chemaxon.struc
Class RgMolecule

java.lang.Object
  chemaxon.struc.MoleculeGraph
      chemaxon.struc.Molecule
          chemaxon.struc.RgMolecule

All Implemented Interfaces:

Incomplecule, chemaxon.struc.MObjectContainer, MTransformable, chemaxon.struc.RgMoleculeGraphIface, StereoConstants, java.io.Serializable

public class RgMolecule
extends Molecule
implements chemaxon.struc.RgMoleculeGraphIface, chemaxon.struc.MObjectContainer

A molecule or reaction containing R-groups.

Since:

Marvin 2.6

Version:

5.3, 10/07/2009

Author:

Peter Csizmadia, Szilveszter Juhos

See Also:

Serialized Form

Field Summary

static int	RG_ID_MASK R-group id mask in R-logic.
static int	RG_ID2_FLAG Other R-group ID's presence flag in R-logic.
static int	RG_ID2_MASK Mask of the other R-group's id in R-logic.
static int	RG_ID2_OFF Offset of the other R-group's id in R-logic.
static int	RG_RESTH The RestH flag in R-logic.

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_CHEMAXON, AROM_DAYLIGHT, 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

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_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, ENDO, EXO, PARITY_ALLENE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_ODD, PARITY_TETRAHEDRAL, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, SYN, TRANS

Constructor Summary

RgMolecule()
Creates a 2 dimensional RgMolecule.

Method Summary

void	add(MolAtom node) Adds an atom to the root structure.
void	add(MolBond edge) Adds a bond to the root structure.
int	addRgroup(int rl, Molecule m) Adds an R-group member.
RgMolecule	addRgroupsTo(Molecule m) Creates a read only RgMolecule from a simple molecule object.
void	aromatize(int method) Aromatizes molecule.
void	aromatize(int method, boolean checkAmbiguity) Aromatizes molecule.
boolean	canBeReactionComponent() Tests whether an object of this class can be a reaction component.
void	checkConsistency() Deprecated.
java.lang.String	checkRlogicRange(int index, java.lang.String range) Checks an R-logic occurence range string for syntax errors and returns a "normalized" string.
protected void	checkSgroupConsistency() Deprecated.
void	cleanupRemovedRgroupMember(MoleculeGraph m, int f) Clean-up after R-group removal.
void	clearForImport(java.lang.String fmt) Clear the edges vector and the properties.
void	clearObjects() Removes all MObjects that belong to a chemical structure.
void	clonecopy(int[] iatoms, MoleculeGraph g) Copies the specified atoms of this graph to another one.
void	clonecopy(MoleculeGraph g) Make another molecule identical to this one.
void	clonelesscopy(MoleculeGraph g) Copy to selection.
Molecule	cloneMolecule() Make an identical copy of the molecule.
boolean	contains(MolAtom node) Checks if the root structure or an R-group contains the specified node.
boolean	contains(MolBond edge) Checks if the root structure or an R-group contains the specified edge.
protected chemaxon.struc.gearch.MoleculeGraphGearch	createGearch()
static Molecule	createMol(java.lang.String fmt) Deprecated. As of Marvin 3.4, MolImportModule.createMol() must be used.
void	endReuse(int n) End reusing atoms.
protected void	fillSelectionMolecule(SelectionMolecule s) Adds all atoms and bonds of the root structure and the R-groups to the specified molecule.
int	findRgroupIndex(int rgid) Finds R-group R#.
protected boolean	fixSelfReferringProperty(MProp prop) Fix a property containing reference to the molecule.
void	fuse(MoleculeGraph g, boolean check) Add the atoms and bonds of another molecule.
protected void	fuse0(MoleculeGraph graph, boolean check) Add those nodes and edges of a graph that are not already elements.
java.util.List<MObject>	getAllObjects() Gets all MObjects that belong to a chemical structure.
MolAtom	getAtom(int i) Gets a node in the graph union.
int	getAtomCount() Gets the number of nodes in the root structure.
int	getAtomCount(int atomicNumber) Gets the number of atoms with the given atomic number in the root structure.
MolBond	getBond(int i) Gets an edge in the graph union.
int	getBondCount() Gets the number of edges in the root structure.
chemaxon.core.util.BondTable	getBondTable() Gets the bond table of the root structre.
int[][]	getBtab() Deprecated. as of Marvin 5.4, please use getBondTable() instead
java.lang.String	getComment() Gets the comment of the root molecule.
int[][]	getCtab() Gets the connection table of the root structure.
protected MDocument	getDocumentForChild(MoleculeGraph g) Gets the parent document for a child graph.
int	getFlags() Gets the dimension and chiral flags.
java.lang.String	getFormula() Gets the molecular formula in Hill order.
MoleculeGraph	getGraphUnion() Gets a graph containing all the atoms and bonds.
int	getLocalParity(int i) Computes the local parity of an atom of the RgMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
int	getLonePairCount(int i) Gets the number of lone pairs.
double	getMass() Calculates the molecular weight of the molecule.
int	getMaxAttachmentPointOrder(int rgroupID) Gets the maximal attachment point order of R-group definition molecules specified by an R-group ID.
protected Molecule	getMostSimplifiedMolecule() Gets the simplified molecule object even if there is a parent document with other objects.
java.lang.String	getName() Gets the name of the root molecule.
int	getObjectCount() Returns the count of the MObjects that belong to a chemical structure.
int	getParity(int i) Computes the parity of an atom of the RgMolecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
int	getRgroupCount() Gets the number of R-groups.
int	getRgroupId(int i) Gets the ID of an R-group.
int	getRgroupIndex(long id) Gets the R-group index from the R-group member ID.
Molecule	getRgroupMember(int i, int j) Gets an R-group member.
int	getRgroupMemberCount(int i) Gets the number of R-group members.
MoleculeGraph	getRgroupMemberG(int i, int j) Gets an R-group member.
long	getRgroupMemberID(MolAtom node) Gets the unique indentifier of the R-group member that contains the specified atom.
int	getRgroupMemberIndex(long id) Gets the R-group member index from the R-group member ID.
int	getRlogic(int i) Gets R-logic flags.
java.lang.String	getRlogicRange(int i) Gets R-logic occurence range.
Molecule	getRoot() Gets the root structure.
MoleculeGraph	getRootG() Gets the root structure.
protected int	getSubGraphCount() Gets the number of all "submolecules".
protected void	getSubGraphs(MoleculeGraph[] arr, int off) Gets all "submolecules".
boolean	hasAtomSet() Tests whether the molecule graph has atom sets.
boolean	hasBondSet() Tests whether the molecule graph has atom sets.
boolean	hasRgroupContainedBy(java.util.Set set) Tests whether the molecule has an R-group that is a subset of the specified set of atoms.
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.
protected void	insertNullAtoms(int i, int count) Insert nulls into the atom array.
protected void	insertNullBonds(int i, int count) Insert nulls into the bond array.
boolean	isAtom() Determines whether the structure represents only one atom and an arbitrary number of bonds.
boolean	isBond() Determines whether the structure represents only one bond and zero or two atoms.
boolean	isEmpty() Ask if the molecule is empty or not.
boolean	isIncompleteReaction() Check whether the reaction is incomplete or not.
boolean	isQuery() Indicates if the molecule has query features.
boolean	isReaction() Checks if the structure represents a reaction or not.
protected boolean	isRealAtomParent() R-group molecule objects cannot be real node parents.
boolean	isSelfReference(MProp p) Tests whether the specified property is a self reference to the molecule.
protected void	makeItSimilar(MoleculeGraph g) Copies some properties of this molecule to the other one specified as argument.
void	mergeAtoms(MolAtom that, MolAtom a) Merges bonds of an atom with another atom, then add the atom to the molecule.
MoleculeGraph	newInstance() Creates a new RgMolecule object.
SelectionMolecule	newSelectionMolecule() Creates a new SelectionMolecule object appropriate for storing selection from this molecule.
MPropertyContainer	properties() Gets the property container.
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() Remove all bonds from the root structure, and from all the R-groups.
void	removeAtom(int i, int cleanupFlags) Removes an atom and its bonds from the root structure.
void	removeAtom(MolAtom node, int cleanupFlags) Removes an atom and its bonds from the root structure and from all the R-groups.
protected void	removeBond(int i, int cleanupFlags) Remove a bond from the root structure.
protected void	removeBond(MolBond edge, int cleanupFlags) Remove a bond from the root structure, and from all the R-groups.
void	removeObject(MObject mo) Removes an MObject that belongs to a chemical structure.
void	replaceAtomsWithNewRgroup(SelectionMolecule sel, int rgid) Replaces selected atoms with a new R-group.
void	replaceBond(MolBond olde, MolBond newe) Replaces an edge by another one.
MolAtom	reuseAtom(int z, int i) Reuse an atom or create a new one.
void	revalidateCoordDependentProps() Revalidate coordinate dependent properties.
int	rgroupIdOf(MolAtom node) Finds the ID of the R-group (the number in R#) that contains the specified atom.
int	rgroupIndexOf(MolAtom node) Finds the index of the R-group (the number in R#) that contains the specified atom.
void	selectAllObjects(boolean s) Selects or deselects all MObjects that belong to a chemical structure.
void	setAbsStereo(boolean c) Sets the absolute stereoconfiguration flag for the root structure and the R-groups.
void	setAbsStereo(boolean c, int i, int j) Deprecated. as of Marvin 5.1.1, please call MoleculeGraph.setAbsStereo(boolean) for the component
void	setAtom(int iu, MolAtom node) Sets the node at the specified index in the graph union.
void	setBond(int iu, MolBond edge) Sets the edge at the specified index in the graph union.
void	setComment(java.lang.String s) Sets the comment of the root molecule.
void	setDim(int d) Sets the dimension of the root structure and the R-groups.
protected void	setFlags(int f) Sets the dimension and chiral flags.
protected void	setFlags(int f, int mask) Sets specified bits in the flags.
void	setInputFormat(java.lang.String format) Sets the input file format.
void	setLocation(DPoint3 p) Set the origin of the molecule.
void	setName(java.lang.String s) Sets the name of the root molecule.
void	setRlogic(int i, int f) Sets R-logic flags.
void	setRlogicRange(int index, java.lang.String range) Sets R-logic occurence range.
void	setRoot(Molecule mol) Sets the root structure.
void	setSgroupParent(MolAtom a, Sgroup sg, boolean set) Sets or unsets an S-group as a parent of an atom in the root structure or an R-group.
void	sortBondsAccordingTo(MolBond[] order) Sort edges in the same order as they appear in the specified array.
boolean	stereoClean() Reset the wedges of the molecule, based on the actual parity information in 2D remove wedges in 3D.
protected void	sumConservedQuantities(MolAtom a, int[] atoms, int sign) For internal use only.
java.lang.String	toString() Overrides Object.toString() to ease debugging.
void	transform(CTransform3D t, boolean incg) Apply a transformation matrix to the atomic coordinates.
int	unRgroupAtoms(java.util.Set set) Ungroup R-groups consisting of the specified atoms and make the be part of root.

Methods inherited from class chemaxon.struc.Molecule

addAtom0, addAtomToFragment, addBond0, addSgroup, addSgroupClones, addSgroupsOf, bondlength, clear, clearExtraLabels, clearProperties, clone, clonecopyWithoutSgroups, cloneMoleculeWithDocument, contractSgroups, convertToFrags, countExpandableContractableSgroups, countOrderedComponentSgroups, dearomatize, expandSgroups, expandSgroups, exportToBinFormat, exportToFormat, exportToObject, exportToObject, findAllSgroupContaining, findContainingMulticenterSgroup, findContractableSgroup, findExpandableSgroup, findFrags, findSgroupContaining, findSgroupOf, findSmallestSgroupContaining, getEndPosition, getGraphUnionAsSelection, getImageSize, getInputFormat, getProperty, getPropertyCount, getPropertyKey, getPropertyKeys, getPropertyObject, getRootSgroups, getSgroup, getSgroupArray, getSgroupCount, getSgroupLigands, getSimplifiedMolecule, getSortedSgroups, getStartPosition, getVisibleCoords, implicitizeHydrogens0, indexOf, isExpandable, isGUIContracted, isMolecule, isSgroup, mergeFrags, removeAllSgroups, removeSgroupFromList, removeSgroupsOf, removeSgroupsOf, reparentSgroups, replaceSgroup, residueSymbolOf, residueTypeOf, setAtom0, setEndPosition, setGUIContracted, setGUIContracted, setProperty, setPropertyObject, setStartPosition, sortSgroupXBonds, toBinFormat, toFormat, toObject, ungroupSgroup, ungroupSgroup, ungroupSgroup, ungroupSgroup, ungroupSgroups, ungroupSgroups

Methods inherited from class chemaxon.struc.MoleculeGraph

addAtomsAndBondsTo, addAtomWithoutChangingIt, addBondWithoutChangingIt, addExplicitHydrogens, addExplicitHydrogens, addExplicitLonePairs, adjustMultiChiralFlag, aromatize, aromatize, arrangeComponents, calcCenter, calcCenter, calcDehydrogenizedGrinv, calcHeight, calcHybridization, calcOutRect, calcOutRect, calcOutRectCenter, calcOutRectCenter, calcWidth, canBeCT, canBeCT, canBeCT, checkBondConsistency, clean, clean, clearCachedInfo, clonecopyMoleculeGraphWithoutSgroups, contains, createBHtab, createCHtab, createDehydrogenizedReadOnlyGraph, createSmolecule, dearomatize, findAtom, findAtomClone, findBasicFrags, findBond, findComponentIds, findComponentIds, findFrag, findFrag, findFragById, findFragById, findFrags, findFrags, findInArray, fuse, getAromaticAndAliphaticRings, getAromrings, getAromrings, getAtomArray, getBondArray, getBonds, getChirality, getCSSR, getDesiredLength, getDesiredLength, getDim, getDocument, getEdge, getEdgeArray, getEdgeCount, getEdgeVector, getEnclosingCube, getExactMass, getExplicitHcount, getExplicitLonePairCount, getForefather, getFormalCharge, getFragCount, getFragCount, getFragIds, getFragIds, getGrinv, getGrinv, getGrinv, getGrinv, getGrinvCC, getGrinvOptions, getImplicitHcount, getLocation, getLock, getMaxRgroupAttachmentPointOrder, getNode, getNodeCount, getNodeVector, getNonAromrings, getNonAromrings, getParent, getParentDocument, getParityType, getPoints, getSmallestRingSizeForIdx, getSSSR, getSSSRBonds, getSSSRBondSet, getSSSRBondSetInLong, getSSSRIdxesForAtoms, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getSubGraphs, getTotalCharge, hasExplicitLonePairs, hasExtraLabelSet, hasImplicitH, hasSelfReferringProperty, hasValenceError, hydrogenize, implicitizeHydrogens, implicitizeHydrogens, implicitizeHydrogens, incGrinvCC, incGrinvCCOnly, insertAtom, insertBond, insertBondInOrder, insertEdge, insertEdgeInOrder, insertNode, isAbsStereo, isGrinvCCValid, isLargeMolecule, isMultiChiral, isolate, isolate, isOnlyFirstAtomInStereoCalculation, isRing, isRingBond, isSimilarTo, isSymmetric, isValenceCheckEnabled, isValidLinkNode, mergeFrags, mergeFrags, mergeNodes, moveTo, pack, partialClean, partialClean, partialClean, qpropCheck, regenCtabs, regenEdges, regenGearch, removeAllEdges, removeAtom, removeAtom, removeBond, removeBond, removeEdge, removeEdge, removeExplicitLonePairs, removeIsolatedAtoms, removeIsolatedBonds, removeNode, removeNode, removeNode, removeNode, replaceEdge, resetCtab, resetGrinvInParents, restoreCache, saveCache, setAtomSetSeqs, setBondSetSeqs, setChirality, setEdge, setGrinvCC, setGrinvOptions, setLinkNodeDefaultOuters, setLocalParity, setLocalParity, setNode, setParity, setParity, setParity, setSetSeqs, setValenceCheckEnabled, smol, sortEdgesAccordingTo, transform, updateDim, useOnlyFirstAtomInStereoCalculation, valenceCheck, valenceCheck

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

RG_ID_MASK

public static final int RG_ID_MASK

R-group id mask in R-logic.

See Also:

getRlogic(int), setRlogic(int, int), Constant Field Values

RG_ID2_FLAG

public static final int RG_ID2_FLAG

Other R-group ID's presence flag in R-logic.

See Also:

getRlogic(int), setRlogic(int, int), Constant Field Values

RG_ID2_OFF

public static final int RG_ID2_OFF

Offset of the other R-group's id in R-logic.

See Also:

getRlogic(int), setRlogic(int, int), Constant Field Values

RG_ID2_MASK

public static final int RG_ID2_MASK

Mask of the other R-group's id in R-logic.

See Also:

getRlogic(int), setRlogic(int, int), Constant Field Values

RG_RESTH

public static final int RG_RESTH

The RestH flag in R-logic.

See Also:

getRlogic(int), setRlogic(int, int), Constant Field Values

Constructor Detail

RgMolecule

public RgMolecule()

Creates a 2 dimensional RgMolecule.

Method Detail

setRoot

public void setRoot(Molecule mol)

Sets the root structure.

Parameters:

mol - the root structure

getRoot

public Molecule getRoot()

Gets the root structure.

Returns:

the root

getRootG

public final MoleculeGraph getRootG()

Gets the root structure.

Specified by:

getRootG in interface chemaxon.struc.RgMoleculeGraphIface

Returns:

the root

getRgroupCount

public int getRgroupCount()

Gets the number of R-groups.

Specified by:

getRgroupCount in interface chemaxon.struc.RgMoleculeGraphIface

Returns:

number of R-groups

getRgroupMemberCount

public int getRgroupMemberCount(int i)

Gets the number of R-group members.

Specified by:

getRgroupMemberCount in interface chemaxon.struc.RgMoleculeGraphIface

Parameters:

i - R-group index

Returns:

number of R-group members

getRgroupMember

public Molecule getRgroupMember(int i,
                                int j)

Gets an R-group member.

Parameters:

i - R-group index

j - member index

Returns:

the R-group member

getRgroupMemberG

public final MoleculeGraph getRgroupMemberG(int i,
                                            int j)

Gets an R-group member.

Specified by:

getRgroupMemberG in interface chemaxon.struc.RgMoleculeGraphIface

Parameters:

i - R-group index

j - member index

Returns:

the R-group member

getRgroupId

public int getRgroupId(int i)

Gets the ID of an R-group.

Specified by:

getRgroupId in interface chemaxon.struc.RgMoleculeGraphIface

Parameters:

i - R-group index

Returns:

number between 0 and MolAtom.RGROUP_MAX

findRgroupIndex

public int findRgroupIndex(int rgid)

Finds R-group R#.

Specified by:

findRgroupIndex in interface chemaxon.struc.RgMoleculeGraphIface

Parameters:

rgid - number between 0 and MolAtom.RGROUP_MAX

Returns:

R-group index, or -1 if not found

addRgroup

public int addRgroup(int rl,
                     Molecule m)

Adds an R-group member.

Parameters:

rl - R-logic flags or an R-group ID number between 0 and MolAtom.RGROUP_MAX

m - the R-group

Returns:

the Rgroup index

hasRgroupContainedBy

public boolean hasRgroupContainedBy(java.util.Set set)

Tests whether the molecule has an R-group that is a subset of the specified set of atoms.

Parameters:

set - set of atoms

Since:

5.0, 02/24/2007

unRgroupAtoms

public int unRgroupAtoms(java.util.Set set)

Ungroup R-groups consisting of the specified atoms and make the be part of root.

Parameters:

set - selected atoms

Returns:

the number of ungrouped R-group members

Since:

5.0, 02/24/2007

replaceAtomsWithNewRgroup

public void replaceAtomsWithNewRgroup(SelectionMolecule sel,
                                      int rgid)

Replaces selected atoms with a new R-group.

Parameters:

sel - selected atoms

rgid - R-group ID

Since:

4.0, 06/30/2005

getRlogic

public int getRlogic(int i)

Gets R-logic flags.

Specified by:

getRlogic in interface chemaxon.struc.RgMoleculeGraphIface

Parameters:

i - R-group index

Returns:

R-logic flags

See Also:

RG_ID_MASK, RG_ID2_FLAG, RG_ID2_OFF, RG_ID2_MASK, RG_RESTH

setRlogic

public void setRlogic(int i,
                      int f)

Sets R-logic flags.

Parameters:

i - R-group index

f - R-logic flags

See Also:

RG_ID_MASK, RG_ID2_FLAG, RG_ID2_OFF, RG_ID2_MASK, RG_RESTH

getRlogicRange

public java.lang.String getRlogicRange(int i)

Gets R-logic occurence range.

Specified by:

getRlogicRange in interface chemaxon.struc.RgMoleculeGraphIface

Parameters:

i - R-group index

Returns:

the occurence range

setRlogicRange

public void setRlogicRange(int index,
                           java.lang.String range)
                    throws java.lang.IllegalArgumentException

Sets R-logic occurence range.

Parameters:

index - R-group index

range - range of occurance

Throws:

java.lang.IllegalArgumentException - bad occurence range

checkRlogicRange

public java.lang.String checkRlogicRange(int index,
                                         java.lang.String range)
                                  throws java.lang.IllegalArgumentException

Checks an R-logic occurence range string for syntax errors and returns a "normalized" string.

Parameters:

index - R-group index

range - range of occurance

Returns:

the normalized occurence range string

Throws:

java.lang.IllegalArgumentException - bad occurence range

Since:

Marvin 3.4

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)

setName

public void setName(java.lang.String s)

Sets the name of the root molecule.

Overrides:

setName in class Molecule

Parameters:

s - the molecule name, empty string or null (null is equivalent to empty string)

getName

public java.lang.String getName()

Gets the name of the root molecule.

Specified by:

getName in interface Incomplecule

Overrides:

getName in class Molecule

Returns:

the molecule name or an empty string

setComment

public void setComment(java.lang.String s)

Sets the comment of the root molecule.

Overrides:

setComment in class Molecule

Parameters:

s - the comment, empty string or null (null is equivalent to empty string)

getComment

public java.lang.String getComment()

Gets the comment of the root molecule.

Overrides:

getComment in class Molecule

Returns:

the comment or empty string

properties

public MPropertyContainer properties()

Gets the property container.

Specified by:

properties in interface Incomplecule

Overrides:

properties in class MoleculeGraph

Returns:

the property container

Since:

Marvin 4.0, 06/20/2005

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

setInputFormat

public void setInputFormat(java.lang.String format)

Sets the input file format.

Overrides:

setInputFormat in class Molecule

Parameters:

format - the input format

See Also:

Molecule.getInputFormat()

reuseAtom

public MolAtom reuseAtom(int z,
                         int i)

Reuse an atom or create a new one. If an atom is reused, all its properties except the corners are initialized.

Overrides:

reuseAtom in class Molecule

Parameters:

z - atomic number

i - atom index

Returns:

the new or old atom

endReuse

public void endReuse(int n)

End reusing atoms.

Overrides:

endReuse in class Molecule

Parameters:

n - number of atoms

Since:

Marvin 2.6

getCtab

public int[][] getCtab()

Gets the connection table of the root structure. 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

getBtab

public int[][] getBtab()

Deprecated. as of Marvin 5.4, please use getBondTable() instead

Gets the bond table of the root structre. If there is no bond table for the molecule, then create it. btab[i][j] will be the index of the bond between atoms i and j, or -1 if there is no bond.

Overrides:

getBtab in class MoleculeGraph

Returns:

the btab array

getBondTable

public chemaxon.core.util.BondTable getBondTable()

Gets the bond table of the root structre. 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

rgroupIdOf

public int rgroupIdOf(MolAtom node)

Finds the ID of the R-group (the number in R#) that contains the specified atom.

Specified by:

rgroupIdOf in interface chemaxon.struc.RgMoleculeGraphIface

Parameters:

node - the atom

Returns:

the R-group ID if found or -1 if not found

rgroupIndexOf

public int rgroupIndexOf(MolAtom node)

Finds the index of the R-group (the number in R#) that contains the specified atom.

Specified by:

rgroupIndexOf in interface chemaxon.struc.RgMoleculeGraphIface

Parameters:

node - the atom

Returns:

the R-group index if found or -1 if not found

getRgroupMemberID

public long getRgroupMemberID(MolAtom node)

Gets the unique indentifier of the R-group member that contains the specified atom.

Specified by:

getRgroupMemberID in interface chemaxon.struc.RgMoleculeGraphIface

Parameters:

node - the atom

Returns:

the ID or -1

Since:

Marvin 4.1, 11/23/2005

getRgroupIndex

public int getRgroupIndex(long id)

Gets the R-group index from the R-group member ID.

Specified by:

getRgroupIndex in interface chemaxon.struc.RgMoleculeGraphIface

Parameters:

id - the R-group member ID or -1

Returns:

the R-group ID or -1

Since:

Marvin 4.1, 11/23/2005

getRgroupMemberIndex

public int getRgroupMemberIndex(long id)

Gets the R-group member index from the R-group member ID.

Specified by:

getRgroupMemberIndex in interface chemaxon.struc.RgMoleculeGraphIface

Parameters:

id - the R-group member ID or -1

Returns:

the R-group member index or -1

Since:

Marvin 4.1, 11/23/2005

setDim

public void setDim(int d)

Sets the dimension of the root structure and the R-groups.

Overrides:

setDim in class Molecule

Parameters:

d - 0, 2 or 3

See Also:

MoleculeGraph.getFlags()

getFlags

public int getFlags()

Gets the dimension and chiral flags.

Overrides:

getFlags in class MoleculeGraph

Returns:

the flags

Since:

Marvin 5.0.1, 02/10/2008

setFlags

protected void setFlags(int f)

Sets the dimension and chiral flags.

Overrides:

setFlags in class MoleculeGraph

Parameters:

f - the flags

Since:

Marvin 5.0.1, 02/10/2008

See Also:

MoleculeGraph.flags

setFlags

protected void setFlags(int f,
                        int mask)

Sets specified bits in the flags.

Overrides:

setFlags in class MoleculeGraph

Parameters:

f - new value of the specified bits

mask - bits to set

setAbsStereo

public void setAbsStereo(boolean c,
                         int i,
                         int j)

Deprecated. as of Marvin 5.1.1, please call MoleculeGraph.setAbsStereo(boolean) for the component

setAbsStereo

public void setAbsStereo(boolean c)

Sets the absolute stereoconfiguration flag for the root structure and the R-groups.

Overrides:

setAbsStereo in class MoleculeGraph

Parameters:

c - the absolute stereoconfiguration flag

See Also:

MoleculeGraph.setFlags(int)

getAtomCount

public int getAtomCount()

Gets the number of nodes in the root structure.

Specified by:

getAtomCount in interface Incomplecule

Overrides:

getAtomCount in class MoleculeGraph

Returns:

number of nodes

getAtomCount

public int getAtomCount(int atomicNumber)

Gets the number of atoms with the given atomic number in the root structure. 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

getAtom

public MolAtom getAtom(int i)

Gets a node in the graph union.

Overrides:

getAtom in class MoleculeGraph

Parameters:

i - node index

Returns:

the node object

setAtom

public void setAtom(int iu,
                    MolAtom node)

Sets the node at the specified index in the graph union.

Overrides:

setAtom in class MoleculeGraph

Parameters:

iu - the atom index

node - the atom

add

public void add(MolAtom node)

Adds an atom to the root structure.

Overrides:

add in class MoleculeGraph

Parameters:

node - the atom

insertNullAtoms

protected void insertNullAtoms(int i,
                               int count)

Insert nulls into the atom array.

Overrides:

insertNullAtoms in class MoleculeGraph

Parameters:

i - starting index

count - number of new entries

Since:

Marvin 3.4

insertNullBonds

protected void insertNullBonds(int i,
                               int count)

Insert nulls into the bond array.

Overrides:

insertNullBonds in class MoleculeGraph

Parameters:

i - starting index

count - number of new entries

Since:

Marvin 3.5.5

getBondCount

public int getBondCount()

Gets the number of edges in the root structure.

Specified by:

getBondCount in interface Incomplecule

Overrides:

getBondCount in class MoleculeGraph

Returns:

number of edges

getBond

public MolBond getBond(int i)

Gets an edge in the graph union.

Overrides:

getBond in class MoleculeGraph

Parameters:

i - edge index

Returns:

the edge object

setBond

public void setBond(int iu,
                    MolBond edge)

Sets the edge at the specified index in the graph union.

Overrides:

setBond in class MoleculeGraph

Parameters:

iu - the bond index

edge - the bond

replaceBond

public void replaceBond(MolBond olde,
                        MolBond newe)

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

add

public void add(MolBond edge)

Adds a bond to the root structure.

Overrides:

add in class MoleculeGraph

Parameters:

edge - the bond to add

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

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

contains

public boolean contains(MolAtom node)

Checks if the root structure or an R-group 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 the root structure or an R-group contains the specified edge.

Overrides:

contains in class MoleculeGraph

Parameters:

edge - the edge object

Returns:

true if the graph contains the object, false otherwise

isEmpty

public boolean isEmpty()

Ask if the molecule is empty or not.

Overrides:

isEmpty in class Molecule

Returns:

true if the graph does not contain any nodes or edges.

isQuery

public boolean isQuery()

Indicates if the molecule has query features.

Overrides:

isQuery in class MoleculeGraph

Returns:

true if there are R-definitions for this molecule or the root has query features.

Since:

Marvin 4.1.2 08/30/2006

See Also:

MolAtom.isQuery(), MolBond.isQuery()

isAtom

public boolean isAtom()

Determines whether the structure represents only one atom and an arbitrary number of bonds.

Overrides:

isAtom in class MoleculeGraph

Returns:

true the root structure represents an atom and there are no R-groups, false otherwise

isBond

public boolean isBond()

Determines whether the structure represents only one bond and zero or two atoms. Determines whether the structure represents only one atom and an arbitrary number of bonds.

Overrides:

isBond in class MoleculeGraph

Returns:

true the root structure represents a bond and there are no R-groups, false otherwise

isReaction

public boolean isReaction()

Checks if the structure represents a reaction or not.

Overrides:

isReaction in class Molecule

Returns:

true if the root structure is a reaction

Since:

Marvin 3.0

canBeReactionComponent

public boolean canBeReactionComponent()

Tests whether an object of this class can be a reaction component. This implementation returns false, an RgMolecule cannot be a reaction component.

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

hasAtomSet

public boolean hasAtomSet()

Tests whether the molecule graph has atom sets.

Overrides:

hasAtomSet in class MoleculeGraph

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

getMostSimplifiedMolecule

protected Molecule getMostSimplifiedMolecule()

Gets the simplified molecule object even if there is a parent document with other objects.

Overrides:

getMostSimplifiedMolecule in class Molecule

Returns:

the root structure if there are no R-groups present, this otherwise

Since:

Marvin 4.1.13, 09/20/2007

getDocumentForChild

protected MDocument getDocumentForChild(MoleculeGraph g)

Gets the parent document for a child graph.

Overrides:

getDocumentForChild in class MoleculeGraph

Parameters:

g - the child graph or this

Returns:

the parent document

Since:

Marvin 4.1.1, 08/23/2006

addRgroupsTo

public RgMolecule addRgroupsTo(Molecule m)

Creates a read only RgMolecule from a simple molecule object.

Parameters:

m - the simple molecule object

Returns:

RgMolecule containing R-groups from this object and the specified molecule as root

Since:

Marvin 3.1

removeAtom

public void removeAtom(MolAtom node,
                       int cleanupFlags)

Removes an atom and its bonds from the root structure and from all the R-groups. 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

removeAtom

public void removeAtom(int i,
                       int cleanupFlags)

Removes an atom and its bonds from the root structure. 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:

i - the atom index

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

cleanupRemovedRgroupMember

public void cleanupRemovedRgroupMember(MoleculeGraph m,
                                       int f)

Clean-up after R-group removal.

Specified by:

cleanupRemovedRgroupMember in interface chemaxon.struc.RgMoleculeGraphIface

Parameters:

m - the removed R-group member

f - clean-up flags

Since:

Marvin 4.1, 11/25/2005

removeBond

protected void removeBond(MolBond edge,
                          int cleanupFlags)

Remove a bond from the root structure, and from all the R-groups.

Overrides:

removeBond in class Molecule

Parameters:

edge - the bond

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(int i,
                          int cleanupFlags)

Remove a bond from the root structure.

Overrides:

removeBond in class Molecule

Parameters:

i - the bond index

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

removeAllBonds

public void removeAllBonds()

Remove all bonds from the root structure, and from all the R-groups.

Overrides:

removeAllBonds in class Molecule

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

isRealAtomParent

protected boolean isRealAtomParent()

R-group molecule objects cannot be real node parents.

Overrides:

isRealAtomParent in class MoleculeGraph

Returns:

false

Since:

Marvin 3.0

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

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

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 location

See Also:

MoleculeGraph.orix

fuse

public void fuse(MoleculeGraph g,
                 boolean check)

Add the atoms and bonds of another molecule.

Overrides:

fuse in class MoleculeGraph

Parameters:

g - 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

checkConsistency

public void checkConsistency()

Deprecated.

Checks the internal consistency of the structure. Use this method for debugging.

Overrides:

checkConsistency in class Molecule

Throws:

java.lang.RuntimeException - if inconsistency found

Since:

Marvin 5.0, 11/06/2007

fuse0

protected void fuse0(MoleculeGraph graph,
                     boolean check)

Add those nodes and edges of a graph that are not already elements. If the graph is a reaction and the root structure is not a reaction then the root structure will become a reaction determined by the reaction arrow corresponding to the graph. For each connected component of the graph checks if it contains an atom connected to an RGgroup in this RgMolecule; if yes then also adds the component to that RGroup, otherwise adds it to the root structure.

Overrides:

fuse0 in class MoleculeGraph

Parameters:

graph - the graph that will be fused into this 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

mergeAtoms

public void mergeAtoms(MolAtom that,
                       MolAtom a)

Merges bonds of an atom with another atom, then add the atom to the molecule.

Overrides:

mergeAtoms in class Molecule

Parameters:

that - the atom

a - the other atom

setSgroupParent

public void setSgroupParent(MolAtom a,
                            Sgroup sg,
                            boolean set)

Sets or unsets an S-group as a parent of an atom in the root structure or an R-group.

Overrides:

setSgroupParent in class Molecule

Parameters:

a - the atom

sg - the S-group

set - set (true) or unset (false)

Throws:

java.lang.IllegalArgumentException - if neither root, nor any R-group contains the atom

Since:

Marvin 3.0

clonecopy

public void clonecopy(MoleculeGraph g)

Make another molecule identical to this one.

Overrides:

clonecopy in class Molecule

Parameters:

g - the target molecule

clonecopy

public void clonecopy(int[] iatoms,
                      MoleculeGraph g)

Copies the specified atoms of this graph to another one. The RgMolecule implementation of this method is incomplete, R-groups are not handled.

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

isSelfReference

public boolean isSelfReference(MProp p)

Tests whether the specified property is a self reference to the molecule.

Overrides:

isSelfReference in class MoleculeGraph

Parameters:

p - the property

Since:

Marvin 4.1.6, 02/11/2007

fixSelfReferringProperty

protected boolean fixSelfReferringProperty(MProp prop)

Fix a property containing reference to the molecule. Called from clonelesscopy().

Overrides:

fixSelfReferringProperty in class Molecule

Parameters:

prop - the property

Since:

Marvin 4.1.6, 02/14/2007

See Also:

MoleculeGraph.clonecopy(MoleculeGraph)

clonelesscopy

public void clonelesscopy(MoleculeGraph g)

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 molecule

cloneMolecule

public Molecule cloneMolecule()

Make an identical copy of the molecule.

Overrides:

cloneMolecule in class Molecule

Returns:

the copy

Since:

Marvin 3.5.1, 11/20/2004

getFormula

public java.lang.String getFormula()

Gets the molecular formula in Hill order.

Overrides:

getFormula in class MoleculeGraph

Returns:

the formula

getMass

public double getMass()

Calculates the molecular weight of the molecule. Returns 0 if the molecule contains R-group or reaction

Overrides:

getMass in class MoleculeGraph

Returns:

the molecular weight

newInstance

public MoleculeGraph newInstance()

Creates a new RgMolecule object. The dimension and the origin coordinates will be the same as in the original molecule.

Overrides:

newInstance in class Molecule

Returns:

an RgMolecule object

newSelectionMolecule

public SelectionMolecule newSelectionMolecule()

Creates a new SelectionMolecule object appropriate for storing selection from this molecule.

Overrides:

newSelectionMolecule in class Molecule

Returns:

an empty selection molecule

Since:

Marvin 4.1, 11/24/2005

makeItSimilar

protected void makeItSimilar(MoleculeGraph g)

Copies some properties of this molecule to the other one specified as argument. Copies properties in the root structures.

Overrides:

makeItSimilar in class Molecule

Parameters:

g - the molecule to change

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 2.9

transform

public void transform(CTransform3D t,
                      boolean incg)

Apply a transformation matrix to the atomic coordinates.

Overrides:

transform in class Molecule

Parameters:

t - the transformation matrix

incg - increase grinvCC or not

createMol

public static Molecule createMol(java.lang.String fmt)

Deprecated. As of Marvin 3.4, MolImportModule.createMol() must be used.

Create molecule object for the specified input file format.

Parameters:

fmt - the file format

Returns:

a Molecule, RgMolecule or RxnMolecule object

getGraphUnion

public MoleculeGraph getGraphUnion()

Gets a graph containing all the atoms and bonds.

Overrides:

getGraphUnion in class MoleculeGraph

Returns:

root.getGraphUnion() if there are no R-groups, getGraphUnionAsSelection() otherwise

Since:

Marvin 3.0, 11/11/2002

See Also:

Molecule.getGraphUnionAsSelection()

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()

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

getLonePairCount

public int getLonePairCount(int i)

Gets the number of lone pairs.

Overrides:

getLonePairCount in class MoleculeGraph

Parameters:

i - atom index

Returns:

the number of lone pairs

aromatize

public void aromatize(int method)

Aromatizes molecule. Changes the bonds.

Overrides:

aromatize in class Molecule

Parameters:

method - Specifies the algorithm for aromatization. Possible values:

• AROM_BASIC - Basic aromatization
• AROM_GENERAL - General (Daylight compatible) aromatization

Limits:

• AROM_BASIC: only up to 18 membered rings are checked
• AROM_GENERAL: no ring system limit

Throws:

java.lang.SecurityException - cannot load module because of a security problem (firewall)

Since:

Marvin 3.4, Marvin 4.1

See Also:

MoleculeGraph.AROM_BASIC, MoleculeGraph.AROM_GENERAL, Document about aromatization

aromatize

public void aromatize(int method,
                      boolean checkAmbiguity)

Aromatizes molecule. Changes the bonds.

Overrides:

aromatize in class Molecule

Parameters:

method - Specifies the algorithm for aromatization. Possible values:

• AROM_BASIC - Basic aromatization
• AROM_GENERAL - General (Daylight compatible) aromatization

Limits:

• AROM_BASIC: only up to 18 membered rings are checked
• AROM_GENERAL: no ring system limit

checkAmbiguity - Specifies whether ANY bonds should be considered during aromatization.

Throws:

java.lang.SecurityException - cannot load module because of a security problem (firewall)

Since:

Marvin 3.4, Marvin 4.1

See Also:

MoleculeGraph.AROM_BASIC, MoleculeGraph.AROM_GENERAL, Document about aromatization

checkSgroupConsistency

protected void checkSgroupConsistency()

Deprecated.

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

toString

public java.lang.String toString()

Overrides Object.toString() to ease debugging.

Overrides:

toString in class MoleculeGraph

Returns:

a string representation of the object

Since:

4.1, 11/28/2005

sumConservedQuantities

protected void sumConservedQuantities(MolAtom a,
                                      int[] atoms,
                                      int sign)

For internal use only.

Overrides:

sumConservedQuantities in class MoleculeGraph

Since:

Marvin 4.1.13, 09/19/2007

See Also:

RxnMolecule.isIncompleteReaction()

createGearch

protected chemaxon.struc.gearch.MoleculeGraphGearch createGearch()

Overrides:

createGearch in class Molecule

getMaxAttachmentPointOrder

public int getMaxAttachmentPointOrder(int rgroupID)

Gets the maximal attachment point order of R-group definition molecules specified by an R-group ID. The attachment point order of an R-gruop definition molecule is the maximal attachment point order of its atoms.

Parameters:

rgroupID - the rgroup identifier to specify the R-group definition molecules.

Returns:

the maximal attachment point order of the definition molecules.

Since:

Marvin 5.4

clearObjects

public void clearObjects()

Description copied from interface: chemaxon.struc.MObjectContainer

Removes all MObjects that belong to a chemical structure.

Specified by:

clearObjects in interface chemaxon.struc.MObjectContainer

Overrides:

clearObjects in class Molecule

getObjectCount

public int getObjectCount()

Description copied from interface: chemaxon.struc.MObjectContainer

Returns the count of the MObjects that belong to a chemical structure.

Specified by:

getObjectCount in interface chemaxon.struc.MObjectContainer

Overrides:

getObjectCount in class Molecule

Returns:

the object count

removeObject

public void removeObject(MObject mo)

Description copied from interface: chemaxon.struc.MObjectContainer

Removes an MObject that belongs to a chemical structure.

Specified by:

removeObject in interface chemaxon.struc.MObjectContainer

Overrides:

removeObject in class Molecule

Parameters:

mo - the object to remove

selectAllObjects

public void selectAllObjects(boolean s)

Description copied from interface: chemaxon.struc.MObjectContainer

Selects or deselects all MObjects that belong to a chemical structure.

Specified by:

selectAllObjects in interface chemaxon.struc.MObjectContainer

Overrides:

selectAllObjects in class Molecule

Parameters:

s - the value to set the selection state of the graphic objects

getAllObjects

public java.util.List<MObject> getAllObjects()

Description copied from interface: chemaxon.struc.MObjectContainer

Gets all MObjects that belong to a chemical structure.

Specified by:

getAllObjects in interface chemaxon.struc.MObjectContainer

Overrides:

getAllObjects in class Molecule

Returns:

the list of objects

getParity

public int getParity(int i)

Computes the parity of an atom of the RgMolecule 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, int, int), MoleculeGraph.getParity(int)

getLocalParity

public int getLocalParity(int i)

Computes the local parity of an atom of the RgMolecule 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, int, int), MoleculeGraph.getLocalParity(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()