RxnMolecule (Marvin API documentation (c) 1998-2020 ChemAxon Ltd.)

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

All Implemented Interfaces:

chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>, chemaxon.core.structure.MoleculeForBuilder, chemaxon.core.structure.ReactionForBuilder, chemaxon.core.structure.RootStructureForBuilder, chemaxon.core.structure.StructureForBuilder, Incomplecule, chemaxon.struc.MObjectContainer, MTransformable, StereoConstants, java.io.Serializable
```
@PublicAPI
public class RxnMolecule
extends Molecule
implements chemaxon.struc.MObjectContainer, chemaxon.core.structure.ReactionForBuilder
```
Reaction.

Since:

Marvin 2.9

Version:

5.3, 10/16/2009

Author:

Peter Csizmadia, Szilveszter Juhos, Erika Biro, Zsuzsanna Szabo

See Also:

Serialized Form

Property Summary
- Properties inherited from class chemaxon.struc.MoleculeGraph
  hasSelfReferringProperty

Nested Class Summary
- Nested classes/interfaces inherited from class chemaxon.struc.MoleculeGraph
  MoleculeGraph.ValenceCheckState

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`AGENTS` "Agent" structure type.
`static int`	`EQUILIBRIUM` Resonance arrow, the same as the two-headed double reaction arrow.
`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`	`RESONANCE` Resonance arrow, the same as the two-headed single reaction arrow.
`static int`	`RETROSYNTHETIC` Retrosynthetic arrow, the same as the regular double reaction arrow.
`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, RM_KEEP_LEAVINGGROUPS, RMCLEANUP_FROMSGROUPS, RMCLEANUP_SGROUPATOMS, RMSG_DEFAULT, RMSG_KEEP_CHILDREN, RMSG_KEEP_MULTICENTER, RMSG_KEEP_PARENT

Fields inherited from class chemaxon.struc.MoleculeGraph
AROM_AMBIGUOUS, AROM_BASIC, AROM_CHUCKEL, AROM_GENERAL, AROM_LOOSE, AROM_SUBSTRUCTURE, atomCount, AUTO_UNGROUP, bondCount, btab, CACHE_REMOVE_ALL, CACHE_REMOVE_AROMATAMODULE, CACHE_REMOVE_CACHEMEMORY, CACHE_REMOVE_GRINVMODULE, CACHE_REMOVE_PARITYMODULE, CACHE_REMOVE_SSSRMODULE, CACHE_REMOVE_TABS, cacheMemory, ctab, DEAROM_GENERAL, DEAROM_HUCKELCHECK, DEAROM_HUCKELCHECK_EX, DIM_MASK, FRAG_BASIC, FRAG_KEEPING_MULTICENTERS, FRAG_KEEPING_SGROUPS, FRAG_TYPE_COUNT, gearch, GRINV_DONT_STORE, GRINV_NOHYDROGEN, GRINV_OLDSTEREO, GRINV_STEREO, GRINV_USEMAPS, GRINV_VALUE_OPTIONS, grinvCC, INITIAL_CAPACITY, INVALID_LINKNODE_MESSAGE, MIN_RING_SIZE_FOR_TRANS_DB, OMIT_POSTCLEAN, orix, oriy, oriz, parentGraph, propertyContainer, RMCLEANUP_ALL, RMCLEANUP_EDGES, RMCLEANUP_FIXCOMPONENT, RMCLEANUP_MOBJECT, RMCLEANUP_NONE, RMCLEANUP_PARENTDOC, RMCLEANUP_STEREO, superGraph, theAtoms, theBonds, useOnlyFirstAtomInStereoCalculation, VALENCE_CHECK, VALENCE_CHECK_AMBIGUOUS

Fields inherited from interface chemaxon.struc.StereoConstants
ANTI, ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_M, CHIRALITY_MASK, CHIRALITY_P, CHIRALITY_r, CHIRALITY_R, CHIRALITY_s, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_ALL_POSSIBLE, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CIS_TRANS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, ENDO, EXO, PARITY_ALLENE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_NONE, PARITY_ODD, PARITY_TETRAHEDRAL, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, SYN, TRANS

Constructor Summary

Constructors
Constructor and Description

RxnMolecule()
Create a reaction.

Constructors
Constructor and Description
`RxnMolecule()` Create a reaction.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`add(MolAtom a)` Adds an atom to a reactant, product or agent structure.
`void`	`add(MolBond e)` Adds a bond to a reactant, product, agent.
`protected void`	`addAtomToFragment(MolAtom a)` Adds an atom to a fragment.
`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.List<Molecule> reactants, java.util.List<Molecule> products, java.util.List<Molecule> agents, chemaxon.struc.graphics.MRArrow arrow, int arrowType)`
`void`	`addSgroup(Sgroup sg, boolean setparent)` Adds an S-group to this object.
`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.
`RxnMolecule`	`clone()` Make an identical copy of the reaction structure.
`void`	`clonecopy(int[] iatoms, MoleculeGraph g)` Copies the specified nodes and edges of this graph to another one.
`void`	`clonecopy(MoleculeGraph g)` Make another molecule identical to this one.
`void`	`clonelesscopy(MoleculeGraph g)` Deprecated. as of Marvin 6.3. Not supported feature.
`RxnMolecule`	`cloneMoleculeWithDocument()` Makes an identical copy of the molecule and its document.
`boolean`	`contains(MolAtom node)` Checks if a reactant, agent or product structure contains the specified node.
`boolean`	`contains(MolBond edge)` Checks if a reactant, agent or product structure contains the specified edge.
`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.
`protected chemaxon.struc.gearch.MoleculeGraphGearch`	`createGearch()`
`static RxnMolecule`	`createReaction(Molecule mol, DPoint3[] arw, int art)` Creates a reaction.
`static RxnMolecule`	`createReaction(MoleculeGraph mol, DPoint3[] arw)` Creates a reaction.
`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`	`fixProperties()` Delegates to tracker's fixProperties().
`void`	`fuse(MoleculeGraph graph, boolean check)` Add the atoms and bonds of another molecule.
`void`	`fuse(RxnMolecule rxnMol)` Fuse and RxnMolecule to this RxnMolecule.
`protected void`	`fuse0(MoleculeGraph 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.
`Molecule[]`	`getAgents()` Gets all agents in an array.
`java.util.List<Molecule>`	`getAllFragments()` Gets the list of reaction fragments (product, reactant, agent components) that build up this reaction.
`java.util.List<MObject>`	`getAllObjects()`
`MPropertyContainer`	`getArrowAsProperty()` Gets the properties (type, endpoint coordinates) of the reaction arrow in this reaction.
`MolAtom`	`getAtom(int i)` Gets a node.
`int`	`getAtomCount()` Returns the number of nodes in the graph union.
`int`	`getAtomCount(int atomicNumber)` Gets the number of atoms with the given atomic number in the unified molecule graph of the reaction.
`IteratorFactory.AtomIterator`	`getAtomIterator()` Returns an iterator over the atoms in this molecule in proper sequence.
`MolBond`	`getBond(int i)` Gets an edge.
`int`	`getBondCount()` Gets the number of edges in the graph union.
`IteratorFactory.BondIterator`	`getBondIterator()` Returns an iterator over the bonds in this molecule in proper sequence.
`BondTable`	`getBondTable()` 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 typeFlag, 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 atom)` Gets the reaction component ID of an atom.
`long`	`getComponentID(MolBond bond)` Gets the reaction component ID of a bond.
`long`	`getComponentID(Molecule molecule)` 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.
`java.lang.String`	`getFormula()` Gets the molecular formula in Hill order.
`MoleculeGraph`	`getGraphUnion()` Gets a graph containing all the atoms and bonds.
`chemaxon.struc.graphics.MRArrow`	`getItsArrow()` Gets the reaction arrow of this reaction.
`int`	`getLocalParity(int i)` Computes the local parity of an atom of the RxnMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
`double`	`getMass()` Calculates the molecular weight of the molecule.
`java.util.Map<chemaxon.struc.graphics.MRArrow,RxnMolecule>`	`getMSLogic()` Deprecated. Multi-step reactions not supported. Method performs no operations.
`int`	`getObjectCount()`
`int`	`getParity(int i)` Computes the parity of an atom of the RxnMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
`Molecule`	`getProduct(int i)` Gets a product.
`int`	`getProductCount()` Gets the number of products.
`Molecule[]`	`getProducts()` Gets all products in an array.
`Molecule`	`getReactant(int i)` Gets a reactant.
`int`	`getReactantCount()` Gets the number of reactants.
`Molecule[]`	`getReactants()` Gets all reactants in an array.
`static RxnMolecule`	`getReaction(MoleculeGraph 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.
`chemaxon.struc.graphics.MRArrow`	`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.List<chemaxon.struc.graphics.MRArrow>`	`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<RxnMolecule>`	`getReactionSteps()` Divides this reaction into simple step reactions if this is a multistep reaction.
`protected int`	`getSubGraphCount()` Gets the number of all "submolecules".
`protected void`	`getSubGraphs(MoleculeGraph[] arr, int off)` Gets all "submolecules".
`int`	`getType(MoleculeGraph selection)` Checks whether the atoms in the selection are all in reactants, products or agents.
`boolean`	`hasAtomSet()` Tests whether the molecule graph has atom sets.
`boolean`	`hasBondSet()` Tests whether the molecule graph has atom sets.
`int`	`indexOf(MolAtom node)` Gets the index of the specified node in the graph union.
`int`	`indexOf(MolBond edge)` Gets the index of the specified edge in the graph union.
`boolean`	`isAtom()` Deprecated. As of Marvin 14.7.7, no replacement. Not supported feature.
`boolean`	`isBond()` Deprecated. As of Marvin 14.7.7, no replacement. Not supported feature.
`boolean`	`isEmpty()` Ask if the reaction is empty or not.
`boolean`	`isIncompleteReaction()` Check whether the reaction is incomplete or not.
`boolean`	`isMergedComponent(MoleculeGraph m)` Check whether given molecule is reaction component with a set of intentionally merged fragments or not.
`boolean`	`isQuery()` Indicates if the molecule has query features: query atoms or query bonds.
`boolean`	`isReaction()` Checks if the structure represents a reaction or not.
`protected boolean`	`isRealAtomParent()` Reaction molecules cannot be real node parents.
`boolean`	`isSingleStepReaction()` Deprecated.
`protected void`	`makeItSimilar(MoleculeGraph g)` Copies some properties of this molecule to the other one specified as argument.
`void`	`mergeAtoms(MolAtom that, MolAtom node)` Deprecated. As of Marvin 6.2, use `MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean)` instead.
`void`	`mergeComponentParts(MoleculeGraph m, int type, boolean isMergeStored)` Finds those component parts that are contained in the molecule graph m and creates a new component containing all atoms of m, splitting them from the previous merges.
`MoleculeGraph`	`newInstance()` Creates a new RxnMolecule object.
`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`	`regenBonds()` 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`	`removeAllBonds()` Removes all bonds from the reactants, products and agents.
`void`	`removeAtom(int iu, int cleanupFlags)` Removes an atom from the reactants, products or agents.
`void`	`removeAtom(MolAtom node, int cleanupFlags)` Removes an atom from the reactants, products or agents.
`protected void`	`removeBond(int iu, int cleanupFlags)` Removes an edge from a reactant, agent or product.
`protected void`	`removeBond(MolBond edge, int cleanupFlags)` Removes a bond from the reactants, products or agents.
`Molecule`	`removeComponent(int flags, int i)` Removes a reactant, product or agent.
`void`	`removeEmptyComponents()` Checks all the componentes and removes those that are empty (node count is zero).
`void`	`removeObject(MObject o)` Removes a graphical object from this.
`void`	`removeReactionArrow()` Removes the reaction arrow of this reacion.
`void`	`replaceBond(MolBond olde, MolBond newe)` Deprecated. as of Marvin 6.2, may constructs inconsistent `MoleculeGraph`. Use `MoleculeGraph.removeBond(MolBond)` for bond removal and `add(MolBond)` for adding a new bond to the molecule.
`void`	`revalidateCoordDependentProps()` Revalidate coordinate dependent properties.
`void`	`selectAllObjects(boolean s)`
`void`	`setAbsStereo(boolean c)` Sets the absolute stereoconfiguration flag for all the structures.
`void`	`setAtom(int iu, MolAtom node)` Deprecated. As of Marvin 6.2, may constructs inconsistent `MoleculeGraph`. Use `MoleculeGraph.removeAtom(MolAtom)` and `add(MolAtom)` to modify the structure.
`void`	`setBond(int iu, MolBond edge)` Deprecated. as of Marvin 6.2, may constructs inconsistent `MoleculeGraph`. Use `MoleculeGraph.removeBond(MolBond)` for bond removal and `add(MolBond)` for adding a new bond to the molecule.
`void`	`setDim(int d)` Sets the dimension for all the structures.
`void`	`setLocation(DPoint3 p)` Set the origin of the molecule.
`void`	`setMSLogic(java.util.Map<chemaxon.struc.graphics.MRArrow,RxnMolecule> ms)` Deprecated. Multi-step reactions not supported. Method performs no operations.
`void`	`setReactionArrow(DPoint3... points)` Sets the endpoint coordinates of the reaction arrow.
`void`	`setReactionArrow(chemaxon.struc.graphics.MRArrow arrow)` Sets the reaction arrow.
`void`	`setReactionArrow0(DPoint3... points)` Sets the reaction arrow.
`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.
`protected void`	`setSupergraph(MoleculeGraph molecule)` Sets the given molecule as the supergraph of this graph and its components.
`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`	`sortBondsAccordingTo(MolBond[] order)` Sort edges in the same order as they appear in the specified array.
`void`	`splitAllDisconnectedComponents()` Replaces all disconnected reaction components by its connected fragments in the structure array.
`void`	`splitComponentParts(MoleculeGraph m, int type)` Finds those component parts that are contained in the molecule graph m and creates separate components from the fragments contained in m, splitting them from the previous merges.
`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.
`boolean`	`stereoClean()` Reset the wedges of the molecule, based on the actual parity information in 2D remove wedges in 3D.
`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
addAtom0, addBond0, addSgroupClones, addSgroupsOf, aromatize, aromatize, bondlength, checkConsistency, clear, clearExtraLabels, clearProperties, cloneAtoms, clonecopyWithoutSgroups, cloneMolecule, connectOriginalBondsToNewAtom, contractSgroups, contractSgroups, convertToFrags, countExpandableContractableSgroups, countOrderedComponentSgroups, dearomatize, endReuse, expandSgroups, expandSgroups, exportToBinFormat, exportToFormat, exportToObject, findAllSgroupContaining, findContainingMulticenterSgroup, findContractableSgroup, findExpandableSgroup, findFrags, findFrags, findSgroupContaining, findSgroupOf, findSmallestSgroupContaining, fixSelfReferringProperty, getBonds, getComment, getEndPosition, getGraphUnionAsSelection, getId, getInputFormat, getMostSimplifiedMolecule, getName, getProperty, getPropertyCount, getPropertyKey, getPropertyKeys, getPropertyObject, getRootSgroups, getSgroup, getSgroupArray, getSgroupCount, getSgroupIterator, getSgroupLigands, getSimplifiedMolecule, getSortedSgroups, getStartPosition, getVisibleCoords, hasContractedSgroup, hasId, implicitizeHydrogens0, indexOf, isExpandable, isGUIContracted, isSgroup, newSelectionMolecule, rearrangeSgroups, removeAllSgroups, removeAtomFromChildren, removeSgroupFromList, removeSgroupsOf, removeSgroupsOf, reparentSgroups, replaceAtom, replaceSgroup, residueSymbolOf, residueTypeOf, reuseAtom, setAtom0, setComment, setEndPosition, setGUIContracted, setGUIContracted, setId, setInputFormat, setName, setProperty, setPropertyObject, setStartPosition, sortSgroupXBonds, toBinFormat, toFormat, toObject, ungroupSgroup, ungroupSgroup, ungroupSgroup, ungroupSgroup, ungroupSgroups, ungroupSgroups, ungroupSgroups

Methods inherited from class chemaxon.struc.MoleculeGraph
add, addAtomsAndBondsTo, addAtomWithoutChangingIt, addBondWithoutChangingIt, addExplicitHydrogens, addExplicitHydrogens, addExplicitLonePairs, addSimpleAtomWithoutChangingIt, adjustMultiChiralFlag, aromatize, aromatize, arrangeComponents, atoms, bonds, calcCenter, calcCenter, calcDehydrogenizedGrinv, calcHeight, calcHybridization, calcOutRect, calcOutRect, calcOutRectCenter, calcOutRectCenter, calcWidth, canBeCT, canBeCT, canBeCT, checkBondConsistency, clean, clean, clearCachedInfo, clonecopyMoleculeGraphWithoutSgroups, contains, createDehydrogenizedReadOnlyGraph, createSmolecule, dearomatize, findAtom, findAtomClone, findBasicFrags, findBond, findComponentIds, findComponentIds, findFrag, findFrag, findFragById, findFrags, findInArray, fuse, getAromaticAndAliphaticRings, getAtomArray, getAtomicNumber, getAtomReferenceList, getBondArray, getBtab, getCharge, getChirality, getCSSR, getCSSRIdxesForAtoms, getDesiredLength, getDesiredLength, getDim, getDocument, getDocumentForChild, getEnclosingCube, getExactMass, getExplicitHcount, getExplicitLonePairCount, getEZStereo, getFlags, getForefather, getFormalCharge, getFragCount, getFragCount, getFragIds, getFreeAttachmentPoints, getGrinv, getGrinv, getGrinv, getGrinv, getGrinvCC, getGrinvOptions, getImplicitHcount, getImplicitHCount, getLigand, getLigandAtno, getLigandBondType, getLigandCount, getLocation, getLock, getLonePairCount, getMaxRgroupAttachmentPointOrder, getParent, getParentDocument, getParityType, getPoints, getPossibleAttachmentPoints, getRadicalCount, getSmallestRingSizeForIdx, getSSSR, getSSSRBonds, getSSSRBondsAsBitSet, getSSSRBondSet, getSSSRBondSetInLong, getSSSRIdxesForAtoms, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getSubGraphs, getTotalCharge, getValenceCheckOptions, getValenceCheckState, getValenceProperty, hasExplicitLonePairs, hasExtraLabelSet, hasImplicitH, hasSelfReferringProperty, hasValenceError, hydrogenize, implicitizeHydrogens, implicitizeHydrogens, implicitizeHydrogens, incGrinvCC, incGrinvCC, incGrinvCCOnly, insertAtom, insertBond, insertBondInOrder, insertNullAtoms, insertNullBonds, isAbsStereo, isAcceptedSpecialLigand, isAtomInRing, isBondParallelWith, isGrinvCCValid, isLargeMolecule, isMolecule, isMultiChiral, isolate, isolate, isOnlyFirstAtomInStereoCalculation, isRing, isRingBond, isSelfReference, isSimilarTo, isSymmetric, isValenceCheckEnabled, isValidLinkNode, mergeFrags, moveTo, pack, partialClean, partialClean, partialClean, properties, qpropCheck, regenBtab, regenCtab, regenGearch, removeAtom, removeAtom, removeBond, removeBond, removeExplicitLonePairs, removeIsolatedAtoms, removeIsolatedBonds, resetCtab, resetGrinvInParents, restoreCache, saveCache, setAtomSetSeqs, setBondSetSeqs, setChirality, setChirality, setFlags, setFlags, setGrinvCC, setGrinvOptions, setLinkNodeDefaultOuters, setLocalParity, setLocalParity, setParity, setParity, setParity, setValenceCheckEnabled, setValenceCheckOptions, setValenceCheckState, smol, sumConservedQuantities, transform, updateDim, useOnlyFirstAtomInStereoCalculation, valenceCheck, valenceCheck

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
  - RESONANCE
```
public static final int RESONANCE
```
    Resonance arrow, the same as the two-headed single reaction arrow.
    
    Since:
    
    Marvin 5.2 27/01/2009
    
    See Also:
    
    Constant Field Values
  - RETROSYNTHETIC
```
public static final int RETROSYNTHETIC
```
    Retrosynthetic arrow, the same as the regular double reaction arrow.
    
    Since:
    
    Marvin 5.2 27/01/2009
    
    See Also:
    
    Constant Field Values
  - EQUILIBRIUM
```
public static final int EQUILIBRIUM
```
    Resonance arrow, the same as the two-headed double reaction arrow.
    
    Since:
    
    Marvin 5.2 27/01/2009
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - RxnMolecule
```
public RxnMolecule()
```
    Create a reaction.
- Method Detail
  - createReaction
```
public static RxnMolecule createReaction(Molecule mol,
                                         DPoint3[] arw,
                                         int art)
```
    Creates a reaction.
    
    Parameters:
    
    mol - contains the atoms of reactants and products
    
    arw - two-element array containing the endpoints of the reaction arrow
    
    art - the arrow type
    
    Returns:
    
    the reaction
  - createReaction
```
public static RxnMolecule createReaction(MoleculeGraph mol,
                                         DPoint3[] arw)
```
    Creates a reaction.
    
    Parameters:
    
    mol - contains the atoms of reactants and products
    
    arw - two-element array containing the endpoints of the reaction arrow
    
    Returns:
    
    the reaction
  - determineArrowDistance
```
public 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'. Return the signed distance of the projected point from the start-point of the arrow divided by the arrow length.
    
    Parameters:
    
    x - is the x coordinate of the point
    
    y - is the y coordinate of the point
    
    z - is the z coordinate of the point
    
    ar - is the reaction arrow
    
    Returns:
    
    the signed distance of the projected point from the start-point of the arrow divided by the arrow length
  - determineType
```
public 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.
    
    Parameters:
    
    x - point x coordinate
    
    y - point y coordinate
    
    z - point z coordinate
    
    ar - reaction arrow
    
    Returns:
    
    REACTANTS, PRODUCTS or AGENTS
  - getReaction
```
public static RxnMolecule getReaction(MoleculeGraph 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
  - add
```
public void add(MolAtom a)
```
    Adds an atom to a reactant, product or agent structure. If a neighbour of the atom is in a reactant, product or agent, then adds the atom to that structure. Otherwise creates a new reactant or product.
    
    Overrides:
    
    add in class MoleculeGraph
    
    Parameters:
    
    a - the new atom
  - add
```
public void add(MolBond e)
```
    Adds a bond to a reactant, product, agent. If an endpoint of the edge is in a reactant, product or agent, then adds the edge to that structure.
    
    Overrides:
    
    add in class Molecule
    
    Parameters:
    
    e - the new edge
  - addComponent
```
public void addComponent(Molecule m,
                         int type)
                  throws java.lang.IllegalArgumentException
```
    Adds a reactant, product or agent. If atoms in the specified structure are already part of some other reactants, products or agents then removes them from those structures.
    
    Parameters:
    
    m - the reactant, product or agent
    
    type - REACTANTS, PRODUCTS or AGENTS
    
    Throws:
    
    java.lang.IllegalArgumentException - if m is of a subclass of Molecule for which the embedding in an RxnMolecule is not supported
  - addComponent
```
public void addComponent(Molecule m,
                         int type,
                         boolean beNew)
                  throws java.lang.IllegalArgumentException
```
    Adds a reactant, product or agent. If atoms in the specified structure are already part of some other reactants, products or agents then removes them from those structures.
    
    Parameters:
    
    m - the reactant, product or agent
    
    type - REACTANTS, PRODUCTS or AGENTS
    
    beNew - m should be a new structure if true
    
    Throws:
    
    java.lang.IllegalArgumentException - if m is of a subclass of Molecule for which the embedding in an RxnMolecule is not supported
  - addReactionStep
```
public void addReactionStep(java.util.List<Molecule> reactants,
                            java.util.List<Molecule> products,
                            java.util.List<Molecule> agents,
                            chemaxon.struc.graphics.MRArrow arrow,
                            int arrowType)
```
  - addSgroup
```
public void addSgroup(Sgroup sg,
                      boolean setparent)
```
    Adds an S-group to this object.
    
    Overrides:
    
    addSgroup in class Molecule
    
    Parameters:
    
    setparent - if true then the parent of the S-group is set to the root or that R-group member of this molecule which contains the S-group and the S-group is removed from the old parent molecule.
    
    sg - the S-group to add.
  - 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
  - clearForImport
```
public void clearForImport(java.lang.String fmt)
```
    Clear the edges vector and the properties.
    
    Overrides:
    
    clearForImport in class Molecule
    
    Parameters:
    
    fmt - input file format. See the text formats on the File Formats in Marvin page.
    
    See Also:
    
    MoleculeGraph.theBonds, MoleculeGraph.orix, MoleculeGraph.oriy, MoleculeGraph.oriz, MoleculeGraph.setFlags(int)
  - clearObjects
```
public void clearObjects()
```
    Deletes the graphical objects from this.
    
    Specified by:
    
    clearObjects in interface chemaxon.struc.MObjectContainer
    
    Overrides:
    
    clearObjects in class Molecule
  - clone
```
public RxnMolecule clone()
```
    Make an identical copy of the reaction structure. Document is not cloned!
    
    Overrides:
    
    clone in class Molecule
    
    Returns:
    
    the copy
  - clonecopy
```
public void clonecopy(int[] iatoms,
                      MoleculeGraph g)
```
    Copies the specified nodes and edges of this graph to another one. The RxnMolecule implementation of this method is incomplete.
    
    Overrides:
    
    clonecopy in class Molecule
    
    Parameters:
    
    iatoms - array of atom indices to copy
    
    g - the target graph
    
    Since:
    
    Marvin 5.0.2, 03/11/2008
  - clonecopy
```
public void clonecopy(MoleculeGraph g)
```
    Make another molecule identical to this one.
    
    Overrides:
    
    clonecopy in class Molecule
    
    Parameters:
    
    g - the target structure
  - clonelesscopy
```
@Deprecated
public void clonelesscopy(MoleculeGraph g)
```
    Deprecated. as of Marvin 6.3.
    Not supported feature.
    
    Copy to selection. Make another molecule identical to this one, but do not clone atoms, bonds, and the props.
    
    Overrides:
    
    clonelesscopy in class Molecule
    
    Parameters:
    
    g - the target structure
  - cloneMoleculeWithDocument
```
public RxnMolecule cloneMoleculeWithDocument()
```
    Description copied from class: Molecule
    
    Makes an identical copy of the molecule and its document. If the molecule does not have a parent, then copies non-molecular data: graphics objects, electron flows, text boxes, atom and bond sets (color, font and thickness). Otherwise (root, rgroup, component molecule) creates a new document.
    
    Overrides:
    
    cloneMoleculeWithDocument in class Molecule
    
    Returns:
    
    the copy
  - contains
```
public boolean contains(MolAtom node)
```
    Checks if a reactant, agent or product structure contains the specified node.
    
    Overrides:
    
    contains in class Molecule
    
    Parameters:
    
    node - the node object
    
    Returns:
    
    true if the graph contains the object, false otherwise
  - contains
```
public boolean contains(MolBond edge)
```
    Checks if a reactant, agent or product structure contains the specified edge.
    
    Overrides:
    
    contains in class MoleculeGraph
    
    Parameters:
    
    edge - the edge object
    
    Returns:
    
    true if the graph contains the object, false otherwise
    
    See Also:
    
    Object.equals(Object)
  - createBHtab
```
public int[][] createBHtab()
```
    Creates the graph union's bond table extended with implicit hydrogen atoms.
    
    Overrides:
    
    createBHtab in class MoleculeGraph
    
    Returns:
    
    the chtab array
    
    Since:
    
    Marvin 3.0
  - createCHtab
```
public int[][] createCHtab()
```
    Creates the graph union's connection table extended with implicit hydrogen atoms.
    
    Overrides:
    
    createCHtab in class MoleculeGraph
    
    Returns:
    
    the chtab array
    
    Since:
    
    Marvin 3.0
  - determineType
```
public int determineType(double x,
                         double y,
                         double z)
```
    Determines whether a point should be in a reactant, in a product or in an agent.
    
    Parameters:
    
    x - point x coordinate
    
    y - point y coordinate
    
    z - point z coordinate
    
    Returns:
    
    REACTANTS, PRODUCTS or AGENTS
  - fixProperties
```
public void fixProperties()
```
    Description copied from class: MoleculeGraph
    
    Delegates to tracker's fixProperties().
    
    Overrides:
    
    fixProperties in class MoleculeGraph
  - fuse
```
public void fuse(MoleculeGraph graph,
                 boolean check)
```
    Add the atoms and bonds of another molecule.
    
    Overrides:
    
    fuse in class MoleculeGraph
    
    Parameters:
    
    graph - the other molecule
    
    check - true if a containment check should be performed to ensure that only those nodes and edges are added that are not already elements - false if the graph is known to be disjoint from this graph and this check can be safely skipped
    
    Since:
    
    Marvin 5.0
  - fuse
```
public void fuse(RxnMolecule rxnMol)
```
    Fuse and RxnMolecule to this RxnMolecule. Adds the reactants of the parameter to the reactants, the agents of the parameter to the agents and the products of the parameter to the products.
    
    Parameters:
    
    rxnMol -
    
    Since:
    
    Marvin 6.2, 09/23/2013
  - getAgent
```
public Molecule getAgent(int i)
```
    Gets an agent.
    
    Parameters:
    
    i - agent index
    
    Returns:
    
    an agent
  - getAgentCount
```
public int getAgentCount()
```
    Gets the number of agents.
    
    Returns:
    
    the number of agents
  - getAgents
```
public Molecule[] getAgents()
```
    Gets all agents in an array.
    
    Returns:
    
    the agents
    
    Since:
    
    Marvin 5.3
  - getAllFragments
```
public java.util.List<Molecule> getAllFragments()
```
    Gets the list of reaction fragments (product, reactant, agent components) that build up this reaction.
    
    Returns:
    
    the list of fragments (Molecule)
    
    Since:
    
    Marvin 5.0, 12/06/2007
    
    See Also:
    
    Molecule
  - getAllObjects
```
public java.util.List<MObject> getAllObjects()
```
    Specified by:
    
    getAllObjects in interface chemaxon.struc.MObjectContainer
    
    Overrides:
    
    getAllObjects in class Molecule
  - getArrowAsProperty
```
public MPropertyContainer getArrowAsProperty()
```
    Gets the properties (type, endpoint coordinates) of the reaction arrow in this reaction.
    
    Returns:
    
    the properties
  - getAtom
```
public MolAtom getAtom(int i)
```
    Gets a node.
    
    Overrides:
    
    getAtom in class MoleculeGraph
    
    Parameters:
    
    i - node index
    
    Returns:
    
    the node object
  - getAtomCount
```
public int getAtomCount()
```
    Returns the number of nodes in the graph union.
    
    Specified by:
    
    getAtomCount in interface chemaxon.core.structure.StructureForBuilder
    
    Specified by:
    
    getAtomCount in interface Incomplecule
    
    Overrides:
    
    getAtomCount in class MoleculeGraph
    
    Returns:
    
    the number of nodes
  - getAtomCount
```
public int getAtomCount(int atomicNumber)
```
    Gets the number of atoms with the given atomic number in the unified molecule graph of the reaction. When atomicNumber is 1, sum includes only explicit Hydrogen atoms (but also D and T isotopes).
    
    Overrides:
    
    getAtomCount in class MoleculeGraph
    
    Parameters:
    
    atomicNumber - atomic number of atoms looked for
    
    Returns:
    
    number of atoms with the given atomic number
    
    Since:
    
    Marvin 5.5, 27/01/2011
  - getAtomIterator
```
public IteratorFactory.AtomIterator getAtomIterator()
```
    Returns an iterator over the atoms in this molecule in proper sequence.
    
    Overrides:
    
    getAtomIterator in class MoleculeGraph
    
    Returns:
    
    an iterator over the atoms in this molecule in proper sequencer
    
    Since:
    
    Marvin 6.2, 2013.09.09.
  - getBond
```
public MolBond getBond(int i)
```
    Gets an edge.
    
    Overrides:
    
    getBond in class MoleculeGraph
    
    Parameters:
    
    i - edge index in the graph union
    
    Returns:
    
    the edge object
  - getBondCount
```
public int getBondCount()
```
    Gets the number of edges in the graph union.
    
    Specified by:
    
    getBondCount in interface Incomplecule
    
    Overrides:
    
    getBondCount in class MoleculeGraph
    
    Returns:
    
    the number of edges
  - getBondIterator
```
public IteratorFactory.BondIterator getBondIterator()
```
    Returns an iterator over the bonds in this molecule in proper sequence.
    
    Overrides:
    
    getBondIterator in class MoleculeGraph
    
    Returns:
    
    an iterator over the bonds in this molecule in proper sequence
    
    Since:
    
    Marvin 6.2, 2013.09.09.
  - getBondTable
```
public BondTable getBondTable()
```
    Gets the bond table for the graph union. If there is no bond table for the molecule, then create it. btab.elementAt(i, j) will be the index of the bond between atoms i and j, or -1 if there is no bond.
    
    Overrides:
    
    getBondTable in class MoleculeGraph
    
    Returns:
    
    the btab array
    
    Since:
    
    Marvin 5.4
  - 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
  - getComponent
```
public Molecule getComponent(int typeFlag,
                             int i)
```
    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:
    
    typeFlag - 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
  - 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)
  - 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
  - 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
  - getComponentID
```
public long getComponentID(MolAtom atom)
```
    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 bond)
```
    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
  - getComponentID
```
public long getComponentID(Molecule molecule)
```
    Gets the ID of a reaction component.
    
    Parameters:
    
    mol - the reaction component
    
    Returns:
    
    the reaction component ID or -1 if not found
    
    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
  - 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
  - getCtab
```
public int[][] getCtab()
```
    Gets the connection table for the graph union. If there is no connection table for the molecule, then create it. ctab[i][j] will be the index of the jth neighbor of the ith atom.
    
    Overrides:
    
    getCtab in class MoleculeGraph
    
    Returns:
    
    the ctab array
  - getFormula
```
public java.lang.String getFormula()
```
    Gets the molecular formula in Hill order.
    
    Overrides:
    
    getFormula in class MoleculeGraph
    
    Returns:
    
    the formula
  - getGraphUnion
```
public MoleculeGraph getGraphUnion()
```
    Gets a graph containing all the atoms and bonds.
    
    Overrides:
    
    getGraphUnion in class MoleculeGraph
    
    Returns:
    
    the unified structure
    
    Since:
    
    Marvin 3.0, 11/11/2002
    
    See Also:
    
    Molecule.getGraphUnionAsSelection()
  - getItsArrow
```
public chemaxon.struc.graphics.MRArrow getItsArrow()
```
    Gets the reaction arrow of this reaction. If the arrow is not yet set creates one.
    
    Returns:
    
    the reaction arrow of this reaction
    
    Since:
    
    Marvin 5.0, 12/06/2007
  - getLocalParity
```
public int getLocalParity(int i)
```
    Computes the local parity of an atom of the RxnMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those. The molecule symmetry is not checked, so even an atom with same ligands can have parity. Leaves the imported parity unchanged. Contracted sgroups must be expanded to achieve consistent result.
    
    Overrides:
    
    getLocalParity in class MoleculeGraph
    
    Parameters:
    
    i - the index of the atom whose parity is to be determined
    
    Returns:
    
    PARITY_ODD or PARITY_EVEN for atoms of odd or even parity, PARITY_EITHER for atoms with wiggly bond 0 for atoms whose parity is unspecified or not known.
    
    Throws:
    
    java.lang.SecurityException - the Parity module cannot be loaded because of security reasons (firewall)
    
    See Also:
    
    StereoConstants.PARITY_ODD, StereoConstants.PARITY_EVEN, StereoConstants.PARITY_EITHER, MoleculeGraph.isAbsStereo(), setAbsStereo(boolean), MoleculeGraph.getLocalParity(int)
  - 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
  - getMSLogic
```
@Deprecated
public java.util.Map<chemaxon.struc.graphics.MRArrow,RxnMolecule> getMSLogic()
```
    Deprecated. Multi-step reactions not supported. Method performs no operations.
    
    Multi-step reactions not supported. Method always returns null.
    
    Returns:
    
    returns the hash that stores the mapping.
  - getObjectCount
```
public int getObjectCount()
```
    Specified by:
    
    getObjectCount in interface chemaxon.struc.MObjectContainer
    
    Overrides:
    
    getObjectCount in class Molecule
  - getParity
```
public int getParity(int i)
```
    Computes the parity of an atom of the RxnMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those. Leaves the imported parity unchanged.
    
    Overrides:
    
    getParity in class MoleculeGraph
    
    Parameters:
    
    i - the index of the atom whose parity is to be determined
    
    Returns:
    
    0 for nonchiral, PARITY_ODD or PARITY_EVEN for atoms of odd or even parity, PARITY_ODD|PARITY_EVEN for atoms whose parity is unspecified or cannot be assigned -as they are defined in MolAtom
    
    Throws:
    
    java.lang.SecurityException - the Parity module cannot be loaded because of security reasons (firewall)
    
    See Also:
    
    StereoConstants.PARITY_ODD, StereoConstants.PARITY_EVEN, MoleculeGraph.isAbsStereo(), setAbsStereo(boolean), MoleculeGraph.getParity(int)
  - getProduct
```
public Molecule getProduct(int i)
```
    Gets a product.
    
    Parameters:
    
    i - product index
    
    Returns:
    
    a product
  - getProductCount
```
public int getProductCount()
```
    Gets the number of products.
    
    Returns:
    
    the number of products
  - getProducts
```
public Molecule[] getProducts()
```
    Gets all products in an array.
    
    Returns:
    
    the products
    
    Since:
    
    Marvin 5.3
  - getReactant
```
public Molecule getReactant(int i)
```
    Gets a reactant.
    
    Parameters:
    
    i - reactant index
    
    Returns:
    
    a reactant
  - getReactantCount
```
public int getReactantCount()
```
    Gets the number of reactants.
    
    Returns:
    
    the number of reactants
  - getReactants
```
public Molecule[] getReactants()
```
    Gets all reactants in an array.
    
    Returns:
    
    the reactants
    
    Since:
    
    Marvin 5.3
  - getReactionArrow
```
public DPoint3[] getReactionArrow()
```
    Gets a two-element array containing the endpoints of the reaction arrow.
    
    Returns:
    
    the arrow
  - getReactionArrow
```
public chemaxon.struc.graphics.MRArrow 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.
  - getReactionArrowList
```
public java.util.List<chemaxon.struc.graphics.MRArrow> getReactionArrowList()
```
    Gets the list of the reaction arrows of this reaction.
    
    Returns:
    
    the list of MRArrow-s
    
    Since:
    
    Marvin 5.0
    
    See Also:
    
    MRArrow
  - 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, RESONANCE, RETROSYNTHETIC, EQUILIBRIUM, 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.RESONANCE or RxnMolecule.TWO_HEADED_SINGLE
    "RETROSYNTHETIC" for arrow type RxnMolecule.RETROSYNTHETIC or RxnMolecule.REGULAR_DOUBLE
    "EQUILIBRIUM" for arrow type RxnMolecule.EQUILIBRIUM or RxnMolecule.TWO_HEADED_DOUBLE
    Since:
    
    Marvin 3.5
  - getReactionSteps
```
public java.util.ArrayList<RxnMolecule> getReactionSteps()
```
    Divides this reaction into simple step reactions if this is a multistep reaction.
    
    Returns:
    
    the list of RxnMolecule-s if this is a multistep reaction empty list otherwise.
    
    Since:
    
    Marvin 5.0
  - getType
```
public int getType(MoleculeGraph selection)
```
    Checks whether the atoms in the selection are all in reactants, products or agents.
    
    Parameters:
    
    selection - the molecule graph containing the selection
    
    Returns:
    
    REACTANTS, PRODUCTS or AGENTS or -1 if not of the same type or there is an atom which is not contained in any component
  - hasAtomSet
```
public boolean hasAtomSet()
```
    Tests whether the molecule graph has atom sets.
    
    Overrides:
    
    hasAtomSet in class Molecule
    
    Returns:
    
    true if there are atom sets, false otherwise
    
    Since:
    
    Marvin 4.0, 03/02/2005
  - hasBondSet
```
public boolean hasBondSet()
```
    Tests whether the molecule graph has atom sets.
    
    Overrides:
    
    hasBondSet in class MoleculeGraph
    
    Returns:
    
    true if there are atom sets, false otherwise
    
    Since:
    
    Marvin 4.0, 03/02/2005
  - indexOf
```
public int indexOf(MolAtom node)
```
    Gets the index of the specified node in the graph union.
    
    Overrides:
    
    indexOf in class MoleculeGraph
    
    Parameters:
    
    node - the node
    
    Returns:
    
    the index, or -1 if not found
    
    Since:
    
    Marvin 2.7
  - indexOf
```
public int indexOf(MolBond edge)
```
    Gets the index of the specified edge in the graph union.
    
    Overrides:
    
    indexOf in class MoleculeGraph
    
    Parameters:
    
    edge - the edge
    
    Returns:
    
    the index, or -1 if not found
    
    Since:
    
    Marvin 2.7
    
    See Also:
    
    Object.equals(Object)
  - isAtom
```
@Deprecated
public boolean isAtom()
```
    Deprecated. As of Marvin 14.7.7, no replacement.
    Not supported feature.
    
    A reaction molecule cannot represent an atom.
    
    Overrides:
    
    isAtom in class MoleculeGraph
    
    Returns:
    
    false
  - isBond
```
@Deprecated
public boolean isBond()
```
    Deprecated. As of Marvin 14.7.7, no replacement.
    Not supported feature.
    
    A reaction molecule cannot represent a bond.
    
    Overrides:
    
    isBond in class MoleculeGraph
    
    Returns:
    
    false
  - 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
  - isIncompleteReaction
```
public boolean isIncompleteReaction()
```
    Check whether the reaction is incomplete or not.
    
    Returns:
    
    true if something is missing, false if it seems to be okay
    
    Since:
    
    Marvin 3.5
  - isMergedComponent
```
public boolean isMergedComponent(MoleculeGraph m)
```
    Check whether given molecule is reaction component with a set of intentionally merged fragments or not.
    
    Parameters:
    
    m - the molecule to check
    
    Returns:
    
    true if merged
  - isQuery
```
public boolean isQuery()
```
    Indicates if the molecule has query features: query atoms or query bonds.
    
    Overrides:
    
    isQuery in class MoleculeGraph
    
    Returns:
    
    true if any of the components has query features
    
    Since:
    
    Marvin 6.0 26/01/2013
    
    See Also:
    
    MolAtom.isQuery(), MolBond.isQuery()
  - isReaction
```
public boolean isReaction()
```
    Checks if the structure represents a reaction or not.
    
    Overrides:
    
    isReaction in class Molecule
    
    Returns:
    
    true
    
    Since:
    
    Marvin 3.0
  - isSingleStepReaction
```
@Deprecated
public boolean isSingleStepReaction()
```
    Deprecated.
    
    Multi-step reactions not supported. Method always returns true.
    
    Returns:
    
    true
  - mergeAtoms
```
@Deprecated
public void mergeAtoms(MolAtom that,
                                   MolAtom node)
```
    Deprecated. As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
    
    Merges bonds of an atom with another atom, then add the atom to the molecule.
    
    Overrides:
    
    mergeAtoms in class Molecule
    
    Parameters:
    
    that - the atom
    
    node - the other atom
  - mergeComponentParts
```
public void mergeComponentParts(MoleculeGraph m,
                                int type,
                                boolean isMergeStored)
                         throws java.lang.IllegalArgumentException
```
    Finds those component parts that are contained in the molecule graph m and creates a new component containing all atoms of m, splitting them from the previous merges.
    
    Parameters:
    
    m - molecule graph that contains atoms of the fragments to merge
    
    type - type of component parts to merge (only parts of components of the same type can be merged)
    
    isMergeStored - if true then merged component remains merged until not splitted intentionnaly
    
    Throws:
    
    java.lang.IllegalArgumentException
    
    See Also:
    
    splitComponentParts(chemaxon.struc.MoleculeGraph, int)
  - newInstance
```
public MoleculeGraph newInstance()
```
    Creates a new RxnMolecule object. The dimension and the origin coordinates will be the same as in the original molecule.
    
    Overrides:
    
    newInstance in class Molecule
    
    Returns:
    
    the new reaction
  - rebuildStructures
```
public 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. Rebuilds the reactant and product vectors accordingly.
  - rebuildStructures
```
public void rebuildStructures(DPoint3[] arw,
                              int art)
```
    Sets the reaction arrow. For each reaction component (reactant or product) determines whether it should be a reactant or a product depending on its the relative position to the reaction arrow. Rebuilds the reactant and product vectors accordingly.
    
    Parameters:
    
    arw - is the new reaction arrow
    
    art - is the new reaction arrow type
  - recalcReactionArrow
```
public void recalcReactionArrow()
```
    Recalculates the coordinates of the reaction arrow from the reactants and products, forced recalculation.
  - regenBonds
```
public void regenBonds()
```
    Regenerate the edge vectors: remove their elements, then put the edge objects from the nodes into it.
    
    Overrides:
    
    regenBonds in class MoleculeGraph
  - removeAll
```
public void removeAll()
```
    Remove all the atoms and bonds from the root structure, and from all the R-groups.
    
    Overrides:
    
    removeAll in class Molecule
  - removeAllBonds
```
public void removeAllBonds()
```
    Removes all bonds from the reactants, products and agents.
    
    Overrides:
    
    removeAllBonds in class Molecule
  - removeAtom
```
public void removeAtom(int iu,
                       int cleanupFlags)
```
    Removes an atom from the reactants, products or agents. This method is for internal use only. Use MoleculeGraph.removeAtom(MolAtom) instead unless you are sure what you are doing.
    
    Overrides:
    
    removeAtom in class Molecule
    
    Parameters:
    
    iu - atom index in the graph union
    
    cleanupFlags - extra clean-up methods
    
    Since:
    
    Marvin 3.1
    
    See Also:
    
    MoleculeGraph.RMCLEANUP_NONE, MoleculeGraph.RMCLEANUP_ALL, MoleculeGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO, Molecule.RMCLEANUP_SGROUPATOMS, Molecule.RMCLEANUP_FROMSGROUPS
  - removeAtom
```
public void removeAtom(MolAtom node,
                       int cleanupFlags)
```
    Removes an atom from the reactants, products or agents. This method is for internal use only. Use MoleculeGraph.removeAtom(MolAtom) instead unless you are sure what you are doing.
    
    Overrides:
    
    removeAtom in class Molecule
    
    Parameters:
    
    node - the atom
    
    cleanupFlags - extra clean-up methods
    
    Since:
    
    Marvin 3.1
    
    See Also:
    
    MoleculeGraph.RMCLEANUP_NONE, MoleculeGraph.RMCLEANUP_ALL, MoleculeGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO, Molecule.RMCLEANUP_SGROUPATOMS, Molecule.RMCLEANUP_FROMSGROUPS
  - removeComponent
```
public Molecule removeComponent(int flags,
                                int i)
```
    Removes 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:
    
    flags - REACTANTS, PRODUCTS or AGENTS, can be combined with RGROUPED
    
    i - reactant, product or agent index
    
    Returns:
    
    the removed reactant, product or agent
    
    Since:
    
    Marvin 4.1, 11/19/2005
  - removeEmptyComponents
```
public void removeEmptyComponents()
```
    Checks all the componentes and removes those that are empty (node count is zero).
  - removeObject
```
public void removeObject(MObject o)
```
    Removes a graphical object from this.
    
    Specified by:
    
    removeObject in interface chemaxon.struc.MObjectContainer
    
    Overrides:
    
    removeObject in class Molecule
    
    Parameters:
    
    o - the graphical object
  - removeReactionArrow
```
public void removeReactionArrow()
```
    Removes the reaction arrow of this reacion.
  - replaceBond
```
@Deprecated
public void replaceBond(MolBond olde,
                                    MolBond newe)
```
    Deprecated. as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and add(MolBond) for adding a new bond to the molecule.
    
    Replaces an edge by another one.
    
    Overrides:
    
    replaceBond in class MoleculeGraph
    
    Parameters:
    
    olde - the old edge
    
    newe - the new edge
    
    Since:
    
    Marvin 4.1, 11/24/2005
  - 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
  - selectAllObjects
```
public void selectAllObjects(boolean s)
```
    Specified by:
    
    selectAllObjects in interface chemaxon.struc.MObjectContainer
    
    Overrides:
    
    selectAllObjects in class Molecule
  - setAbsStereo
```
public void setAbsStereo(boolean c)
```
    Sets the absolute stereoconfiguration flag for all the structures.
    
    Overrides:
    
    setAbsStereo in class MoleculeGraph
    
    Parameters:
    
    c - the absolute stereoconfiguration flag
    
    See Also:
    
    MoleculeGraph.setFlags(int)
  - setAtom
```
@Deprecated
public void setAtom(int iu,
                                MolAtom node)
```
    Deprecated. As of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeAtom(MolAtom) and add(MolAtom) to modify the structure.
    
    Sets the node at the specified index.
    
    Overrides:
    
    setAtom in class MoleculeGraph
    
    Parameters:
    
    iu - node index in the graph union
    
    node - new node reference
  - setBond
```
@Deprecated
public void setBond(int iu,
                                MolBond edge)
```
    Deprecated. as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use MoleculeGraph.removeBond(MolBond) for bond removal and add(MolBond) for adding a new bond to the molecule.
    
    Sets the edge at the specified index.
    
    Overrides:
    
    setBond in class MoleculeGraph
    
    Parameters:
    
    iu - edge index in the graph union
    
    edge - new node reference
  - setDim
```
public void setDim(int d)
```
    Sets the dimension for all the structures.
    
    Overrides:
    
    setDim in class Molecule
    
    Parameters:
    
    d - 0, 2 or 3
    
    See Also:
    
    MoleculeGraph.getFlags()
  - setLocation
```
public void setLocation(DPoint3 p)
```
    Set the origin of the molecule. The MolAtom coordinates are relative to this origin.
    
    Overrides:
    
    setLocation in class MoleculeGraph
    
    Parameters:
    
    p - the origin
    
    See Also:
    
    MoleculeGraph.orix
  - setMSLogic
```
@Deprecated
public void setMSLogic(java.util.Map<chemaxon.struc.graphics.MRArrow,RxnMolecule> ms)
```
    Deprecated. Multi-step reactions not supported. Method performs no operations.
    
    Multi-step reactions not supported. Method performs no operations. Method declaration kept for compatibility reasons.
    
    Parameters:
    
    ms - mapping store.
  - setReactionArrow
```
public void setReactionArrow(DPoint3... points)
```
    Sets the endpoint coordinates of the reaction arrow. Sets the stored reaction arrow to its calculated value if no argument passed.
    
    Parameters:
    
    points - endpoint coordinates of the reaction arrow
    
    Throws:
    
    java.lang.IllegalArgumentException - if argument contains one point only.
  - setReactionArrow
```
public void setReactionArrow(chemaxon.struc.graphics.MRArrow arrow)
```
    Sets the reaction arrow.
    
    Parameters:
    
    arrow -
  - setReactionArrow0
```
public void setReactionArrow0(DPoint3... points)
```
    Sets the reaction arrow. Sets the stored reaction arrow 'arrowPoints' to its calculated value if no argument passed.
    
    Parameters:
    
    points - is the new reaction arrow.
    
    Throws:
    
    java.lang.IllegalArgumentException - if argument contains one point only.
  - setReactionArrowEndPoints
```
public void setReactionArrowEndPoints(DPoint3[] points)
```
    Sets the endpoints of the reaction arrow in this reaction. If the arrow is not yet set creates one with the given endpoint coordinates.
    
    Parameters:
    
    points - the endpoint coordinates of the arrow
    
    Since:
    
    Marvin 5.0, 12/06/2007
  - 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
  - setSgroupParent
```
public 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.
    
    Overrides:
    
    setSgroupParent in class Molecule
    
    Parameters:
    
    a - the atom
    
    sg - the S-group
    
    set - set (true) or unset (false)
    
    Throws:
    
    java.lang.IllegalArgumentException - neither reactants, nor products or agents contain the atom
    
    Since:
    
    Marvin 3.0
  - simplifyIncompleteReactionToMolecule
```
public Molecule simplifyIncompleteReactionToMolecule()
```
    Simplify a reaction to a molecule if possible. If the reaction is incomplete and it only contains one reactant, one product or one agent, then that object is returned. Otherwise, simplification is impossible and this is returned.
    
    Returns:
    
    a reactant, product, agent or this
    
    Since:
    
    Marvin 4.0
    
    See Also:
    
    Molecule.getSimplifiedMolecule()
  - simplifyToMolecule
```
public Molecule simplifyToMolecule()
```
    Simplifies this RxnMolecule by moving the atoms and bonds from the reactants, products, and agents to a Molecule. Clears reactans, products, agents.
    
    Returns:
    
    the simplified molecule
    
    Since:
    
    Marvin 5.0
  - sortBondsAccordingTo
```
public void sortBondsAccordingTo(MolBond[] order)
```
    Sort edges in the same order as they appear in the specified array.
    
    Overrides:
    
    sortBondsAccordingTo in class MoleculeGraph
    
    Parameters:
    
    order - the array
    
    Since:
    
    Marvin 3.5, 09/02/2004
  - splitAllDisconnectedComponents
```
public void splitAllDisconnectedComponents()
```
    Replaces all disconnected reaction components by its connected fragments in the structure array.
    
    Since:
    
    Marvin 5.4, 07/07/2010
    
    See Also:
    
    splitDisconnectedComponent(int, int)
  - splitComponentParts
```
public void splitComponentParts(MoleculeGraph m,
                                int type)
                         throws java.lang.IllegalArgumentException
```
    Finds those component parts that are contained in the molecule graph m and creates separate components from the fragments contained in m, splitting them from the previous merges.
    
    Parameters:
    
    m - molecule graph that contains atoms of the fragments to split
    
    type - type of component parts to merge (only parts of components of the same type can be merged)
    
    Throws:
    
    java.lang.IllegalArgumentException
  - splitDisconnectedComponent
```
public void splitDisconnectedComponent(int type,
                                       int index)
```
    Replaces a disconnected reaction component by its connected fragments in the structure array.
    
    Parameters:
    
    type - is the structure type: REACTANTS, PRODUCTS or AGENTS
    
    index - is the structure index
    
    Since:
    
    Marvin 4.1, 11/19/2005
  - splitDisconnectedComponent
```
public void splitDisconnectedComponent(long id)
```
    Replaces a disconnected reaction component by its connected fragments in the structure array.
    
    Parameters:
    
    id - the reaction component ID
    
    Since:
    
    Marvin 4.1, 11/19/2005
    
    See Also:
    
    splitDisconnectedComponent(int, int)
  - stereoClean
```
public boolean stereoClean()
```
    Reset the wedges of the molecule, based on the actual parity information in 2D remove wedges in 3D. Take care of expanding the molecule if neccessary.
    
    Overrides:
    
    stereoClean in class MoleculeGraph
    
    Returns:
    
    true if succesful
    
    See Also:
    
    MoleculeGraph.stereoClean()
  - toString
```
public java.lang.String toString()
```
    Overrides Object.toString() to ease debugging.
    
    Overrides:
    
    toString in class MoleculeGraph
    
    Returns:
    
    a string representation of the object
  - transform
```
public void transform(CTransform3D t,
                      boolean incg)
```
    Apply a transformation matrix to the atomic coordinates and the reaction arrow.
    
    Overrides:
    
    transform in class Molecule
    
    Parameters:
    
    t - the transformation matrix
    
    incg - increase grinvCC or not
  - updateComponentRoles
```
public void updateComponentRoles()
```
    Updates fragment roles in the molecule. roles are like: - nodes that are sources only: are REACTANTS - nodes that are sinks only: are PRODUCTS - all other nodes: are AGENTS For single step reactions: if the reaction is stored as single step, does nothing. If the single reaction is stored in the hash, transforms it into a single step one.
  - addAtomToFragment
```
protected void addAtomToFragment(MolAtom a)
```
    Adds an atom to a fragment. S-groups are added only if all atoms are already in the molecule.
    
    Overrides:
    
    addAtomToFragment in class Molecule
    
    Parameters:
    
    a - the atom reference
  - checkSgroupConsistency
```
protected void checkSgroupConsistency()
```
    Checks the consistency of S-groups.
    
    Overrides:
    
    checkSgroupConsistency in class Molecule
    
    Throws:
    
    java.lang.RuntimeException - if inconsistency found
    
    Since:
    
    Marvin 5.0, 11/06/2007
  - createGearch
```
protected chemaxon.struc.gearch.MoleculeGraphGearch createGearch()
```
    Overrides:
    
    createGearch in class Molecule
  - fillSelectionMolecule
```
protected void fillSelectionMolecule(SelectionMolecule s)
```
    Adds all atoms and bonds of the root structure and the R-groups to the specified molecule.
    
    Overrides:
    
    fillSelectionMolecule in class Molecule
    
    Parameters:
    
    s - the selection molecule
    
    Since:
    
    Marvin 3.0, 11/05/2002
  - fuse0
```
protected void fuse0(MoleculeGraph graph,
                     boolean check)
```
    Add those nodes and edges of a graph that are not already elements. If the graph has an atom connected to a reactant or product, then also adds the graph to that structure. Handles one connected component.
    
    Overrides:
    
    fuse0 in class Molecule
    
    Parameters:
    
    graph - the structure to fuse into this one
    
    check - true if a containment check should be performed to ensure that only those nodes and edges are added that are not already elements - false if the graph is known to be disjoint from this graph and this check can be safely skipped
    
    Since:
    
    Marvin 5.0
  - getSubGraphCount
```
protected final int getSubGraphCount()
```
    Gets the number of all "submolecules".
    
    Overrides:
    
    getSubGraphCount in class MoleculeGraph
    
    Returns:
    
    the number of submolecules
    
    Since:
    
    Marvin 4.1.2
    
    See Also:
    
    MoleculeGraph.getSubGraphs(MoleculeGraph[], int)
  - getSubGraphs
```
protected final void getSubGraphs(MoleculeGraph[] arr,
                                  int off)
```
    Gets all "submolecules".
    
    Overrides:
    
    getSubGraphs in class MoleculeGraph
    
    Parameters:
    
    arr - the output array
    
    off - offset
    
    Since:
    
    Marvin 4.1.2
    
    See Also:
    
    MoleculeGraph.getSubGraphs(), MoleculeGraph.getSubGraphCount()
  - isRealAtomParent
```
protected boolean isRealAtomParent()
```
    Reaction molecules cannot be real node parents.
    
    Overrides:
    
    isRealAtomParent in class MoleculeGraph
    
    Returns:
    
    false
    
    Since:
    
    Marvin 3.0
  - makeItSimilar
```
protected void makeItSimilar(MoleculeGraph g)
```
    Copies some properties of this molecule to the other one specified as argument. Copies the reaction arrow.
    
    Overrides:
    
    makeItSimilar in class Molecule
    
    Parameters:
    
    g - the molecule to change
  - removeBond
```
protected void removeBond(int iu,
                          int cleanupFlags)
```
    Removes an edge from a reactant, agent or product.
    
    Overrides:
    
    removeBond in class Molecule
    
    Parameters:
    
    iu - edge index in the graph union
    
    cleanupFlags - extra clean-up methods
    
    Since:
    
    Marvin 3.1
    
    See Also:
    
    MoleculeGraph.RMCLEANUP_NONE, MoleculeGraph.RMCLEANUP_ALL, MoleculeGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO, Molecule.RMCLEANUP_SGROUPATOMS, Molecule.RMCLEANUP_FROMSGROUPS
  - removeBond
```
protected void removeBond(MolBond edge,
                          int cleanupFlags)
```
    Removes a bond from the reactants, products or agents.
    
    Overrides:
    
    removeBond in class Molecule
    
    Parameters:
    
    edge - the edge
    
    cleanupFlags - extra clean-up methods
    
    Since:
    
    Marvin 3.1
    
    See Also:
    
    MoleculeGraph.RMCLEANUP_NONE, MoleculeGraph.RMCLEANUP_ALL, MoleculeGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO, Molecule.RMCLEANUP_SGROUPATOMS, Molecule.RMCLEANUP_FROMSGROUPS
  - setSupergraph
```
protected void setSupergraph(MoleculeGraph molecule)
```
    Sets the given molecule as the supergraph of this graph and its components.
    
    Overrides:
    
    setSupergraph in class MoleculeGraph
    
    Parameters:
    
    molecule - the molecule
    
    Since:
    
    Marvin 14.7.7, Jul 2, 2014
  - transformReactionArrow
```
protected void transformReactionArrow(CTransform3D t)
```
    Apply a transformation matrix to the reaction arrow.
    
    Parameters:
    
    t - the transformation matrix

Class RxnMolecule

Property Summary

Properties inherited from class chemaxon.struc.MoleculeGraph

Nested Class Summary

Nested classes/interfaces inherited from class chemaxon.struc.MoleculeGraph

Field Summary

Fields inherited from class chemaxon.struc.Molecule

Fields inherited from class chemaxon.struc.MoleculeGraph

Fields inherited from interface chemaxon.struc.StereoConstants

Constructor Summary

Method Summary

Methods inherited from class chemaxon.struc.Molecule

Methods inherited from class chemaxon.struc.MoleculeGraph

Methods inherited from class java.lang.Object

Field Detail

TYPE_COUNT

REACTANTS

PRODUCTS

AGENTS

RGROUPED

TYPE_MASK

REGULAR_SINGLE

TWO_HEADED_SINGLE

REGULAR_DOUBLE

TWO_HEADED_DOUBLE

RESONANCE

RETROSYNTHETIC

EQUILIBRIUM

Constructor Detail

RxnMolecule

Method Detail

createReaction

createReaction

determineArrowDistance

determineType

getReaction

add

add

addComponent

addComponent

addReactionStep

addSgroup

canBeReactionComponent

clearForImport

clearObjects

clone

clonecopy

clonecopy

clonelesscopy

cloneMoleculeWithDocument

contains

contains

createBHtab

createCHtab

determineType

fixProperties

fuse

fuse

getAgent

getAgentCount

getAgents

getAllFragments

getAllObjects

getArrowAsProperty

getAtom

getAtomCount

getAtomCount

getAtomIterator

getBond

getBondCount

getBondIterator

getBondTable

getCenter

getComponent

getComponent

getComponentCount

getComponentFlags

getComponentID

getComponentID

getComponentID