Uses of Class
com.actelion.research.chem.reaction.Reaction
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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)
Reaction
SmilesParser. parseReaction(java.lang.String 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)
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Uses of Reaction in com.actelion.research.chem.chemicalspaces
Methods in com.actelion.research.chem.chemicalspaces with parameters of type Reaction Modifier and Type Method Description static boolean
ChemicalSpaceCreator. matchesReactionRole(Reaction rxn, SSSearcherWithIndex[] searchers, int component, StereoMolecule reactant, long[] index)
Method parameters in com.actelion.research.chem.chemicalspaces with type arguments of type Reaction Modifier and Type Method Description void
ChemicalSpaceCreator. setReactions(java.util.List<Reaction> reactions)
Constructor parameters in com.actelion.research.chem.chemicalspaces with type arguments of type Reaction Constructor Description ChemicalSpaceCreator(java.util.Set<java.lang.String> bbs, java.util.List<Reaction> reactions, java.io.File outdirectory)
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Uses of Reaction in com.actelion.research.chem.chemicalspaces.synthon
Methods in com.actelion.research.chem.chemicalspaces.synthon that return Reaction Modifier and Type Method Description static Reaction[]
SynthonCreator. create(Reaction rxn)
only works for reactions with a single productMethods in com.actelion.research.chem.chemicalspaces.synthon with parameters of type Reaction Modifier and Type Method Description static Reaction[]
SynthonCreator. create(Reaction rxn)
only works for reactions with a single product -
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)
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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)
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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 reaction, SSSearcher sss)
Reaction
MCSReactionMapper. matchReaction(Reaction reaction)
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 reaction, SSSearcher sss)
Reaction
MCSReactionMapper. matchReaction(Reaction reaction)
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.chem.reaction.mapping
Methods in com.actelion.research.chem.reaction.mapping that return Reaction Modifier and Type Method Description Reaction
ChemicalRuleEnhancedReactionMapper. mapReaction(Reaction rxn, SSSearcher sss)
Methods in com.actelion.research.chem.reaction.mapping with parameters of type Reaction Modifier and Type Method Description void
SimilarityGraphBasedReactionMapper. copyMapNosToReaction(Reaction rxn, int[] reactantMapNo, int[] productMapNo, int graphMapNoCount)
Copies the generated mapping numbers from the merged reactant/product molecules into the original reaction.void
ChemicalRuleEnhancedReactionMapper. map(Reaction rxn)
void
SimilarityGraphBasedReactionMapper. map(Reaction rxn)
Entirely maps the given reaction by setting all reactant's and product's mapping numbers.Reaction
ChemicalRuleEnhancedReactionMapper. mapReaction(Reaction rxn, SSSearcher sss)
void
SimilarityGraphBasedReactionMapper. mergeReactantsAndProducts(Reaction rxn)
Copies all reactant/product molecules into one StereoMolecule for easier processing Use getReactant() and getProduct() from outside to access these. -
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()
Deprecated.Reaction
JDrawDialog. getReaction()
Deprecated.Reaction
JEditableChemistryView. getReaction()
Reaction
JDrawArea. getReactionAndDrawings()
Deprecated.Reaction
JDrawDialog. getReactionAndDrawings()
Deprecated.Methods in com.actelion.research.gui with parameters of type Reaction Modifier and Type Method Description protected JDrawDialog
JEditableChemistryView. createDrawDialog(java.lang.String title, Reaction reaction)
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)
Deprecated.Constructors in com.actelion.research.gui with parameters of type Reaction Constructor Description JDrawDialog(java.awt.Dialog owner, Reaction rxn, java.lang.String title, java.awt.Dialog.ModalityType modalityType)
Deprecated.JDrawDialog(java.awt.Frame owner, Reaction rxn)
Deprecated.JDrawDialog(java.awt.Frame owner, Reaction rxn, java.awt.Dialog.ModalityType modalityType)
Deprecated.JDrawDialog(java.awt.Frame owner, Reaction rxn, java.lang.String title)
Deprecated.JDrawDialog(java.awt.Frame owner, Reaction rxn, java.lang.String title, java.awt.Dialog.ModalityType modalityType)
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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 ClipboardReaction
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 molfileboolean
IClipboardHandler. copyReaction(Reaction r)
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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)
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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)
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Uses of Reaction in com.actelion.research.gui.editor
Methods in com.actelion.research.gui.editor that return Reaction Modifier and Type Method Description Reaction
GenericDrawArea. getReaction()
Reaction
SwingEditorDialog. getReaction()
Reaction
GenericDrawArea. getReactionAndDrawings()
Reaction
SwingEditorDialog. getReactionAndDrawings()
Methods in com.actelion.research.gui.editor with parameters of type Reaction Modifier and Type Method Description void
GenericDrawArea. setReaction(Reaction rxn)
Constructors in com.actelion.research.gui.editor with parameters of type Reaction Constructor Description SwingEditorDialog(java.awt.Dialog owner, Reaction rxn)
Creates a modal chemical editor dialog to edit a chemical reaction.SwingEditorDialog(java.awt.Dialog owner, Reaction rxn, java.awt.Dialog.ModalityType modalityType)
Creates a modal chemical editor dialog to edit a chemical reaction.SwingEditorDialog(java.awt.Frame owner, Reaction rxn)
Creates a modal chemical editor dialog to edit a chemical reaction.SwingEditorDialog(java.awt.Frame owner, Reaction rxn, java.awt.Dialog.ModalityType modalityType)
Creates a modal chemical editor dialog to edit a chemical reaction.SwingEditorPanel(Reaction rxn)
Creates a chemical editor panel to edit the given chemical reaction. -
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)
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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)
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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)
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