RxnMolecule (Marvin API documentation (c) 1998-2008 ChemAxon Ltd.)

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chemaxon.struc
Class RxnMolecule

java.lang.Object
  chemaxon.struc.CGraph
      chemaxon.struc.MoleculeGraph
          chemaxon.struc.Molecule
              chemaxon.struc.RxnMolecule

All Implemented Interfaces:: chemaxon.struc.MObjectContainer, MTransformable, chemaxon.struc.ReadableMolecule, StereoConstants, java.io.Serializable, java.lang.Cloneable

public class RxnMolecule
extends Molecule
implements chemaxon.struc.MObjectContainer
extends Molecule
implements chemaxon.struc.MObjectContainer

Reaction.

Since:: Marvin 2.9
Version:: 5.1.1, 08/28/2008
Author:: Peter Csizmadia, Szilveszter Juhos
See Also:: Serialized Form

Field Summary
`static int`	`AGENTS` "Agent" structure type.
`static int`	`PRODUCTS` "Product" structure type.
`static int`	`REACTANTS` "Reactant" structure type.
`static int`	`REGULAR_DOUBLE` Regular double reaction arrow type.
`static int`	`REGULAR_SINGLE` Regular single reaction arrow type.
`static int`	`RGROUPED` Add R-groups to component structure.
`static int`	`TWO_HEADED_DOUBLE` Two headed double reaction arrow type.
`static int`	`TWO_HEADED_SINGLE` Two headed single reaction arrow type.
`static int`	`TYPE_COUNT` Number of structure types.
`static int`	`TYPE_MASK` Component type mask.

Fields inherited from class chemaxon.struc.Molecule
`DEFAULT_UNGROUP, RECURSIVE_UNGROUP, RMCLEANUP_FROMSGROUPS, RMCLEANUP_SGROUPATOMS, RMSG_DEFAULT, RMSG_KEEP_CHILDREN, RMSG_KEEP_MULTICENTER, RMSG_KEEP_PARENT`

Fields inherited from class chemaxon.struc.MoleculeGraph
`AROM_BASIC, AROM_CHEMAXON, AROM_DAYLIGHT, AROM_GENERAL, CACHE_REMOVE_AROMATAMODULE, CACHE_REMOVE_GRINVMODULE, CACHE_REMOVE_PARITYMODULE, CACHE_REMOVE_SSSRMODULE, DIM_MASK, GRINV_DONT_STORE, GRINV_NOHYDROGEN, GRINV_OLDSTEREO, GRINV_STEREO, GRINV_USEMAPS, GRINV_VALUE_OPTIONS, INVALID_LINKNODE_MESSAGE, MIN_RING_SIZE_FOR_TRANS_DB, OMIT_POSTCLEAN, orix, oriy, oriz, propertyContainer, RMCLEANUP_MOBJECT, RMCLEANUP_PARENTDOC, RMCLEANUP_STEREO, useOnlyFirstAtomInStereoCalculation`

Fields inherited from class chemaxon.struc.MoleculeGraph

AROM_BASIC, AROM_CHEMAXON, AROM_DAYLIGHT, AROM_GENERAL, CACHE_REMOVE_AROMATAMODULE, CACHE_REMOVE_GRINVMODULE, CACHE_REMOVE_PARITYMODULE, CACHE_REMOVE_SSSRMODULE, DIM_MASK, GRINV_DONT_STORE, GRINV_NOHYDROGEN, GRINV_OLDSTEREO, GRINV_STEREO, GRINV_USEMAPS, GRINV_VALUE_OPTIONS, INVALID_LINKNODE_MESSAGE, MIN_RING_SIZE_FOR_TRANS_DB, OMIT_POSTCLEAN, orix, oriy, oriz, propertyContainer, RMCLEANUP_MOBJECT, RMCLEANUP_PARENTDOC, RMCLEANUP_STEREO, useOnlyFirstAtomInStereoCalculation

Fields inherited from class chemaxon.struc.CGraph
`btab, CACHE_REMOVE_ALL, CACHE_REMOVE_CACHEMEMORY, cacheMemory, cssr, ctab, edgeCount, edges, fragIds, grinv, grinvCC, grinvOptions, INITIAL_CAPACITY, nFrags, nGrinv, nodeCount, nodes, parentGraph, RMCLEANUP_ALL, RMCLEANUP_EDGES, RMCLEANUP_FIXCOMPONENT, RMCLEANUP_NONE, sssr, sssr2idx, sssrl2idx, superGraph`

Fields inherited from interface chemaxon.struc.ReadableMolecule
`HS_S, HS_SP, HS_SP2, HS_SP3, HS_UNKNOWN`

Fields inherited from interface chemaxon.struc.StereoConstants
`ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_MASK, CHIRALITY_R, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_ODD, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, TRANS`

Constructor Summary
`RxnMolecule()` Create a reaction.

Method Summary
`void`	`add(CEdge e)` Adds a bond to a reactant, product, agent.
`void`	`add(CNode node)` Adds an atom to a reactant, product or agent structure.
`void`	`addComponent(Molecule m, int type)` Adds a reactant, product or agent.
`void`	`addComponent(Molecule m, int type, boolean beNew)` Adds a reactant, product or agent.
`void`	`addReactionStep(java.util.ArrayList reactants, java.util.ArrayList products, java.util.ArrayList agents, chemaxon.struc.graphics.MRArrow arrow, int arrowType)`
`void`	`addStructure(Molecule m, int type)` Deprecated. as of Marvin 4.1, replaced by `addComponent(Molecule, int)`
`void`	`addStructure(Molecule m, int type, boolean beNew)` Deprecated. as of Marvin 4.1, replaced by `addComponent(Molecule, int, boolean)`
`boolean`	`canBeReactionComponent()` Tests whether an object of this class can be a reaction component.
`protected void`	`checkSgroupConsistency()` Checks the consistency of S-groups.
`void`	`clearForImport(java.lang.String fmt)` Clear the edges vector and the properties.
`void`	`clearObjects()` Deletes the graphical objects from this.
`void`	`clonecopy(CGraph g)` Make another molecule identical to this one.
`void`	`clonecopy(int[] iatoms, MoleculeGraph g)` Copies the specified nodes and edges of this graph to another one.
`void`	`clonelesscopy(CGraph g)` Copy to selection.
`Molecule`	`cloneMolecule()` Make an identical copy of the molecule.
`boolean`	`contains(CEdge edge)` Checks if a reactant, agent or product structure contains the specified edge.
`boolean`	`contains(CNode node)` Checks if a reactant, agent or product structure contains the specified node.
`int[][]`	`createBHtab()` Creates the graph union's bond table extended with implicit hydrogen atoms.
`int[][]`	`createCHtab()` Creates the graph union's connection table extended with implicit hydrogen atoms.
`static RxnMolecule`	`createReaction(Molecule mol, DPoint3[] arw, int art)` Creates a reaction.
`static RxnMolecule`	`createReaction(MoleculeGraph mol, DPoint3[] pos)`
`static double`	`determineArrowDistance(double x, double y, double z, DPoint3[] ar)` Project the point (x,y,z) to the line of the reaction arrow 'ar'.
`int`	`determineType(double x, double y, double z)` Determines whether a point should be in a reactant, in a product or in an agent.
`static int`	`determineType(double x, double y, double z, DPoint3[] ar)` Determines whether a point should be in a reactant, in a product or in an agent.
`protected void`	`fillSelectionMolecule(SelectionMolecule s)` Adds all atoms and bonds of the root structure and the R-groups to the specified molecule.
`void`	`fuse(CGraph graph, boolean check)` Add the atoms and bonds of another molecule.
`protected void`	`fuse0(CGraph graph, boolean check)` Add those nodes and edges of a graph that are not already elements.
`Molecule`	`getAgent(int i)` Gets an agent.
`int`	`getAgentCount()` Gets the number of agents.
`java.util.ArrayList`	`getAllFragments()` Gets the list of reaction fragments (product, reactant, agent components) that build up this reaction.
`MPropertyContainer`	`getArrowAsProperty()` Gets the properties (type, endpoint coordinates) of the reaction arrow in this reaction.
`int[][]`	`getBtab()` Gets the bond table for the graph union.
`DPoint3`	`getCenter(int type, int i)` Gets the geometrical center of a reaction component.
`Molecule`	`getComponent(int flags, int i)` Gets a reactant, product or agent.
`Molecule`	`getComponent(long id)` Gets a reactant, product or agent.
`int`	`getComponentCount(int type)` Gets the number of reactants, products or agents.
`int`	`getComponentFlags(long id)` Gets the reaction component type flags from the ID.
`long`	`getComponentID(MolAtom a)` Gets the reaction component ID of an atom.
`long`	`getComponentID(MolBond b)` Gets the reaction component ID of a bond.
`long`	`getComponentID(Molecule m)` Gets the ID of a reaction component.
`int`	`getComponentIndex(long id)` Gets the reactant, product or agent index from the ID.
`int`	`getComponentType(long id)` Gets the reaction component type from the ID.
`int[][]`	`getCtab()` Gets the connection table for the graph union.
`CEdge`	`getEdge(int i)` Gets an edge.
`int`	`getEdgeCount()` Gets the number of edges in the graph union.
`java.util.Vector`	`getEdgeVector()` Gets the edges.
`java.lang.String`	`getFormula()` Gets the molecular formula in Hill order.
`MoleculeGraph`	`getGraphUnion()` Gets a graph containing all the atoms and bonds.
`protected int[]`	`getGrinv()` Gets the graph invariants for the graph union.
`int`	`getGrinv(int[] gi)` Gets the graph invariants for the graph union.
`MObject`	`getItsArrow()` Gets the reaction arrow of this reaction.
`double`	`getMass()` Calculates the molecular weight of the molecule.
`java.util.Hashtable`	`getMSLogic()` Gets the hash that stores arrow - reaction mapping.
`CNode`	`getNode(int i)` Gets a node.
`int`	`getNodeCount()` Returns the number of nodes in the graph union.
`java.util.Vector`	`getNodeVector()` Gets the nodes.
`MObject`	`getObject(int index)` Returns the graphical object that belongs to a chemical structure.
`int`	`getObjectCount()` Returns the count of the graphical objects that belong to a chemical structure.
`Molecule`	`getProduct(int i)` Gets a product.
`int`	`getProductCount()` Gets the number of products.
`Molecule`	`getReactant(int i)` Gets a reactant.
`int`	`getReactantCount()` Gets the number of reactants.
`static RxnMolecule`	`getReaction(CGraph g)` Returns the reaction represented by the given molecule if exists, otherwise null.
`DPoint3[]`	`getReactionArrow()` Gets a two-element array containing the endpoints of the reaction arrow.
`MObject`	`getReactionArrow(boolean generate)` Gets the reaction arrow of this reaction with the possibility to generate an arrow if the arrow is not yet set.
`java.util.ArrayList`	`getReactionArrowList()` Gets the list of the reaction arrows of this reaction.
`int`	`getReactionArrowType()` Gets the reaction arrow type.
`java.lang.String`	`getReactionArrowTypeName()` Gets the reaction arrow type name.
`java.util.ArrayList`	`getReactionSteps()` Divides this reaction into simple step reactions if this is a multistep reaction.
`Molecule`	`getStructure(int flags, int i)` Deprecated. as of Marvin 4.1, replaced by `getComponent(int, int)`
`int`	`getStructureCount(int type)` Deprecated. as of Marvin 4.1, replaced by `getComponentCount(int)`
`protected int`	`getSubGraphCount()` Gets the number of all "submolecules".
`protected void`	`getSubGraphs(MoleculeGraph[] arr, int off)` Gets all "submolecules".
`boolean`	`hasAtomSet()` Tests whether the molecule graph has atom sets.
`boolean`	`hasBondSet()` Tests whether the molecule graph has atom sets.
`void`	`implicitizeHydrogens(int f, MolAtom[] atoms)` Removes explicit bound Hydrogens from the graph and converts them to implicit.
`int`	`indexOf(CEdge edge)` Gets the index of the specified edge in the graph union.
`int`	`indexOf(CNode node)` Gets the index of the specified node in the graph union.
`int`	`indexOf(MObject mo)` Searches for an object that belongs to a chemical structure.
`boolean`	`isAtom()` A reaction molecule cannot represent an atom.
`boolean`	`isBond()` A reaction molecule cannot represent a bond.
`boolean`	`isEmpty()` Ask if the reaction is empty or not.
`boolean`	`isIncompleteReaction()` Check whether the reaction is incomplete or not.
`boolean`	`isReaction()` Checks if the structure represents a reaction or not.
`protected boolean`	`isRealNodeParent()` Reaction molecules cannot be real node parents.
`boolean`	`isSingleStepReaction()` Decides wheter this reaction is a singlestep or multistep reaction.
`protected void`	`makeItSimilar(CGraph g)` Copies some properties of this molecule to the other one specified as argument.
`void`	`mergeNodes(CNode that, CNode node)` Merges bonds of an atom with another atom, then add the atom to the molecule.
`CGraph`	`newInstance()` Creates a new RxnMolecule object.
`protected void`	`postClean()` Operations performed after cleaning.
`void`	`rebuildStructures()` For each structure (reactant or product) determines whether it should be a reactant or a product depending on its the relative position to the reaction arrow.
`void`	`rebuildStructures(DPoint3[] arw, int art)` Sets the reaction arrow.
`void`	`recalcReactionArrow()` Recalculates the coordinates of the reaction arrow from the reactants and products, forced recalculation.
`void`	`regenEdges()` Regenerate the edge vectors: remove their elements, then put the edge objects from the nodes into it.
`void`	`removeAll()` Remove all the atoms and bonds from the root structure, and from all the R-groups.
`void`	`removeAllEdges()` Removes all bonds from the reactants, products and agents.
`Molecule`	`removeComponent(int flags, int i)` Removes a reactant, product or agent.
`protected void`	`removeEdge(CEdge edge, int cleanupFlags)` Removes a bond from the reactants, products or agents.
`protected void`	`removeEdge(int iu, int cleanupFlags)` Removes an edge from a reactant, agent or product.
`void`	`removeEmptyComponents()` Checks all the componentes and removes those that are empty (node count is zero).
`void`	`removeNode(CNode node, int cleanupFlags)` Removes an atom from the reactants, products or agents.
`void`	`removeNode(int iu, int cleanupFlags)` Removes an atom from the reactants, products or agents.
`void`	`removeObject(MObject o)` Removes a graphical object from this.
`void`	`removeReactionArrow()` Removes the reaction arrow of this reacion.
`Molecule`	`removeStructure(int flags, int i)` Deprecated. as of Marvin 4.1, replaced by `removeComponent(int, int)`
`void`	`replaceEdge(CEdge olde, CEdge newe)` Replaces an edge by another one.
`void`	`revalidateCoordDependentProps()` Revalidate coordinate dependent properties.
`void`	`selectAllObjects(boolean s)` Selects or deselects all objects that belong to a chemical structure.
`void`	`setAbsStereo(boolean c)` Sets the absolute stereoconfiguration flag for all the structures.
`void`	`setDim(int d)` Sets the dimension for all the structures.
`void`	`setEdge(int iu, CEdge edge)` Sets the edge at the specified index.
`void`	`setLocation(DPoint3 p)` Set the origin of the molecule.
`void`	`setMSLogic(java.util.Hashtable ms)` Sets the hash that stores arrow - reaction mapping.
`void`	`setNode(int iu, CNode node)` Sets the node at the specified index.
`void`	`setReactionArrow()` Sets the stored reaction arrow to its calculated value.
`void`	`setReactionArrow(DPoint3[] arw)` Sets the endpoint coordinates of the reaction arrow.
`void`	`setReactionArrow(chemaxon.struc.graphics.MRArrow arrow)` Sets the reaction arrow.
`void`	`setReactionArrow0()` Sets the stored reaction arrow 'arrowPoints' to its calculated value.
`void`	`setReactionArrowEndPoints(DPoint3[] points)` Sets the endpoints of the reaction arrow in this reaction.
`void`	`setReactionArrowType(int type)` Sets the reaction arrow type.
`void`	`setReactionArrowType(java.lang.String name)` Sets the reaction arrow type from type name.
`void`	`setSgroupParent(MolAtom a, Sgroup sg, boolean set)` Sets or unsets an S-group as a parent of an atom in reactants, products or agents.
`Molecule`	`simplifyIncompleteReactionToMolecule()` Simplify a reaction to a molecule if possible.
`Molecule`	`simplifyToMolecule()` Simplifies this RxnMolecule by moving the atoms and bonds from the reactants, products, and agents to a Molecule.
`void`	`sortEdgesAccordingTo(CEdge[] order)` Sort edges in the same order as they appear in the specified array.
`void`	`splitDisconnectedComponent(int type, int index)` Replaces a disconnected reaction component by its connected fragments in the structure array.
`void`	`splitDisconnectedComponent(long id)` Replaces a disconnected reaction component by its connected fragments in the structure array.
`java.lang.String`	`toString()` Overrides Object.toString() to ease debugging.
`void`	`transform(CTransform3D t, boolean incg)` Apply a transformation matrix to the atomic coordinates and the reaction arrow.
`protected void`	`transformReactionArrow(CTransform3D t)` Apply a transformation matrix to the reaction arrow.
`void`	`updateComponentRoles()` Updates fragment roles in the molecule.

Methods inherited from class chemaxon.struc.Molecule
addNode0, addSgroup, addSgroupClones, addSgroupsOf, aromatize, bondlength, checkConsistency, clean, cleanSgroups, clear, clearExtraLabels, clearProperties, clone, clonecopyWithoutSgroups, cloneMoleculeWithDocument, contractExpandedSgroups, contractSgroups, convertToFrags, countExpandableContractableSgroups, countOrderedComponentSgroups, dearomatize, draw, endReuse, expandSgroups, expandSgroups, exportToBinFormat, exportToFormat, exportToObject, findAllSgroupContaining, findContainingMulticenterSgroup, findContractableSgroup, findExpandableSgroup, findFrags, findFrags, findSgroupContaining, findSgroupOf, findSmallestSgroupContaining, fixSelfReferringProperty, getComment, getEndPosition, getGraphUnionAsSelection, getImageSize, getInputFormat, getMostSimplifiedMolecule, getName, getProperty, getPropertyCount, getPropertyKey, getPropertyKeys, getPropertyObject, getSgroup, getSgroupArray, getSgroupCount, getSgroupLigands, getSimplifiedMolecule, getSortedSgroups, getStartPosition, getVisibleCoords, indexOf, isExpandable, isGUIContracted, isPeptideChain, isSgroup, makeBiopolymerSnake, newSelectionMolecule, partialClean, regenFragIds, removeAllSgroups, removeSgroupFromList, removeSgroupsOf, removeSgroupsOf, reparentSgroups, residueSymbolOf, residueTypeOf, reuseAtom, setComment, setEndPosition, setGUIContracted, setInputFormat, setName, setNode0, setProperty, setPropertyObject, setStartPosition, sortSgroupXBonds, toBinFormat, toFormat, toObject, ungroupSgroup, ungroupSgroup, ungroupSgroup, ungroupSgroup, ungroupSgroups

Methods inherited from class chemaxon.struc.Molecule

addNode0, addSgroup, addSgroupClones, addSgroupsOf, aromatize, bondlength, checkConsistency, clean, cleanSgroups, clear, clearExtraLabels, clearProperties, clone, clonecopyWithoutSgroups, cloneMoleculeWithDocument, contractExpandedSgroups, contractSgroups, convertToFrags, countExpandableContractableSgroups, countOrderedComponentSgroups, dearomatize, draw, endReuse, expandSgroups, expandSgroups, exportToBinFormat, exportToFormat, exportToObject, findAllSgroupContaining, findContainingMulticenterSgroup, findContractableSgroup, findExpandableSgroup, findFrags, findFrags, findSgroupContaining, findSgroupOf, findSmallestSgroupContaining, fixSelfReferringProperty, getComment, getEndPosition, getGraphUnionAsSelection, getImageSize, getInputFormat, getMostSimplifiedMolecule, getName, getProperty, getPropertyCount, getPropertyKey, getPropertyKeys, getPropertyObject, getSgroup, getSgroupArray, getSgroupCount, getSgroupLigands, getSimplifiedMolecule, getSortedSgroups, getStartPosition, getVisibleCoords, indexOf, isExpandable, isGUIContracted, isPeptideChain, isSgroup, makeBiopolymerSnake, newSelectionMolecule, partialClean, regenFragIds, removeAllSgroups, removeSgroupFromList, removeSgroupsOf, removeSgroupsOf, reparentSgroups, residueSymbolOf, residueTypeOf, reuseAtom, setComment, setEndPosition, setGUIContracted, setInputFormat, setName, setNode0, setProperty, setPropertyObject, setStartPosition, sortSgroupXBonds, toBinFormat, toFormat, toObject, ungroupSgroup, ungroupSgroup, ungroupSgroup, ungroupSgroup, ungroupSgroups

Methods inherited from class chemaxon.struc.MoleculeGraph
addAtomsAndBondsTo, addExplicitHydrogens, addExplicitHydrogens, addExplicitLonePairs, adjustMultiChiralFlag, aromatize, aromatize, arrangeComponents, calcCenter, calcCenter, calcDehydrogenizedGrinv, calcHeight, calcHybridization, calcOutRect, calcOutRect, calcOutRectCenter, calcOutRectCenter, calcWidth, canBeCT, canBeCT, clean, clearCachedInfo, clonecopyCGraphWithoutSgroups, contains, createDehydrogenizedReadOnlyGraph, findAtomClone, getAromaticAndAliphaticRings, getAromrings, getAromrings, getAtom, getAtomArray, getAtomCount, getBond, getBondArray, getBondCount, getCharge, getChirality, getDesiredLength, getDesiredLength, getDim, getDocument, getDocumentForChild, getEdgeArray, getExactMass, getExplicitHcount, getExplicitLonePairCount, getFlags, getFormalCharge, getGrinv, getGrinv, getGrinvOptions, getHybridizationState, getImplicitHcount, getLocalChirality, getLocalParity, getLocation, getLonePairCount, getMassno, getNeighbor, getNeighborCount, getNonAromrings, getNonAromrings, getParentDocument, getParity, getPoints, getRadical, getSSSRBondSet, getSSSRBondSetInLong, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getSubGraphs, getTotalCharge, hasExplicitLonePairs, hasExtraLabelSet, hasImplicitH, hasSelfReferringProperty, hasValenceError, hydrogenize, implicitizeHydrogens, implicitizeHydrogens, isAbsStereo, isMultiChiral, isOnlyFirstAtomInStereoCalculation, isQuery, isRingBond, isSelfReference, isSimilarTo, isValidLinkNode, moveTo, partialClean, properties, qpropCheck, removeExplicitLonePairs, restoreCache, saveCache, setAtomSetSeqs, setBondSetSeqs, setChirality, setFlags, setGrinvOptions, setLinkNodeDefaultOuters, setLocalParity, setParity, setParity, setParity, setSetSeqs, stereoClean, sumConservedQuantities, transform, updateDim, useOnlyFirstAtomInStereoCalculation, valenceCheck, valenceCheck

Methods inherited from class chemaxon.struc.MoleculeGraph

addAtomsAndBondsTo, addExplicitHydrogens, addExplicitHydrogens, addExplicitLonePairs, adjustMultiChiralFlag, aromatize, aromatize, arrangeComponents, calcCenter, calcCenter, calcDehydrogenizedGrinv, calcHeight, calcHybridization, calcOutRect, calcOutRect, calcOutRectCenter, calcOutRectCenter, calcWidth, canBeCT, canBeCT, clean, clearCachedInfo, clonecopyCGraphWithoutSgroups, contains, createDehydrogenizedReadOnlyGraph, findAtomClone, getAromaticAndAliphaticRings, getAromrings, getAromrings, getAtom, getAtomArray, getAtomCount, getBond, getBondArray, getBondCount, getCharge, getChirality, getDesiredLength, getDesiredLength, getDim, getDocument, getDocumentForChild, getEdgeArray, getExactMass, getExplicitHcount, getExplicitLonePairCount, getFlags, getFormalCharge, getGrinv, getGrinv, getGrinvOptions, getHybridizationState, getImplicitHcount, getLocalChirality, getLocalParity, getLocation, getLonePairCount, getMassno, getNeighbor, getNeighborCount, getNonAromrings, getNonAromrings, getParentDocument, getParity, getPoints, getRadical, getSSSRBondSet, getSSSRBondSetInLong, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getSubGraphs, getTotalCharge, hasExplicitLonePairs, hasExtraLabelSet, hasImplicitH, hasSelfReferringProperty, hasValenceError, hydrogenize, implicitizeHydrogens, implicitizeHydrogens, isAbsStereo, isMultiChiral, isOnlyFirstAtomInStereoCalculation, isQuery, isRingBond, isSelfReference, isSimilarTo, isValidLinkNode, moveTo, partialClean, properties, qpropCheck, removeExplicitLonePairs, restoreCache, saveCache, setAtomSetSeqs, setBondSetSeqs, setChirality, setFlags, setGrinvOptions, setLinkNodeDefaultOuters, setLocalParity, setParity, setParity, setParity, setSetSeqs, stereoClean, sumConservedQuantities, transform, updateDim, useOnlyFirstAtomInStereoCalculation, valenceCheck, valenceCheck

Methods inherited from class chemaxon.struc.CGraph
addEdge0, addEdgeWithoutChangingIt, addNodeWithoutChangingIt, checkEdgeConsistency, findBasicFrags, findComponentIds, findComponentIds, findEdge, findFrag, findFragById, findInArray, findNode, fuse, fuse0, getCSSR, getEdgeList, getForefather, getFragCount, getFragIds, getGrinvCC, getLock, getParent, getSmallestRingSizeForIdx, getSSSR, getSSSREdges, getSSSRIdxesForAtoms, incGrinvCC, incGrinvCCOnly, insertEdge, insertEdgeInOrder, insertNode, insertNullEdges, insertNullNodes, isGrinvCCValid, isolate, isolate, isRing, isSymmetric, mergeFrags, pack, regenCtabs, removeEdge, removeEdge, removeIsolatedEdges, removeIsolatedNodes, removeNode, removeNode, resetCtab, resetGrinvInParents, setGrinvCC

Methods inherited from class chemaxon.struc.CGraph

addEdge0, addEdgeWithoutChangingIt, addNodeWithoutChangingIt, checkEdgeConsistency, findBasicFrags, findComponentIds, findComponentIds, findEdge, findFrag, findFragById, findInArray, findNode, fuse, fuse0, getCSSR, getEdgeList, getForefather, getFragCount, getFragIds, getGrinvCC, getLock, getParent, getSmallestRingSizeForIdx, getSSSR, getSSSREdges, getSSSRIdxesForAtoms, incGrinvCC, incGrinvCCOnly, insertEdge, insertEdgeInOrder, insertNode, insertNullEdges, insertNullNodes, isGrinvCCValid, isolate, isolate, isRing, isSymmetric, mergeFrags, pack, regenCtabs, removeEdge, removeEdge, removeIsolatedEdges, removeIsolatedNodes, removeNode, removeNode, resetCtab, resetGrinvInParents, setGrinvCC

Methods inherited from class java.lang.Object
`equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait`

Field Detail

TYPE_COUNT

public static final int TYPE_COUNT

Number of structure types. Currently 3: REACTANTS, PRODUCTS, AGENTS.

See Also:: Constant Field Values

REACTANTS

public static final int REACTANTS

"Reactant" structure type.

See Also:: getComponent(int, int), Constant Field Values

PRODUCTS

public static final int PRODUCTS

"Product" structure type.

See Also:: getComponent(int, int), Constant Field Values

AGENTS

public static final int AGENTS

"Agent" structure type.

See Also:: getComponent(int, int), Constant Field Values

RGROUPED

public static final int RGROUPED

Add R-groups to component structure.

Since:: Marvin 3.1
See Also:: Constant Field Values

TYPE_MASK

public static final int TYPE_MASK

Component type mask.

Since:: Marvin 3.1
See Also:: REACTANTS, PRODUCTS, AGENTS, Constant Field Values

REGULAR_SINGLE

public static final int REGULAR_SINGLE

Regular single reaction arrow type.

Since:: Marvin 5.1, 02/28/2008
See Also:: Constant Field Values

TWO_HEADED_SINGLE

public static final int TWO_HEADED_SINGLE

Two headed single reaction arrow type.

Since:: Marvin 5.1, 02/28/2008
See Also:: Constant Field Values

REGULAR_DOUBLE

public static final int REGULAR_DOUBLE

Regular double reaction arrow type.

Since:: Marvin 5.1, 02/28/2008
See Also:: Constant Field Values

TWO_HEADED_DOUBLE

public static final int TWO_HEADED_DOUBLE

Two headed double reaction arrow type.

Since:: Marvin 5.1, 02/28/2008
See Also:: Constant Field Values

Constructor Detail

RxnMolecule

public RxnMolecule()

Create a reaction.

Method Detail

isEmpty

public boolean isEmpty()

Ask if the reaction is empty or not.

Overrides:: isEmpty in class Molecule

Returns:: true if there are no reactants, products or agents

isAtom

public boolean isAtom()

A reaction molecule cannot represent an atom.

Overrides:: isAtom in class MoleculeGraph

Returns:: false

isBond

public boolean isBond()

A reaction molecule cannot represent a bond.

Overrides:: isBond in class MoleculeGraph

Returns:: false

isReaction

public boolean isReaction()

Checks if the structure represents a reaction or not.

Overrides:: isReaction in class Molecule

Returns:: true
Since:: Marvin 3.0

canBeReactionComponent

public boolean canBeReactionComponent()

Tests whether an object of this class can be a reaction component. This implementation returns false, RxnMolecules cannot be embedded in each other.

Overrides:: canBeReactionComponent in class Molecule

Returns:: true if it can be a reactant, product or agent, false if adding it to an RxnMolecule is not supported
Since:: Marvin 4.1.13, 09/19/2007

getFormula

public java.lang.String getFormula()

Gets the molecular formula in Hill order.

Overrides:: getFormula in class MoleculeGraph

Returns:: the formula

getMass

public double getMass()

Calculates the molecular weight of the molecule. Always returns 0 for reactions

Overrides:: getMass in class MoleculeGraph

Returns:: the molecular weight

getReaction

public static RxnMolecule getReaction(CGraph g)

Returns the reaction represented by the given molecule if exists, otherwise null. The corresponding reaction molecule is either the molecule itself or its root structure.

Parameters:: g - the molecule graph
Returns:: the corresponding reaction molecule

getReactantCount

public int getReactantCount()

Gets the number of reactants.

Returns:: the number of reactants

getProductCount

public int getProductCount()

Gets the number of products.

Returns:: the number of products

getAgentCount

public int getAgentCount()

Gets the number of agents.

Returns:: the number of agents

getComponentCount

public int getComponentCount(int type)

Gets the number of reactants, products or agents.

Parameters:: type - REACTANTS, PRODUCTS or AGENTS
Returns:: the number of reactants, products or agents
Since:: Marvin 4.1, 11/19/2005

getReactant

public Molecule getReactant(int i)

Gets a reactant.

Parameters:: i - reactant index
Returns:: a reactant

getProduct

public Molecule getProduct(int i)

Gets a product.

Parameters:: i - product index
Returns:: a product

getAgent

public Molecule getAgent(int i)

Gets an agent.

Parameters:: i - agent index
Returns:: an agent

getComponentID

public long getComponentID(Molecule m)

Gets the ID of a reaction component.

Parameters:: m - the reaction component
Returns:: the reaction component ID or -1 if not found
Since:: Marvin 4.1, 11/19/2005

getComponentID

public long getComponentID(MolAtom a)

Gets the reaction component ID of an atom.

Parameters:: a - the atom
Returns:: the reaction component ID or -1 if not found
Since:: Marvin 4.1, 11/19/2005

getComponentID

public long getComponentID(MolBond b)

Gets the reaction component ID of a bond.

Parameters:: b - the bond
Returns:: the reaction component ID or -1 if not found
Since:: Marvin 4.1, 11/19/2005

getComponentType

public int getComponentType(long id)

Gets the reaction component type from the ID.

Parameters:: id - the reaction component ID or -1
Returns:: the reaction component type or -1
Since:: Marvin 4.1, 11/19/2005

getComponentFlags

public int getComponentFlags(long id)

Gets the reaction component type flags from the ID.

Parameters:: id - the reaction component ID or -1
Returns:: the reaction component type or -1
Since:: Marvin 4.1, 11/19/2005

getComponentIndex

public int getComponentIndex(long id)

Gets the reactant, product or agent index from the ID.

Parameters:: id - the reaction component ID or -1
Returns:: the reaction component index or -1
Since:: Marvin 4.1, 11/19/2005

getComponent

public Molecule getComponent(long id)

Gets a reactant, product or agent.

Warning! The RGROUPED flag returns an RgMolecule object having the same atom objects as the original reactant/product/agent. The parent of the atom objects is unchanged (it is the original reactant/product/agent).

Parameters:: id - the reaction component ID
Returns:: a reactant, product or agent
Since:: Marvin 4.1, 11/19/2005
See Also:: getComponent(int, int)

getComponent

public Molecule getComponent(int flags,
                             int i)

Gets a reactant, product or agent.

Parameters:: flags - REACTANTS, PRODUCTS or AGENTS, can be combined with RGROUPED; i - reactant, product or agent index
Returns:: a reactant, product or agent
Since:: Marvin 4.1, 11/19/2005

getCenter

public DPoint3 getCenter(int type,
                         int i)

Gets the geometrical center of a reaction component.

Parameters:: type - REACTANTS, PRODUCTS or AGENTS; i - reactant, product or agent index
Returns:: the center of mass

revalidateCoordDependentProps

public void revalidateCoordDependentProps()

Revalidate coordinate dependent properties. This method should be called at molecule import, after all atomic coordinates and bonds are parsed.

Overrides:: revalidateCoordDependentProps in class MoleculeGraph

Since:: Marvin 4.1, 08/03/2006

setReactionArrow0

public void setReactionArrow0()

Sets the stored reaction arrow 'arrowPoints' to its calculated value.

getReactionArrowType

public int getReactionArrowType()

Gets the reaction arrow type.

Returns:: the reaction arrow type, REGULAR_SINGLE if no reaction arrow is set.
Since:: Marvin 3.5
See Also:: REGULAR_SINGLE, REGULAR_DOUBLE, TWO_HEADED_SINGLE, TWO_HEADED_DOUBLE

getReactionArrowTypeName

public java.lang.String getReactionArrowTypeName()

Gets the reaction arrow type name. Used in molecule export.

Returns:

the reaction arrow type name:

"DEFAULT" for arrow type RxnMolecule.REGULAR_SINGLE or in case if no reaction arrow is set.
"RESONANCE" for arrow type RxnMolecule.REGULAR_DOUBLE
"RETROSYNTHETIC" for arrow type RxnMolecule.TWO_HEADED_SINGLE
"EQUILIBRIUM" for arrow type RxnMolecule.TWO_HEADED_DOUBLE

Since:

Marvin 3.5

setReactionArrowType

public void setReactionArrowType(int type)

Sets the reaction arrow type.

Parameters:: type - the reaction arrow type
Since:: Marvin 3.5

setReactionArrowType

public void setReactionArrowType(java.lang.String name)

Sets the reaction arrow type from type name. Used in molecule import.

Parameters:: name - the reaction arrow type name
Throws:: java.lang.IllegalArgumentException - for invalid type name
Since:: Marvin 3.5

getReactionArrow

public DPoint3[] getReactionArrow()

Gets a two-element array containing the endpoints of the reaction arrow.

Returns:: the arrow

getReactionArrow

public MObject getReactionArrow(boolean generate)

Gets the reaction arrow of this reaction with the possibility to generate an arrow if the arrow is not yet set.

Parameters:: generate - if true then arrow is generated in case when the arrow is not yet set.
Returns:: the arrow of this reaction, null if the arrow is not set and the generate parameter was false.

setReactionArrow

public void setReactionArrow(DPoint3[] arw)

Sets the endpoint coordinates of the reaction arrow.

Parameters:: arw - endpoint coordinates of the reaction arrow

setReactionArrow

public void setReactionArrow()

Sets the stored reaction arrow to its calculated value.

setReactionArrow

public void setReactionArrow(chemaxon.struc.graphics.MRArrow arrow)

Sets the reaction arrow.

Parameters:: arrow -

removeReactionArrow

public void removeReactionArrow()

Removes the reaction arrow of this reacion.

setMSLogic

public void setMSLogic(java.util.Hashtable ms)

Sets the hash that stores arrow - reaction mapping.

Parameters:: ms - the hash that stores the mapping.

getMSLogic

public java.util.Hashtable getMSLogic()

Gets the hash that stores arrow - reaction mapping.

Returns:: returns the hash that stores the

chemaxon.struc Class RxnMolecule

TYPE_COUNT

REACTANTS

PRODUCTS

AGENTS

RGROUPED

TYPE_MASK

REGULAR_SINGLE

TWO_HEADED_SINGLE

REGULAR_DOUBLE

TWO_HEADED_DOUBLE

RxnMolecule

isEmpty

isAtom

isBond

isReaction

canBeReactionComponent

getFormula

getMass

getReaction

getReactantCount

getProductCount

getAgentCount

getComponentCount

getReactant

getProduct

getAgent

getComponentID

getComponentID

getComponentID

getComponentType

getComponentFlags

getComponentIndex

getComponent

getComponent

getCenter

revalidateCoordDependentProps

setReactionArrow0

getReactionArrowType

getReactionArrowTypeName

setReactionArrowType

setReactionArrowType

getReactionArrow

getReactionArrow

setReactionArrow

setReactionArrow

setReactionArrow

removeReactionArrow

setMSLogic

getMSLogic

chemaxon.struc
Class RxnMolecule