RgMolecule (Marvin API documentation (c) 1998-2012 ChemAxon Ltd.)

Overview

Package

Class

Tree

Deprecated

Index

Help

PREV CLASS NEXT CLASS

FRAMES NO FRAMES

SUMMARY: NESTED | FIELD | CONSTR | METHOD

DETAIL: FIELD | CONSTR | METHOD

chemaxon.struc
Class RgMolecule

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

All Implemented Interfaces:: chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>, Incomplecule, chemaxon.struc.MObjectContainer, chemaxon.struc.MoleculeForBuilder, MTransformable, chemaxon.struc.RgMoleculeGraphIface, StereoConstants, java.io.Serializable

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

Nested Class Summary

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

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, VALENCE_CHECK_AMBIGUOUS

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, 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_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`

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.
`protected void`	`addAtomToFragment(MolAtom atom)` Adds an atom to a fragment.
`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()` Checks the consistency of S-groups.
`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()`
`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()`
`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()`
`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)`
`void`	`removeRgroup(int definition)` Removes an R-group Note: the R-group definitions are always indexed continuously starting with 0
`void`	`removeRgroupMember(int definition, int member)` Removes an R-group member.
`void`	`removeRgroupMembers(int definition, int[] members)` Removes R-group members.
`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)`
`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, addBond0, addSgroup, addSgroupClones, addSgroupsOf, bondlength, clear, clearExtraLabels, clearProperties, clone, clonecopyWithoutSgroups, cloneMoleculeWithDocument, contractSgroups, convertToFrags, countExpandableContractableSgroups, countOrderedComponentSgroups, dearomatize, expandSgroups, expandSgroups, exportToBinFormat, exportToFormat, exportToObject, findAllSgroupContaining, findContainingMulticenterSgroup, findContractableSgroup, findExpandableSgroup, findFrags, findSgroupContaining, findSgroupOf, findSmallestSgroupContaining, getEndPosition, getFreeAttachmentPoints, getFreeAttachmentPoints, getGraphUnionAsSelection, 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.Molecule

addAtom0, addBond0, addSgroup, addSgroupClones, addSgroupsOf, bondlength, clear, clearExtraLabels, clearProperties, clone, clonecopyWithoutSgroups, cloneMoleculeWithDocument, contractSgroups, convertToFrags, countExpandableContractableSgroups, countOrderedComponentSgroups, dearomatize, expandSgroups, expandSgroups, exportToBinFormat, exportToFormat, exportToObject, findAllSgroupContaining, findContainingMulticenterSgroup, findContractableSgroup, findExpandableSgroup, findFrags, findSgroupContaining, findSgroupOf, findSmallestSgroupContaining, getEndPosition, getFreeAttachmentPoints, getFreeAttachmentPoints, getGraphUnionAsSelection, 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, getAtomicNumber, getAtomReferenceList, getBondArray, getBonds, getCharge, 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, getImplicitHCount, getLigand, getLigandAtno, getLigandBondType, getLigandCount, getLocation, getLock, getMaxRgroupAttachmentPointOrder, getNode, getNodeCount, getNodeVector, getNonAromrings, getNonAromrings, getParent, getParentDocument, getParityType, getPoints, getPossibleAttachmentPoints, getRadicalCount, getSmallestRingSizeForIdx, getSSSR, getSSSRBonds, getSSSRBondSet, getSSSRBondSetInLong, getSSSRIdxesForAtoms, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getSubGraphs, getTotalCharge, getValenceCheckState, getValenceProperty, hasExplicitLonePairs, hasExtraLabelSet, hasImplicitH, hasSelfReferringProperty, hasValenceError, hydrogenize, implicitizeHydrogens, implicitizeHydrogens, implicitizeHydrogens, incGrinvCC, incGrinvCCOnly, insertAtom, insertBond, insertBondInOrder, insertEdge, insertEdgeInOrder, insertNode, isAbsStereo, isAcceptedSpecialLigand, isAtomInRing, 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, setValenceCheckState, smol, sortEdgesAccordingTo, transform, updateDim, useOnlyFirstAtomInStereoCalculation, valenceCheck, valenceCheck

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, getAtomicNumber, getAtomReferenceList, getBondArray, getBonds, getCharge, 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, getImplicitHCount, getLigand, getLigandAtno, getLigandBondType, getLigandCount, getLocation, getLock, getMaxRgroupAttachmentPointOrder, getNode, getNodeCount, getNodeVector, getNonAromrings, getNonAromrings, getParent, getParentDocument, getParityType, getPoints, getPossibleAttachmentPoints, getRadicalCount, getSmallestRingSizeForIdx, getSSSR, getSSSRBonds, getSSSRBondSet, getSSSRBondSetInLong, getSSSRIdxesForAtoms, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getSubGraphs, getTotalCharge, getValenceCheckState, getValenceProperty, hasExplicitLonePairs, hasExtraLabelSet, hasImplicitH, hasSelfReferringProperty, hasValenceError, hydrogenize, implicitizeHydrogens, implicitizeHydrogens, implicitizeHydrogens, incGrinvCC, incGrinvCCOnly, insertAtom, insertBond, insertBondInOrder, insertEdge, insertEdgeInOrder, insertNode, isAbsStereo, isAcceptedSpecialLigand, isAtomInRing, 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, setValenceCheckState, 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

removeRgroupMember

public void removeRgroupMember(int definition,
                               int member)
                        throws chemaxon.struc.IllegalRgroupDefinitionException,
                               chemaxon.struc.IllegalRgroupMemberException

Removes an R-group member. If it is the last member to be removed then the whole R-group definition will be removed Note: the R-group members are always indexed continuously starting with 0

Parameters:: definition - the iteration number of the R-group definition; member - the iteration number of the member
Throws:: IllegalRgroupDefinitionException - If the definition index is not valid; IllegalRgroupMemberException - If the member index is not valid
Since:: 5.10 2012.05.10

removeRgroupMembers

public void removeRgroupMembers(int definition,
                                int[] members)
                         throws chemaxon.struc.IllegalRgroupDefinitionException,
                                chemaxon.struc.IllegalRgroupMemberException

Removes R-group members. If the last member is removed then the whole R-group definition will be removed Note: the R-group members are always indexed continuously starting with 0

Parameters:: definition - the iteration number of the R-group definition; members - the array of the iteration numbers of the members
Throws:: IllegalRgroupDefinitionException - If the definition index is not valid; IllegalRgroupMemberException - If a member index is not valid
Since:: 5.10 2012.05.10

removeRgroup

public void removeRgroup(int definition)
                  throws chemaxon.struc.IllegalRgroupDefinitionException

Removes an R-group Note: the R-group definitions are always indexed continuously starting with 0

Parameters:: definition - the iteration number of the R-group definition
Throws:: IllegalRgroupDefinitionException - If the definition index is not valid
Since:: 5.10 2012.05.10

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

addAtomToFragment

protected void addAtomToFragment(MolAtom atom)

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:: atom - the atom reference

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

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

checkSgroupConsistency

protected void checkSgroupConsistency()

Checks the consistency of S-groups.

Overrides:: checkSgroupConsistency in class Molecule

Throws:: java.lang.RuntimeException - if inconsistency found
Since:: Marvin 5.0, 11/06/2007

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()

Specified by:: clearObjects in interface chemaxon.struc.MObjectContainer
Overrides:: clearObjects in class Molecule

getObjectCount

public int getObjectCount()

Specified by:: getObjectCount in interface chemaxon.struc.MObjectContainer
Overrides:: getObjectCount in class Molecule

removeObject

public void removeObject(MObject mo)

Specified by:: removeObject in interface chemaxon.struc.MObjectContainer
Overrides:: removeObject in class Molecule

selectAllObjects

public void selectAllObjects(boolean s)

Specified by:: selectAllObjects in interface chemaxon.struc.MObjectContainer
Overrides:: selectAllObjects in class Molecule

getAllObjects

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

Specified by:: getAllObjects in interface chemaxon.struc.MObjectContainer
Overrides:: getAllObjects in class Molecule

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()

Overview

Package

Class

Tree

Deprecated

Index

Help

PREV CLASS NEXT CLASS

FRAMES NO FRAMES

SUMMARY: NESTED | FIELD | CONSTR | METHOD

DETAIL: FIELD | CONSTR | METHOD

chemaxon.struc Class RgMolecule

RG_ID_MASK

RG_ID2_FLAG

RG_ID2_OFF

RG_ID2_MASK

RG_RESTH

RgMolecule

setRoot

getRoot

getRootG

getRgroupCount

getRgroupMemberCount

getRgroupMember

getRgroupMemberG

getRgroupId

findRgroupIndex

addRgroup

removeRgroupMember

removeRgroupMembers

removeRgroup

hasRgroupContainedBy

unRgroupAtoms

replaceAtomsWithNewRgroup

getRlogic

setRlogic

getRlogicRange

setRlogicRange

checkRlogicRange

clearForImport

setName

getName

setComment

getComment

properties

revalidateCoordDependentProps

setInputFormat

reuseAtom

endReuse

getCtab

getBtab

getBondTable

rgroupIdOf

rgroupIndexOf

getRgroupMemberID

getRgroupIndex

getRgroupMemberIndex

setDim

getFlags

setFlags

setFlags

setAbsStereo

setAbsStereo

getAtomCount

getAtomCount

getAtom

setAtom

add

addAtomToFragment

insertNullAtoms

insertNullBonds

getBondCount

getBond

setBond

replaceBond

add

indexOf

indexOf

contains

contains

isEmpty

isQuery

isAtom

isBond

isReaction

canBeReactionComponent

hasAtomSet

hasBondSet

getMostSimplifiedMolecule

getDocumentForChild

addRgroupsTo

chemaxon.struc
Class RgMolecule