Uses of Class
com.actelion.research.chem.reaction.Reaction

Packages that use Reaction

Package	Description
com.actelion.research.chem
com.actelion.research.chem.descriptor
com.actelion.research.chem.io
com.actelion.research.chem.reaction
com.actelion.research.gui
com.actelion.research.gui.clipboard
com.actelion.research.gui.clipboard.external
com.actelion.research.gui.dnd
com.actelion.research.share.gui.editor
com.actelion.research.share.gui.editor.chem
com.actelion.research.util

Uses of Reaction in com.actelion.research.chem

Methods in com.actelion.research.chem that return Reaction

Modifier and Type	Method	Description
Reaction	ExtendedDepictor.getReaction()
Reaction	SmilesParser.parseReaction(byte[] smiles)

Methods in com.actelion.research.chem with parameters of type Reaction

Modifier and Type	Method	Description
static void	ChemistryHelper.arrangeReaction(Reaction rxn, java.awt.Dimension size)
static java.lang.String	IsomericSmilesCreator.createReactionSmiles(Reaction rxn)
static java.awt.geom.Rectangle2D.Double	ChemistryHelper.getArrowBoundingRect(Reaction r)
static double	ChemistryHelper.getAverageBondLength(Reaction r)
static java.awt.geom.Rectangle2D.Double	ChemistryHelper.getBoundingRect(Reaction r, boolean includearrows)
static ExtendedMolecule[]	ChemistryHelper.getProducts(Reaction r)
static java.awt.geom.Rectangle2D	ChemistryHelper.getProductsBoundingRect(Reaction r)
static ExtendedMolecule[]	ChemistryHelper.getReactants(Reaction r)
static java.awt.geom.Rectangle2D.Double	ChemistryHelper.getReactantsBoundingRect(Reaction r)
static int	ChemistryHelper.getReactionType(Reaction r)
static void	ChemistryHelper.scaleInto(Reaction reaction, double x, double y, double width, double height, double arrowSize)
static void	ChemistryHelper.scaleIntoF(Reaction reaction, double x, double y, double width, double height, double arrowSize)
static void	ChemistryHelper.scaleIntoOld(Reaction reaction, double x, double y, double width, double height, double arrowSize)
static void	ChemistryHelper.setAverageBondLength(Reaction rxn, double bndlen)
static void	ChemistryHelper.transformReaction(Reaction r, double offsetx, double offsety, double scale)

Constructors in com.actelion.research.chem with parameters of type Reaction

Constructor	Description
ExtendedDepictor(Reaction reaction, DrawingObjectList drawingObjectList, boolean layoutReaction, boolean useGraphics2D)

Uses of Reaction in com.actelion.research.chem.descriptor

Methods in com.actelion.research.chem.descriptor that return types with arguments of type Reaction

Modifier and Type	Method	Description
DescriptorHandler<long[],Reaction>	DescriptorHandlerReactionFP.getThreadSafeCopy()

Methods in com.actelion.research.chem.descriptor with parameters of type Reaction

Modifier and Type	Method	Description
long[]	DescriptorHandlerReactionFP.createDescriptor(Reaction rxn)

Uses of Reaction in com.actelion.research.chem.io

Methods in com.actelion.research.chem.io that return Reaction

Modifier and Type	Method	Description
Reaction	RDFileParser.getNextReaction()	RD-files may contains lists of molecules or lists of reactions.
Reaction	NativeMDLReactionReader.getReaction(int reaction, int variation)
Reaction	RXNFileParser.getReaction(java.io.File file)
Reaction	RXNFileParser.getReaction(java.io.File file, boolean ignoreIdCode)
Reaction	RXNFileParser.getReaction(java.lang.String buffer)
Reaction	RXNFileParser.getReaction(java.lang.String buffer, boolean ignoreIdCode)

Methods in com.actelion.research.chem.io with parameters of type Reaction

Modifier and Type	Method	Description
boolean	RXNFileParser.parse(Reaction theReaction, java.io.BufferedReader theReader)
boolean	RXNFileParser.parse(Reaction theReaction, java.io.BufferedReader theReader, boolean ignoreIdCode)
boolean	RXNFileParser.parse(Reaction theReaction, java.io.File file)
boolean	RXNFileParser.parse(Reaction theReaction, java.io.File file, boolean ignoreIdCode)
boolean	RXNFileParser.parse(Reaction theReaction, java.lang.String buffer)
boolean	RXNFileParser.parse(Reaction theReaction, java.lang.String buffer, boolean ignoreIdCode)
void	CompoundFileHelper.saveRXNFile(Reaction rxn)

Constructors in com.actelion.research.chem.io with parameters of type Reaction

Constructor	Description
RXNFileCreator(Reaction rxn)
RXNFileCreator(Reaction r, java.lang.String programName)
RXNFileV3Creator(Reaction rxn)
RXNFileV3Creator(Reaction r, java.lang.String programName)

Uses of Reaction in com.actelion.research.chem.reaction

Subclasses of Reaction in com.actelion.research.chem.reaction

Modifier and Type	Class	Description
class	DatabaseReaction

Methods in com.actelion.research.chem.reaction that return Reaction

Modifier and Type	Method	Description
static Reaction	ReactionEncoder.decode(byte[] rxnCode, byte[] rxnMapping, byte[] rxnCoords, java.lang.String rxnObjects, byte[] rxnCatalysts, boolean ensureCoordinates)	Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class.
static Reaction	ReactionEncoder.decode(java.lang.String s, boolean ensureCoordinates)
static Reaction	ReactionEncoder.decode(java.lang.String s, boolean ensureCoordinates, Reaction rxn)	Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class and are passed OBJECT_DELIMITER-delimited within one string.
static Reaction	ReactionEncoder.decode(java.lang.String s, int includeOptions, Reaction rxn)	Creates a Reaction object by interpreting a reaction string encoded by this class.
static Reaction	ReactionEncoder.decode(java.lang.String rxnCode, java.lang.String rxnMapping, java.lang.String rxnCoords, java.lang.String rxnObjects, java.lang.String rxnCatalysts, boolean ensureCoordinates, Reaction rxn)	Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class.
Reaction[]	Reactor.getFullyMappedReactions()	After instantiating the Reactor with MODE_FULLY_MAP_REACTIONS and after supplying real reactants, this method may be used to construct the fully mapped reaction.
Reaction	Reaction.getMergedCopy()	Merges all reactants into one molecule and all products into another ad creates a new Reaction object from those.
Reaction	IReactionMapper.mapReaction(Reaction r, SSSearcher sss)
Reaction	MCSReactionMapper.mapReaction(Reaction r, SSSearcher sss)
Reaction	MCSReactionMapper.matchReaction(Reaction r)

Methods in com.actelion.research.chem.reaction with parameters of type Reaction

Modifier and Type	Method	Description
int	ReactionClassifier.classify(int indexToCreate, Reaction theReaction)
int	ReactionClassifier.classify(Reaction theReaction)
static Reaction	ReactionEncoder.decode(java.lang.String s, boolean ensureCoordinates, Reaction rxn)	Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class and are passed OBJECT_DELIMITER-delimited within one string.
static Reaction	ReactionEncoder.decode(java.lang.String s, int includeOptions, Reaction rxn)	Creates a Reaction object by interpreting a reaction string encoded by this class.
static Reaction	ReactionEncoder.decode(java.lang.String rxnCode, java.lang.String rxnMapping, java.lang.String rxnCoords, java.lang.String rxnObjects, java.lang.String rxnCatalysts, boolean ensureCoordinates, Reaction rxn)	Creates a Reaction object by interpreting a reaction code, mapping, coordinates and drawing objects that were earlier created by this class.
static java.lang.String[]	ReactionEncoder.encode(Reaction reaction, boolean keepAbsoluteCoordinates)	Creates a String containing a unique reaction code by creating idcodes of every reactant and product and concatenating them in lexical order.
static java.lang.String	ReactionEncoder.encode(Reaction reaction, boolean keepAbsoluteCoordinates, int mode)	Creates a String containing a reaction code by creating idcodes of every reactant and product and concatenating them in original (if mode includes RETAIN_REACTANT_AND_PRODUCT_ORDER) or in lexical order.
static com.actelion.research.chem.reaction.CommonSubGraphHelper.Result	CommonSubGraphHelper.getMCS(Reaction reaction, boolean[] exclude, SSSearcher sss)
Reaction	IReactionMapper.mapReaction(Reaction r, SSSearcher sss)
Reaction	MCSReactionMapper.mapReaction(Reaction r, SSSearcher sss)
Reaction	MCSReactionMapper.matchReaction(Reaction r)
void	MCSReactionMapper.removeMapping(Reaction reaction)
void	MCSReactionMapper.resetFragments(Reaction rxn)
void	SRSearcher.setQuery(Reaction query)	This defines the query reaction (or transformation).
void	SRSearcher.setQuery(Reaction query, long[] reactantFFP, long[] productFFP)	This defines the query reaction (or transformation).
void	SRSearcher.setReaction(Reaction reaction)
void	SRSearcher.setReaction(Reaction reaction, long[] reactantFFP, long[] productFFP)	This defines the query reaction (or transformation).

Constructors in com.actelion.research.chem.reaction with parameters of type Reaction

Constructor	Description
Reaction(Reaction rxn)
Reactor(Reaction reaction)	Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants.
Reactor(Reaction reaction, boolean retainCoordinates)	Constructs a Reactor that is able to construct products from a generic reaction (transformation) and a list of real world reactants.
Reactor(Reaction reaction, boolean retainCoordinates, boolean fullyMapReactions, int maxProducts, boolean uniqueOnly)	Deprecated.
Reactor(Reaction reaction, int mode, int maxProducts)	Constructs a Reactor that is able to build products from a generic reaction (transformation) and a list of real world reactants.

Uses of Reaction in com.actelion.research.gui

Methods in com.actelion.research.gui that return Reaction

Modifier and Type	Method	Description
Reaction	JDrawArea.getReaction()
Reaction	JDrawDialog.getReaction()
Reaction	JEditableChemistryView.getReaction()
Reaction	JDrawArea.getReactionAndDrawings()
Reaction	JDrawDialog.getReactionAndDrawings()

Methods in com.actelion.research.gui with parameters of type Reaction

Modifier and Type	Method	Description
void	JChemistryView.setContent(Reaction rxn)
void	JChemistryView.setContent(Reaction rxn, DrawingObjectList drawingObjectList)
void	JEditableChemistryView.setContent(Reaction rxn)
void	JEditableChemistryView.setContent(Reaction rxn, DrawingObjectList drawingObjectList)
void	JDrawArea.setReaction(Reaction rxn)

Constructors in com.actelion.research.gui with parameters of type Reaction

Constructor	Description
JDrawDialog(java.awt.Frame owner, Reaction rxn)
JDrawDialog(java.awt.Frame owner, Reaction rxn, java.lang.String title)

Uses of Reaction in com.actelion.research.gui.clipboard

Methods in com.actelion.research.gui.clipboard that return Reaction

Modifier and Type	Method	Description
Reaction	ClipboardHandler.pasteReaction()	Get a Reaction from the Clipboard
Reaction	IClipboardHandler.pasteReaction()
Reaction	ClipboardHandler.pasteReactionWindowsNative()

Methods in com.actelion.research.gui.clipboard with parameters of type Reaction

Modifier and Type	Method	Description
boolean	ClipboardHandler.copyReaction(Reaction r)	Copies a reaction to the clipboard in various formats: MDLSK Sketch MDLCT MDL molfile
boolean	IClipboardHandler.copyReaction(Reaction r)

Uses of Reaction in com.actelion.research.gui.clipboard.external

Methods in com.actelion.research.gui.clipboard.external with parameters of type Reaction

Modifier and Type	Method	Description
byte[]	ChemDrawCDX.getChemDrawBuffer(Reaction rxn)

Uses of Reaction in com.actelion.research.gui.dnd

Fields in com.actelion.research.gui.dnd declared as Reaction

Modifier and Type	Field	Description
protected Reaction	ReactionTransferable.mReaction

Methods in com.actelion.research.gui.dnd that return Reaction

Modifier and Type	Method	Description
protected Reaction	ReactionDropAdapter.createFromDataFlavor(java.awt.datatransfer.DataFlavor chosen, java.lang.Object o)

Methods in com.actelion.research.gui.dnd with parameters of type Reaction

Modifier and Type	Method	Description
void	ReactionDropAdapter.onDropReaction(Reaction rxn, java.awt.Point pt)

Constructors in com.actelion.research.gui.dnd with parameters of type Reaction

Constructor	Description
ReactionTransferable(Reaction rxn)

Uses of Reaction in com.actelion.research.share.gui.editor

Methods in com.actelion.research.share.gui.editor that return Reaction

Modifier and Type	Method	Description
Reaction	Model.getReaction()
Reaction	Model.getSelectedReaction()
abstract Reaction	Model.pasteReaction(double cx, double cy)

Methods in com.actelion.research.share.gui.editor with parameters of type Reaction

Modifier and Type	Method	Description
void	Model.setReaction(Reaction rxn)
void	Model.setValue(Reaction rxn)

Uses of Reaction in com.actelion.research.share.gui.editor.chem

Constructors in com.actelion.research.share.gui.editor.chem with parameters of type Reaction

Constructor	Description
AbstractExtendedDepictor(Reaction reaction, java.util.List<IDrawingObject> drawingObjectList, boolean layoutReaction, boolean useGraphics2D, DrawConfig cfg)

Uses of Reaction in com.actelion.research.util

Methods in com.actelion.research.util with parameters of type Reaction

Modifier and Type	Method	Description
static boolean	Sketch.createReactionFromSketchBuffer(Reaction rxn, byte[] buffer)
static boolean	Sketch.createReactionFromSketchFile(Reaction rxn, java.lang.String szFileName)
static byte[]	Sketch.createSketchFromReaction(Reaction r)
static byte[]	Sketch.createSketchFromReactionOLd(Reaction rxn)
static boolean	Sketch.writeReactionSketchFile(Reaction rxn, java.io.OutputStream os)
static boolean	Sketch.writeReactionSketchFile(Reaction rxn, java.lang.String filename)