MoleculeGraph (Marvin API documentation (c) 1998-2008 ChemAxon Ltd.)

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chemaxon.struc
Class MoleculeGraph

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

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

Direct Known Subclasses:: Molecule, SelectionMolecule

public class MoleculeGraph
extends CGraph
implements chemaxon.struc.ReadableMolecule, MTransformable, StereoConstants
extends CGraph
implements chemaxon.struc.ReadableMolecule, MTransformable, StereoConstants

A graph consisting of MolAtom vertices and MolBond edges.

Since:: Marvin 3.0, 10/11/2002
Version:: 5.0.2, 03/11/2008
Author:: Peter Csizmadia, Ferenc Csizmadia, Andras Volford, Gyorgy Pirok, Szilveszter Juhos, Szabolcs Csepregi, Erika Biro
See Also:: MolAtom, MolBond, Serialized Form

Field Summary
`static int`	`AROM_BASIC` Basic aromatization.
`static int`	`AROM_CHEMAXON` Deprecated. please use AROM_BASIC instead. Chemaxon aromatization.
`static int`	`AROM_DAYLIGHT` Deprecated. please use AROM_GENERAL instead. Daylight aromatization (modified Huckel rule).
`static int`	`AROM_GENERAL` General (Daylight conform) aromatization.
`static int`	`CACHE_REMOVE_AROMATAMODULE` Cache removal option for remove module used in aromatization.
`static int`	`CACHE_REMOVE_GRINVMODULE` Cache removal option for remove module used in graph invariant calculation.
`static int`	`CACHE_REMOVE_PARITYMODULE` Cache removal option for remove module used in parity calculation.
`static int`	`CACHE_REMOVE_SSSRMODULE` Cache removal option for remove module used in sssr.
`protected static int`	`DIM_MASK` Dimension bits in flags.
`static int`	`GRINV_DONT_STORE` Graph invariant option to instruct that the graph invariant should not be stored in MoleculeGraph.
`static int`	`GRINV_NOHYDROGEN` Graph invariant option for ignoring explicit hydrogens.
`static int`	`GRINV_OLDSTEREO` Graph invariant option for calculating graph invariants using the old stereo method.
`static int`	`GRINV_STEREO` Graph invariant option for calculating graph invariants using stereo information.
`static int`	`GRINV_USEMAPS` Graph invariant option for calculating graph invariants considering atom maps also.
`static int`	`GRINV_VALUE_OPTIONS` Unified mask of graph invariant options affecting grinv value.
`static java.lang.String`	`INVALID_LINKNODE_MESSAGE`
`static int`	`MIN_RING_SIZE_FOR_TRANS_DB` The minimal size of the ring for the existence of TRANS double bond.
`static int`	`OMIT_POSTCLEAN` Omit arranging process after the hydrogen addition.
`protected double`	`orix` Origin x.
`protected double`	`oriy` Origin y.
`protected double`	`oriz` Origin z.
`protected MPropertyContainer`	`propertyContainer`
`static int`	`RMCLEANUP_MOBJECT` Remove graphics objects containing the removed node.
`static int`	`RMCLEANUP_PARENTDOC` Remove atom from parent document.
`static int`	`RMCLEANUP_STEREO` When removing a H atom, keep stereo information unchanged.
`protected boolean`	`useOnlyFirstAtomInStereoCalculation`

Fields inherited from class chemaxon.struc.CGraph
`btab, CACHE_REMOVE_ALL, CACHE_REMOVE_CACHEMEMORY, cacheMemory, cssr, ctab, edgeCount, edges, fragIds, grinv, grinvCC, grinvOptions, INITIAL_CAPACITY, nFrags, nGrinv, nodeCount, nodes, parentGraph, RMCLEANUP_ALL, RMCLEANUP_EDGES, RMCLEANUP_FIXCOMPONENT, RMCLEANUP_NONE, sssr, sssr2idx, 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
`MoleculeGraph()` Construct a molecule.
`MoleculeGraph(MoleculeGraph p, int na, int nb)` Construct a molecule or fragment with the specified number of atoms and bonds.

Method Summary
`protected void`	`addAtomsAndBondsTo(MoleculeGraph s)` Adds all atoms and bonds to the specified molecule.
`boolean`	`addExplicitHydrogens(int f)` Adds explicit H atoms instead of the current implicit ones.
`boolean`	`addExplicitHydrogens(int f, MolAtom[] atoms)` Adds explicit H atoms instead of the current implicit ones.
`void`	`addExplicitLonePairs()` Adds explicit lone pairs.
`void`	`adjustMultiChiralFlag()` Checks whether the molecule has multiple chiral centres
`void`	`aromatize()` Aromatize molecule using the default general aromatization method.
`void`	`aromatize(boolean a)` Aromatize (using the default general aromatization method) or dearomatize molecule.
`void`	`aromatize(int method)` Aromatize molecule.
`void`	`arrangeComponents()` Arranges molecule components (reactants, agents, products, R-group definitions) nicely.
`double`	`bondlength()` Calculates the regular bond length.
`DPoint3`	`calcCenter()` Calculates the geometrical center.
`void`	`calcCenter(DPoint3 p)` Calculates the geometrical center.
`int`	`calcDehydrogenizedGrinv(int[] gi)` Calculates the graph invariants with the assumption that hydrogens are removed.
`double`	`calcHeight()` Calculates the molecule height.
`void`	`calcHybridization()` Calculates and sets hybridazation state for each atom.
`DPoint3`	`calcOutRect()` Calculates the outer rectangle.
`void`	`calcOutRect(DPoint3 p)` Calculates the outer rectangle.
`DPoint3`	`calcOutRectCenter()` Calculates the center of the outer rectangle.
`void`	`calcOutRectCenter(DPoint3 p)`
`double`	`calcWidth()` Calculates the molecule width.
`boolean`	`canBeCT(int i2, int i3)` Determines whether the bond between the specified atoms can be a CIS/TRANS or not.
`boolean`	`canBeCT(int i2, int i3, boolean grcheck)` Determines whether the bond between the specified atoms can be a CIS/TRANS or not.
`boolean`	`clean(int dim, java.lang.String opts)` Calculates atom coordinates.
`boolean`	`clean(int dim, java.lang.String opts, MProgressMonitor pmon)` Calculates atom coordinates.
`void`	`clear()` Clears the molecule.
`void`	`clearCachedInfo(int options)` Deletes the cached information depending on the given options.
`void`	`clearForImport(java.lang.String format)` Clears the edges vector, the properties, the flags, and sets the origin coordinates to 0.
`java.lang.Object`	`clone()` Make an identical copy of the molecule.
`void`	`clonecopy(CGraph g)` Make another molecule identical to this one.
`void`	`clonecopy(int[] iatoms, MoleculeGraph g)` Copies the specified nodes of this molecule graph to another one.
`protected boolean`	`clonecopyCGraphWithoutSgroups(int[] cnodes, CEdge[] cedges, int nb, CGraph g)` Copies the specified nodes and edges of this graph to another one.
`void`	`clonelesscopy(CGraph g)` Copy to selection.
`boolean`	`contains(CGraph graph)` Does the graph contain the specified fragment?
`int[][]`	`createBHtab()` Creates the bond table extended with implicit hydrogen atoms.
`int[][]`	`createCHtab()` Creates the connection table extended with implicit hydrogen atoms.
`protected MoleculeGraph`	`createDehydrogenizedReadOnlyGraph()` Creates a dehydrogenized version of the molecule.
`boolean`	`dearomatize()` Dearomatize molecule.
`MolAtom`	`findAtomClone(MolAtom a)` Finds the clone of an atom.
`protected boolean`	`fixSelfReferringProperty(MProp prop)` Fix a property containing reference to the molecule.
`protected void`	`fuse0(CGraph g, boolean check)` Add the atoms and bonds of another molecule.
`int[][][]`	`getAromaticAndAliphaticRings(int aromatizationType, boolean onlyAromrings, boolean aromatize, int maxRingSize, int ringsLimit)` Get aromatic and or aliphatic ring atom indexes.
`int[][]`	`getAromrings()` Deprecated. please use getAromaticAndAliphaticRings instead.
`int[][]`	`getAromrings(int size)` Deprecated. please use getAromaticAndAliphaticRings instead.
`MolAtom`	`getAtom(int n)` Gets the nth atom.
`MolAtom[]`	`getAtomArray()` Creates an array of atoms.
`int`	`getAtomCount()` Gets the number of atoms.
`MolBond`	`getBond(int n)` Gets the nth bond.
`MolBond[]`	`getBondArray()` Creates an array of bonds.
`int`	`getBondCount()` Gets the number of bonds.
`int`	`getCharge(int k)` Gets the charge of an atom.
`int`	`getChirality(int i)` Computes the chirality of an atom of the Molecule instance based on both the coordinates of the neighbouring atoms and the stereo information of the bonds to those.
`double`	`getDesiredLength(int atno1, int atno2, int type)` Gets the ideal bond length in Angstroms.
`double`	`getDesiredLength(MolBond b)` Gets the ideal bond length in Angstroms.
`int`	`getDim()` Gets the dimension.
`MDocument`	`getDocument()` Gets the document object.
`protected MDocument`	`getDocumentForChild(MoleculeGraph g)` Gets the parent document for a child graph.
`CEdge[]`	`getEdgeArray()` Creates an array of bonds.
`java.util.Vector`	`getEdgeVector()` Creates an array of atoms.
`double`	`getExactMass()` Calculates the molecular exact weight of the molecule.
`int`	`getExplicitHcount()` Gets the total number of explicit hydrogens attached to the molecule.
`int`	`getExplicitLonePairCount(int i)`
`int`	`getFlags()` Gets the dimension and chiral flags.
`java.lang.String`	`getFormula()` Gets the molecular formula.
`MoleculeGraph`	`getGraphUnion()` Gets a graph containing all the atoms and bonds.
`int`	`getGrinv(int[] gi)` Gets the graph invariants.
`int`	`getGrinv(int[] gi, boolean uniqueFlag)` Deprecated. Please use getGrinv(int[], int) instead.
`int`	`getGrinv(int[] gi, int options)` Gets the graph invariants (canonical labels).
`int`	`getGrinvOptions()` Gets graph invariant calculation options passed to the module.
`int`	`getHybridizationState(int k)` Gets the hybridization state.
`int`	`getImplicitHcount()` Gets the total number of implicit hydrogens attached to the molecule.
`int`	`getLocalChirality(int idx, int[] ch)` Get local chirality.
`int`	`getLocalParity(int i)` Computes the local parity of an atom of the Molecule instance based on both the coordinates of the neighbouring atoms and the stereo information of the bonds to those.
`DPoint3`	`getLocation()` Gets the origin of the molecule.
`int`	`getLonePairCount(int i)` Gets the number of lone pairs.
`double`	`getMass()` Calculates the molecular weight of the molecule.
`int`	`getMassno(int k)` Gets the mass number of an atom.
`java.lang.String`	`getName()` Gets the molecule name.
`int`	`getNeighbor(int k, int i)` Gets the index of a neighbor of an atom.
`int`	`getNeighborCount(int k)` Gets the number of neighbors of an atom.
`java.util.Vector`	`getNodeVector()` Creates an array of atoms.
`int[][]`	`getNonAromrings()` Deprecated. please use getAromaticAndAliphaticRings instead.
`int[][]`	`getNonAromrings(int size)` Deprecated. please use getAromaticAndAliphaticRings instead.
`protected MDocument`	`getParentDocument()` Gets the document or the document of the parent graph.
`int`	`getParity(int i)` Computes the parity of an atom of the Molecule instance based on both the coordinates of the neighbouring atoms and the stereo information of the bonds to those.
`DPoint3[]`	`getPoints()` Gets an array containing the atom coordinates.
`int`	`getRadical(int k)` Gets the radical value of an atom.
`int[]`	`getSSSRBondSet()` Deprecated. please use getSSSRBondSetInLong() instead.
`long[]`	`getSSSRBondSetInLong()` Get SSSR bond bitsets in long array.
`int`	`getStereo2(CNode a1, int i2, int i3, CNode a4)` Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
`int`	`getStereo2(int i1, int i2, int i3, int i4)` Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
`int`	`getStereo2(MolBond b)` Gets cis/trans (Z/E) stereo information for the given bond.
`int`	`getStereo2(MolBond b, CNode a1, CNode a4)` Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
`int`	`getStereo2(MolBond b, CNode a1, CNode a4, boolean grcheck)` Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
`protected int`	`getStereo2(MolBond b, CNode a1, int i2, int i3, CNode a4)` Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
`protected int`	`getStereo2(MolBond b, CNode a1, int i2, int i3, CNode a4, boolean grcheck)` Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
`protected int`	`getSubGraphCount()` Gets the number of all "submolecules".
`MoleculeGraph[]`	`getSubGraphs()` Gets all "submolecules".
`protected void`	`getSubGraphs(MoleculeGraph[] m, int off)` Gets all "submolecules".
`int`	`getTotalCharge()` Gets the total (formal) charge of the molecule.
`double[]`	`getVisibleCoords(MolAtom ma)` Returns the coordinates of the given atom (contained in the molecule).
`boolean`	`hasAtomSet()` Tests whether the molecule graph has atom sets.
`boolean`	`hasBondSet()` Tests whether the molecule graph has atom sets.
`boolean`	`hasExplicitLonePairs()` Tests whether the molecule has implicit explici lone pair nodes.
`boolean`	`hasExtraLabelSet()`
`boolean`	`hasImplicitH()` Indicates, whether the molecule has implicit hydrogen atoms.
`boolean`	`hasSelfReferringProperty()` Tests whether the property list contains the molecule.
`boolean`	`hasValenceError()` Determines if this molecule has a valence error on any of its atoms.
`boolean`	`hydrogenize(boolean add)` Implicit/explicit Hydrogen conversion.
`void`	`implicitizeHydrogens(int f)` Removes explicit bound Hydrogens from the graph and converts them to implicit.
`void`	`implicitizeHydrogens(int f, MolAtom[] atoms)` Removes explicit bound Hydrogens from the graph and converts them to implicit.
`void`	`implicitizeHydrogens(int f, MolAtom[] atoms, boolean check)` Removes explicit bound Hydrogens from the graph and converts them to implicit.
`boolean`	`isAbsStereo()` Gets the absolute stereoconfiguration flag.
`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`	`isMultiChiral()` Returns the multiple chirality flag.
`boolean`	`isOnlyFirstAtomInStereoCalculation()` Get how parity module interpret wedes.
`boolean`	`isQuery()` Indicates if the molecule has query features.
`boolean`	`isRingBond(int idx)` Is this bond in ring?
`boolean`	`isSelfReference(MProp p)` Tests whether the specified property is a self reference to the molecule.
`boolean`	`isSimilarTo(CGraph g)` Checks if the graph is similar to another graph.
`boolean`	`isValidLinkNode(int linkAtomIdx, int outer1, int outer2)` Checks whether the specified link atom is valid or not.
`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 edges of a node with another node, then adds the node to the molecule.
`void`	`moveTo(DPoint3 o)` Move the molecule.
`CGraph`	`newInstance()` Creates a new MoleculeGraph object.
`boolean`	`partialClean(int dim, int[] fixed, java.lang.String opts)` Calculates atom coordinates by using fixed atoms.
`boolean`	`partialClean(MoleculeGraph template, int[] map, java.lang.String opts)` Calculates atom coordinates by using the given template molecule.
`MPropertyContainer`	`properties()` Gets the property container.
`void`	`qpropCheck(java.util.Vector v)` Check for query property errors.
`protected void`	`removeEdge(int i, int cleanupFlags)` Removes an edge by reference.
`void`	`removeExplicitLonePairs()` Removes explicit lone pairs.
`void`	`removeNode(CNode node, int cleanupFlags)` Removes a node and its edges with extra options.
`void`	`removeNode(int i, int cleanupFlags)` Removes a node and its edges with extra options.
`protected java.lang.Object[]`	`restoreCache(int n)` Restores caches like connection table, bond table, etc.
`void`	`revalidateCoordDependentProps()` Revalidate coordinate dependent properties.
`protected java.lang.Object[]`	`saveCache(int n)` Saves caches like connection table, bond table, etc.
`void`	`setAbsStereo(boolean c)` Sets the absolute stereoconfiguration flag.
`void`	`setAtomSetSeqs(int id)` Sets the set sequence number of all atoms.
`void`	`setBondSetSeqs(int id)` Sets the set sequence number of all bonds.
`boolean`	`setChirality(int i, int c)` Set chirality of an atom of the Molecule instance based on both the coordinates of the neighbouring atoms and the stereo information of the bonds to those.
`void`	`setDim(int d)` Sets the dimension.
`void`	`setEdge(int i, CEdge edge)` Sets the edge at the specified index.
`protected void`	`setFlags(int f)` Sets the dimension and chiral flags.
`void`	`setGrinvOptions(int opt)` Sets graph invariant calculation options passed to the module.
`void`	`setLinkNodeDefaultOuters(MolAtom atom)` Sets link node outer atoms to default values, if they are not set yet; making sure that the resulting link node configuration is valid.
`boolean`	`setLocalParity(int[] p, boolean useActualWedges)` In case of 2D molecule change the bonds flag (UP/DOWN), in case of 0D molecule set the atom flags to achieve the specified parity array.
`void`	`setLocation(DPoint3 o)` Set the origin of the molecule.
`protected void`	`setNode0(int i, CNode node)` Sets the node at the specified index.
`boolean`	`setParity(int[] p)` Change the bonds flag (UP/DOWN) connected to the whole molecule to achieve the specified parity array.
`boolean`	`setParity(int[] p, boolean useActualWedges)` Change the bonds flag (UP/DOWN) connected to the whole molecule to achieve the specified parity array.
`boolean`	`setParity(int i, int p)` Change the bonds flag (UP/DOWN) connected to the given atom to achieve the specified parity.
`void`	`setSetSeqs(int id)` Deprecated. as of Marvin 4.0, replaced by setAtomSetSeq
`boolean`	`stereoClean()` Reset the wedges of the molecule, based on the actual parity information.
`protected void`	`sumConservedQuantities(MolAtom a, int[] atoms, int sign)` For internal use only.
`java.lang.String`	`toString()` Overrides CGraph.toString() to ease debugging.
`void`	`transform(CTransform3D t)` Apply a transformation matrix to the atomic coordinates.
`void`	`transform(CTransform3D t, boolean incg)` Apply a transformation matrix to the atomic coordinates.
`protected void`	`updateDim(MoleculeGraph m)` Updates the dimensions when fusing two structures.
`void`	`useOnlyFirstAtomInStereoCalculation(boolean f)` Set how parity module should interpret wedes.
`void`	`valenceCheck()` Check valence and query property errors for each atoms.
`void`	`valenceCheck(java.util.Vector v)` Check valence and query property errors.

Methods inherited from class chemaxon.struc.CGraph
add, add, addEdge0, addEdgeWithoutChangingIt, addNode0, addNodeWithoutChangingIt, checkConsistency, checkEdgeConsistency, contains, contains, findBasicFrags, findComponentIds, findComponentIds, findEdge, findFrag, findFragById, findFrags, findInArray, findNode, fuse, fuse, fuse0, getBtab, getCSSR, getCtab, getEdge, getEdgeCount, getEdgeList, getForefather, getFragCount, getFragIds, getGrinv, getGrinvCC, getLock, getNode, getNodeCount, getParent, getSmallestRingSizeForIdx, getSSSR, getSSSREdges, getSSSRIdxesForAtoms, incGrinvCC, incGrinvCCOnly, indexOf, indexOf, insertEdge, insertEdgeInOrder, insertNode, insertNullEdges, insertNullNodes, isEmpty, isGrinvCCValid, isolate, isolate, isRealNodeParent, isRing, isSymmetric, mergeFrags, pack, regenCtabs, regenEdges, regenFragIds, removeAll, removeAllEdges, removeEdge, removeEdge, removeEdge, removeIsolatedEdges, removeIsolatedNodes, removeNode, removeNode, replaceEdge, resetCtab, resetGrinvInParents, setGrinvCC, setNode, sortEdgesAccordingTo

Methods inherited from class chemaxon.struc.CGraph

add, add, addEdge0, addEdgeWithoutChangingIt, addNode0, addNodeWithoutChangingIt, checkConsistency, checkEdgeConsistency, contains, contains, findBasicFrags, findComponentIds, findComponentIds, findEdge, findFrag, findFragById, findFrags, findInArray, findNode, fuse, fuse, fuse0, getBtab, getCSSR, getCtab, getEdge, getEdgeCount, getEdgeList, getForefather, getFragCount, getFragIds, getGrinv, getGrinvCC, getLock, getNode, getNodeCount, getParent, getSmallestRingSizeForIdx, getSSSR, getSSSREdges, getSSSRIdxesForAtoms, incGrinvCC, incGrinvCCOnly, indexOf, indexOf, insertEdge, insertEdgeInOrder, insertNode, insertNullEdges, insertNullNodes, isEmpty, isGrinvCCValid, isolate, isolate, isRealNodeParent, isRing, isSymmetric, mergeFrags, pack, regenCtabs, regenEdges, regenFragIds, removeAll, removeAllEdges, removeEdge, removeEdge, removeEdge, removeIsolatedEdges, removeIsolatedNodes, removeNode, removeNode, replaceEdge, resetCtab, resetGrinvInParents, setGrinvCC, setNode, sortEdgesAccordingTo

Methods inherited from class java.lang.Object
`equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait`

Field Detail

AROM_BASIC

public static final int AROM_BASIC

Basic aromatization.

Since:: Marvin 4.1, 12/09/2005
See Also:: aromatize(int), Constant Field Values

AROM_CHEMAXON

public static final int AROM_CHEMAXON

Deprecated. please use AROM_BASIC instead. Chemaxon aromatization.

Since:: Marvin 3.4, 05/10/2004
See Also:: aromatize(int), Constant Field Values

AROM_GENERAL

public static final int AROM_GENERAL

General (Daylight conform) aromatization.

Since:: Marvin 4.1, 12/09/2005
See Also:: aromatize(int), Constant Field Values

AROM_DAYLIGHT

public static final int AROM_DAYLIGHT

Deprecated. please use AROM_GENERAL instead. Daylight aromatization (modified Huckel rule).

Since:: Marvin 3.4, 05/10/2004
See Also:: aromatize(int), Constant Field Values

INVALID_LINKNODE_MESSAGE

public static final java.lang.String INVALID_LINKNODE_MESSAGE

See Also:: Constant Field Values

DIM_MASK

protected static final int DIM_MASK

Dimension bits in flags.

See Also:: getFlags(), Constant Field Values

RMCLEANUP_STEREO

public static final int RMCLEANUP_STEREO

When removing a H atom, keep stereo information unchanged.

Since:: Marvin 3.1
See Also:: removeNode(CNode, int), removeNode(int, int), CGraph.RMCLEANUP_ALL, Constant Field Values

RMCLEANUP_MOBJECT

public static final int RMCLEANUP_MOBJECT

Remove graphics objects containing the removed node.

Since:: Marvin 4.1, 03/07/2006
See Also:: removeNode(CNode, int), removeNode(int, int), CGraph.RMCLEANUP_ALL, Constant Field Values

RMCLEANUP_PARENTDOC

public static final int RMCLEANUP_PARENTDOC

Remove atom from parent document.

Since:: Marvin 4.1.13, 09/06/2007
See Also:: removeNode(CNode, int), removeNode(int, int), CGraph.RMCLEANUP_ALL, Constant Field Values

GRINV_NOHYDROGEN

public static final int GRINV_NOHYDROGEN

Graph invariant option for ignoring explicit hydrogens.

See Also:: getGrinv(int[], int), Constant Field Values

GRINV_STEREO

public static final int GRINV_STEREO

Graph invariant option for calculating graph invariants using stereo information. (Chirality & E/Z)

See Also:: getGrinv(int[], int), Constant Field Values

GRINV_OLDSTEREO

public static final int GRINV_OLDSTEREO

Graph invariant option for calculating graph invariants using the old stereo method. (Chirality only.)

See Also:: getGrinv(int[], int), Constant Field Values

GRINV_USEMAPS

public static final int GRINV_USEMAPS

Graph invariant option for calculating graph invariants considering atom maps also.

See Also:: getGrinv(int[], int), Constant Field Values

GRINV_VALUE_OPTIONS

public static final int GRINV_VALUE_OPTIONS

Unified mask of graph invariant options affecting grinv value. But see values below that are not included into this value when introducing a new one to avoid undesired side-effects.

See Also:: Constant Field Values

GRINV_DONT_STORE

public static final int GRINV_DONT_STORE

Graph invariant option to instruct that the graph invariant should not be stored in MoleculeGraph.

See Also:: getGrinv(int[], int), Constant Field Values

CACHE_REMOVE_GRINVMODULE

public static final int CACHE_REMOVE_GRINVMODULE

Cache removal option for remove module used in graph invariant calculation.

See Also:: clearCachedInfo(int), Constant Field Values

CACHE_REMOVE_PARITYMODULE

public static final int CACHE_REMOVE_PARITYMODULE

Cache removal option for remove module used in parity calculation.

See Also:: clearCachedInfo(int), Constant Field Values

CACHE_REMOVE_AROMATAMODULE

public static final int CACHE_REMOVE_AROMATAMODULE

Cache removal option for remove module used in aromatization.

See Also:: clearCachedInfo(int), Constant Field Values

CACHE_REMOVE_SSSRMODULE

public static final int CACHE_REMOVE_SSSRMODULE

Cache removal option for remove module used in sssr.

See Also:: clearCachedInfo(int), Constant Field Values

MIN_RING_SIZE_FOR_TRANS_DB

public static final int MIN_RING_SIZE_FOR_TRANS_DB

The minimal size of the ring for the existence of TRANS double bond.

See Also:: Constant Field Values

OMIT_POSTCLEAN

public static final int OMIT_POSTCLEAN

Omit arranging process after the hydrogen addition.

See Also:: addExplicitHydrogens(int), Constant Field Values

orix

protected transient double orix

Origin x.

oriy

protected transient double oriy

Origin y.

oriz

protected transient double oriz

Origin z.

propertyContainer

protected transient MPropertyContainer propertyContainer

useOnlyFirstAtomInStereoCalculation

protected transient boolean useOnlyFirstAtomInStereoCalculation

Constructor Detail

MoleculeGraph

public MoleculeGraph(MoleculeGraph p,
                     int na,
                     int nb)

Construct a molecule or fragment with the specified number of atoms and bonds.

Parameters:: p - the molecule that contains the created fragment; na - no reallocation needed until the number of atoms is less than this value; nb - no reallocation needed until the number of bonds is less than this value

MoleculeGraph

public MoleculeGraph()

Construct a molecule.

Method Detail

getDocument

public MDocument getDocument()

Gets the document object.

Returns:: a Marvin document object
Since:: Marvin 3.3

getParentDocument

protected MDocument getParentDocument()

Gets the document or the document of the parent graph. Moved to separate method because R-groups in RgMolecule should not have a normal document parent. If two R-groups would have a common document parent, then their bounds would be determined incorrectly because the graphics objects are common.

Returns:: the parent document
Since:: Marvin 4.1.1, 08/23/2006

getDocumentForChild

protected MDocument getDocumentForChild(MoleculeGraph g)

Gets the parent document for a child graph.

Parameters:: g - the child graph or this
Returns:: the parent document
Since:: Marvin 4.1.1, 08/23/2006

setDim

public void setDim(int d)

Sets the dimension.

Parameters:: d - 0, 2, or 3
See Also:: setFlags(int)

getDim

public int getDim()

Gets the dimension.

Returns:: 0, 2, or 3
See Also:: getFlags()

getFlags

public int getFlags()

Gets the dimension and chiral flags.

Returns:: the flags
Since:: Marvin 5.0.1, 02/10/2008

setFlags

protected void setFlags(int f)

Sets the dimension and chiral flags.

Parameters:: f - the flags
Since:: Marvin 5.0.1, 02/10/2008

isAbsStereo

public boolean isAbsStereo()

Gets the absolute stereoconfiguration flag. "Chiral flag" in MDL molfiles.

Returns:: true for absolute, false for relative configuration
See Also:: getFlags()

setAbsStereo

public void setAbsStereo(boolean c)

Sets the absolute stereoconfiguration flag.

Parameters:: c - the absolute stereoconfiguration flag
See Also:: setFlags(int)

clear

public void clear()

Clears the molecule. Does the same as clearForImport() but also clears the nodes vector.

See Also:: clearForImport(java.lang.String), CGraph.nodes

clearForImport

public void clearForImport(java.lang.String format)

Clears the edges vector, the properties, the flags, and sets the origin coordinates to 0. The molecule dimension is set to 2.

Parameters:: format - input file format, neglected
See Also:: CGraph.edges, orix, oriy, oriz, setFlags(int)

removeNode

public void removeNode(CNode node,
                       int cleanupFlags)

Removes a node and its edges with extra options. This method is for internal use only. Use CGraph.removeNode(CNode) instead unless you are sure what you are doing.

Overrides:: removeNode in class CGraph

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

removeNode

public void removeNode(int i,
                       int cleanupFlags)

Removes a node and its edges with extra options. This method is for internal use only. Use CGraph.removeNode(CNode) instead unless you are sure what you are doing.

Overrides:: removeNode in class CGraph

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

removeEdge

protected void removeEdge(int i,
                          int cleanupFlags)

Removes an edge by reference.

Overrides:: removeEdge in class CGraph

Parameters:: edge - the edge; cleanupFlags - extra clean-up methods
See Also:: CGraph.RMCLEANUP_NONE, CGraph.RMCLEANUP_ALL, CGraph.RMCLEANUP_EDGES

setNode0

protected void setNode0(int i,
                        CNode node)

Sets the node at the specified index.

Overrides:: setNode0 in class CGraph

Parameters:: i - node index; node - new node reference

setEdge

public void setEdge(int i,
                    CEdge edge)

Sets the edge at the specified index.

Overrides:: setEdge in class CGraph

Parameters:: i - edge index; edge - the edge reference

setAtomSetSeqs

public final void setAtomSetSeqs(int id)

Sets the set sequence number of all atoms.

Parameters:: id - the set sequence number
Since:: Marvin 4.0

setBondSetSeqs

public final void setBondSetSeqs(int id)

Sets the set sequence number of all bonds.

Parameters:: id - the set sequence number
Since:: Marvin 4.0

setSetSeqs

public final void setSetSeqs(int id)

Deprecated. as of Marvin 4.0, replaced by setAtomSetSeq

Parameters:: id - the set sequence number
Since:: Marvin 2.9.1

addExplicitHydrogens

public boolean addExplicitHydrogens(int f)

Adds explicit H atoms instead of the current implicit ones.

Parameters:: f - flags specifying special features, otherwise if f is 0, then the result equals with hydrogenize(true).
Returns:: true for success, false if an error occured
Throws:: java.lang.SecurityException - cannot load module because of a security problem (firewall)
Since:: Marvin 4.1.3, 02/11/2006
See Also:: OMIT_POSTCLEAN

addExplicitHydrogens

public boolean addExplicitHydrogens(int f,
                                    MolAtom[] atoms)

Adds explicit H atoms instead of the current implicit ones.

Parameters:: f - flags specifying special features, otherwise if f is 0, then the result equals with hydrogenize(true).; atoms - add hydrogens to these atoms only
Returns:: true for success, false if an error occured
Throws:: java.lang.SecurityException - cannot load module because of a security problem (firewall)
Since:: Marvin 5.0, 02/23/2007
See Also:: OMIT_POSTCLEAN

hydrogenize

public boolean hydrogenize(boolean add)

Implicit/explicit Hydrogen conversion. Adds explicit H atoms instead of the current implicit ones, or removes explicit H atoms and increases the number of implicit hydrogens.

Parameters:: add - add explicit H atoms if true, remove if false
Returns:: true for success, false if an error occured
Throws:: java.lang.SecurityException - cannot load module because of a security problem (firewall)

addExplicitLonePairs

public void addExplicitLonePairs()

Adds explicit lone pairs.

Throws:: java.lang.SecurityException - cannot load module because of a security problem (firewall)
Since:: Marvin 3.5, 07/06/2004

removeExplicitLonePairs

public void removeExplicitLonePairs()

Removes explicit lone pairs.

Throws:: java.lang.SecurityException - cannot load module because of a security problem (firewall)
Since:: Marvin 3.5, 07/06/2004

implicitizeHydrogens

public

chemaxon.struc Class MoleculeGraph

AROM_BASIC

AROM_CHEMAXON

AROM_GENERAL

AROM_DAYLIGHT

INVALID_LINKNODE_MESSAGE

DIM_MASK

RMCLEANUP_STEREO

RMCLEANUP_MOBJECT

RMCLEANUP_PARENTDOC

GRINV_NOHYDROGEN

GRINV_STEREO

GRINV_OLDSTEREO

GRINV_USEMAPS

GRINV_VALUE_OPTIONS

GRINV_DONT_STORE

CACHE_REMOVE_GRINVMODULE

CACHE_REMOVE_PARITYMODULE

CACHE_REMOVE_AROMATAMODULE

CACHE_REMOVE_SSSRMODULE

MIN_RING_SIZE_FOR_TRANS_DB

OMIT_POSTCLEAN

orix

oriy

oriz

propertyContainer

useOnlyFirstAtomInStereoCalculation

MoleculeGraph

MoleculeGraph

getDocument

getParentDocument

getDocumentForChild

setDim

getDim

getFlags

setFlags

isAbsStereo

setAbsStereo

clear

clearForImport

removeNode

removeNode

removeEdge

setNode0

setEdge

setAtomSetSeqs

setBondSetSeqs

setSetSeqs

addExplicitHydrogens

addExplicitHydrogens

hydrogenize

addExplicitLonePairs

removeExplicitLonePairs

implicitizeHydrogens

chemaxon.struc
Class MoleculeGraph