdk.interfaces.IReactionSet

Returns the Iterable over Reactions of this container.

reactionSchemes() - Method in interface org.openscience.cdk.interfaces.IReactionScheme

Returns an Iterable for looping over all IMolecularScheme in this ReactionScheme.

read(T) - Method in interface org.openscience.cdk.io.ISimpleChemObjectReader

Reads an IChemObject of type "object" from input.

ReaderEvent - Class in org.openscience.cdk.io

Signals that something has happened in a file reader.

ReaderEvent(Object) - Constructor for class org.openscience.cdk.io.ReaderEvent

Creates a reader event.

readRecord(int) - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader

relatedChemObjects() - Method in interface org.openscience.cdk.interfaces.IMapping

Returns an Iterable to the two IChemObjects.

remove(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes all atoms and electronContainers of a given atomcontainer from this container.

removeAllAtomContainers() - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Removes all AtomContainer from this container.

removeAllBonds() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes all Bonds from this container.

removeAllElectronContainers() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes electronContainers from this container.

removeAllElements() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes all atoms, bonds and stereo elements from this container.

removeAllIsotopes() - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Removes all isotopes of this molecular formula.

removeAllMolecularFormulas() - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet

Removes all IMolecularFormula of this IMolecularFormulaSet.

removeAllReactions() - Method in interface org.openscience.cdk.interfaces.IReactionSet

Removes all reactions from this set.

removeAllReactionSchemes() - Method in interface org.openscience.cdk.interfaces.IReactionScheme

Removes all IReactionScheme from this chemObject.

removeAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Safely remove an atom from the container.

removeAtom(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Safely remove an atom from the container.

removeAtomAndConnectedElectronContainers(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Deprecated.

Method has be renamed IAtomContainer.removeAtom(IAtom).

removeAtomContainer(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Removes an AtomContainer from this container.

removeAtomContainer(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Removes an AtomContainer from this container.

removeAtomOnly(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Unsafely remove atom at index.

removeAtomOnly(IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Unsafely remove atom.

removeBond(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes the bond at the given position from the AtomContainer.

removeBond(IAtom, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes the bond that connects the two given atoms.

removeBond(IBond) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes the bond from this container.

removeChemModel(int) - Method in interface org.openscience.cdk.interfaces.IChemSequence

Remove a ChemModel from this ChemSequence.

removeChemObjectIOListener(IChemObjectIOListener) - Method in interface org.openscience.cdk.io.IChemObjectIO

Removes a IChemObjectIOListener from this IChemObjectIO.

removeChemSequence(int) - Method in interface org.openscience.cdk.interfaces.IChemFile

Removes the IChemSequence at the given position from this container.

removeElectronContainer(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes the bond at the given position from this container.

removeElectronContainer(IElectronContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes this ElectronContainer from this container.

removeIsotope(IIsotope) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Removes the given isotope from the MolecularFormula.

removeListener(IChemObjectListener) - Method in interface org.openscience.cdk.interfaces.IChemObject

Use this to remove a ChemObjectListener from the ListenerList of this IChemObject.

removeLonePair(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes the lone pair at the given position from the AtomContainer.

removeLonePair(ILonePair) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes the lone pair from the AtomContainer.

removeMapping(int) - Method in interface org.openscience.cdk.interfaces.IReaction

Removes a mapping between the reactant and product side to this Reaction.

removeMolecularFormula(IMolecularFormula) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet

Removes the given IMolecularFormula from the IMolecularFormulaSet.

removeMolecularFormula(int) - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet

Removes the IMolecularFormula at the given position from the IMolecularFormulaSet.

removeMonomer(String) - Method in interface org.openscience.cdk.interfaces.IPolymer

Removes a particular monomer, specified by its name.

removeMonomer(String) - Method in interface org.openscience.cdk.interfaces.IStrand

Removes a particular monomer, specified by its name.

removeProperty(Object) - Method in interface org.openscience.cdk.interfaces.IChemObject

Removes a property for a IChemObject.

removeProperty(Object) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Removes a property for a IChemObject.

removeReaction(int) - Method in interface org.openscience.cdk.interfaces.IReactionSet

Remove a reaction from this set.

removeReaction(IReaction) - Method in interface org.openscience.cdk.interfaces.IReactionSet

Removes all instances of a reaction from this IReactionSet.

removeReactionScheme(IReactionScheme) - Method in interface org.openscience.cdk.interfaces.IReactionScheme

Removes an IReactionScheme from this chemObject.

removeSingleElectron(int) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes the single electron at the given position from the AtomContainer.

removeSingleElectron(ISingleElectron) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Removes the single electron from the AtomContainer.

removeStrand(String) - Method in interface org.openscience.cdk.interfaces.IBioPolymer

Removes a particular strand, specified by its name.

replaceAtomContainer(int, IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Replace the AtomContainer at a specific position (array has to be large enough).

RIGHT - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

S

setA(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal

Sets the A unit cell axes in carthesian coordinates in a eucledian space.

setAltLoc(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

set the Alternate location indicator of this atom.

setAtom(int, IAtom) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Set the atom at idx, the index must have an existing atom and therefore be in the range 0 ≤ idx < mol.getAtomCount().

setAtom(IAtom, int) - Method in interface org.openscience.cdk.interfaces.IBond

Sets an Atom in this bond.

setAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.ILonePair

Sets the associated Atom.

setAtom(IAtom) - Method in interface org.openscience.cdk.interfaces.ISingleElectron

Sets the associated Atom.

setAtomicNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IElement

Sets the atomic number of this element.

setAtoms(IAtom[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Sets the array of atoms of this AtomContainer.

setAtoms(IAtom[]) - Method in interface org.openscience.cdk.interfaces.IBond

Sets the array of atoms making up this bond.

setAtomTypeName(String) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the if attribute of the AtomType object.

setAttachPointNum(int) - Method in interface org.openscience.cdk.interfaces.IPseudoAtom

Set the attachment point number.

setB(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal

Sets the B unit cell axes in carthesian coordinates.

setBondOrderSum(Double) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the the exact bond order sum attribute of the AtomType object.

setBonds(IBond[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Sets the array of bonds of this AtomContainer.

setC(Vector3d) - Method in interface org.openscience.cdk.interfaces.ICrystal

Sets the C unit cell axes in carthesian coordinates.

setChainID(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

set the Chain identifier of this atom.

setChainID(String) - Method in interface org.openscience.cdk.interfaces.IPDBMonomer

Sets the Chain ID of this monomer.

setCharge(Integer) - Method in interface org.openscience.cdk.interfaces.IAdductFormula

Sets the partial charge of this adduct formula.

setCharge(Double) - Method in interface org.openscience.cdk.interfaces.IAtom

Sets the partial charge of this atom.

setCharge(Integer) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Sets the charge of this IMolecularFormula, since there is no atom associated with the charge the number of a given isotope is not modified.

setConfigOrder(int) - Method in interface org.openscience.cdk.interfaces.IStereoElement

Set the configuration order of the stereochemistry.

setCovalentRadius(Double) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the covalent radius for this AtomType.

setCrystal(ICrystal) - Method in interface org.openscience.cdk.interfaces.IChemModel

Sets the Crystal contained in this ChemModel.

setDirection(IReaction.Direction) - Method in interface org.openscience.cdk.interfaces.IReaction

Sets the direction of the reaction.

setElectronCount(Integer) - Method in interface org.openscience.cdk.interfaces.IElectronContainer

Sets the number of electrons in this electron container.

setEndChainID(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure

set the ending Chain identifier of this structure.

setEndInsertionCode(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure

set the ending Code for insertion of residues of this structure.

setEndSequenceNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IPDBStructure

set the ending sequence number of this structure.

setErrorHandler(IChemObjectReaderErrorHandler) - Method in interface org.openscience.cdk.io.IChemObjectReader

Sets an error handler that is sent events when file format issues occur.

setExactMass(Double) - Method in interface org.openscience.cdk.interfaces.IIsotope

Sets the ExactMass attribute of the Isotope object.

setExpanded(boolean) - Method in interface org.openscience.cdk.interfaces.IFragmentAtom

Sets whether this atom is to be fully drawn and not just in the abbreviated form.

setFlag(int, boolean) - Method in interface org.openscience.cdk.interfaces.IChemObject

Sets the value of some flag.

setFlags(boolean[]) - Method in interface org.openscience.cdk.interfaces.IChemObject

Sets the whole set of flags.

setFormalCharge(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the formal charge of this atom.

setFormalNeighbourCount(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the formal neighbour count of this atom.

setFractionalPoint3d(Point3d) - Method in interface org.openscience.cdk.interfaces.IAtom

Sets a point specifying the location of this atom in a Crystal unit cell.

setFragment(IAtomContainer) - Method in interface org.openscience.cdk.interfaces.IFragmentAtom

Sets the fully expended form of the IFragmentAtom.

setHetAtom(Boolean) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

Mark the atom as a heteroatom.

setHybridization(IAtomType.Hybridization) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the hybridization of this atom.

setICode(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

set the Code for insertion of residues of this atom.

setICode(String) - Method in interface org.openscience.cdk.interfaces.IPDBMonomer

Sets the ICode of this monomer.

setID(String) - Method in interface org.openscience.cdk.interfaces.IChemObject

Sets the identifier (ID) of this object.

setImplicitHydrogenCount(Integer) - Method in interface org.openscience.cdk.interfaces.IAtom

Sets the implicit hydrogen count of this atom.

setIsAromatic(boolean) - Method in interface org.openscience.cdk.interfaces.IAtom

Mark this atom as being aromatic.

setIsAromatic(boolean) - Method in interface org.openscience.cdk.interfaces.IBond

Mark this bond as being aromatic.

setIsInRing(boolean) - Method in interface org.openscience.cdk.interfaces.IAtom

Mark this atom as being in a ring.

setIsInRing(boolean) - Method in interface org.openscience.cdk.interfaces.IBond

Mark this bond as being in a ring.

setLabel(String) - Method in interface org.openscience.cdk.interfaces.IPseudoAtom

Sets the label of this PseudoAtom.

setLoggingToolClass(Class<? extends ILoggingTool>) - Static method in class org.openscience.cdk.tools.LoggingToolFactory

Sets the ILoggingTool implementation to be used.

setMassNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IIsotope

Sets the atomic mass of this element.

setMaxBondOrder(IBond.Order) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the MaxBondOrder attribute of the AtomType object.

setMoleculeSet(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IChemModel

Sets the IAtomContainerSet of this ChemModel.

setMonomerName(String) - Method in interface org.openscience.cdk.interfaces.IMonomer

Set the name of the Monomer object.

setMonomerType(String) - Method in interface org.openscience.cdk.interfaces.IMonomer

Set the type of the Monomer object.

setMultiplier(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Sets the coefficient of a AtomContainer to a given value.

setMultiplier(int, Double) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Sets the coefficient of a AtomContainer to a given value.

setMultipliers(Double[]) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Sets the multipliers of the AtomContainers.

setName(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

set the Atom name of this atom.

setNaturalAbundance(Double) - Method in interface org.openscience.cdk.interfaces.IIsotope

Sets the NaturalAbundance attribute of the Isotope object.

setNotification(boolean) - Method in interface org.openscience.cdk.interfaces.IChemObject

Set a flag to use or not use notification.

setOccupancy(Double) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

set the Occupancy of this atom.

setOrder(IBond.Order) - Method in interface org.openscience.cdk.interfaces.IBond

Sets the bond order of this bond.

setOutputWriter(Writer) - Method in class org.openscience.cdk.io.listener.PropertiesListener

Overwrites the default writer to which the output is directed.

setOxt(Boolean) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

Change the state of this atom in being the PDB OXT atom.

setPoint2d(Point2d) - Method in interface org.openscience.cdk.interfaces.IAtom

Sets a point specifying the location of this atom in a 2D space.

setPoint3d(Point3d) - Method in interface org.openscience.cdk.interfaces.IAtom

Sets a point specifying the location of this atom in 3D space.

setProductCoefficient(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction

Sets the coefficient of a a product to a given value.

setProductCoefficients(Double[]) - Method in interface org.openscience.cdk.interfaces.IReaction

Sets the coefficient of the products.

setProducts(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IReaction

Assigns a IAtomContaineSet to the products of this reaction.

setProperties(Map<Object, Object>) - Method in interface org.openscience.cdk.interfaces.IChemObject

Set the properties of this object to the provided map (shallow copy).

setProperties(Map<Object, Object>) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Sets the properties of this object.I should integrate into ChemObject.

setProperty(Object, Object) - Method in interface org.openscience.cdk.interfaces.IChemObject

Sets a property for a IChemObject.

setProperty(Object, Object) - Method in interface org.openscience.cdk.interfaces.IMolecularFormula

Sets a property for a IChemObject.

setReactantCoefficient(IAtomContainer, Double) - Method in interface org.openscience.cdk.interfaces.IReaction

Sets the coefficient of a a reactant to a given value.

setReactantCoefficients(Double[]) - Method in interface org.openscience.cdk.interfaces.IReaction

Sets the coefficients of the reactants.

setReactants(IAtomContainerSet) - Method in interface org.openscience.cdk.interfaces.IReaction

Assigns a IAtomContaineSet to the reactants in this reaction.

setReactionSet(IReactionSet) - Method in interface org.openscience.cdk.interfaces.IChemModel

Sets the ReactionSet contained in this ChemModel.

setReader(Reader) - Method in interface org.openscience.cdk.io.IChemObjectReader

Sets the Reader from which this ChemObjectReader should read the contents.

setReader(InputStream) - Method in interface org.openscience.cdk.io.IChemObjectReader

Sets the InputStream from which this ChemObjectReader should read the contents.

setReaderMode(IChemObjectReader.Mode) - Method in interface org.openscience.cdk.io.IChemObjectReader

Sets the reader mode.

setRecord(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

Set one entire line from the PDB entry file which describe the IPDBAtom.

setResName(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

set the Residue name of this atom.

setResSeq(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

set the Residue sequence number of this atom.

setResSeq(String) - Method in interface org.openscience.cdk.interfaces.IPDBMonomer

Sets the sequence identifier of this monomer.

setRingSet(IRingSet) - Method in interface org.openscience.cdk.interfaces.IChemModel

Sets the RingSet of this ChemModel.

setSegID(String) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

set the Segment identifier, left-justified of this atom.

setSerial(Integer) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

set the Atom serial number of this atom.

setSetting(String) - Method in class org.openscience.cdk.io.setting.IOSetting

Sets the setting for a certain question.

setSpaceGroup(String) - Method in interface org.openscience.cdk.interfaces.ICrystal

Sets the space group of this crystal.

setStackLength(int) - Method in interface org.openscience.cdk.tools.ILoggingTool

Sets the number of StackTraceElements to be printed in DEBUG mode when calling debug(Throwable).

setStartChainID(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure

set the start Chain identifier of this structure.

setStartInsertionCode(Character) - Method in interface org.openscience.cdk.interfaces.IPDBStructure

set the start Chain identifier of this structure.

setStartSequenceNumber(Integer) - Method in interface org.openscience.cdk.interfaces.IPDBStructure

set the start sequence number of this structure.

setStereo(IBond.Stereo) - Method in interface org.openscience.cdk.interfaces.IBond

Sets the stereo descriptor for this bond.

setStereo(ITetrahedralChirality.Stereo) - Method in interface org.openscience.cdk.interfaces.ITetrahedralChirality

Set the stereochemistry of this tetrahedral centre.

setStereoElements(List<IStereoElement>) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Set the stereo elements - this will replace the existing instance with a new instance.

setStereoParity(Integer) - Method in interface org.openscience.cdk.interfaces.IAtom

Deprecated.

use IStereoElements for storing stereochemistry

setStrandName(String) - Method in interface org.openscience.cdk.interfaces.IStrand

Set the name of the Strand object.

setStrandType(String) - Method in interface org.openscience.cdk.interfaces.IStrand

Set the type of the Strand object.

setStructureType(String) - Method in interface org.openscience.cdk.interfaces.IPDBStructure

set the Structure Type of this structure.

setSymbol(String) - Method in interface org.openscience.cdk.interfaces.IElement

Sets the element symbol of this element.

setTempFactor(Double) - Method in interface org.openscience.cdk.interfaces.IPDBAtom

set the Temperature factor of this atom.

setting - Variable in class org.openscience.cdk.io.setting.IOSetting

setTitle(String) - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Modify the title of the record.

setValency(Integer) - Method in interface org.openscience.cdk.interfaces.IAtomType

Sets the the exact electron valency of the AtomType object.

setWriter(Writer) - Method in interface org.openscience.cdk.io.IChemObjectWriter

Sets the Writer from which this ChemObjectWriter should write the contents.

setWriter(OutputStream) - Method in interface org.openscience.cdk.io.IChemObjectWriter

Sets the OutputStream from which this ChemObjectWriter should write the contents.

setZ(Integer) - Method in interface org.openscience.cdk.interfaces.ICrystal

Sets the number of assymmetric parts in the unit cell.

singleElectrons() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns an Iterable for looping over all single electrons in this container.

size() - Method in interface org.openscience.cdk.interfaces.IMolecularFormulaSet

Returns the number of MolecularFormulas in this IMolecularFormulaSet.

size() - Method in interface org.openscience.cdk.io.random.IRandomAccessChemObjectReader

sortAtomContainers(Comparator<IAtomContainer>) - Method in interface org.openscience.cdk.interfaces.IAtomContainerSet

Sort the AtomContainers using a provided Comparator.

SP - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Square Planar (SP-4) (e.g.

SP4 - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Square Planar Configutation in 4 Shape

SPU - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Square Planar Configutation in U Shape

SPY - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Square Pyramidal (SPY-5)

SPZ - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Square Planar Configutation in Z Shape

SquarePlanar - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Square Planar (SP-4) (e.g.

SquarePyramidal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Square Pyramidal (SPY-5)

stateChanged(EventObject) - Method in interface org.openscience.cdk.event.ICDKChangeListener

Invoked when the target of the listener has changed its state.

stateChanged(IChemObjectChangeEvent) - Method in interface org.openscience.cdk.interfaces.IChemObjectListener

Called by objects to notify objects that implemented this interface and registered with them as ChemObjectListeners.

STDOUT_LOGGING_TOOL_CLASS - Static variable in class org.openscience.cdk.tools.LoggingToolFactory

Back-up logging tool.

stereoElements() - Method in interface org.openscience.cdk.interfaces.IAtomContainer

Returns the stereo elements defined for this atom container.

T

TBPY - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Trigonal Bipyramidal (TBPY-5)

Tetrahedral - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Tetrahedral (T-4) (e.g.

TH - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Tetrahedral (T-4) (e.g.

timeout(long) - Static method in exception org.openscience.cdk.exception.Intractable

Utility for creating a message which indicates an operation timed out after a given time in milliseconds, t.

timeout(String, long) - Static method in exception org.openscience.cdk.exception.Intractable

Utility for creating a message which indicates an operation timed out after a given time in milliseconds, t.

toConfig(IDoubleBondStereochemistry.Conformation) - Static method in enum org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation

toConfig(ITetrahedralChirality.Stereo) - Static method in enum org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo

toConformation(int) - Static method in enum org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation

TOGETHER - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

toStereo(int) - Static method in enum org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo

toString() - Method in interface org.openscience.cdk.interfaces.IChemObject

Returns a one line description of this IChemObject.

TrigonalBipyramidal - Static variable in interface org.openscience.cdk.interfaces.IStereoElement

Trigonal Bipyramidal (TBPY-5)

U

UnsupportedChemObjectException - Exception in org.openscience.cdk.exception

UnsupportedChemObjectException(String) - Constructor for exception org.openscience.cdk.exception.UnsupportedChemObjectException

V

valueOf(String) - Static method in enum org.openscience.cdk.interfaces.IAtomType.Hybridization

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.openscience.cdk.interfaces.IBond.Order

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.openscience.cdk.interfaces.IBond.Stereo

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.openscience.cdk.interfaces.IReaction.Direction

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.openscience.cdk.io.IChemObjectReader.Mode

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.openscience.cdk.io.setting.IOSetting.Importance

Returns the enum constant of this type with the specified name.

valueOf(String) - Static method in enum org.openscience.cdk.ReactionRole

Returns the enum constant of this type with the specified name.

values() - Static method in enum org.openscience.cdk.interfaces.IAtomType.Hybridization

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.openscience.cdk.interfaces.IBond.Order

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.openscience.cdk.interfaces.IBond.Stereo

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.openscience.cdk.interfaces.IDoubleBondStereochemistry.Conformation

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.openscience.cdk.interfaces.IReaction.Direction

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.openscience.cdk.interfaces.ITetrahedralChirality.Stereo

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.openscience.cdk.io.IChemObjectReader.Mode

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.openscience.cdk.io.setting.IOSetting.Importance

Returns an array containing the constants of this enum type, in the order they are declared.

values() - Static method in enum org.openscience.cdk.ReactionRole

Returns an array containing the constants of this enum type, in the order they are declared.

W

warn(Object) - Method in interface org.openscience.cdk.tools.ILoggingTool

Shows WARN output for the Object.

warn(Object, Object...) - Method in interface org.openscience.cdk.tools.ILoggingTool

Shows WARN output for the given Object's.

write(IChemObject) - Method in interface org.openscience.cdk.io.IChemObjectWriter

Writes the content of "object" to output.

A B C D E F G H I L M N O P Q R S T U V W