RgMolecule (Marvin API documentation (c) 1998-2006 ChemAxon Ltd.)

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chemaxon.struc
Class RgMolecule

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

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

public class RgMolecule
extends Molecule
implements chemaxon.struc.RgMoleculeGraphIface

A molecule or reaction containing R-groups.

Since:: Marvin 2.6
Version:: 4.1.2, 09/20/2006
Author:: Peter Csizmadia
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

RMCLEANUP_FROMSGROUPS, RMCLEANUP_SGROUPATOMS

Fields inherited from class chemaxon.struc.MoleculeGraph

AROM_BASIC, AROM_CHEMAXON, AROM_DAYLIGHT, AROM_GENERAL, CACHE_REMOVE_AROMATAMODULE, CACHE_REMOVE_GRINVMODULE, CACHE_REMOVE_PARITYMODULE, CACHE_REMOVE_SSSRMODULE, DIM_MASK, flags, GRINV_DONT_STORE, GRINV_NOHYDROGEN, GRINV_OLDSTEREO, GRINV_STEREO, GRINV_VALUE_OPTIONS, INVALID_LINKNODE_MESSAGE, isMultiChiral, MIN_RING_SIZE_FOR_TRANS_DB, orix, oriy, oriz, propertyContainer, RMCLEANUP_MOBJECT, RMCLEANUP_STEREO

Fields inherited from class chemaxon.struc.CGraph

btab, CACHE_REMOVE_ALL, CACHE_REMOVE_CACHEMEMORY, cacheMemory, ctab, edgeCount, edges, fragIds, grinv, grinvCC, grinvOptions, INITIAL_CAPACITY, nFrags, nGrinv, nodeCount, nodes, parentGraph, RMCLEANUP_ALL, RMCLEANUP_EDGES, RMCLEANUP_NONE, sssr, sssrl2idx, superGraph

Fields inherited from interface chemaxon.struc.ReadableMolecule

HS_S, HS_SP, HS_SP2, HS_SP3, HS_UNKNOWN

Fields inherited from interface chemaxon.struc.StereoConstants

ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_MASK, CHIRALITY_R, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_ODD, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, TRANS

Constructor Summary
`RgMolecule()` Creates an RgMolecule.

Method Summary
`void`	`add(CEdge edge)` Adds a bond to the root structure.
`void`	`add(CNode node)` Adds an atom 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)` Aromatize molecule.
`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.
`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`	`clonecopy(CGraph g)` Make another molecule identical to this one.
`void`	`clonelesscopy(CGraph g)` Copy to selection.
`Molecule`	`cloneMolecule()` Make an identical copy of the molecule.
`boolean`	`contains(java.lang.Object o)` Checks if the root structure or an R-group contains the specified node or edge.
`static Molecule`	`createMol(java.lang.String fmt)` Deprecated. As of Marvin 3.4, `MolImportIface.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#.
`void`	`fuse(CGraph g)` Add the atoms and bonds of another molecule.
`protected void`	`fuse0(CGraph graph)` Add those nodes and edges of a graph that are not already elements.
`int[][]`	`getBtab()` Gets the bond table of the root structre.
`int[][]`	`getCtab()` Gets the connection table of the root structure.
`protected MDocument`	`getDocumentForChild(MoleculeGraph g)` Gets the parent document for a child graph.
`CEdge`	`getEdge(int i)` Gets an edge in the graph union.
`int`	`getEdgeCount()` Gets the number of edges in the root structure.
`java.lang.String`	`getFormula()` Gets the molecular formula in Hill order.
`MoleculeGraph`	`getGraphUnion()` Gets a graph containing all the atoms and bonds.
`protected int[]`	`getGrinv()` Gets the graph invariants of the root structure.
`int`	`getGrinv(int[] gi)` Gets the graph invariants of the root structure.
`int`	`getGrinv(int[] gi, int options)` Gets the graph invariants (canonical labels).
`double`	`getMass()` Calculates the molecular weight of the molecule.
`java.lang.String`	`getName()` Gets the name of the root molecule.
`CNode`	`getNode(int i)` Gets a node in the graph union.
`int`	`getNodeCount()` Gets the number of nodes in the root structure.
`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(CNode 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.
`Molecule`	`getSimplifiedMolecule()` Gets the simplified molecule object.
`protected int`	`getSubGraphCount()` Gets the number of all "submolecules".
`protected void`	`getSubGraphs(MoleculeGraph[] arr, int off)` Gets all "submolecules".
`boolean`	`hasAtomSet()` Tests whether the molecule graph has atom sets.
`boolean`	`hasBondSet()` Tests whether the molecule graph has atom sets.
`void`	`implicitizeHydrogens(int f)` Removes explicit bound Hydrogens from the graph and converts them to implicit.
`int`	`indexOf(CEdge edge)` Gets the index of the specified edge in the graph union.
`int`	`indexOf(CNode node)` Gets the index of the specified node in the graph union.
`protected void`	`insertNullEdges(int i, int count)` Insert nulls into the bond array.
`protected void`	`insertNullNodes(int i, int count)` Insert nulls into the atom 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`	`isRealNodeParent()` R-group molecule objects cannot be real node parents.
`protected void`	`makeItSimilar(CGraph g)` Copies some properties of this molecule to the other one specified as argument.
`void`	`mergeNodes(CNode that, CNode a)` Merges bonds of an atom with another atom, then add the atom to the molecule.
`CGraph`	`newInstance()` Creates a new RgMolecule object.
`SelectionMolecule`	`newSelectionMolecule()` Creates a new SelectionMolecule object appropriate for storing selection from this molecule.
`protected void`	`postClean()` Operations performed after cleaning.
`MPropertyContainer`	`properties()` Gets the property container.
`void`	`regenEdges()` Regenerate the edge vectors: remove their elements, then put the edge objects from the nodes into it.
`void`	`removeAll()` Remove all the atoms and bonds from the root structure, and from all the R-groups.
`void`	`removeAllEdges()` Remove all bonds from the root structure, and from all the R-groups.
`protected void`	`removeEdge(CEdge edge, int cleanupFlags)` Remove a bond from the root structure, and from all the R-groups.
`protected void`	`removeEdge(int i, int cleanupFlags)` Remove a bond from the root structure.
`void`	`removeNode(CNode node, int cleanupFlags)` Removes an atom and its bonds from the root structure and from all the R-groups.
`void`	`removeNode(int i, int cleanupFlags)` Removes an atom and its bonds from the root structure.
`void`	`replaceAtomsWithNewRgroup(SelectionMolecule sel, int rgid)` Replaces selected atoms with a new R-group.
`void`	`replaceEdge(CEdge olde, CEdge 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(CNode node)` Finds the ID of the R-group (the number in R#) that contains the specified atom.
`int`	`rgroupIndexOf(CNode node)` Finds the index of the R-group (the number in R#) that contains the specified atom.
`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)` Sets the absolute stereoconfiguration flag for the root structure and the R-groups.
`void`	`setDim(int d)` Sets the dimension of the root structure and the R-groups.
`void`	`setEdge(int iu, CEdge edge)` Sets the edge at the specified index in the graph union.
`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`	`setNode(int iu, CNode node)` Sets the node at the specified index in the graph union.
`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`	`sortEdgesAccordingTo(CEdge[] order)` Sort edges in the same order as they appear in the specified array.
`java.lang.String`	`toString()` Overrides Object.toString() to ease debugging.
`void`	`transform(CTransform3D t, boolean incg)` Apply a transformation matrix to the atomic coordinates.

Methods inherited from class chemaxon.struc.Molecule

addNode0, addSgroupClones, addSgroupsOf, bondlength, clean, cleanSgroups, clear, clearExtraLabels, clearProperties, clone, clonecopyWithoutSgroups, cloneMoleculeWithDocument, contractSgroups, convertToFrags, dearomatize, draw, expandSgroups, expandSgroups, exportToBinFormat, exportToFormat, exportToObject, findContractableSgroup, findExpandableSgroup, findFrags, findFrags, findSgroupContaining, findSgroupOf, findSmallestSgroupContaining, getComment, getEndPosition, getGraphUnionAsSelection, getImageSize, getInputFormat, getOrderedComponentSgroupCount, getProperty, getPropertyCount, getPropertyKey, getPropertyKeys, getPropertyObject, getSgroup, getSgroupArray, getSgroupCount, getSgroupLigands, getSortedSgroups, getStartPosition, getVisibleCoords, indexOf, isExpandable, isGUIContracted, isSgroup, removeAllSgroups, removeSgroupFromList, removeSgroupsOf, reparentSgroups, residueSymbolOf, residueTypeOf, setComment, setEndPosition, setGUIContracted, setNode0, setProperty, setPropertyObject, setStartPosition, toBinFormat, toFormat, toObject, ungroupSgroup, ungroupSgroup, ungroupSgroups

Methods inherited from class chemaxon.struc.MoleculeGraph

addAtomsAndBondsTo, addExplicitLonePairs, adjustMultiChiralFlag, aromatize, aromatize, arrangeComponents, calcCenter, calcCenter, calcDehydrogenizedGrinv, calcHeight, calcHybridization, calcOutRect, calcOutRect, calcOutRectCenter, calcOutRectCenter, calcWidth, canBeCT, canBeCT, clean, clearCachedInfo, contains, createBHtab, createCHtab, createDehydrogenizedReadOnlyGraph, findAtomClone, getAromaticAndAliphaticRings, getAromrings, getAromrings, getAtom, getAtomArray, getAtomCount, getBond, getBondArray, getBondCount, getCharge, getChirality, getDesiredLength, getDesiredLength, getDim, getDocument, getEdgeArray, getEdgeVector, getExactMass, getExplicitHcount, getGrinv, getHybridizationState, getImplicitHcount, getLocalChirality, getLocalParity, getLocation, getLonePairCount, getMassno, getNeighbor, getNeighborCount, getNodeVector, getNonAromrings, getNonAromrings, getParentDocument, getParity, getPoints, getRadical, getSSSRBondSet, getSSSRBondSetInLong, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getSubGraphs, hasExplicitLonePairs, hasExtraLabelSet, hasImplicitH, hasValenceError, hydrogenize, isAbsStereo, isMultiChiral, isRingBond, isSimilarTo, isValidLinkNode, moveTo, partialClean, qpropCheck, removeExplicitLonePairs, restoreCache, saveCache, setAtomSetSeqs, setBondSetSeqs, setChirality, setLinkNodeDefaultOuters, setParity, setParity, setParity, setSetSeqs, stereoClean, transform, updateDim, valenceCheck, valenceCheck

Methods inherited from class chemaxon.struc.CGraph

addEdge0, addEdgeWithoutChangingIt, addNodeWithoutChangingIt, findComponentIds, findComponentIds, findEdge, findFrag, findFragById, findNode, getForefather, getFragCount, getFragIds, getGrinvCC, getLock, getParent, getSmallestRingSizeForIdx, getSSSR, incGrinvCC, incGrinvCCOnly, insertEdge, insertNode, isRing, isSymmetric, pack, regenCtabs, removeEdge, removeEdge, removeNode, removeNode, resetCtab, resetGrinvInParents, setGrinvCC

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 an 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

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.

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 chemaxon.struc.ReadableMolecule
Overrides:: getName in class Molecule

Returns:: the molecule name or an empty string

properties

public MPropertyContainer properties()

Gets the property container.

Specified by:: properties in interface chemaxon.struc.ReadableMolecule
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 CGraph

Returns:: the ctab array

getBtab

public int[][] getBtab()

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 CGraph

Returns:: the btab array

getGrinv

public int getGrinv(int[] gi)

Gets the graph invariants of the root structure.

Overrides:: getGrinv in class MoleculeGraph

Parameters:: gi - the output array
Returns:: zero

getGrinv

protected int[] getGrinv()

Gets the graph invariants of the root structure.

Overrides:: getGrinv in class CGraph

Returns:: the graph invariants array

getGrinv

public int getGrinv(int[] gi,
                    int options)

Gets the graph invariants (canonical labels). Same like getGrinv() but depending on the options chiral info is also added to invariants (needed for unique SMILES) and/or hydrogens are ignored. In the latter case -1 graph invariant is assigned to explicit hydrogens.

Overrides:: getGrinv in class MoleculeGraph

Parameters:: gi - output array, its length must be equal to the number of atoms; options - options for the generation of graph invariants
Returns:: the number of different graph invariants
Throws:: java.lang.SecurityException - the GraphInvariants module cannot be loaded because of security reasons (firewall)
Since:: Marvin 4.0 7/08/2005
See Also:: MoleculeGraph.GRINV_NOHYDROGEN, MoleculeGraph.GRINV_STEREO

rgroupIdOf

public int rgroupIdOf(CNode 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(CNode 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(CNode 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.flags

setAbsStereo

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

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

Parameters:: c - the absolute stereoconfiguration flag

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.flags

getNodeCount

public int getNodeCount()

Gets the number of nodes in the root structure.

Overrides:: getNodeCount in class CGraph

Returns:: number of nodes

getNode

public CNode getNode(int i)

Gets a node in the graph union.

Overrides:: getNode in class CGraph

Parameters:: i - node index
Returns:: the node object

setNode

public void setNode(int iu,
                    CNode node)

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

Overrides:: setNode in class CGraph

Parameters:: iu - the atom index; node - the atom

add

public void add(CNode node)

Adds an atom to the root structure.

Overrides:: add in class CGraph

Parameters:: node - the atom

insertNullNodes

protected void insertNullNodes(int i,
                               int count)

Insert nulls into the atom array.

Overrides:: insertNullNodes in class CGraph

Parameters:: i - starting index; count - number of new entries
Since:: Marvin 3.4

insertNullEdges

protected void insertNullEdges(int i,
                               int count)

Insert nulls into the bond array.

Overrides:: insertNullEdges in class CGraph

Parameters:: i - starting index; count - number of new entries
Since:: Marvin 3.5.5

getEdgeCount

public int getEdgeCount()

Gets the number of edges in the root structure.

Overrides:: getEdgeCount in class CGraph

Returns:: number of edges

getEdge

public CEdge getEdge(int i)

Gets an edge in the graph union.

Overrides:: getEdge in class CGraph

Parameters:: i - edge index
Returns:: the edge object

setEdge

public void setEdge(int iu,
                    CEdge edge)

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

Overrides:: setEdge in class MoleculeGraph

Parameters:: iu - the bond index; edge - the bond

replaceEdge

public void replaceEdge(CEdge olde,
                        CEdge newe)

Replaces an edge by another one.

Overrides:: replaceEdge in class CGraph

Parameters:: olde - the old edge; newe - the new edge
Since:: Marvin 4.1, 11/24/2005

add

public void add(CEdge edge)

Adds a bond to the root structure.

Overrides:: add in class CGraph

Parameters:: edge - the bond to add

indexOf

public int indexOf(CNode node)

Gets the index of the specified node in the graph union.

Overrides:: indexOf in class CGraph

Parameters:: node - the node
Returns:: the index, or -1 if not found

indexOf

public int indexOf(CEdge edge)

Gets the index of the specified edge in the graph union.

Overrides:: indexOf in class CGraph

Parameters:: edge - the edge
Returns:: the index, or -1 if not found

contains

public boolean contains(java.lang.Object o)

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

Overrides:: contains in class CGraph

Parameters:: o - the node or 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

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

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

getSimplifiedMolecule

public Molecule getSimplifiedMolecule()

Gets the simplified molecule object.

Overrides:: getSimplifiedMolecule in class Molecule

Returns:: the root structure if there are no R-groups present, this otherwise
Since:: Marvin 3.0.1

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

removeNode

public void removeNode(CNode 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 CGraph.removeNode(CNode) instead unless you are sure what you are doing.

Overrides:: removeNode in class Molecule

Parameters:: node - the atom; cleanupFlags - extra clean-up methods
Since:: Marvin 3.1
See Also:: CGraph.RMCLEANUP_NONE, CGraph.RMCLEANUP_ALL, CGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO, Molecule.RMCLEANUP_SGROUPATOMS, Molecule.RMCLEANUP_FROMSGROUPS

removeNode

public void removeNode(int i,
                       int cleanupFlags)

Removes an atom and its bonds from the root structure. This method is for internal use only. Use CGraph.removeNode(CNode) instead unless you are sure what you are doing.

Overrides:: removeNode in class Molecule

Parameters:: i - the atom index; cleanupFlags - extra clean-up methods
Since:: Marvin 3.1
See Also:: CGraph.RMCLEANUP_NONE, CGraph.RMCLEANUP_ALL, CGraph.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

removeEdge

protected void removeEdge(CEdge edge,
                          int cleanupFlags)

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

Overrides:: removeEdge in class Molecule

Parameters:: edge - the bond; cleanupFlags - extra clean-up methods
Since:: Marvin 3.1
See Also:: CGraph.RMCLEANUP_NONE, CGraph.RMCLEANUP_ALL, CGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO, Molecule.RMCLEANUP_SGROUPATOMS, Molecule.RMCLEANUP_FROMSGROUPS

removeEdge

protected void removeEdge(int i,
                          int cleanupFlags)

Remove a bond from the root structure.

Overrides:: removeEdge in class Molecule

Parameters:: i - the bond index; cleanupFlags - extra clean-up methods
Since:: Marvin 3.1
See Also:: CGraph.RMCLEANUP_NONE, CGraph.RMCLEANUP_ALL, CGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO, Molecule.RMCLEANUP_SGROUPATOMS, Molecule.RMCLEANUP_FROMSGROUPS

removeAllEdges

public void removeAllEdges()

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

Overrides:: removeAllEdges 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

isRealNodeParent

protected boolean isRealNodeParent()

R-group molecule objects cannot be real node parents.

Overrides:: isRealNodeParent in class CGraph

Returns:: false
Since:: Marvin 3.0

regenEdges

public void regenEdges()

Regenerate the edge vectors: remove their elements, then put the edge objects from the nodes into it.

Overrides:: regenEdges in class CGraph

sortEdgesAccordingTo

public void sortEdgesAccordingTo(CEdge[] order)

Sort edges in the same order as they appear in the specified array.

Overrides:: sortEdgesAccordingTo in class CGraph

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(CGraph g)

Add the atoms and bonds of another molecule.

Overrides:: fuse in class CGraph

Parameters:: g - the other molecule

fuse0

protected void fuse0(CGraph graph)

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

mergeNodes

public void mergeNodes(CNode that,
                       CNode a)

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

Overrides:: mergeNodes 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(CGraph g)

Make another molecule identical to this one.

Overrides:: clonecopy in class Molecule

Parameters:: g - the target molecule

clonelesscopy

public void clonelesscopy(CGraph 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 CGraph 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(CGraph 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, MolImportIface.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

implicitizeHydrogens

public void implicitizeHydrogens(int f)

Removes explicit bound Hydrogens from the graph and converts them to implicit. Only those explicit H atoms are converted for which MolAtom.isImplicitizableH(int) returns true.

Overrides:: implicitizeHydrogens in class MoleculeGraph

Parameters:: f - flags specifying special H atom types to include
Since:: Marvin 3.1
See Also:: MolAtom.LONELY_H, MolAtom.ISOTOPE_H, MolAtom.CHARGED_H, MolAtom.RADICAL_H, MolAtom.MAPPED_H, MolAtom.WEDGED_H, MolAtom.HCONNECTED_H

aromatize

public void aromatize(int method)

Aromatize molecule. Change 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

postClean

protected void postClean()

Operations performed after cleaning. Makes a 2D clean, calculates atom coordinates and creates a peptide snake if needed

Overrides:: postClean in class Molecule

Since:: Marvin 4.1, 07/31/2006

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

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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

replaceAtomsWithNewRgroup

getRlogic

setRlogic

getRlogicRange

setRlogicRange

checkRlogicRange

clearForImport

setName

getName

properties

revalidateCoordDependentProps

setInputFormat

reuseAtom

endReuse

getCtab

getBtab

getGrinv

getGrinv

getGrinv

rgroupIdOf

rgroupIndexOf

getRgroupMemberID

getRgroupIndex

getRgroupMemberIndex

setDim

setAbsStereo

setAbsStereo

getNodeCount

getNode

setNode

add

insertNullNodes

insertNullEdges

getEdgeCount

getEdge

setEdge

replaceEdge

add

indexOf

indexOf

contains

isEmpty

isQuery

isAtom

isBond

isReaction

hasAtomSet

hasBondSet

getSimplifiedMolecule

getDocumentForChild

addRgroupsTo

removeNode

removeNode

cleanupRemovedRgroupMember

removeEdge

removeEdge

removeAllEdges

removeAll

isRealNodeParent

regenEdges

sortEdgesAccordingTo

setLocation

fuse

chemaxon.struc
Class RgMolecule