Package chemaxon.struc

Class RxnMolecule

java.lang.Object

chemaxon.struc.MoleculeGraph

chemaxon.struc.Molecule

chemaxon.struc.RxnMolecule

All Implemented Interfaces:

MoleculeWithValence<MolAtom>, chemaxon.core.structure.MoleculeForBuilder, chemaxon.core.structure.ReactionForBuilder, chemaxon.struc.MObjectContainer, MTransformable, StereoConstants, Serializable

@PublicApi
public class RxnMolecule
extends Molecule
implements chemaxon.struc.MObjectContainer, chemaxon.core.structure.ReactionForBuilder

Reaction.

Since:

Marvin 2.9

See Also:

• Serialized Form

Nested Class Summary

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

MoleculeGraph.ValenceCheckState

Field Summary

Fields

Modifier and Type	Field	Description
static final int	AGENTS	"Agent" structure type.
static final int	EQUILIBRIUM	Resonance arrow, the same as the two-headed double reaction arrow.
static final int	PRODUCTS	"Product" structure type.
static final int	REACTANTS	"Reactant" structure type.
static final int	REGULAR_DOUBLE	Regular double reaction arrow type.
static final int	REGULAR_SINGLE	Regular single reaction arrow type.
static final int	RESONANCE	Resonance arrow, the same as the two-headed single reaction arrow.
static final int	RETROSYNTHETIC	Retrosynthetic arrow, the same as the regular double reaction arrow.
static final int	RGROUPED	Add R-groups to component structure.
static final int	TWO_HEADED_DOUBLE	Two headed double reaction arrow type.
static final int	TWO_HEADED_SINGLE	Two headed single reaction arrow type.
static final int	TYPE_COUNT	Number of structure types.
static final 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_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	Description
RxnMolecule()	Create a reaction.

Method Summary

Modifier and Type	Method	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	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(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.
protected chemaxon.struc.gearch.MoleculeGraphGearch	createGearch()
static RxnMolecule	createReaction(MoleculeGraph mol, DPoint3[] arw)	Creates a reaction.
static RxnMolecule	createReaction(Molecule mol, DPoint3[] arw, int art)	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.
List<Molecule>	getAllFragments()	Gets the list of reaction fragments (product, reactant, agent components) that build up this reaction.
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.
String	getFormula()	Gets the molecular formula in Hill order.
MoleculeGraph	getGraphUnion()	Gets a graph containing all the atoms and bonds.
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.
Map<MRArrow,RxnMolecule>	getMSLogic()	Deprecated, for removal: This API element is subject to removal in a future version. Multi-step reactions not supported.
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.
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.
List<MRArrow>	getReactionArrowList()	Gets the list of the reaction arrows of this reaction.
int	getReactionArrowType()	Gets the reaction arrow type.
String	getReactionArrowTypeName()	Gets the reaction arrow type name.
protected final int	getSubGraphCount()	Gets the number of all "submolecules".
protected final 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, for removal: This API element is subject to removal in a future version.
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, for removal: This API element is subject to removal in a future version. 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, for removal: This API element is subject to removal in a future version. as of Marvin 6.2, may constructs inconsistent MoleculeGraph.
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.
void	setBond(int iu, MolBond edge)	Deprecated. as of Marvin 6.2, may constructs inconsistent MoleculeGraph.
void	setDim(int d)	Sets the dimension for all the structures.
void	setLocation(DPoint3 p)	Set the origin of the molecule.
void	setMSLogic(Map<MRArrow,RxnMolecule> ms)	Deprecated, for removal: This API element is subject to removal in a future version. Multi-step reactions not supported.
void	setReactionArrow(DPoint3... points)	Sets the endpoint coordinates of the reaction arrow.
void	setReactionArrow(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(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.
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, 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 Details

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 Details

RxnMolecule

public RxnMolecule()

Create a reaction.

Method Details

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 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:

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 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:

IllegalArgumentException - if m is of a subclass of Molecule for which the embedding in an RxnMolecule is not supported

addSgroup

public void addSgroup(Sgroup sg,
 boolean setparent)

Adds an S-group to this object.

Overrides:

addSgroup in class Molecule

Parameters:

sg - the S-group to add.

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.

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(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)

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.

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 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 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.

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.

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:

atom - 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:

bond - 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:

molecule - 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 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 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:

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(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2025)
public Map<MRArrow,RxnMolecule> getMSLogic()

Deprecated, for removal: This API element is subject to removal in a future version.

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:

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 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 List<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 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

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
@SubjectToRemoval(date=JUL_01_2025)
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
@SubjectToRemoval(date=JUL_01_2025)
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(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2025)
public boolean isSingleStepReaction()

Deprecated, for removal: This API element is subject to removal in a future version.

Multi-step reactions not supported. Method always returns true.

Returns:

true

mergeAtoms

@Deprecated(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2025)
public void mergeAtoms(MolAtom that,
 MolAtom node)

Deprecated, for removal: This API element is subject to removal in a future version.

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 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:

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(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2025)
public void replaceBond(MolBond olde,
 MolBond newe)

Deprecated, for removal: This API element is subject to removal in a future version.

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(forRemoval=true)
@SubjectToRemoval(date=JUL_01_2025)
public void setMSLogic(Map<MRArrow,RxnMolecule> ms)

Deprecated, for removal: This API element is subject to removal in a future version.

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:

IllegalArgumentException - if argument contains one point only.

setReactionArrow

public void setReactionArrow(MRArrow arrow)

Sets the reaction 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:

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(String name)

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

Parameters:

name - the reaction arrow type name

Throws:

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:

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 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:

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 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)

Description copied from class: Molecule

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:

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