MoleculeGraph (Marvin API documentation (c) 1998-2021 ChemAxon Ltd.)

java.lang.Object
- chemaxon.struc.MoleculeGraph

All Implemented Interfaces:

chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>, chemaxon.core.structure.MoleculeForBuilder, chemaxon.core.structure.RootStructureForBuilder, chemaxon.core.structure.StructureForBuilder, Incomplecule, MTransformable, StereoConstants, java.io.Serializable

Direct Known Subclasses:

Molecule, SelectionMolecule
```
@PublicAPI
public class MoleculeGraph
extends java.lang.Object
implements chemaxon.core.structure.MoleculeForBuilder, Incomplecule, MTransformable, StereoConstants, java.io.Serializable, chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>
```
A graph consisting of MolAtom nodes and MolBond edges.

Since:

Marvin 3.0, 10/11/2002

Version:

14.7.7

Author:

Peter Csizmadia, Ferenc Csizmadia, Andras Volford, Gyorgy Pirok, Szilveszter Juhos, Szabolcs Csepregi, Erika Biro, Janos Kendi

See Also:

MolAtom, MolBond, Serialized Form

Property Summary

All Methods Instance Methods Concrete Methods
Type Property and Description

boolean hasSelfReferring
Tests whether the property list contains the molecule.

All Methods Instance Methods Concrete Methods
Type	Property and Description
`boolean`	`hasSelfReferring` Tests whether the property list contains the molecule.

Nested Class Summary

Nested Classes
Modifier and Type	Class and Description
`static class`	`MoleculeGraph.ValenceCheckState` Deprecated. As of Marvin 6.0, replaced by `setValenceCheckOptions(ValenceCheckOptions)` and `ValenceCheckOptions`.

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`AROM_AMBIGUOUS` Aromatization type for ambiguous 5-membered rings.
`static int`	`AROM_BASIC` Basic aromatization.
`static int`	`AROM_CHUCKEL` Huckel aromatization.
`static int`	`AROM_GENERAL` General (Daylight conform) aromatization.
`static int`	`AROM_LOOSE` Loose aromatization.
`static int`	`AROM_SUBSTRUCTURE` Substructure aromatization.
`protected int`	`atomCount` The number of atoms.
`protected static int`	`AUTO_UNGROUP` Automatic ungroup bit in flags.
`protected int`	`bondCount` The number of bonds.
`protected BondTable`	`btab` Bond table.
`static int`	`CACHE_REMOVE_ALL` Cache removal option for clearing all cached info.
`static int`	`CACHE_REMOVE_AROMATAMODULE` Cache removal option for remove module used in aromatization.
`static int`	`CACHE_REMOVE_CACHEMEMORY` Cache removal option for cacheMemory.
`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.
`static int`	`CACHE_REMOVE_TABS` Cache remove option to clear ctab and btab.
`protected java.util.List<java.lang.Object[]>`	`cacheMemory`
`protected int[][]`	`ctab` Connection table.
`static int`	`DEAROM_GENERAL` General dearomatization.
`static int`	`DEAROM_HUCKELCHECK` Dearomatize method which dearomatizes only that molecules which fullfills the Huckel's rule.
`static int`	`DEAROM_HUCKELCHECK_EX` Dearomatize method which dearomatizes only that molecules which fullfills the Huckel's rule.
`protected static int`	`DIM_MASK` Dimension bits in flags.
`static int`	`FRAG_BASIC` Basic fragmentation, only atom - atom connections (bond) are considered.
`static int`	`FRAG_KEEPING_MULTICENTERS` Fragmentation without breaking multicenter S-groups.
`static int`	`FRAG_KEEPING_SGROUPS` Fragmentation without breaking S-groups.
`static int`	`FRAG_TYPE_COUNT` Number of fragmentation types.
`chemaxon.struc.gearch.MoleculeGraphGearch`	`gearch`
`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.
`protected long`	`grinvCC` Graph invariant change count.
`protected static int`	`INITIAL_CAPACITY` Initial capacity of the atoms and bonds vectors.
`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 MoleculeGraph`	`parentGraph` The structure that contains this molecule graph as a substructure.
`protected MPropertyContainer`	`propertyContainer`
`static int`	`RMCLEANUP_ALL` Perform all clean-up methods when removing an atom or a bond.
`static int`	`RMCLEANUP_EDGES` When removing an atom or a bond, also remove the bond(s) from the atom object(s).
`protected static int`	`RMCLEANUP_FIXCOMPONENT` Remove called from RxnMolecule.fixComponent.
`static int`	`RMCLEANUP_MOBJECT` Remove graphics objects containing the removed atom.
`static int`	`RMCLEANUP_NONE` Do not perform any clean-up methods when removing an atom or a bond.
`static int`	`RMCLEANUP_PARENTDOC` Remove atom from parent document.
`static int`	`RMCLEANUP_STEREO` When removing a H atom, keep stereo information unchanged.
`protected MoleculeGraph`	`superGraph` Parent of all parents.
`protected MolAtom[]`	`theAtoms` The atoms (nodes).
`protected MolBond[]`	`theBonds` The bonds (edges).
`protected boolean`	`useOnlyFirstAtomInStereoCalculation`
`protected static int`	`VALENCE_CHECK` Valence check calculation bit in flags.
`protected static int`	`VALENCE_CHECK_AMBIGUOUS` Deprecated. As of Marvin 6.0, replaced by `ValenceCheckOptions`.

Fields inherited from interface chemaxon.struc.StereoConstants
ANTI, ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_M, CHIRALITY_MASK, CHIRALITY_P, CHIRALITY_r, CHIRALITY_R, CHIRALITY_s, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_ALL_POSSIBLE, CHIRALITYSUPPORT_NONE, CHIRALITYSUPPORT_SELECTED, CIS, CIS_TRANS, CTUMASK, CTUNKNOWN, CTUNSPEC, DBS_ALL, DBS_MARKED, DBS_NONE, ENDO, EXO, PARITY_ALLENE, PARITY_EITHER, PARITY_EVEN, PARITY_MASK, PARITY_NONE, PARITY_ODD, PARITY_TETRAHEDRAL, PARITY_UNSPEC, STGRP_ABS, STGRP_AND, STGRP_NONE, STGRP_OR, SYN, TRANS

Constructor Summary

Constructors
Constructor and Description
`MoleculeGraph()` Construct a 2 dimensional molecule.
`MoleculeGraph(MoleculeGraph p, int na, int nb)` Construct a molecule or fragment with the specified number of atoms and bonds.

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`add(MolAtom atom)` Adds an atom to the molecule.
`void`	`add(MolBond bond)` Adds a bond to the molecule.
`void`	`add(MolBond bond, boolean checkParallel)` Add a bond to the molecule.
`protected void`	`addAtom0(MolAtom atom)` Adds an atom.
`protected void`	`addAtomsAndBondsTo(MoleculeGraph s)` Adds all atoms and bonds to the specified molecule.
`protected void`	`addAtomToFragment(MolAtom atom)` Adds an atom to a fragment.
`protected int`	`addAtomWithoutChangingIt(MolAtom atom)` Adds an atom without setting its parentGraph and index fields.
`protected void`	`addBond0(MolBond bond)` Adds a bond.
`protected int`	`addBondWithoutChangingIt(MolBond bond)` Adds a bond without setting its parentGraph and index fields.
`boolean`	`addExplicitHydrogens(int f)` Deprecated. As of Marvin 5.7, replaced by `Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int)`. Usage: Hydrogenize.convertImplicitHToExplicit(molecule, null, f);
`boolean`	`addExplicitHydrogens(int f, MolAtom[] atoms)` Deprecated. As of Marvin 5.7, replaced by `Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int)`. Usage: Hydrogenize.convertImplicitHToExplicit(molecule, atoms, f);
`void`	`addExplicitLonePairs()` Deprecated. As of Marvin 5.7, replaced by `Hydrogenize.convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[])`. Usage: Hydrogenize.convertImplicitLonePairsToExplicit(molecule, null);
`protected int`	`addSimpleAtomWithoutChangingIt(MolAtom atom)` Adds a non-SgroupAtom atom without setting its parentGraph and index fields.
`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)` Aromatizes molecule.
`void`	`aromatize(int method, boolean checkAmbiguity)` Aromatizes molecule.
`boolean`	`arrangeComponents()` Deprecated. As of Marvin 5.7, replaced by `CleanUtil.arrangeComponents(MoleculeGraph, boolean, boolean)`. Usage: CleanUtil.arrangeComponents(molecule, true, true);
`java.util.List<MolAtom>`	`atoms()` Provides a list view of the atoms in the molecule.
`double`	`bondlength()` Calculates the regular bond length.
`java.util.List<MolBond>`	`bonds()` Provides a list view of the bonds in the molecule.
`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)` Calculates the center of the outer rectangle.
`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`	`canBeCT(MolBond bond)` Determines whether the given bond can be a CIS/TRANS or not.
`protected void`	`checkBondConsistency()`
`void`	`checkConsistency()` Deprecated. As of Marvin 5.7, no replacement. Not intended for public use, it was intended only for internal debugging.
`boolean`	`clean(int dim, java.lang.String opts)` Deprecated. As of Marvin 5.7, replaced by `Cleaner.clean(MoleculeGraph, int, String)`.
`boolean`	`clean(int dim, java.lang.String opts, MProgressMonitor pmon)` Deprecated. As of Marvin 5.7, replaced by `Cleaner.clean(MoleculeGraph, int, String, MProgressMonitor)`.
`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 bonds vector, the properties, the flags, and sets the origin coordinates to 0.
`MoleculeGraph`	`clone()` Make an identical copy of the molecule.
`protected int`	`cloneAtoms(int[] cnodes, MoleculeGraph graph)` Copies the specified atoms.
`void`	`clonecopy(int[] iatoms, MoleculeGraph g)` Copies the specified atoms of this molecule graph to another one.
`void`	`clonecopy(MoleculeGraph m)` Make another molecule identical to this one.
`protected boolean`	`clonecopyMoleculeGraphWithoutSgroups(int[] cnodes, MolBond[] cedges, int nb, MoleculeGraph graph)` Copies the specified atoms and bonds of this molecule graph to another one.
`void`	`clonelesscopy(MoleculeGraph graph)` Deprecated. as of Marvin 6.3. Not supported feature.
`protected void`	`connectOriginalBondsToNewAtom(MolAtom newAtom, MolAtom orig, MolBond[] bonds)` Sets the original connections to the new atom.
`boolean`	`contains(MolAtom atom)` Checks if the molecule graph contains the specified atom.
`boolean`	`contains(MolBond bond)` Checks if the molecule graph contains the specified bond, or a bond which is equals with the given bond.
`boolean`	`contains(MoleculeGraph graph)` Does the molecule graph contain the specified fragment?
`int[][]`	`createCHtab()` Deprecated. As of version 20.22, no replacement.
`protected MoleculeGraph`	`createDehydrogenizedReadOnlyGraph()` Creates a dehydrogenized version of the molecule.
`protected chemaxon.struc.gearch.MoleculeGraphGearch`	`createGearch()`
`protected Smolecule`	`createSmolecule()` Creates a `Smolecule` represenation of this molecule.
`boolean`	`dearomatize()` Dearomatize molecule.
`boolean`	`dearomatize(int method)` Dearomatize molecule.
`protected int`	`findAtom(MolAtom atom)` Finds an atom in the atoms array.
`MolAtom`	`findAtomClone(MolAtom a)` Finds the clone of an atom.
`<C extends MoleculeGraph> C[]`	`findBasicFrags(java.lang.Class<C> cl)` Determines the disconnected fragments and puts them into an array.
`protected int`	`findBond(MolBond bond)` Finds a bond in the bonds array.
`int[]`	`findComponentIds()` Deprecated. As of Marvin 6.0, replaced by `getFragIds(int)` and `FRAG_BASIC`. Usage: mol.getFragIds(MoleculeGraph.FRAG_BASIC);
`int[]`	`findComponentIds(int[] inds)` Assigns a component ID to each connected component formed by the specified atom indexes.
`void`	`findFrag(int i, int fragmentationType, MoleculeGraph frag)` Determines the subgraph connected to the specified atom.
`void`	`findFrag(int i, MoleculeGraph frag)` Deprecated. As of Marvin 5.6, replaced by `findFrag(int, int, MoleculeGraph)` and `FRAG_KEEPING_MULTICENTERS`. Usage: mol.findFrag(i, MoleculeGraph.FRAG_KEEPING_MULTICENTERS, frag);
`void`	`findFragById(int fragId, int fragmentationType, MoleculeGraph frag)` Determines the subgraph corresponding to the specific fragment ID.
`<C extends MoleculeGraph> C[]`	`findFrags(java.lang.Class<C> cl)` Deprecated. As of Marvin 5.6, replaced by `findFrags(Class, int)` and `FRAG_KEEPING_MULTICENTERS`. Usage: mol.findFrags(cl, MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
`<C extends MoleculeGraph> C[]`	`findFrags(java.lang.Class<C> cl, int fragmentationType)` Determines the disconnected fragments and puts them into an array.
`protected static int`	`findInArray(java.lang.Object[] array, int[] indices, int n, java.lang.Object o)` Finds an object in an array.
`void`	`fixProperties()` Delegates to tracker's fixProperties().
`protected boolean`	`fixSelfReferringProperty(MProp prop)` Fix a property containing reference to the molecule.
`void`	`fuse(MoleculeGraph graph)` Adds those atoms and bonds of another molecule to this one that are not already elements.
`void`	`fuse(MoleculeGraph graph, boolean check)` Adds atoms and bonds of another molecule to this one.
`protected void`	`fuse0(MoleculeGraph g, boolean check)` Adds the atoms and bonds of another molecule to this one.
`int[][][]`	`getAromaticAndAliphaticRings(int aromatizationType, boolean onlyAromrings, boolean aromatize, int maxRingSize, int ringsLimit)` Returns the aromatic and or aliphatic ring atom indexes. Note: This method does not aromatize the already aromatized rings.
`MolAtom`	`getAtom(int n)` Gets the nth atom.
`MolAtom[]`	`getAtomArray()` Creates an array of atoms.
`int`	`getAtomCount()` Gets the number of atoms.
`int`	`getAtomCount(int atomicNumber)` Gets the number of atoms with the given atomic number.
`int`	`getAtomicNumber(MolAtom atom)`
`IteratorFactory.AtomIterator`	`getAtomIterator()` Returns an iterator over the atoms in this molecule in proper sequence.
`java.util.List<MolAtom>`	`getAtomReferenceList()` Deprecated. Use `atoms()` instead.
`MolBond`	`getBond(int n)` Gets the nth bond.
`MolBond[]`	`getBondArray()` Creates an array of bonds.
`int`	`getBondCount()` Gets the number of bonds.
`IteratorFactory.BondIterator`	`getBondIterator()` Returns an iterator over the bonds in this molecule in proper sequence.
`protected MolBond[]`	`getBonds(MolAtom atom)` Returns the bonds attached to the given atom in this molecule graph.
`BondTable`	`getBondTable()` Gets the bond (edge) table.
`int`	`getCharge(MolAtom atom)`
`int`	`getChirality(int i)` Computes the chirality of an atom of the Molecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
`int[][]`	`getCSSR()` Gets the Complete Set of Smallest Ring atom indexes array.
`int[][]`	`getCSSRIdxesForAtoms()` Get the cssr ring indexes in which the atom (specified with it's index) can be located.
`int[][]`	`getCtab()` Gets the connection table.
`double`	`getDesiredLength(int atno1, int atno2, int type)` Deprecated. As of Marvin 5.11, replaced by `MolBond.desiredLength(int, int, int, int)` and `getDim()`. Usage: MolBond.desiredLength(atno1, atno2, type, getDim());
`double`	`getDesiredLength(MolBond b)` Deprecated. As of Marvin 5.11, replaced by `MolBond.desiredLength(int, int, int, int)`, `MolBond.getType()` and `getDim()`. Usage: MolBond.desiredLength(atno1, atno2, b.getType, getDim());
`int`	`getDim()` Gets the dimension.
`MDocument`	`getDocument()` Gets the document object.
`protected MDocument`	`getDocumentForChild(MoleculeGraph g)` Gets the parent document for a child molecule graph.
`DPoint3[]`	`getEnclosingCube()` Gets the cube that encloses the atoms of molecule graph.
`double`	`getExactMass()` Calculates the molecular weight of the molecule using the mass of the most frequent natural isotope of the atoms.
`int`	`getExplicitHcount()` Gets the total number of explicit hydrogens attached to the molecule.
`int`	`getExplicitLonePairCount(int i)` Deprecated. use `MDocument.getExplicitLonePairCount()` instead
`chemaxon.struc.stereo.EZConfiguration`	`getEZStereo(MolBond bond)` Deprecated. as of Marvin 15.2.16 replaced by `CIPStereoCalculator.calculateCIPStereoDescriptors(MoleculeGraph, boolean)`.
`int`	`getFlags()` Gets the dimension and chiral flags.
`MoleculeGraph`	`getForefather()` Gets the first parent.
`int`	`getFormalCharge()` Gets the (total) formal charge of the molecule.
`java.lang.String`	`getFormula()` Gets the molecular formula.
`int`	`getFragCount()` Deprecated. As of Marvin 5.6, replaced by `getFragCount(int)` and `FRAG_KEEPING_MULTICENTERS`. Usage: mol.getFragCount(MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
`int`	`getFragCount(int fragmentationType)` Returns the number of fragments for the given fragmentation type.
`int[]`	`getFragIds(int fragmentationType)` Gets an array containing the fragment id for each atom for the given fragmentation type.
`int`	`getFreeAttachmentPoints(MolAtom atom)`
`MoleculeGraph`	`getGraphUnion()` Gets a molecule graph containing all the atoms and bonds.
`protected int[]`	`getGrinv()` Gets the graph invariants array.
`int`	`getGrinv(int[] gi)` Gets the graph invariants (canonical labels).
`int`	`getGrinv(int[] gi, boolean uniqueFlag)` Deprecated. As of Marvin 4.0, replaced by `getGrinv(int[], int)`. Usage: getGrinv(gi, uniqueFlag ? GRINV_OLDSTEREO : 0);
`int`	`getGrinv(int[] gi, int options)` Gets the graph invariants (canonical labels).
`long`	`getGrinvCC()` Gets the graph invariant change count.
`int`	`getGrinvOptions()` Gets graph invariant calculation options passed to the module.
`int`	`getImplicitHcount()` Gets the total number of implicit hydrogens attached to the molecule.
`int`	`getImplicitHCount(MolAtom atom)`
`MolAtom`	`getLigand(MolAtom atom, int n)`
`int`	`getLigandAtno(MolAtom atom, int n)`
`chemaxon.struc.BondType`	`getLigandBondType(MolAtom atom, int i)`
`int`	`getLigandCount(MolAtom atom)`
`int`	`getLocalParity(int i)` Computes the local parity of an atom of the Molecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those.
`DPoint3`	`getLocation()` Gets the origin of the molecule.
`java.lang.Object`	`getLock()` Gets the lock object for synchronization.
`int`	`getLonePairCount(int i)` Deprecated. use `MDocument.getLonePairCount()` instead
`double`	`getMass()` Calculates the molecular weight of the molecule.
`int`	`getMaxRgroupAttachmentPointOrder()` Returns the maximal attachment point order of R-group attachment point atoms in this molecule graph.
`java.lang.String`	`getName()` Gets the molecule title/name.
`MoleculeGraph`	`getParent()` Gets the parent graph that contains this substructure.
`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 neighboring atoms and the stereo information of the bonds to those.
`int`	`getParityType(int idx)` Gets parity type.
`DPoint3[]`	`getPoints()` Gets an array containing the atom coordinates.
`protected int`	`getPossibleAttachmentPoints(MolAtom molAtom)` Deprecated. As of Marvin 6.0, replaced by `SuperatomSgroup.getAttachmentPointOrders(MolAtom)` and `MolAtom.getAttachParentSgroup()`. Usage: SuperatomSgroup group = (SuperatomSgroup)molAtom.getAttachParentSgroup()); List<Integer> orders = group.getAttachmentPointOrders(molAtom);
`int`	`getRadicalCount(MolAtom atom)`
`int[]`	`getSmallestRingSizeForIdx()` Get the smallest ring size in which the atom (specified with it's index) can be located.
`int[][]`	`getSSSR()` Gets the Smallest Set of Smallest Ring atom indexes array.
`int[][]`	`getSSSRBonds()` Gets the Smallest Set of Smallest Ring bond indexes array.
`java.util.BitSet[]`	`getSSSRBondsAsBitSet()` Gets the Smallest Set of Smallest Ring edges as an array of BitSets, one BitSet for each ring.
`java.util.BitSet`	`getSSSRBondSet()` Get SSSR bond index bitset.
`long[]`	`getSSSRBondSetInLong()` Deprecated. as of 15.09.2014, use `getSSSRBondSet()` instead
`int[][]`	`getSSSRIdxesForAtoms()` Get the sssr ring indexes in which the atom (specified with it's index) can be located.
`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(MolAtom a1, int i2, int i3, MolAtom a4)` Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
`int`	`getStereo2(MolBond b)` Deprecated. as of Marvin 6.3 replaced by `getEZStereo(MolBond)`.
`protected int`	`getStereo2(MolBond b, MolAtom a1, int i2, int i3, MolAtom a4)` Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
`protected int`	`getStereo2(MolBond b, MolAtom a1, int i2, int i3, MolAtom a4, boolean grcheck)` Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
`int`	`getStereo2(MolBond b, MolAtom a1, MolAtom a4)` Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration.
`int`	`getStereo2(MolBond b, MolAtom a1, MolAtom 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.
`ValenceCheckOptions`	`getValenceCheckOptions()` Returns the options for valence checking.
`MoleculeGraph.ValenceCheckState`	`getValenceCheckState()` Deprecated. As of Marvin 6.0, replaced by `getValenceCheckOptions()` and `isValenceCheckEnabled()`. Usage: // Same as getValenceCheckState() == ValenceCheckState.OFF: isValenceCheckEnabled() == true; // Same as getValenceCheckState() == ValenceCheckState.AMBIGUOUS_AROMATIC_ATOMS_IGNORED: getValenceCheckOptions.isLocalAromatic() == true; // Same as getValenceCheckState() == ValenceCheckState.FULL: getValenceCheckOptions.isLocalAromatic() == false;
`int`	`getValenceProperty(MolAtom atom)`
`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()` Deprecated. use `MDocument.hasExplicitLonePairs()` instead
`boolean`	`hasExtraLabelSet()`
`boolean`	`hasImplicitH()` Tests 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)` Deprecated. As of Marvin 5.7, replaced by `Hydrogenize.convertImplicitHToExplicit(MoleculeGraph)` and `Hydrogenize.convertExplicitHToImplicit(MoleculeGraph)`.
`void`	`implicitizeHydrogens(int f)` Deprecated. As of Marvin 5.7, replaced by `Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int)`. Usage: Hydrogenize.convertExplicitHToImplicit(molecule, f);
`void`	`implicitizeHydrogens(int f, MolAtom[] atoms)` Deprecated. As of Marvin 5.7, replaced by `Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int)`. Usage: Hydrogenize.convertExplicitHToImplicit(mol, atoms, f);
`void`	`implicitizeHydrogens(int f, MolAtom[] atoms, boolean check)` Deprecated. As of Marvin 5.7, replaced by `Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean)`. Usage: Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);
`protected boolean`	`implicitizeHydrogens0(int f, MolAtom[] atoms, boolean check)` Deprecated. As of Marvin 5.7, replaced by `Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean)`. Usage: Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);
`protected void`	`incGrinvCC()` Increases the graph invariant change count and sets grinv to null.
`protected void`	`incGrinvCC(boolean isSSSRReset)`
`void`	`incGrinvCCOnly()` Increases the graph invariant change count, but does not change grinv.
`int`	`indexOf(MolAtom atom)` Gets the index of the specified atom.
`int`	`indexOf(MolBond bond)` Gets the index of the specified bond.
`void`	`insertAtom(int i, MolAtom atom)` Deprecated. as of Marvin 6.2, may construct inconsistent `MoleculeGraph`. Similar functionality is performed by `add(MolAtom)`.
`void`	`insertBond(int i, MolBond bond)` Deprecated. as of Marvin 6.2, may constructs inconsistent `MoleculeGraph`. Similar functionality is performed by `add(MolBond)`.
`void`	`insertBondInOrder(MolBond e, MolBond[] order)` Insert a bond in the order specified as the second argument.
`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`	`isAbsStereo()` Gets the absolute stereoconfiguration flag.
`boolean`	`isAcceptedSpecialLigand(MolAtom atom)`
`boolean`	`isAtom()` Deprecated. As of Marvin 14.7.7, no replacement. Not supported feature.
`boolean`	`isAtomInRing(MolAtom atom)`
`boolean`	`isBond()` Deprecated. As of Marvin 14.7.7, no replacement. Not supported feature.
`protected boolean`	`isBondParallelWith(MolBond b)` Checks if there is a bond parallel (having same endpoints) with the given bond in this MoleculeGraph.
`boolean`	`isEmpty()` Tests whether the molecule graph is empty.
`protected boolean`	`isGrinvCCValid()` Tests whether the graph invariant change count is valid.
`boolean`	`isLargeMolecule()` Returns `true` if large molecule (number of atoms exceeds `1000`).
`boolean`	`isMolecule()` Deprecated. as of Marvin 14.7.7, no replacement. Usage: use `myObject instanceof Molecule` instead
`boolean`	`isMultiChiral()` Returns the multiple chirality flag.
`protected void`	`isolate(MolAtom node)` Isolates atom: a more efficient way of removing an atom than `removeAtom(chemaxon.struc.MolAtom)`, especially for large molecule graphs.
`protected void`	`isolate(MolBond edge)` Isolates bond: a more efficient way of removing a bond than `removeBond(chemaxon.struc.MolBond)`, especially for large molecule graphs.
`boolean`	`isOnlyFirstAtomInStereoCalculation()` Get how parity module interpret wedges.
`boolean`	`isQuery()` Indicates if the molecule has query features: query atoms or query bonds.
`protected boolean`	`isRealAtomParent()` Can it be a real atom parent?
`boolean`	`isRing()` Deprecated. As of Marvin 14.7.7, no replacement. Not supported feature.
`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(MoleculeGraph g)` Tests if the molecule graph is similar to another graph.
`boolean`	`isSymmetric()` Tests whether the molecule graph is symmetric.
`boolean`	`isValenceCheckEnabled()` Determines whether valence check is enabled on this molecule graph.
`boolean`	`isValidLinkNode(int linkAtomIdx, int outer1, int outer2)` Checks whether the specified link atom is valid or not.
`protected void`	`makeItSimilar(MoleculeGraph g)` Copies some properties of this molecule to the other one specified as argument.
`void`	`mergeAtoms(MolAtom replacementAtom, MolAtom origAtom)` Deprecated. As of Marvin 6.2, use `MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean)` instead.
`int`	`mergeFrags(int id1, int id2, int fragmentationType)` Merges two connected components of the given fragmentation type.
`void`	`moveTo(DPoint3 o)` Move the molecule.
`MoleculeGraph`	`newInstance()` Creates a new MoleculeGraph object.
`void`	`pack()` Reduce memory usage.
`boolean`	`partialClean(int dim, int[] fixed, java.lang.String opts)` Deprecated. As of Marvin 5.7, replaced by `Cleaner.partialClean(MoleculeGraph, int, int[], String)`.
`boolean`	`partialClean(Molecule[] template, java.lang.String opts)` Deprecated. As of Marvin 5.7, replaced by `Cleaner.partialClean(Molecule, Molecule[], String)`.
`boolean`	`partialClean(MoleculeGraph template, int[] map, java.lang.String opts)` Deprecated. As of Marvin 5.7, replaced by `Cleaner.partialClean(MoleculeGraph, MoleculeGraph, int[], String)`.
`MPropertyContainer`	`properties()` Gets the property container.
`void`	`qpropCheck(java.util.List<MolAtom> v)` Check for query property errors.
`void`	`regenBonds()` Regenerates the bond vector: remove its elements, then put the bond objects from the atoms into it.
`protected void`	`regenBtab()` Regenerates the bond table.
`protected void`	`regenCtab()` Regenerates the connection table.
`protected void`	`regenGearch()` Recreate graph search results object.
`void`	`removeAll()` Removes all the atoms and bonds.
`void`	`removeAllBonds()` Removes all bonds.
`void`	`removeAtom(int i)` Removes an atom and its bonds by index.
`void`	`removeAtom(int i, int cleanupFlags)` Removes an atom and its bonds with extra clean-up options.
`void`	`removeAtom(MolAtom atom)` Removes an atom and its bonds by reference.
`void`	`removeAtom(MolAtom atom, int cleanupFlags)` Removes an atom and its bonds with extra clean-up options.
`void`	`removeBond(int i)` Removes a bond by index.
`protected void`	`removeBond(int i, int cleanupFlags)` Removes a bond by index.
`void`	`removeBond(MolBond bond)` Removes a bond by reference.
`protected void`	`removeBond(MolBond bond, int cleanupFlags)` Removes a bond by reference.
`void`	`removeExplicitLonePairs()` Deprecated. As of Marvin 5.7, replaced by `Hydrogenize.convertExplicitLonePairsToImplicit(MoleculeGraph)`.
`protected void`	`removeIsolatedAtoms()` Removes the `null` atom entries in the atoms array and sets the index fields appropriately.
`protected void`	`removeIsolatedBonds()` Removes the `null` bond entries in the bonds array and sets the index fields appropriately.
`void`	`replaceAtom(int i, MolAtom newAtom)` Replaces the atom on the given index with the parameter atom and removes the parameter atom from its original parent molecule if needed.
`void`	`replaceBond(MolBond oldb, MolBond newb)` Deprecated. as of Marvin 6.2, may constructs inconsistent `MoleculeGraph`. Use `removeBond(MolBond)` for removal and `add(MolBond)` for adding a new bond to the molecule.
`protected void`	`resetCtab()` An operation performed that changed the connection table and the graph invariants.
`protected void`	`resetGrinvInParents()` Graph invariants must be recalculated for this graph and all parent graphs.
`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`	`setAtom(int i, MolAtom atom)` Deprecated. as of Marvin 6.2, may construct inconsistent `MoleculeGraph`. Use `removeAtom(int)` for atom removal and `add(MolAtom)` for adding new atoms.
`protected void`	`setAtom0(int i, MolAtom atom)` Sets the atom at the specified index.
`void`	`setAtomSetSeqs(int id)` Sets the set sequence number of all atoms.
`void`	`setBond(int i, MolBond b)` Deprecated. as of Marvin 6.2, may constructs inconsistent `MoleculeGraph`. Use `removeBond(MolBond)` for bond removal and `add(MolBond)` for adding a new bond to the molecule.
`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 neighboring atoms and the stereo information of the bonds to those.
`boolean`	`setChirality(java.util.Map<java.lang.Integer,java.lang.Integer> chiralities)` Sets the chiralities of atoms.
`void`	`setDim(int d)` Sets the dimension.
`protected void`	`setFlags(int f)` Sets the flags of the molecule.
`protected void`	`setFlags(int f, int mask)` Sets specified bits in the flags.
`protected void`	`setGrinvCC(long g)` Sets the graph invariant change count.
`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.
`boolean`	`setLocalParity(int[] idxes, int[] p, boolean useActualWedges)` Set given local parity for the given atomic indexes.
`void`	`setLocation(DPoint3 o)` Set the origin of the molecule.
`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.
`protected void`	`setSupergraph(MoleculeGraph molecule)` Sets the given molecule as the supergraph of this graph.
`void`	`setValenceCheckEnabled(boolean b)` Enables or disables valence check on this molecule graph, depending on the value of the parameter b.
`void`	`setValenceCheckOptions(ValenceCheckOptions options)` Sets the options for valence checking.
`void`	`setValenceCheckState(MoleculeGraph.ValenceCheckState state)` Deprecated. As of Marvin 6.0, replaced by `setValenceCheckOptions(ValenceCheckOptions)` and `setValenceCheckEnabled(boolean)`. Usage: // Same as setValenceCheckState(ValenceCheckState.OFF): setValenceCheckEnabled(false); // Same as setValenceCheckState(ValenceCheckState.AMBIGUOUS_AROMATIC_ATOMS_IGNORED): setValenceCheckOptions(ValenceCheckOptions.DEFAULT); // Same as setValenceCheckState(ValenceCheckState.FULL): setValenceCheckOptions(new ValenceCheckOptions(false, true));
`Smolecule`	`smol()` Gets a `Smolecule` representation of this molecule.
`void`	`sortBondsAccordingTo(MolBond[] order)` Sorts bonds in the same order as they appear in another chemical graph.
`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 MoleculeGraph.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 atoms.
`void`	`valenceCheck(java.util.List<MolAtom> v)` Check valence and query property errors.

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

Property Detail
- hasSelfReferring
```
public final boolean hasSelfReferringProperty
```
  Tests whether the property list contains the molecule.
  
  Since:
  
  Marvin 4.1.6, 02/11/2007

Field Detail
- INITIAL_CAPACITY
```
protected static final int INITIAL_CAPACITY
```
  Initial capacity of the atoms and bonds vectors.
  
  See Also:
  
  Constant Field Values
- 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_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_LOOSE
```
public static final int AROM_LOOSE
```
  Loose aromatization.
  
  Since:
  
  Marvin 5.2, 01/11/2008
  
  See Also:
  
  aromatize(int), Constant Field Values
- AROM_SUBSTRUCTURE
```
public static final int AROM_SUBSTRUCTURE
```
  Substructure aromatization. Used internally.
  
  Since:
  
  Marvin 5.3, 09/14/2009
  
  See Also:
  
  aromatize(int), Constant Field Values
- AROM_AMBIGUOUS
```
public static final int AROM_AMBIGUOUS
```
  Aromatization type for ambiguous 5-membered rings. This option of aromatization checks 5-membered rings with bond pattern similar to pyrrole and having A, AH, Q, QH, atom list (with ambiguous atom types) or not list at the N position (with the two single bonds). In that particular ring, the bonds are replaced by "single or aromatic" and "double or aromatic" bonds. Fusion with aromatic rings are tricky, the aromatic rings should be aromatized first.
  
  Since:
  
  Marvin 5.4, 08/14/2010
  
  See Also:
  
  aromatize(int), Constant Field Values
- AROM_CHUCKEL
```
public static final int AROM_CHUCKEL
```
  Huckel aromatization.
  
  Since:
  
  Marvin 16.12, 09/12/2016
  
  See Also:
  
  CHuckelAromatization, Constant Field Values
- DEAROM_GENERAL
```
public static final int DEAROM_GENERAL
```
  General dearomatization.
  
  Since:
  
  Marvin 5.2.3, 06/29/2008
  
  See Also:
  
  dearomatize(int), Constant Field Values
- DEAROM_HUCKELCHECK
```
public static final int DEAROM_HUCKELCHECK
```
  Dearomatize method which dearomatizes only that molecules which fullfills the Huckel's rule.
  
  Since:
  
  Marvin 5.2.3, 06/29/2008
  
  See Also:
  
  dearomatize(int), Constant Field Values
- DEAROM_HUCKELCHECK_EX
```
public static final int DEAROM_HUCKELCHECK_EX
```
  Dearomatize method which dearomatizes only that molecules which fullfills the Huckel's rule. The same as DEAROM_HUCKELCHECK but throws exception if dearomatization fails.
  
  Since:
  
  Marvin 5.2.3, 06/29/2008
  
  See Also:
  
  dearomatize(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
- AUTO_UNGROUP
```
protected static final int AUTO_UNGROUP
```
  Automatic ungroup bit in flags. Specified changes will result in an automatic ungroup of the affected S-groups. Changes causing ungroup:
  - changes in atom type
  - changes in bond type
  See Also:
  
  Constant Field Values
- VALENCE_CHECK
```
protected static final int VALENCE_CHECK
```
  Valence check calculation bit in flags. Valence check will be called according to this flag.
  
  Since:
  
  Marvin 5.4
  
  See Also:
  
  Constant Field Values
- VALENCE_CHECK_AMBIGUOUS
```
@Deprecated
protected static final int VALENCE_CHECK_AMBIGUOUS
```
  Deprecated. As of Marvin 6.0, replaced by ValenceCheckOptions.
  
  Valence check calculation bit in flags for checking ambiguous aromatic atoms requiring . Valence check of ambiguous atoms will be called according to this flag.
  
  Since:
  
  Marvin 5.9
  
  See Also:
  
  Constant Field Values
- RMCLEANUP_NONE
```
public static final int RMCLEANUP_NONE
```
  Do not perform any clean-up methods when removing an atom or a bond.
  
  Since:
  
  Marvin 3.1
  
  See Also:
  
  removeAtom(MolAtom, int), removeAtom(int, int), removeBond(MolBond, int), removeBond(int, int), Constant Field Values
- RMCLEANUP_FIXCOMPONENT
```
protected static final int RMCLEANUP_FIXCOMPONENT
```
  Remove called from RxnMolecule.fixComponent. For internal use only.
  
  Since:
  
  Marvin 4.1.3, 11/16/2006
  
  See Also:
  
  RMCLEANUP_ALL, Constant Field Values
- RMCLEANUP_ALL
```
public static final int RMCLEANUP_ALL
```
  Perform all clean-up methods when removing an atom or a bond.
  
  Since:
  
  Marvin 3.1
  
  See Also:
  
  removeAtom(MolAtom, int), removeAtom(int, int), removeBond(MolBond, int), removeBond(int, int), Constant Field Values
- RMCLEANUP_EDGES
```
public static final int RMCLEANUP_EDGES
```
  When removing an atom or a bond, also remove the bond(s) from the atom object(s).
  
  Since:
  
  Marvin 3.1
  
  See Also:
  
  removeAtom(MolAtom, int), removeAtom(int, int), removeBond(MolBond, int), removeBond(int, int), Constant Field Values
- CACHE_REMOVE_ALL
```
public static final int CACHE_REMOVE_ALL
```
  Cache removal option for clearing all cached info.
  
  See Also:
  
  clearCachedInfo(int), Constant Field Values
- CACHE_REMOVE_CACHEMEMORY
```
public static final int CACHE_REMOVE_CACHEMEMORY
```
  Cache removal option for cacheMemory.
  
  See Also:
  
  cacheMemory, clearCachedInfo(int), 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:
  
  removeAtom(MolAtom, int), removeAtom(int, int), RMCLEANUP_ALL, Constant Field Values
- RMCLEANUP_MOBJECT
```
public static final int RMCLEANUP_MOBJECT
```
  Remove graphics objects containing the removed atom.
  
  Since:
  
  Marvin 4.1, 03/07/2006
  
  See Also:
  
  removeAtom(MolAtom, int), removeAtom(int, int), 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:
  
  removeAtom(MolAtom, int), removeAtom(int, int), 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
- CACHE_REMOVE_TABS
```
public static final int CACHE_REMOVE_TABS
```
  Cache remove option to clear ctab and btab.
  
  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
- FRAG_BASIC
```
public static final int FRAG_BASIC
```
  Basic fragmentation, only atom - atom connections (bond) are considered.
  
  See Also:
  
  Constant Field Values
- FRAG_KEEPING_MULTICENTERS
```
public static final int FRAG_KEEPING_MULTICENTERS
```
  Fragmentation without breaking multicenter S-groups.
  
  See Also:
  
  Constant Field Values
- FRAG_KEEPING_SGROUPS
```
public static final int FRAG_KEEPING_SGROUPS
```
  Fragmentation without breaking S-groups.
  
  See Also:
  
  Constant Field Values
- FRAG_TYPE_COUNT
```
public static final int FRAG_TYPE_COUNT
```
  Number of fragmentation types.
  
  See Also:
  
  Constant Field Values
- superGraph
```
protected transient MoleculeGraph superGraph
```
  Parent of all parents.
- parentGraph
```
protected transient MoleculeGraph parentGraph
```
  The structure that contains this molecule graph as a substructure.
- theAtoms
```
protected transient MolAtom[] theAtoms
```
  The atoms (nodes).
- atomCount
```
protected transient int atomCount
```
  The number of atoms.
- theBonds
```
protected transient MolBond[] theBonds
```
  The bonds (edges).
- bondCount
```
protected transient int bondCount
```
  The number of bonds.
- orix
```
protected transient double orix
```
  Origin x.
- oriy
```
protected transient double oriy
```
  Origin y.
- oriz
```
protected transient double oriz
```
  Origin z.
- grinvCC
```
protected transient long grinvCC
```
  Graph invariant change count. The number of times the molecule (and the corresponding graph invariants) may have changed since the creation of the molecule.
  
  See Also:
  
  getGrinvCC(), incGrinvCC(), incGrinvCCOnly(), getGrinv(int[])
- cacheMemory
```
protected transient java.util.List<java.lang.Object[]> cacheMemory
```
- ctab
```
protected transient int[][] ctab
```
  Connection table.
- btab
```
protected transient BondTable btab
```
  Bond table.
- gearch
```
public transient chemaxon.struc.gearch.MoleculeGraphGearch gearch
```
- 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 2 dimensional molecule.

Method Detail

getParent
```
public final MoleculeGraph getParent()
```
Gets the parent graph that contains this substructure.

Returns:

the parent, or null if this is the supergraph

Since:

Marvin 2.6

getForefather
```
public final MoleculeGraph getForefather()
```
Gets the first parent.

Returns:

parent of all parents

Since:

Marvin 2.9.11

getLock
```
public final java.lang.Object getLock()
```
Gets the lock object for synchronization. The lock object is the top parent.

Returns:

the lock object

Since:

Marvin 2.6

add
```
public void add(MolAtom atom)
```
Adds an atom to the molecule.

Parameters:

atom - the atom object

add
```
public void add(MolBond bond)
```
Adds a bond to the molecule. If the molecule graph is a superGraph, the bond is also added to its endpoints (two MolAtom objects).

Parameters:

bond - the bond object

add
```
public void add(MolBond bond,
                boolean checkParallel)
```
Add a bond to the molecule. If the second parameter is true, there an exception thrown when there is already a bond between the given MolAtoms. There is no checking if either is SgroupAtom. If the molecule graph is a superGraph, the bond is also added to its endpoints (two MolAtom objects).

Parameters:

bond - the bond object

checkParallel -

addAtom0
```
protected void addAtom0(MolAtom atom)
```
Adds an atom.

Parameters:

atom - the atom reference

addAtomWithoutChangingIt
```
protected int addAtomWithoutChangingIt(MolAtom atom)
```
Adds an atom without setting its parentGraph and index fields.

Parameters:

atom - the atom reference

Returns:

the new atom index

addSimpleAtomWithoutChangingIt
```
protected int addSimpleAtomWithoutChangingIt(MolAtom atom)
```
Adds a non-SgroupAtom atom without setting its parentGraph and index fields.

Parameters:

atom - the atom reference

Returns:

the new atom index

addAtomToFragment
```
protected void addAtomToFragment(MolAtom atom)
```
Adds an atom to a fragment.

Parameters:

atom - the atom reference

addBond0
```
protected void addBond0(MolBond bond)
```
Adds a bond.

Parameters:

bond - the bond reference

addBondWithoutChangingIt
```
protected final int addBondWithoutChangingIt(MolBond bond)
```
Adds a bond without setting its parentGraph and index fields.

Parameters:

bond - the bond reference

Returns:

the new bond index

pack
```
public void pack()
```
Reduce memory usage.

removeAtom
```
public void removeAtom(MolAtom atom)
```
Removes an atom and its bonds by reference.

Parameters:

atom - the atom

Since:

Marvin 5.3, 04/30/2009

removeAtom
```
public void removeAtom(int i)
```
Removes an atom and its bonds by index.

Parameters:

i - the atom index

Since:

Marvin 5.3, 04/30/2009

removeBond
```
public void removeBond(MolBond bond)
```
Removes a bond by reference.

Parameters:

bond - the bond

Since:

Marvin 5.3, 04/30/2009

removeBond
```
public void removeBond(int i)
```
Removes a bond by index.

Parameters:

i - the bond index

Since:

Marvin 5.3, 04/30/2009

removeAllBonds
```
public void removeAllBonds()
```
Removes all bonds.

Since:

Marvin 5.3, 04/30/2009

removeAll
```
public void removeAll()
```
Removes all the atoms and bonds.

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 molecule graph.

Parameters:

g - the child graph or this

Returns:

the parent document

Since:

Marvin 4.1.1, 08/23/2006

smol
```
public final Smolecule smol()
```
Gets a Smolecule representation of this molecule.

Returns:

the Smolecule implementation

Since:

Marvin 5.2.2, 04/24/2009

createSmolecule
```
protected final Smolecule createSmolecule()
```
Creates a Smolecule represenation of this molecule.

Returns:

the new Smolecule

Since:

Marvin 5.2.2, 04/24/2009

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 flags of the molecule.

Parameters:

f - the flags

Since:

Marvin 5.0.1, 02/10/2008

See Also:

flags

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 atoms vector.

See Also:

clearForImport(java.lang.String), theAtoms

clearForImport
```
public void clearForImport(java.lang.String format)
```
Clears the bonds 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:

theBonds, orix, oriy, oriz, setFlags(int)

removeAtom
```
public void removeAtom(MolAtom atom,
                       int cleanupFlags)
```
Removes an atom and its bonds with extra clean-up options. This method is for internal use only. Use removeAtom(MolAtom) instead unless you are sure what you are doing.

Parameters:

atom - the atom

cleanupFlags - extra clean-up methods

Since:

Marvin 5.3, 04/30/2009

See Also:

RMCLEANUP_NONE, RMCLEANUP_ALL, RMCLEANUP_EDGES

removeAtom
```
public void removeAtom(int i,
                       int cleanupFlags)
```
Removes an atom and its bonds with extra clean-up options. This method is for internal use only. Use removeAtom(int) instead unless you are sure what you are doing.

Parameters:

i - the atom index

cleanupFlags - extra clean-up methods

Since:

Marvin 5.3, 04/30/2009

See Also:

RMCLEANUP_NONE, RMCLEANUP_ALL, RMCLEANUP_EDGES

setAtom0

protected void setAtom0(int i,
                        MolAtom atom)

Sets the atom at the specified index.

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

setBond
```
@Deprecated
public void setBond(int i,
                                MolBond b)
```
Deprecated. as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use removeBond(MolBond) for bond removal and add(MolBond) for adding a new bond to the molecule.

Sets the bond at the specified index.

Parameters:

i - bond index

b - the bond reference

replaceBond
```
@Deprecated
public void replaceBond(MolBond oldb,
                                    MolBond newb)
```
Deprecated. as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Use removeBond(MolBond) for removal and add(MolBond) for adding a new bond to the molecule.

Replaces an bond by another one.

Parameters:

oldb - the old bond

newb - the new bond

Since:

Marvin 5.3, 04/30/2009

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

getGrinv
```
public int getGrinv(int[] gi)
```
Gets the graph invariants (canonical labels). The graph invariants are copied into the specified array, that must have the same length as the number of atoms in the molecule.
Notes: 1. For normal molecules and R-groups, graph invariants are recalculated only if an atom or bond changed, removed or added.
2. For selections, graph invariants are recalculated each time this function is called, because atoms and bonds cannot notify selections about their changes.

Parameters:

gi - output array, its length must be equal to the number of atoms

Returns:

the number of different graph invariants

Throws:

java.lang.SecurityException - the GraphInvariants module cannot be loaded because of security reasons (firewall)

getGrinv
```
@Deprecated
public int getGrinv(int[] gi,
                                boolean uniqueFlag)
```
Deprecated.
As of Marvin 4.0, replaced by getGrinv(int[], int).
Usage:
```
             getGrinv(gi, uniqueFlag ? GRINV_OLDSTEREO : 0);
             
```
Gets the graph invariants (canonical labels). Same like the former method but if the boolean flag is true, chiral info is also added to invariants (needed for unique SMILES).

Parameters:

gi - output array, its length must be equal to the number of atoms

uniqueFlag - boolean flag

Returns:

the number of different graph invariants

Throws:

java.lang.SecurityException - the GraphInvariants module cannot be loaded because of security reasons (firewall)

Since:

Marvin 3.3

See Also:

getGrinv(int[], int)

getGrinv
```
public int getGrinv(int[] gi,
                    int options)
```
Gets the graph invariants (canonical labels). Optionally, chiral info can be added to the invariants and hydrogens can be ignored. Graph invariants are copied into the specified array, that must have the same length as the number of atoms in the molecule.
Notes: 1. For normal molecules and R-groups, graph invariants are recalculated only if an atom or bond changed, removed or added.
2. For selections, graph invariants are recalculated each time this function is called, because atoms and bonds cannot notify selections about their changes.

Parameters:

gi - output array, its length must be equal to the number of atoms

options - graph invariant generation options

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:

GRINV_NOHYDROGEN, GRINV_STEREO, GRINV_DONT_STORE

calcDehydrogenizedGrinv
```
public int calcDehydrogenizedGrinv(int[] gi)
```
Calculates the graph invariants with the assumption that hydrogens are removed. Entries corresponding to hydrogens are filled with -1 values in the output array. Only normal Hydrogen atoms are removed, isotopes (Deuterium and Tricium) are not.

Parameters:

gi - output array, its length must be equal to the number of atoms

Returns:

the number of different graph invariants

Throws:

java.lang.SecurityException - the GraphInvariants module cannot be loaded because of security reasons (firewall)

Since:

Marvin 3.1

See Also:

getGrinv(int[])

createDehydrogenizedReadOnlyGraph
```
protected MoleculeGraph createDehydrogenizedReadOnlyGraph()
```
Creates a dehydrogenized version of the molecule. The same atom and bond objects are used as in the original molecule, so the returned structure must be used for reading only. Hydrogen isotopes (Deuterium and Tricium) are not removed.

Returns:

dehydrogenized structure

Since:

Marvin 3.1

getGrinv
```
protected int[] getGrinv()
```
Gets the graph invariants array. This array is cached, so clone it if you plan to modify it.

Returns:

the grinv field

Since:

Marvin 3.0

See Also:

grinvCC

getGrinvCC
```
public final long getGrinvCC()
```
Gets the graph invariant change count. Returns the number of times the graph invariants may have changed since the creation of the molecule.

Returns:

graph invariant change count

See Also:

grinvCC, incGrinvCC(), incGrinvCCOnly(), getGrinv(int[])

setGrinvCC
```
protected final void setGrinvCC(long g)
```
Sets the graph invariant change count.

Parameters:

g - graph invariant change count

Since:

Marvin 3.4

See Also:

grinvCC, getGrinvCC()

incGrinvCC
```
protected final void incGrinvCC()
```
Increases the graph invariant change count and sets grinv to null. Incremented in the following cases:
- atom, bond addition, removal, property change
- atomic coordinate change
- dimension change
Since:

Marvin 3.5

See Also:

incGrinvCCOnly(), grinvCC, getGrinvCC(), getGrinv(int[])

incGrinvCC

protected final void incGrinvCC(boolean isSSSRReset)

incGrinvCCOnly
```
public final void incGrinvCCOnly()
```
Increases the graph invariant change count, but does not change grinv. Handle with care, it may force certain data to be recalculated!

Since:

Marvin 4.0 5/07/2005

See Also:

incGrinvCC(), grinvCC, getGrinvCC(), getGrinv(int[])

resetCtab
```
protected void resetCtab()
```
An operation performed that changed the connection table and the graph invariants.

Since:

Marvin 2.6

resetGrinvInParents
```
protected final void resetGrinvInParents()
```
Graph invariants must be recalculated for this graph and all parent graphs.

regenCtab
```
protected void regenCtab()
```
Regenerates the connection table. See getCtab().

Since:

Marvin 16.6.6

regenBtab
```
protected void regenBtab()
```
Regenerates the bond table. See #getBtab().

Since:

Marvin 16.6.6

addExplicitHydrogens
```
@Deprecated
public boolean addExplicitHydrogens(int f)
```
Deprecated.
As of Marvin 5.7, replaced by Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int).
Usage:
```
             Hydrogenize.convertImplicitHToExplicit(molecule, null, 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 occurred

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
```
@Deprecated
public boolean addExplicitHydrogens(int f,
                                                MolAtom[] atoms)
```
Deprecated.
As of Marvin 5.7, replaced by Hydrogenize.convertImplicitHToExplicit(MoleculeGraph, MolAtom[], int).
Usage:
```
             Hydrogenize.convertImplicitHToExplicit(molecule, atoms, 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).

atoms - add hydrogens to these atoms only

Returns:

true for success, false if an error occurred

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
```
@Deprecated
public boolean hydrogenize(boolean add)
```
Deprecated. As of Marvin 5.7, replaced by Hydrogenize.convertImplicitHToExplicit(MoleculeGraph) and Hydrogenize.convertExplicitHToImplicit(MoleculeGraph).

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 occurred

Throws:

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

addExplicitLonePairs
```
@Deprecated
public void addExplicitLonePairs()
```
Deprecated.
As of Marvin 5.7, replaced by Hydrogenize.convertImplicitLonePairsToExplicit(MoleculeGraph, MolAtom[]).
Usage:
```
             Hydrogenize.convertImplicitLonePairsToExplicit(molecule, null);
             
```
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
```
@Deprecated
public void removeExplicitLonePairs()
```
Deprecated. As of Marvin 5.7, replaced by Hydrogenize.convertExplicitLonePairsToImplicit(MoleculeGraph).

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
```
@Deprecated
public final void implicitizeHydrogens(int f)
```
Deprecated.
As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int).
Usage:
```
             Hydrogenize.convertExplicitHToImplicit(molecule, f);
             
```
Removes explicit bound Hydrogens from the molecule graph and converts them to implicit.

Parameters:

f - flags specifying special H atom types to include

Since:

Marvin 3.1

implicitizeHydrogens
```
@Deprecated
public void implicitizeHydrogens(int f,
                                             MolAtom[] atoms)
```
Deprecated.
As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int).
Usage:
```
             Hydrogenize.convertExplicitHToImplicit(mol, atoms, f);
             
```
Removes explicit bound Hydrogens from the molecule graph and converts them to implicit.

Parameters:

f - flags specifying special H atom types to include

atoms - the subset of H atoms to include or null for all

Since:

Marvin 4.1.3, 11/09/2006

implicitizeHydrogens
```
@Deprecated
public void implicitizeHydrogens(int f,
                                             MolAtom[] atoms,
                                             boolean check)
```
Deprecated.
As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean).
Usage:
```
             Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);
             
```
Removes explicit bound Hydrogens from the molecule graph and converts them to implicit.

Parameters:

f - flags specifying special H atom types to include

atoms - the subset of H atoms to include or null for all

check - false if H atoms not belonging to the molecule should be skipped, true if such atoms should generate a RuntimeException

Since:

Marvin 5.0, 06/29/2007

implicitizeHydrogens0

@Deprecated
protected boolean implicitizeHydrogens0(int f,
                                                    MolAtom[] atoms,
                                                    boolean check)

Deprecated. As of Marvin 5.7, replaced by Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, MolAtom[], int, boolean).
Usage:

             Hydrogenize.convertExplicitHToImplicit(mol, atoms, f, check);

Parameters:: f -; atoms -; check -
Returns:: true if success else false

fuse
```
public void fuse(MoleculeGraph graph,
                 boolean check)
```
Adds atoms and bonds of another molecule to this one.

Parameters:

graph - the other molecule graph

check - true if a containment check should be performed to ensure that only those atoms and bonds are added that are not already elements - false if the molecule is known to be disjoint from this one and this check can be safely skipped

Since:

Marvin 5.0

fuse
```
public final void fuse(MoleculeGraph graph)
```
Adds those atoms and bonds of another molecule to this one that are not already elements. Made final in Marvin 5.0. From Marvin 5.0, subclasses should implement fuse(chemaxon.struc.MoleculeGraph, boolean) instead.

Parameters:

graph - the other molecule graph

fuse0
```
protected void fuse0(MoleculeGraph g,
                     boolean check)
```
Adds the atoms and bonds of another molecule to this one.

Parameters:

g - the other molecule

check - true if a containment check should be performed to ensure that only those atoms and bonds are added that are not already elements - false if the molecule is known to be disjoint from this one and this check can be safely skipped

Since:

Marvin 5.0

checkConsistency
```
@Deprecated
public void checkConsistency()
```
Deprecated. As of Marvin 5.7, no replacement.
Not intended for public use, it was intended only for internal debugging.

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

Throws:

java.lang.RuntimeException - if inconsistency found

Since:

Marvin 5.0, 11/06/2007

checkBondConsistency
```
protected void checkBondConsistency()
```

updateDim
```
protected final void updateDim(MoleculeGraph m)
```
Updates the dimensions when fusing two structures.

Parameters:

m - the other molecule

Since:

Marvin 4.0.2, 08/26/2005

mergeAtoms
```
@Deprecated
public void mergeAtoms(MolAtom replacementAtom,
                                   MolAtom origAtom)
```
Deprecated. As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.

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

Parameters:

replacementAtom - the atom which will take place in the molecule after the merge

origAtom - the original atom which's bonds will be added to the new atom

hasValenceError
```
public boolean hasValenceError()
```
Determines if this molecule has a valence error on any of its atoms.

Returns:

true if there is an atom with valence error, false if there is no valence error

Since:

Marvin 4.1

See Also:

valenceCheck(), MolAtom.hasValenceError()

valenceCheck
```
public void valenceCheck()
```
Check valence and query property errors for atoms. During this check implicit hydrogens are calculated and the valence error flag is set in case of error. It can be set by a previous call of setValenceCheckOptions(ValenceCheckOptions); which atoms are checked.

See Also:

MolAtom.valenceCheck(), MolAtom.getImplicitHcount(), hasValenceError(), setValenceCheckOptions(ValenceCheckOptions), getValenceCheckOptions()

valenceCheck
```
public void valenceCheck(java.util.List<MolAtom> v)
```
Check valence and query property errors. Check all the atoms if the argument is null. During this check implicit hydrogens are calculated and the valence error flag is set in case of error.

Parameters:

v - contains the atoms to check

See Also:

MolAtom.valenceCheck(), valenceCheck()

qpropCheck
```
public void qpropCheck(java.util.List<MolAtom> v)
```
Check for query property errors. Check all the atoms if the argument is null.

Parameters:

v - contains the atoms to check

See Also:

MolAtom.qpropCheck()

isSimilarTo
```
public boolean isSimilarTo(MoleculeGraph g)
```
Tests if the molecule graph is similar to another graph. Two graphs are similar if:
1. they have the same number of atoms and bonds,
2. for each atom ai in the first graph, there is a corresponding atom aj in the other graph, with the same graph invariant, "equal properties" and "similar bonds".
Parameters:

g - the molecule graph

Returns:

true if the graphs are similar, false otherwise

Since:

Marvin 3.4.1, 07/21/2004

See Also:

MolAtom.haveEqualProperties(MolAtom), MolAtom.haveSimilarBonds(MolAtom)

isAtom
```
@Deprecated
public boolean isAtom()
```
Deprecated. As of Marvin 14.7.7, no replacement.
Not supported feature.

Determines whether the structure represents only one atom and an arbitrary number of bonds. Note: a one-atom structure has bonds only if it is a fragment.

Returns:

true if the number of atoms is one

isBond
```
@Deprecated
public boolean isBond()
```
Deprecated. As of Marvin 14.7.7, no replacement.
Not supported feature.

Determines whether the structure represents only one bond and zero or two Carbon or MolAtom.EMPTY atoms.

Returns:

true if the structure is the representation of a bond

isRing
```
@Deprecated
public boolean isRing()
```
Deprecated. As of Marvin 14.7.7, no replacement.
Not supported feature.

Tests whether the molecule graph represents a ring.

Returns:

true if the graph is a ring, false otherwise

Since:

Marvin 4.1, 01/27/2006

isSymmetric
```
public boolean isSymmetric()
```
Tests whether the molecule graph is symmetric. The graph is symmetric if each atom has the same graph invariant value.

Returns:

true if the graph is a symmetric, false otherwise

Since:

Marvin 4.1, 01/27/2006

getName
```
public java.lang.String getName()
```
Gets the molecule title/name. This method is implemented for the Incomplecule interface but it returns empty string in this basic implementation.

Specified by:

getName in interface Incomplecule

Returns:

empty string

Since:

Marvin 4.1, 05/28/2006

properties
```
public MPropertyContainer properties()
```
Gets the property container.

Specified by:

properties in interface Incomplecule

Returns:

the property container

Since:

Marvin 4.1, 05/28/2006

revalidateCoordDependentProps
```
public void revalidateCoordDependentProps()
```
Revalidate coordinate dependent properties. This method should be called at molecule import, after all atomic coordinates and bonds are parsed.

Since:

Marvin 4.1, 08/03/2006

getAtomCount
```
public int getAtomCount()
```
Gets the number of atoms.

Specified by:

getAtomCount in interface chemaxon.core.structure.StructureForBuilder

Specified by:

getAtomCount in interface Incomplecule

Returns:

the number of atoms

getAtomCount
```
public int getAtomCount(int atomicNumber)
```
Gets the number of atoms with the given atomic number. When atomicNumber is 1, sum includes only explicit Hydrogen atoms (but also D and T isotopes).

Parameters:

atomicNumber - atomic number of atoms looked for

Returns:

number of atoms with the given atomic number

Since:

Marvin 5.5, 27/01/2011

getBondCount
```
public int getBondCount()
```
Gets the number of bonds.

Specified by:

getBondCount in interface Incomplecule

Returns:

number of bonds

getFormalCharge
```
public int getFormalCharge()
```
Gets the (total) formal charge of the molecule.

Returns:

the formal charge of the molecule

Since:

Marvin 5.1.3

getTotalCharge
```
public int getTotalCharge()
```
Gets the total (formal) charge of the molecule. Does the same as the getFormalCharge() method.

Returns:

the total charge of the molecule

Since:

Marvin 4.1.10

isRealAtomParent
```
protected boolean isRealAtomParent()
```
Can it be a real atom parent?

Returns:

true

Since:

Marvin 3.0

getAtom
```
public MolAtom getAtom(int n)
```
Gets the nth atom.

Parameters:

n - the atom index

Returns:

the atom object

getBond
```
public MolBond getBond(int n)
```
Gets the nth bond.

Parameters:

n - the bond index

Returns:

the bond object

setAtom
```
@Deprecated
public void setAtom(int i,
                                MolAtom atom)
```
Deprecated. as of Marvin 6.2, may construct inconsistent MoleculeGraph. Use removeAtom(int) for atom removal and add(MolAtom) for adding new atoms.

Sets the atom at the specified index.

Parameters:

i - atom index

atom - new atom reference

Since:

Marvin 5.3, 04/30/2009

insertAtom
```
@Deprecated
public final void insertAtom(int i,
                                         MolAtom atom)
```
Deprecated. as of Marvin 6.2, may construct inconsistent MoleculeGraph. Similar functionality is performed by add(MolAtom).

Inserts the atom at the specified index.

Parameters:

i - atom index

atom - new atom reference

Since:

Marvin 5.3, 04/30/2009

insertNullAtoms
```
protected void insertNullAtoms(int i,
                               int count)
```
Insert nulls into the atom array.

Parameters:

i - starting index

count - number of new entries

Since:

Marvin 5.3, 04/30/2009

insertBond
```
@Deprecated
public final void insertBond(int i,
                                         MolBond bond)
```
Deprecated. as of Marvin 6.2, may constructs inconsistent MoleculeGraph. Similar functionality is performed by add(MolBond).

Inserts the bond at the specified index.

Parameters:

i - bond index

bond - new bond reference

Since:

Marvin 5.3, 04/30/2009

insertBondInOrder
```
public void insertBondInOrder(MolBond e,
                              MolBond[] order)
```
Insert a bond in the order specified as the second argument.

Parameters:

e - the bond to insert

order - array of bonds defining the order

Since:

Marvin 5.3, 04/30/2009

insertNullBonds
```
protected void insertNullBonds(int i,
                               int count)
```
Insert nulls into the bond array.

Parameters:

i - starting index

count - number of new entries

Since:

Marvin 5.3, 04/30/2009

sortBondsAccordingTo
```
public void sortBondsAccordingTo(MolBond[] order)
```
Sorts bonds in the same order as they appear in another chemical graph.

Parameters:

order - the bonds in the other chemical graph

Since:

Marvin 5.3, 04/30/2009

getAtomArray
```
public MolAtom[] getAtomArray()
```
Creates an array of atoms.

Returns:

array of atom objects

Since:

Marvin 2.6

getBondArray
```
public MolBond[] getBondArray()
```
Creates an array of bonds.

Returns:

array of bond objects

Since:

Marvin 3.5, 09/02/2004

calcCenter
```
public void calcCenter(DPoint3 p)
```
Calculates the geometrical center.

Parameters:

p - reference to the object that will hold the result

Since:

Marvin 2.7

calcOutRect
```
public DPoint3 calcOutRect()
```
Calculates the outer rectangle.

Returns:

the outer rectangle (x, y, and z direction width of the outer rectangle)

Since:

Marvin 4.1

calcOutRect
```
public void calcOutRect(DPoint3 p)
```
Calculates the outer rectangle.

Parameters:

p - reference to the object that will hold the result (x, y, and z direction width of the outer rectangle)

Since:

Marvin 4.1

calcOutRectCenter
```
public DPoint3 calcOutRectCenter()
```
Calculates the center of the outer rectangle.

Returns:

the center

Since:

Marvin 4.1

calcOutRectCenter
```
public void calcOutRectCenter(DPoint3 p)
```
Calculates the center of the outer rectangle.

Parameters:

p - reference to the object that will hold the result

calcCenter
```
public DPoint3 calcCenter()
```
Calculates the geometrical center.

Returns:

center point

calcWidth
```
public double calcWidth()
```
Calculates the molecule width.

Returns:

the molecule width

Since:

Marvin 3.0

calcHeight
```
public double calcHeight()
```
Calculates the molecule height.

Returns:

the molecule height

Since:

Marvin 3.0

getDesiredLength
```
@Deprecated
public double getDesiredLength(int atno1,
                                           int atno2,
                                           int type)
```
Deprecated.
As of Marvin 5.11, replaced by MolBond.desiredLength(int, int, int, int) and getDim().
Usage:
```
             MolBond.desiredLength(atno1, atno2, type, getDim());
             
```
Gets the ideal bond length in Angstroms.

Parameters:

atno1 - atomic number of first molecule

atno2 - atomic number of second molecule

type - bond type

Returns:

the ideal bond length

getDesiredLength
```
@Deprecated
public double getDesiredLength(MolBond b)
```
Deprecated.
As of Marvin 5.11, replaced by MolBond.desiredLength(int, int, int, int), MolBond.getType() and getDim().
Usage:
```
             MolBond.desiredLength(atno1, atno2, b.getType, getDim());
             
```
Gets the ideal bond length in Angstroms.

Parameters:

b - the bond

Returns:

the ideal bond length

Since:

Marvin 2.7

bondlength
```
public double bondlength()
```
Calculates the regular bond length.

Returns:

the calculated length in Angstroms, or MolBond.CCLENGTH if the molecule has no bonds

getLocation
```
public DPoint3 getLocation()
```
Gets the origin of the molecule.

Returns:

the origin

Since:

Marvin 2.7

See Also:

orix

setLocation
```
public void setLocation(DPoint3 o)
```
Set the origin of the molecule.

Parameters:

o - the origin

Since:

Marvin 2.7

See Also:

orix

moveTo
```
public void moveTo(DPoint3 o)
```
Move the molecule.

Parameters:

o - the new origin

Since:

Marvin 2.7

See Also:

orix

transform
```
public void transform(CTransform3D t)
```
Apply a transformation matrix to the atomic coordinates.

Specified by:

transform in interface MTransformable

Parameters:

t - the transformation matrix

Since:

Marvin 2.7

transform
```
public void transform(CTransform3D t,
                      boolean incg)
```
Apply a transformation matrix to the atomic coordinates.

Parameters:

t - the transformation matrix

incg - graph invariants are changed (true) or not (false)

Since:

Marvin 3.0

getPoints
```
public DPoint3[] getPoints()
```
Gets an array containing the atom coordinates.

Returns:

atom coordinates array

Since:

Marvin 2.9.1

getEnclosingCube
```
public DPoint3[] getEnclosingCube()
```
Gets the cube that encloses the atoms of molecule graph.

Returns:

Array of the two corners of the cube: bottom left and top right

Since:

Marvin 5.3.2

clonecopy
```
public void clonecopy(MoleculeGraph m)
```
Make another molecule identical to this one.

Parameters:

m - the target molecule

clonecopy
```
public void clonecopy(int[] iatoms,
                      MoleculeGraph g)
```
Copies the specified atoms of this molecule graph to another one.

Parameters:

iatoms - array of atom indices to copy or null

g - the target molecule graph

Since:

Marvin 5.0.2, 03/11/2008

clonecopyMoleculeGraphWithoutSgroups
```
protected boolean clonecopyMoleculeGraphWithoutSgroups(int[] cnodes,
                                                       MolBond[] cedges,
                                                       int nb,
                                                       MoleculeGraph graph)
```
Copies the specified atoms and bonds of this molecule graph to another one.

Parameters:

cnodes - array of atom indices to copy or null

cedges - array of bonds to copy or null to copy bonds in cnodes only

nb - number of bonds

graph - the target molecule graph

Returns:

false if the atoms array contains all bond end points, true if there is at least one external bond

Since:

Marvin 5.0.2, 03/07/2008

cloneAtoms
```
protected int cloneAtoms(int[] cnodes,
                         MoleculeGraph graph)
```
Copies the specified atoms.

Parameters:

cnodes - array of atom indices to copy or null

graph - the target molecule graph

Returns:

the atom count

Since:

Marvin 6.0, 2013.02.25.

getBonds
```
protected MolBond[] getBonds(MolAtom atom)
```
Returns the bonds attached to the given atom in this molecule graph. By default, returns the bond array stored in the atom.

Parameters:

atom - the atom

Returns:

the bonds attached to the given atom in this molecule graph

Since:

Marvin 5.5

findInArray

protected static final int findInArray(java.lang.Object[] array,
                                       int[] indices,
                                       int n,
                                       java.lang.Object o)

Finds an object in an array.

Parameters:: array - the array; indices - array indices or null; n - the number of elements
Returns:: the object index or -1 if not found
Since:: Marvin 5.0.2, 03/07/2008

clonelesscopy
```
@Deprecated
public void clonelesscopy(MoleculeGraph graph)
```
Deprecated. as of Marvin 6.3.
Not supported feature.

Copy to selection. Copies without cloning. Make another molecule identical to this one, but do not clone atoms, bonds, and the properties.

Parameters:

graph - the target molecule graph (the selection)

hasSelfReferringProperty
```
public final boolean hasSelfReferringProperty()
```
Tests whether the property list contains the molecule.

Since:

Marvin 4.1.6, 02/11/2007

isSelfReference
```
public boolean isSelfReference(MProp p)
```
Tests whether the specified property is a self reference to the molecule.

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().

Parameters:

prop - the property

Since:

Marvin 4.1.6, 02/14/2007

See Also:

clonecopy(MoleculeGraph)

toString
```
public java.lang.String toString()
```
Overrides MoleculeGraph.toString() to ease debugging. Returns a string consisting of the classname (without the package name!), the at-sign character `@', and the unsigned hexadecimal representation of the hash code of the object. If the graph is not empty and it has more than one atom, then the string also contains the number of atoms and bonds in "[Na,Mb]" form. If there is only one atom, then its symbol appears between the square brackets.

Overrides:

toString in class java.lang.Object

Returns:

a string representation of the object

clone
```
public MoleculeGraph clone()
```
Make an identical copy of the molecule. The clone is deep clone including atom and bond cloning.

Overrides:

clone in class java.lang.Object

Returns:

the copy

getParityType
```
public int getParityType(int idx)
```
Gets parity type. Currently tetrahedral and allene type parity supported. Only basic parity conditions are checked so return value not 0 does not mean that the atom has parity value different from 0.

Parameters:

idx - the index of the atom whose parity type is to be determined

Returns:

PARITY_ALLENE type for atoms having two double bond, and PARITY_TETRAHEDRAL for atoms having 3 or 4 bonds, else 0.

See Also:

StereoConstants.PARITY_ALLENE, StereoConstants.PARITY_TETRAHEDRAL

getParity
```
public int getParity(int i)
```
Computes the parity of an atom of the Molecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those. Leaves the imported parity unchanged.
Parity for tetrahedral center is defined as follows:
Number the atoms surrounding the stereo center with 1, 2, 3, and 4 in order of increasing atom number (position in the atom block) (a hydrogen atom should be considered the highest numbered atom, in this case atom 4). View the center from a position such that the bond connecting the highest-numbered atom (4) projects behind the plane formed by atoms 1, 2, and 3. Sighting towards atom number 4 through the plane (123), you see that the three remaining atoms can be arranged in either a clockwise or counterclockwise direction in ascending numerical order. Parity value of ODD is for a clockwise arrangement at the stereo center and EVEN for counterclockwise.
Allene like parity is defined as follows:
The two pair of atoms which connects to the central atom through one single and odd number of double bond connections defines a tetrahedron. Number the tetrahedron atoms with 1, 2, 3, and 4 in order of increasing atom number (position in the atom block). Hydrogen atom should be considered the highest numbered atom, in this case atom 4. We may have two Hydrogen atoms for allene like parity type. So the two Hydrogen atoms are differentiated by the atom indexes connected to the central atom with double bond. The Hydrogen atom which is on the same side of the double bond connecting to the central atom with higher atom index's ligand gets the smaller value (3). View the center from a position such that the bond connecting the highest-numbered atom (4) projects behind the plane formed by atoms 1, 2, and 3. Sighting towards atom number 4 through the plane (123), you see that the three remaining atoms can be arranged in either a clockwise or counterclockwise direction in ascending numerical order. Parity value ODD is assigned for a clockwise arrangement at the stereo center and EVEN for counterclockwise.

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, isAbsStereo(), setAbsStereo(boolean)

getLocalParity
```
public int getLocalParity(int i)
```
Computes the local parity of an atom of the Molecule 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.

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. Corresponding PARITY_UNSPEC flag is also returned if set.

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, StereoConstants.PARITY_UNSPEC, isAbsStereo(), setAbsStereo(boolean)

setParity
```
public boolean setParity(int i,
                         int p)
```
Change the bonds flag (UP/DOWN) connected to the given atom to achieve the specified parity. If all atom parities will be set then setParity(int[] p) is more efficient.

Parameters:

i - the index of the atom whose parity is to be set

p - parity to be set (PARITY_ODD,PARITY_EVEN)

Returns:

true if successful

Throws:

java.lang.SecurityException - the Parity module cannot be loaded because of security reasons (firewall)

See Also:

StereoConstants.PARITY_ODD, StereoConstants.PARITY_EVEN, MolBond.UP, MolBond.DOWN, setParity(int[] p), getParity(int i)

setParity
```
public boolean setParity(int[] p)
```
Change the bonds flag (UP/DOWN) connected to the whole molecule to achieve the specified parity array. Take care of expanding the molecule if necessary. In 2D, use actual wedge setup and change it if necessary.

Parameters:

p - the parity for each atom in the molecule

Returns:

true if successful

See Also:

StereoConstants.PARITY_ODD, StereoConstants.PARITY_EVEN, isAbsStereo(), setAbsStereo(boolean), MolBond.UP, MolBond.DOWN, getParity(int i)

setParity
```
public boolean setParity(int[] p,
                         boolean useActualWedges)
```
Change the bonds flag (UP/DOWN) connected to the whole molecule to achieve the specified parity array. Take care of expanding the molecule if necessary.

Parameters:

p - the parity for each atom in the molecule

useActualWedges - if true use actual wedge setup and change it if necessary, otherwise remove the wedges and set them again

Returns:

true if successful

Since:

Marvin 3.5, 12/18/2004

See Also:

StereoConstants.PARITY_ODD, StereoConstants.PARITY_EVEN, isAbsStereo(), setAbsStereo(boolean), MolBond.UP, MolBond.DOWN, getParity(int i)

setLocalParity
```
public 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. Parity setting is allowed for non-stereogenic center. (This means that the central carbon of an isobutane can get parity value.) The molecule is not expanded. Parity calculation use only the narrow end of a wedge in case of 2D molecules (useOnlyFirstAtomInStereoCalculation = true). If useOnlyFirstAtomInStereoCalculation is false then the function returns false.

Parameters:

p - the parity for each atom in the molecule

useActualWedges - if true use actual wedge setup and change it if necessary, otherwise remove the wedges and set them again

Returns:

true if successful

Since:

Marvin 5.0.1, 01/18/2008

See Also:

StereoConstants.PARITY_ODD, StereoConstants.PARITY_EVEN, isAbsStereo(), setAbsStereo(boolean), useOnlyFirstAtomInStereoCalculation, MolBond.UP, MolBond.DOWN

setLocalParity
```
public boolean setLocalParity(int[] idxes,
                              int[] p,
                              boolean useActualWedges)
```
Set given local parity for the given atomic indexes. 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. Parity setting is allowed for non-stereogenic center. (This means that the central carbon of an isobutane can get parity value.) The molecule is not expanded. Parity calculation use only the narrow end of a wedge in case of 2D molecules (useOnlyFirstAtomInStereoCalculation = true). If useOnlyFirstAtomInStereoCalculation is false then the function returns false.

Parameters:

idxes - atom indexes to set the local parity for

p - the corresponding local parity information

useActualWedges - if true use actual wedge setup and change it if necessary, otherwise remove the wedges and set them again

Returns:

true if successful

Since:

Marvin 5.3.6, 06/30/2010

See Also:

StereoConstants.PARITY_ODD, StereoConstants.PARITY_EVEN, isAbsStereo(), setAbsStereo(boolean), useOnlyFirstAtomInStereoCalculation, MolBond.UP, MolBond.DOWN

getChirality
```
public int getChirality(int i)
```
Computes the chirality of an atom of the Molecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those. Leaves the imported configuration unchanged. Contracted sgroups are expanded for calculation purposes. Though this method works only for valid atom indices.

Parameters:

i - the index of the atom whose chirality is to be determined

Returns:

0 for nonchiral, CHIRALITY_R, CHIRALITY_S, CHIRALITY_r, CHIRALITY_s, CHIRALITY_M, CHIRALITY_P for atoms of R, S or r, s or M, P configuration, PARITY_EITHER for atoms whose configuration 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.CHIRALITY_R, StereoConstants.CHIRALITY_S, StereoConstants.CHIRALITY_r, StereoConstants.CHIRALITY_s, StereoConstants.CHIRALITY_M, StereoConstants.CHIRALITY_P

setChirality
```
public boolean setChirality(java.util.Map<java.lang.Integer,java.lang.Integer> chiralities)
```
Sets the chiralities of atoms. Using this method, R, S, r, s chirality values can be set. Use StereoConstants.CHIRALITY_R, StereoConstants.CHIRALITY_S, StereoConstants.CHIRALITY_r, and StereoConstants.CHIRALITY_s to define chirality. If chirality settings on at least on atom was not successful, chirality values on all atoms are reverted back to their original state.

Parameters:

chiralities - Map of integers, where the key is the atom index, value is the chirality value.

Returns:

true, if setting chirality on all atom was successful; false otherwise.

Since:

version 14.7.7.

setChirality
```
public boolean setChirality(int i,
                            int c)
```
Set chirality of an atom of the Molecule instance based on both the coordinates of the neighboring atoms and the stereo information of the bonds to those. Take care of expanding the molecule if necessary.
Possible chirality values to set:

CHIRALITY_R

set the stereocenter to R chirality value

CHIRALITY_S

set the stereocenter to S chirality value

CHIRALITY_R|CHIRALITY_S, PARITY_EITHER or 0

remove chirality value

Parameters:

i - the index of the atom whose chirality is to be set

c - chirality to be set (CHIRALITY_R,CHIRALITY_S. 0 or (CHIRALITY_R|CHIRALITY_S) to remove chirality)

Returns:

true if successful

Throws:

java.lang.SecurityException - the Parity module cannot be loaded because of security reasons (firewall)

See Also:

StereoConstants.CHIRALITY_R, StereoConstants.CHIRALITY_S

getStereo2
```
public int getStereo2(int i1,
                      int i2,
                      int i3,
                      int i4)
```
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration. Calculates the stereo information if the molecule is 2D or 3D, reports previously set information if it is 0D. Not checking atom equivalences using graph invariants. Not checking if the bond is in small ring (MIN_RING_SIZE_FOR_TRANS_DB (so chemically the double bond with its ring ligand can be cis only), but due to the perspective depiction in two dimension the double bond ligand arrangement looks trans. In this case the chemically incorrect trans returned.

Parameters:

i1 - index of atom A1

i2 - index of atom A2

i3 - index of atom A3

i4 - index of atom A4

Returns:

the cis/trans information, or 0 if A2 and A3 are not connected

See Also:

StereoConstants.CTUMASK, MolBond.calcStereo2(), for detailed examples.

getStereo2

public int getStereo2(MolAtom a1,
                      int i2,
                      int i3,
                      MolAtom a4)

Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration. Calculates the stereo information if the molecule is 2D or 3D, reports previously set information if it is 0D. Not checking atom equivalences using graph invariants. Not checking if the bond is in small ring (MIN_RING_SIZE_FOR_TRANS_DB (so chemically the double bond with its ring ligand can be cis only), but due to the perspective depiction in two dimension the double bond ligand arrangement looks trans. In this case the chemically incorrect trans returned.

Parameters:

a1 - atom A1

i2 - index of atom A2

i3 - index of atom A3

a4 - atom A4

Returns:

the cis/trans information, or 0 if A2 and A3 are not connected

Returned values for the four Carbons ("O" means set flag):

Dihedral	Returned flags			Remark
Dihedral	CIS	TRANS	CTUNSPEC	Remark
SMARTS bonds:
C/C=C/C	-	O	-
C/C=C\C	O	-	-
CC=CC	O	O	-
C/?C=C/C	-	O	O
C/?C=C\C	O	-	O
ISIS bonds:
C-C=C-C	O	O	-	180 degrees
C-C X C-C	O	O	-	"Cis" or "Trans" bond
C/C="C/T?"=C/C	-	O	O	"Not Cis" bond
C/C="C/T?"=C\C	O	-	O	"Not trans" bond
C-C="C/T?"=C-C	O	O	O	180 degrees

getStereo2
```
public int getStereo2(MolBond b,
                      MolAtom a1,
                      MolAtom a4)
```
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration. Calculates the stereo information if the molecule is 2D or 3D, reports previously set information if it is 0D. Atoms A2 and A3 are atom1 and atom2 of the specified bond. Both (A2, A3) = (atom1, atom2) and (A2, A3) = (atom2, atom1) works. Not checking atom equivalences using graph invariants. Not checking if the bond is in small ring (MIN_RING_SIZE_FOR_TRANS_DB (so chemically the double bond with its ring ligand can be cis only), but due to the perspective depiction in two dimension the double bond ligand arrangement looks trans. In this case the chemically incorrect trans returned.

Parameters:

b - the bond

a1 - atom A1

a4 - atom A4

Returns:

the stereo flags

See Also:

StereoConstants.CTUMASK, MolBond.calcStereo2(), for detailed examples.

getStereo2
```
public int getStereo2(MolBond b,
                      MolAtom a1,
                      MolAtom a4,
                      boolean grcheck)
```
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration. Calculates the stereo information if the molecule is 2D or 3D, reports previously set information if it is 0D. Atoms A2 and A3 are atom1 and atom2 of the specified bond. Both (A2, A3) = (atom1, atom2) and (A2, A3) = (atom2, atom1) works. If A1 or A4 is null 0 is returned. Not checking if the bond is in small ring (MIN_RING_SIZE_FOR_TRANS_DB (so chemically the double bond with its ring ligand can be cis only), but due to the perspective depiction in two dimension the double bond ligand arrangement looks trans. In this case the chemically incorrect trans returned.

Parameters:

b - the bond

a1 - atom A1

a4 - atom A4

grcheck - true if check atom equivalences using graph invariants

Returns:

the stereo flags

See Also:

StereoConstants.CTUMASK, MolBond.calcStereo2(), for detailed examples.

getEZStereo
```
@Deprecated
public chemaxon.struc.stereo.EZConfiguration getEZStereo(MolBond bond)
```
Deprecated. as of Marvin 15.2.16 replaced by CIPStereoCalculator.calculateCIPStereoDescriptors(MoleculeGraph, boolean).
Gets E/Z stereo information for the given double bond. The calculation considers the following:
- If the bond is ring bond then EZConfiguration.NONE is returned
- If the molecule is zero dimensional then no calculation is performed but the values stored in the bond's flags are taken into consideration
- The CIP (Cahn-Ingold-Prelog) rules are used to determine the highest priority ligands around the double bond
- No graph invariant checking is performed
Furthermore a little clarification of the connection between CIS/TRANS stereoisomerism and E/Z stereo by giving an insight into the algorithm calculating the result:
- The highest priority ligands are calculated (using the CIP rules), one ligand connected to each end atom of the double bond
- The CIS/TRANS stereo value is calculated for these two atoms and the double bond's end atoms
- The CIS/TRANS value is converted to E/Z by:
  - CIS configuration is converted to EZConfiguration.Z
  - TRANS configuration is converted to EZConfiguration.E
  - CIS/TRANS configuration is converted to EZConfiguration.E_OR_Z
  - CIS/UNSPEC configuration is converted to EZConfiguration.Z_OR_UNSPEC
  - TRANS/UNSPEC configuration is converted to EZConfiguration.E_OR_UNSPEC
  - no configuration is converted to EZConfiguration.NONE
Parameters:

bond - the bond for which the E/Z stereo will be calculated

Returns:

the E/Z stereo value that is specified by the given bond

getStereo2
```
@Deprecated
public int getStereo2(MolBond b)
```
Deprecated. as of Marvin 6.3 replaced by getEZStereo(MolBond).

Gets cis/trans (Z/E) stereo information for the given bond. Use the CIP rules to determine the A1, A4 atoms in A1-A2=A3-A4 atom configuration. Calculates the stereo information if the molecule is 2D or 3D, reports previously set information if it is 0D. For ring bonds 0 is returned. Not checking atom equivalences using graph invariants.

Parameters:

b - the bond

Returns:

CIP stereo values for the given bond: CIS for Z stereo configuration, TRANS for E stereo configuration, CIS|TRANS for E/Z stereo configuration or 0

Since:

Marvin 4.1 4/13/2006

See Also:

StereoConstants.CTUMASK, StereoConstants.CIS, StereoConstants.TRANS, MolBond.calcStereo2(), for detailed examples.

getStereo2
```
protected final int getStereo2(MolBond b,
                               MolAtom a1,
                               int i2,
                               int i3,
                               MolAtom a4)
```
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration. Calculates the stereo information if the molecule is 2D or 3D, reports previously set information if it is 0D. Not checking atom equivalences using graph invariants.

Parameters:

b - the bond

a1 - atom A1

i2 - index of atom A2

i3 - index of atom A3

a4 - atom A4

Returns:

the stereo flags

See Also:

StereoConstants.CTUMASK, MolBond.calcStereo2(), for detailed examples.

getStereo2
```
protected final int getStereo2(MolBond b,
                               MolAtom a1,
                               int i2,
                               int i3,
                               MolAtom a4,
                               boolean grcheck)
```
Gets cis/trans stereo information for an A1-A2=A3-A4 atom configuration. Calculates the stereo information if the molecule is 2D or 3D, reports previously set information if it is 0D.

Parameters:

b - the bond

a1 - atom A1

i2 - index of atom A2

i3 - index of atom A3

a4 - atom A4

grcheck - true if check atom equivalences using graph invariants

Returns:

the stereo flags

See Also:

StereoConstants.CTUMASK, MolBond.calcStereo2(), for detailed examples.

removeBond
```
protected void removeBond(MolBond bond,
                          int cleanupFlags)
```
Removes a bond by reference.

Parameters:

bond - the bond

cleanupFlags - extra clean-up methods

Since:

Marvin 3.1

See Also:

RMCLEANUP_NONE, RMCLEANUP_ALL, RMCLEANUP_EDGES

removeBond
```
protected void removeBond(int i,
                          int cleanupFlags)
```
Removes a bond by index.

Parameters:

i - the bond index

cleanupFlags - extra clean-up methods

Since:

Marvin 3.1

See Also:

RMCLEANUP_NONE, RMCLEANUP_ALL, RMCLEANUP_EDGES

regenBonds
```
public void regenBonds()
```
Regenerates the bond vector: remove its elements, then put the bond objects from the atoms into it.

isolate
```
protected void isolate(MolAtom node)
```
Isolates atom: a more efficient way of removing an atom than removeAtom(chemaxon.struc.MolAtom), especially for large molecule graphs. Removes the atom but instead of shifting the atoms array, simply sets the corresponding entry to null. After isolating some atoms, call removeIsolatedAtoms() to get a valid molecule graph.

Parameters:

node - the atom

Since:

Marvin 5.0

isolate
```
protected void isolate(MolBond edge)
```
Isolates bond: a more efficient way of removing a bond than removeBond(chemaxon.struc.MolBond), especially for large molecule graphs. Removes the bond but instead of shifting the bonds array, simply sets the corresponding entry to null. After isolating some bonds, call removeIsolatedBonds() to get a valid molecule graph.

Parameters:

edge - the bond

Since:

Marvin 5.0

removeIsolatedAtoms
```
protected void removeIsolatedAtoms()
```
Removes the null atom entries in the atoms array and sets the index fields appropriately. Clean-up method after calling isolate(chemaxon.struc.MolAtom) for some atoms.

Since:

Marvin 5.0

removeIsolatedBonds
```
protected void removeIsolatedBonds()
```
Removes the null bond entries in the bonds array and sets the index fields appropriately. Clean-up method after calling isolate(chemaxon.struc.MolBond) for some bonds.

Since:

Marvin 5.0

canBeCT
```
public boolean canBeCT(int i2,
                       int i3)
```
Determines whether the bond between the specified atoms can be a CIS/TRANS or not. In case of ring bonds the ring sizes of the ring for the existence of CIS/TRANS specific bond should be checked before calling this method as ring sizes are not checked in this method.

Parameters:

i2 - index of the first atom

i3 - index of the second atom

Returns:

true if this is a double bond that can be either CIS, TRANS or EITHER, false otherwise.

canBeCT
```
public boolean canBeCT(int i2,
                       int i3,
                       boolean grcheck)
```
Determines whether the bond between the specified atoms can be a CIS/TRANS or not. In case of ring bonds the ring sizes of the ring for the existence of CIS/TRANS specific bond should be checked before calling this method as ring sizes are not checked in this method.

Parameters:

i2 - index of the first atom

i3 - index of the second atom

grcheck - true if check atom equivalences using graph invariants

Returns:

true if this is a double bond that can be either CIS, TRANS or EITHER, false otherwise.

Since:

Marvin 4.0 1/23/2005

canBeCT
```
public boolean canBeCT(MolBond bond)
```
Determines whether the given bond can be a CIS/TRANS or not. In case of ring bonds the ring sizes of the ring for the existence of CIS/TRANS specific bond should be checked before calling this method as ring sizes are not checked in this method.

Parameters:

bond - the bond to check

Returns:

true if this is a double bond that can be either CIS, TRANS or EITHER, false otherwise.

Since:

Marvin 5.5

getLonePairCount
```
@Deprecated
public int getLonePairCount(int i)
```
Deprecated. use MDocument.getLonePairCount() instead

Gets the number of lone pair atoms.

Parameters:

i - atom index

Returns:

the number of lone pair atoms connected to this atoms

Since:

Marvin 3.5, 09/29/2004

getExplicitLonePairCount
```
@Deprecated
public int getExplicitLonePairCount(int i)
```
Deprecated. use MDocument.getExplicitLonePairCount() instead

Gets the explicit lone pair count of the submitted atom.

Parameters:

i - atom index

Returns:

the number of the explicit lone pairs

Since:

Marvin 4.1.2, 10/06/2005

aromatize
```
public void aromatize(boolean a)
               throws java.lang.SecurityException
```
Aromatize (using the default general aromatization method) or dearomatize molecule.

Parameters:

a - aromatize (true) or dearomatize (false)

Throws:

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

Since:

Marvin 2.8

See Also:

AROM_GENERAL, Document about aromatization

aromatize
```
public final void aromatize()
```
Aromatize molecule using the default general aromatization method. Only single or double bonds are changed to aromatic, aromatic bonds are not changed.

Throws:

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

Since:

Marvin 3.4, 05/10/2004

See Also:

AROM_GENERAL, Document about aromatization

dearomatize
```
public boolean dearomatize()
```
Dearomatize molecule.

Returns:

true if success, else false.

Throws:

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

Since:

Marvin 5.0.1, 01/05/2008

dearomatize
```
public boolean dearomatize(int method)
```
Dearomatize molecule.
Parameters:
method - Specifies the algorithm for dearomatization. Possible values:
- DEAROM_GENERAL - General dearomatization
- DEAROM_HUCKELCHECK - Check Huckel rule during dearomatization.
- DEAROM_HUCKELCHECK_EX - The same as DEAROM_HUCKELCHECK but throw exception if dearomatization is not successful.
Returns:

true if success, else false.

Throws:

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

java.lang.RuntimeException - the molecule cannot be dearomatized with method DEAROM_HUCKELCHECK_EX

Since:

Marvin 5.2.3, 06/29/2008

aromatize
```
public void aromatize(int method)
```
Aromatizes molecule. Only single or double bonds are changed to aromatic, aromatic bonds are not changed. For query molecules if the molecule contains ANY bond, then the aromaticity is checked as if the ANY bonds were aromatic bonds. If a ring or a ring system found to be aromatic then the single bonds are changed to SINGLE_OR_AROMATIC and the double bonds to DOUBLE_OR_AROMATIC type.
Parameters:
method - Specifies the algorithm for aromatization. Possible values:
- AROM_BASIC - Basic aromatization
- AROM_GENERAL - General (Daylight compatible) aromatization
- AROM_LOOSE - Loose 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

See Also:

AROM_BASIC, AROM_GENERAL, AROM_LOOSE, Document about aromatization

aromatize
```
public void aromatize(int method,
                      boolean checkAmbiguity)
```
Aromatizes molecule. Only single or double bonds are changed to aromatic, aromatic bonds are not changed. For query molecules if checkAmbiguity set to true and the molecule contains ANY bond, then the aromaticity is checked as if the ANY bonds were aromatic bonds. If a ring or a ring system found to be aromatic then the single bonds are changed to SINGLE_OR_AROMATIC and the double bonds to DOUBLE_OR_AROMATIC type. Otherwise if checkAmbiguity is set to false a bond containing ANY bond cannot be aromatic.
Parameters:
method - Specifies the algorithm for aromatization. Possible values:
- AROM_BASIC - Basic aromatization
- AROM_GENERAL - General (Daylight compatible) aromatization
- AROM_LOOSE - Loose 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

See Also:

AROM_BASIC, AROM_GENERAL, AROM_LOOSE, Document about aromatization

calcHybridization
```
public void calcHybridization()
```
Calculates and sets hybridazation state for each atom. The calculation is based on simple rules that cannot be customized in the present implementation. However, setHybridizationState( int ) can be called to set the appropriate value directly. This sp-hybridization state reflects the spatial configuration of the C,N and O atoms rather than the sp-hybridization of the electron bands. It doesn't cover all the mixed orbitals of Si,S and P atoms. For hydrogens the "s" MolAtom.HS_S state, for atoms with query bonds the unknown state MolAtom.HS_UNKNOWN is set. If the atom has aromatic bonds the sp2 state is set. Otherwise the sp-hybridization state is determined based on the number of double and tripple bonds. If the atom has a tripple bond or two double bonds the sp state is set. If the atom has one double bond the sp2 state is set. If the atom has more then one tripple bond or more than two double bonds the unknown state is set. If a heavy atom has only single bonds the sp3 state is set.

Since:

Marvin 3.5

See Also:

LonePairCounter

getFormula
```
public java.lang.String getFormula()
```
Gets the molecular formula.

Returns:

the formula

getMass
```
public double getMass()
```
Calculates the molecular weight of the molecule. Returns a double value.

Returns:

the molecular weight

getExactMass
```
public double getExactMass()
```
Calculates the molecular weight of the molecule using the mass of the most frequent natural isotope of the atoms. Returns a double value.

Returns:

the molecular exact weight

makeItSimilar
```
protected void makeItSimilar(MoleculeGraph g)
```
Copies some properties of this molecule to the other one specified as argument. Copies the flags and the origin coordinates.

Parameters:

g - the molecule to change

newInstance
```
public MoleculeGraph newInstance()
```
Creates a new MoleculeGraph object. The dimension and the origin coordinates will be the same as in the original molecule.

Returns:

a MoleculeGraph object

getGraphUnion
```
public MoleculeGraph getGraphUnion()
```
Gets a molecule graph containing all the atoms and bonds.

Returns:

this object (in the default implementation)

Since:

Marvin 3.0, 11/11/2002

indexOf
```
public int indexOf(MolAtom atom)
```
Gets the index of the specified atom.

Parameters:

atom - the atom

Returns:

the index, or -1 if not found

Since:

Marvin 2.7

indexOf
```
public int indexOf(MolBond bond)
```
Gets the index of the specified bond. This method uses MolBond.equals() for the bond comparison.

Parameters:

bond - the bond

Returns:

the index, or -1 if not found

Since:

Marvin 2.7

See Also:

Object.equals(Object)

findAtom
```
protected final int findAtom(MolAtom atom)
```
Finds an atom in the atoms array.

Returns:

the atom index or -1 if not found

findBond
```
protected final int findBond(MolBond bond)
```
Finds a bond in the bonds array.

Returns:

the bond index or -1 if not found

contains
```
public boolean contains(MolAtom atom)
```
Checks if the molecule graph contains the specified atom.

Parameters:

atom - the atom object

Returns:

true if the graph contains the object, false otherwise

contains
```
public boolean contains(MolBond bond)
```
Checks if the molecule graph contains the specified bond, or a bond which is equals with the given bond.

Parameters:

bond - the bond object

Returns:

true if the graph contains the object, false otherwise

See Also:

Object.equals(Object)

contains
```
public boolean contains(MoleculeGraph graph)
```
Does the molecule graph contain the specified fragment?

Parameters:

graph - the fragment

Returns:

true if it contains the graph, false if not

isEmpty
```
public boolean isEmpty()
```
Tests whether the molecule graph is empty.

Returns:

true if the graph does not contain any atoms or bonds, false otherwise

getSubGraphs
```
public final MoleculeGraph[] getSubGraphs()
```
Gets all "submolecules".

Since:

Marvin 4.1.2

See Also:

getSubGraphCount()

getSubGraphCount
```
protected int getSubGraphCount()
```
Gets the number of all "submolecules". Submolecules are R-groups and the root structure in case of an RgMolecule, reactants, products and agents of an RxnMolecule etc.

Returns:

the number of submolecules

Since:

Marvin 4.1.2

See Also:

getSubGraphs(MoleculeGraph[], int)

getSubGraphs
```
protected void getSubGraphs(MoleculeGraph[] m,
                            int off)
```
Gets all "submolecules".

Parameters:

m - the output array

off - offset

Since:

Marvin 4.1.2

See Also:

getSubGraphs(), getSubGraphCount()

addAtomsAndBondsTo
```
protected void addAtomsAndBondsTo(MoleculeGraph s)
```
Adds all atoms and bonds to the specified molecule.

Parameters:

s - the selection molecule

Since:

Marvin 4.1, 11/25/2005

hasExplicitLonePairs
```
@Deprecated
public boolean hasExplicitLonePairs()
```
Deprecated. use MDocument.hasExplicitLonePairs() instead

Tests whether the molecule has explicit lone pair atoms.

Returns:

true if it has lone pair atoms, false otherwise

Since:

3.5.1, 11/24/2004

hasImplicitH
```
public boolean hasImplicitH()
```
Tests whether the molecule has implicit hydrogen atoms.

Returns:

true, if the molecule has at least one implicit hydrogen atom

Since:

Marvin 3.3, 01/14/2004

hasAtomSet
```
public boolean hasAtomSet()
```
Tests whether the molecule graph has atom sets.

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.

Returns:

true if there are atom sets, false otherwise

Since:

Marvin 4.0, 03/02/2005

hasExtraLabelSet
```
public boolean hasExtraLabelSet()
```

clean
```
@Deprecated
public boolean clean(int dim,
                                 java.lang.String opts)
```
Deprecated. As of Marvin 5.7, replaced by Cleaner.clean(MoleculeGraph, int, String).

Calculates atom coordinates.

Parameters:

dim - dimensions

opts - cleaning options

Returns:

true for success, false if an error occurred

Throws:

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

partialClean
```
@Deprecated
public boolean partialClean(Molecule[] template,
                                        java.lang.String opts)
```
Deprecated. As of Marvin 5.7, replaced by Cleaner.partialClean(Molecule, Molecule[], String).

Calculates atom coordinates by using the given template molecule array. Works only in 2D. Set the x and y coordinates for the substructure of this molecule which first match a molecule from template molecule array. Partially clean the rest atoms. Remark, that only the first matching template molecule is used despite any later match in the template molecules. If the template has no wedges, try to keep the wedges of the original molecule. Otherwise try to keep the template wedge settings.

Parameters:

template - template molecule array (substructure of the target)

opts - cleaning options

Returns:

true for success, false if no template match found or an error occurred

Throws:

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

Since:

Marvin 5.4, 02/23/2010

partialClean
```
@Deprecated
public boolean partialClean(MoleculeGraph template,
                                        int[] map,
                                        java.lang.String opts)
```
Deprecated. As of Marvin 5.7, replaced by Cleaner.partialClean(MoleculeGraph, MoleculeGraph, int[], String).

Calculates atom coordinates by using the given template molecule. Works only in 2D. Set the x and y coordinates of the molecule from the given template using the given mapping. Partially clean the rest atoms. Map length should be equal the atomcount of the template. If the template has no wedges, try to keep the wedges of the original molecule. Otherwise try to keep the template wedge settings.

Parameters:

template - template molecule (substructure of the target)

map - hit list which describes the atom mapping (the size equals to the number of atoms in the template, contains target atom indexes or -1 to exclude)

opts - cleaning options

Returns:

true for success, false if an error occurred

Throws:

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

Since:

Marvin 5.0, 09/09/2007

partialClean
```
@Deprecated
public boolean partialClean(int dim,
                                        int[] fixed,
                                        java.lang.String opts)
```
Deprecated. As of Marvin 5.7, replaced by Cleaner.partialClean(MoleculeGraph, int, int[], String).

Calculates atom coordinates by using fixed atoms. Internal use only. Works only in 2D. Store the needed stereo information in the atomflags!

Parameters:

dim - dimensions

fixed - atom indexes to be fixed

opts - cleaning options

Returns:

true for success, false if an error occurred

Throws:

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

Since:

Marvin 3.5.2, 01/01/2005

clean
```
@Deprecated
public boolean clean(int dim,
                                 java.lang.String opts,
                                 MProgressMonitor pmon)
```
Deprecated. As of Marvin 5.7, replaced by Cleaner.clean(MoleculeGraph, int, String, MProgressMonitor).

Calculates atom coordinates. In a 3D it works only for Molecules (not for MoleculeGraphs).

Parameters:

dim - dimensions

opts - cleaning options

pmon - progress monitor or null

Returns:

true for success, false if an error occurred (for example 3D case for MoleculeGraphs).

Throws:

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

Since:

Marvin 3.4, 05/06/2004

See Also:

clean(int, java.lang.String)

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 necessary. Only rings smaller then 19 atoms are examined.

Returns:

true if successful

isGrinvCCValid
```
protected boolean isGrinvCCValid()
```
Tests whether the graph invariant change count is valid.

Returns:

true

Since:

Marvin 5.0, 11/30/2007

getAromaticAndAliphaticRings
```
public int[][][] getAromaticAndAliphaticRings(int aromatizationType,
                                              boolean onlyAromrings,
                                              boolean aromatize,
                                              int maxRingSize,
                                              int ringsLimit)
```
Returns the aromatic and or aliphatic ring atom indexes.
Note: This method does not aromatize the already aromatized rings. Use first the dearomatize() or dearomatize(int) methods to convert the molecule to Kekule form.
Handle maxRingSize, ringsLimit parameters with care, otherwise the calculation can take extremly long time or result in OutOfMemoryError. Suggested values are 18 for maxRingSize and 1000 for ringsLimit parameter.
Parameters:
aromatizationType - use aromatization:
- 0 - No aromatization. The molecule is used as it is.
- AROM_BASIC - basic aromatization
- AROM_GENERAL - general aromatization
onlyAromrings - get only the aromatic rings (Aromatic ring detection is faster than calculating Aliphatic and Aromatic rings in case of BASIC aromatization, in case of GENERAL aromatization there is no difference in the speed),

aromatize - whether to set the bonds to aromatic (true), or keep the original form (false),

maxRingSize - the maximum ring size during ring detection (0: no limit)

ringsLimit - limit of the number of rings (0: no limit)

Returns:

the aromatic ring atom indexes in the array 0th position, the aliphatic ring atom indexes in the array 1st position

Since:

Marvin 4.1

See Also:

AROM_BASIC, AROM_GENERAL

getSSSR
```
public final int[][] getSSSR()
```
Gets the Smallest Set of Smallest Ring atom indexes array. It follows all kind of bonds including MolBond.ANY, MolBond.COORDINATE, MolBond.HYDROGEN. If the SSSR array is not calculated for the molecule, then create it. sssr[i][j] is the j-th atom index at the i-th SSSR ring in the molecule. This array is cached, so clone it if you plan to modify it.

Returns:

the sssr atom index arrays

Since:

Marvin 3.0

See Also:

grinvCC

getCSSR
```
public final int[][] getCSSR()
```
Gets the Complete Set of Smallest Ring atom indexes array. CSSR is generated by adding the ring to CSSR which are xor of the SSSR but size smaller then 14 and also size not larger then the largest ring in the SSSR. If the CSSR array is not calculated for the molecule, then create it. cssr[i][j] is the j-th atom index at the i-th CSSR ring in the molecule. This array is cached, so clone it if you plan to modify it.

Returns:

the cssr atom index arrays

Since:

Marvin 5.0

See Also:

grinvCC

getSSSRBonds
```
public final int[][] getSSSRBonds()
```
Gets the Smallest Set of Smallest Ring bond indexes array. Values are recalculated each time from the array of BitSets. The bond indexes are not in connection order. Use TopologyUtil.convertSSSRBondSetsToConnectedBondIndexArray(BitSet[], MoleculeGraph) to get bond indexes with connection order. WARNING! Using getSSSRBondsAsBitSet() may be more efficient and requires less memory usage.

Returns:

the sssr bond index arrays

Since:

Marvin 5.1.2

See Also:

grinvCC

getSSSRIdxesForAtoms
```
public int[][] getSSSRIdxesForAtoms()
```
Get the sssr ring indexes in which the atom (specified with it's index) can be located. This array is cached, so clone it if you plan to modify it.

Returns:

sssr ring indexes for each atom index.

Since:

Marvin 4.1.8 4/17/2007

See Also:

getCSSRIdxesForAtoms(), grinvCC

getCSSRIdxesForAtoms
```
public int[][] getCSSRIdxesForAtoms()
```
Get the cssr ring indexes in which the atom (specified with it's index) can be located.

Returns:

cssr ring indexes for each atom index.

Since:

Marvin 16.11.7.0

See Also:

getSSSRIdxesForAtoms(), grinvCC

getSSSRBondSet
```
public java.util.BitSet getSSSRBondSet()
```
Get SSSR bond index bitset. Values are not recalculated but the result of a previous calculation returned. If no previous calculation result found the values are calculated.

Returns:

the SSSR ring bond indexes in bitset.

Since:

Marvin 5.10

getSSSRBondsAsBitSet
```
public final java.util.BitSet[] getSSSRBondsAsBitSet()
```
Gets the Smallest Set of Smallest Ring edges as an array of BitSets, one BitSet for each ring. Values are cached.

Returns:

the sssr bonds as an array of BitSets, one BitSet for each ring

getSSSRBondSetInLong
```
@Deprecated
public long[] getSSSRBondSetInLong()
```
Deprecated. as of 15.09.2014, use getSSSRBondSet() instead
Get SSSR bond bitsets in long array. To get if the given 'n' bond is in the sssr long array 'r', use the following code:
```
 static boolean get(int n, long[] r) {
    return (r[n/64] & (((long)1) << (63-(n % 64)))) != 0 ;

 }
 
```
Returns:

the SSSR ring bond indexes in long array.

Since:

Marvin 4.1

See Also:

grinvCC

getSmallestRingSizeForIdx
```
public int[] getSmallestRingSizeForIdx()
```
Get the smallest ring size in which the atom (specified with it's index) can be located. This array is cached, so clone it if you plan to modify it.

Returns:

smallest ring size for each atom index.

Since:

Marvin 4.1 4/13/2006

See Also:

grinvCC

isRingBond
```
public boolean isRingBond(int idx)
```
Is this bond in ring?

Parameters:

idx - the bond index

Returns:

true if the bond is in ring else false.

createCHtab
```
@Deprecated
 @SubjectToRemoval(date=JAN_01_2022)
public int[][] createCHtab()
```
Deprecated. As of version 20.22, no replacement.

Creates the connection table extended with implicit hydrogen atoms. The implicit H atoms are indexed by free index numbers starting from the atom count and proceeding one-by-one from there. The current implementation always creates the table, the molecule does not store its extended connection table. chtab[i][j] will be the index of the j-th neighbor of the i-th atom, where atom indices greater than or equal to the atom count mean implicit hydrogen atoms.

Returns:

the chtab array

Since:

Marvin 3.0

getImplicitHcount
```
public int getImplicitHcount()
```
Gets the total number of implicit hydrogens attached to the molecule.

Returns:

the implicit hydrogen count or the number of query hydrogens

getExplicitHcount
```
public int getExplicitHcount()
```
Gets the total number of explicit hydrogens attached to the molecule.

Returns:

the explicit hydrogen count

Since:

Marvin 3.4

findAtomClone
```
public MolAtom findAtomClone(MolAtom a)
```
Finds the clone of an atom.

Parameters:

a - the original atom

Returns:

the clone or null if not found

Since:

Marvin 3.4.1, 07/06/2004

isValidLinkNode
```
public boolean isValidLinkNode(int linkAtomIdx,
                               int outer1,
                               int outer2)
```
Checks whether the specified link atom is valid or not. Invalid link atoms are those where repetition is impossible due to rings.

Parameters:

linkAtomIdx - atom index to be set to link atom.

outer1 - outer bond to be set by setLinkNodeOuterAtom(0)

outer2 - outer bond to be set by setLinkNodeOuterAtom(1)

Returns:

whether repetition is possible on the given atom and outer bonds.

Since:

Marvin 4.0 12/29/2004

setLinkNodeDefaultOuters
```
public 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.

Parameters:

atom - Atom to set to link node.

Throws:

java.lang.IllegalArgumentException - if it is an invalid link node configuration.

Since:

Marvin 4.0 12/29/2004

See Also:

MolAtom.setLinkNodeDefaultOuters(), MolAtom.setLinkNodeOuterAtom(int, int)

getVisibleCoords
```
public double[] getVisibleCoords(MolAtom ma)
```
Returns the coordinates of the given atom (contained in the molecule).

Parameters:

ma - The atom to be queried.

Returns:

The coordinates of ma.

Since:

Marvin 4.0 8/07/2005

saveCache
```
protected java.lang.Object[] saveCache(int n)
```
Saves caches like connection table, bond table, etc.

Since:

Marvin 3.4

restoreCache
```
protected java.lang.Object[] restoreCache(int n)
```
Restores caches like connection table, bond table, etc.

Since:

Marvin 3.4

isMultiChiral
```
public boolean isMultiChiral()
```
Returns the multiple chirality flag. To speed up the canonical label calculations, add chirality invariant to only those molecules that has at least two possible chiral centres.

Since:

Marvin 3.3

adjustMultiChiralFlag
```
public void adjustMultiChiralFlag()
```
Checks whether the molecule has multiple chiral centres

Since:

Marvin 3.3

isMolecule
```
@Deprecated
public boolean isMolecule()
```
Deprecated.
as of Marvin 14.7.7, no replacement.
Usage:
```
 use myObject instanceof Molecule instead
             
```
Checks if the object is an instance of Molecule or not. x.isMolecule() is equivalent to x instanceof Molecule, only faster.

Returns:

false

Since:

Marvin 5.2

isQuery
```
public boolean isQuery()
```
Indicates if the molecule has query features: query atoms or query bonds.

Returns:

true if the molecule has query features

Since:

Marvin 4.0 04/02/2005

See Also:

MolAtom.isQuery(), MolBond.isQuery()

clearCachedInfo
```
public void clearCachedInfo(int options)
```
Deletes the cached information depending on the given options.

Parameters:

options - options for the cache clearing

Since:

Marvin 4.0.2 09/20/2005

See Also:

CACHE_REMOVE_GRINVMODULE, CACHE_REMOVE_PARITYMODULE, CACHE_REMOVE_AROMATAMODULE, CACHE_REMOVE_SSSRMODULE, CACHE_REMOVE_TABS, CACHE_REMOVE_ALL

arrangeComponents
```
@Deprecated
public boolean arrangeComponents()
```
Deprecated.
As of Marvin 5.7, replaced by CleanUtil.arrangeComponents(MoleculeGraph, boolean, boolean).
Usage:
```
             CleanUtil.arrangeComponents(molecule, true, true);
             
```
Arranges molecule components (fragments, reactants, agents, products, R-group definitions) nicely. Also arranges molecule fragments in root / main molecule, attached data and Sgroup brackets.

Returns:

true if coordinates changed, false if unchanged

Since:

Marvin 4.1

setGrinvOptions
```
public void setGrinvOptions(int opt)
```
Sets graph invariant calculation options passed to the module.

Parameters:

opt - the graph invariant calculation option

Since:

Marvin 4.1.6

See Also:

GRINV_NOHYDROGEN, GRINV_DONT_STORE, GRINV_OLDSTEREO, GRINV_STEREO, GRINV_USEMAPS, GRINV_VALUE_OPTIONS

getGrinvOptions
```
public int getGrinvOptions()
```
Gets graph invariant calculation options passed to the module.

Returns:

the graph invariant calculation option

Since:

Marvin 4.1.6

See Also:

GRINV_NOHYDROGEN, GRINV_DONT_STORE, GRINV_OLDSTEREO, GRINV_STEREO, GRINV_USEMAPS, GRINV_VALUE_OPTIONS

useOnlyFirstAtomInStereoCalculation
```
public void useOnlyFirstAtomInStereoCalculation(boolean f)
```
Set how parity module should interpret wedes. The difference between the two ideas wheter to interpret both (narrow and wide) endpoints of the wedge as chiral center or just the first atom (which is the narrow end of the MDL wedge).

Parameters:

f - wheter to use only the first atom of the wedge for calculations

Since:

Marvin 5.0

isOnlyFirstAtomInStereoCalculation
```
public boolean isOnlyFirstAtomInStereoCalculation()
```
Get how parity module interpret wedges. The difference between the two ideas whether to interpret both (narrow and wide) endpoints of the wedge as chiral center (return false) or just the first atom (which is the narrow end of the MDL wedge) (return true).

Returns:

true if just the first atom of the bond is considered as chiral center, else false.

Since:

Marvin 5.0

sumConservedQuantities

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

For internal use only.

Since:: Marvin 4.1.13, 09/19/2007
See Also:: RxnMolecule.isIncompleteReaction()

getCtab
```
public int[][] getCtab()
```
Gets the connection table. If there is no connection table for the molecule graph, then creates it. ctab[i][j] will be the index of the j-th neighbor of the i-th atom. This array is cached, so clone it if you plan to modify it.

Returns:

the ctab array

Since:

Marvin 2.6

getBondTable
```
public BondTable getBondTable()
```
Gets the bond (edge) table. If there is no bond table for the molecule, then creates it. btab.elementOf(i, j) will be the index of the bond between atoms i and j, or -1 if there is no bond. This array is cached, so clone it if you plan to modify it.

Returns:

the BondTable of this molecule graph.

Since:

Marvin 5.4

findFrags
```
@Deprecated
public <C extends MoleculeGraph> C[] findFrags(java.lang.Class<C> cl)
```
Deprecated.
As of Marvin 5.6, replaced by findFrags(Class, int) and FRAG_KEEPING_MULTICENTERS.
Usage:
```
             mol.findFrags(cl, MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
             
```
Determines the disconnected fragments and puts them into an array. Multicenter groups are kept in the same fragment. Atoms are removed from the original molecule object unless the fragment class is SelectionMolecule.class. The original atom order is preserved in the returned fragments. Fragment order is also determined by the original atom order. The first fragment is the one containing atom 0, the second fragment is the one containing the smallest indexed atom not in the first fragment, etc.

Type Parameters:

C - the class of the fragments

Parameters:

cl - create fragment objects of this class

Returns:

array of fragments

Since:

Marvin 3.0

See Also:

findFrags(Class, int)

findFrags
```
public <C extends MoleculeGraph> C[] findFrags(java.lang.Class<C> cl,
                                               int fragmentationType)
```
Determines the disconnected fragments and puts them into an array. Atoms are removed from the original molecule object unless the fragment class is SelectionMolecule.class. The original atom order is preserved in the returned fragments. Fragment order is also determined by the original atom order. The first fragment is the one containing atom 0, the second fragment is the one containing the smallest indexed atom not in the first fragment, etc. Fragmentation is performed depending on fragmentation type:
- Merge only fragmented multicenter S-groups (see FRAG_KEEPING_MULTICENTERS)
- Merge all types of S-groups (see FRAG_KEEPING_SGROUPS)
- Keep all fragments separately, do not take into account the S-groups (see FRAG_BASIC)
Type Parameters:

C - the class of the fragments

Parameters:

cl - create fragment objects of this class

fragmentationType - determines the type of fragmentation

Returns:

array of fragments

Since:

Marvin 5.6

See Also:

FRAG_BASIC, FRAG_KEEPING_MULTICENTERS, FRAG_KEEPING_SGROUPS

findComponentIds
```
@Deprecated
public final int[] findComponentIds()
```
Deprecated.
As of Marvin 6.0, replaced by getFragIds(int) and FRAG_BASIC.
Usage:
```
             mol.getFragIds(MoleculeGraph.FRAG_BASIC);
             
```
Assigns a component ID to each connected component. S-groups are ignored. Do not modify the result array!

Returns:

the component ID array (the i-th ID is the component ID for atom i)

Since:

Marvin 4.0

findComponentIds
```
public final int[] findComponentIds(int[] inds)
```
Assigns a component ID to each connected component formed by the specified atom indexes. S-groups are ignored. Do not modify the result array!

Parameters:

inds - atom index array, null means all atoms

Returns:

the corresponding component ID array (the i-th ID is the component ID for atom inds[i] or atom i if the atom index array is null)

Since:

Marvin 4.0

getFragCount
```
@Deprecated
public final int getFragCount()
```
Deprecated.
As of Marvin 5.6, replaced by getFragCount(int) and FRAG_KEEPING_MULTICENTERS.
Usage:
```
             mol.getFragCount(MoleculeGraph.FRAG_KEEPING_MULTICENTERS);
             
```
Returns the number of fragments for fragmentation keeping multicenters.

Returns:

the number of fragments

Since:

Marvin 3.01

See Also:

getFragCount(int)

getFragCount
```
public final int getFragCount(int fragmentationType)
```
Returns the number of fragments for the given fragmentation type.

Parameters:

fragmentationType - type of fragmentation

Returns:

the number of fragments

Since:

Marvin 5.6

See Also:

FRAG_BASIC, FRAG_KEEPING_MULTICENTERS, FRAG_KEEPING_SGROUPS

getFragIds
```
public final int[] getFragIds(int fragmentationType)
```
Gets an array containing the fragment id for each atom for the given fragmentation type. This array is cached, so clone it if you plan to modify it.

Parameters:

fragmentationType - type of fragmentation

Returns:

array of fragment identifiers

Since:

Marvin 5.6

See Also:

FRAG_BASIC, FRAG_KEEPING_MULTICENTERS, FRAG_KEEPING_SGROUPS

regenGearch
```
protected final void regenGearch()
```
Recreate graph search results object.

findFrag
```
@Deprecated
public final void findFrag(int i,
                                       MoleculeGraph frag)
```
Deprecated.
As of Marvin 5.6, replaced by findFrag(int, int, MoleculeGraph) and FRAG_KEEPING_MULTICENTERS.
Usage:
```
             mol.findFrag(i, MoleculeGraph.FRAG_KEEPING_MULTICENTERS, frag);
             
```
Determines the subgraph connected to the specified atom, considering multicenter S-groups as one fragment. Subsequent calls with different atom (i) argument are possible because only those atoms and bonds are added that are still not elements of frag. Atoms are removed from the original molecule graph unless the frag is a SelectionMolecule.

Parameters:

i - atom index

frag - add the atoms and bonds to this MoleculeGraph

Since:

Marvin 2.6

See Also:

findFrag(int, int, MoleculeGraph)

findFrag
```
public final void findFrag(int i,
                           int fragmentationType,
                           MoleculeGraph frag)
```
Determines the subgraph connected to the specified atom. Subsequent calls with different atom (i) argument are possible because only those atoms and bonds are added that are still not elements of frag. Atoms are removed from the original molecule graph unless the frag is a SelectionMolecule.

Parameters:

i - atom index

fragmentationType - type of fragmentation

frag - add the atoms and bonds to this MoleculeGraph

Since:

Marvin 5.6

See Also:

FRAG_BASIC, FRAG_KEEPING_MULTICENTERS, FRAG_KEEPING_SGROUPS

findFragById
```
public final void findFragById(int fragId,
                               int fragmentationType,
                               MoleculeGraph frag)
```
Determines the subgraph corresponding to the specific fragment ID. Atoms are removed from the original molecule graph unless the frag is a SelectionMolecule.

Parameters:

fragId - fragment ID

fragmentationType - type of fragmentation

frag - add the atoms and bonds to this MoleculeGraph

Since:

Marvin 5.6

See Also:

getFragIds(int), FRAG_BASIC, FRAG_KEEPING_MULTICENTERS, FRAG_KEEPING_SGROUPS

findBasicFrags
```
public final <C extends MoleculeGraph> C[] findBasicFrags(java.lang.Class<C> cl)
```
Determines the disconnected fragments and puts them into an array. Atoms are removed from the original molecule object unless the fragment class is SelectionMolecule.class. The original atom order is preserved in the returned fragments. Fragment order is also determined by the original atom order. The first fragment is the one containing atom 0, the second fragment is the one containing the smallest indexed atom not in the first fragment, etc. This method provides the basic fragmentation that relies on classical graph theory and is not overwritten by successor class. DO NOT USE WITH OTHER FRAGMENTATION RELATED METHODS like getFragCount()! The length of the returned array and the returned value of getFragCount() might be different in successor classes.

Parameters:

cl - create fragment objects of this class

Returns:

array of fragments

Since:

Marvin 5.0

createGearch

protected chemaxon.struc.gearch.MoleculeGraphGearch createGearch()

getMaxRgroupAttachmentPointOrder
```
public int getMaxRgroupAttachmentPointOrder()
```
Returns the maximal attachment point order of R-group attachment point atoms in this molecule graph.

Returns:

the maximal attachment point order

Since:

Marvin 5.4

See Also:

MolAtom.RGROUP_ATTACHMENT, MolAtom.getRgroupAttachmentPointOrder()

mergeFrags
```
public int mergeFrags(int id1,
                      int id2,
                      int fragmentationType)
```
Merges two connected components of the given fragmentation type.

Parameters:

id1 - index of first atom to be merged into one fragment

id2 - index of second atom to be merged into one fragment

fragmentationType - determines the type of fragmentation

Returns:

the new ID of the merged connected components

See Also:

FRAG_BASIC, FRAG_KEEPING_MULTICENTERS, FRAG_KEEPING_SGROUPS

setFlags
```
protected void setFlags(int f,
                        int mask)
```
Sets specified bits in the flags.

Parameters:

f - new value of the specified bits

mask - bits to set

setValenceCheckEnabled
```
public void setValenceCheckEnabled(boolean b)
```
Enables or disables valence check on this molecule graph, depending on the value of the parameter b. Enabled valence check means that the valence check is called for all atoms in this molecule graph when needed.
Valence check is enabled initially by default. To configure the options of the valence check see setValenceCheckOptions(ValenceCheckOptions)

Parameters:

b - - If true, the valence check is enabled on this molecule graph; otherwise valence check is disabled

Since:

Marvin 5.4

See Also:

isValenceCheckEnabled()

isValenceCheckEnabled
```
public boolean isValenceCheckEnabled()
```
Determines whether valence check is enabled on this molecule graph. Enabled valence check means that the valence check is called for all atoms in this molecule graph when needed. Disabling means that valence check is not called anywhere. Valence check may be enabled or disabled by calling the setValenceCheckEnabled method.
To configure the options of the valence check see setValenceCheckOptions(ValenceCheckOptions)

Returns:

true if the valence check is enabled, false otherwise

Since:

Marvin 5.4

See Also:

setValenceCheckEnabled(boolean b)

setValenceCheckState
```
@Deprecated
public void setValenceCheckState(MoleculeGraph.ValenceCheckState state)
```
Deprecated.
As of Marvin 6.0, replaced by setValenceCheckOptions(ValenceCheckOptions) and setValenceCheckEnabled(boolean).
Usage:
```
             // Same as setValenceCheckState(ValenceCheckState.OFF):
             setValenceCheckEnabled(false);
             // Same as setValenceCheckState(ValenceCheckState.AMBIGUOUS_AROMATIC_ATOMS_IGNORED):
             setValenceCheckOptions(ValenceCheckOptions.DEFAULT);
             // Same as setValenceCheckState(ValenceCheckState.FULL):
             setValenceCheckOptions(new ValenceCheckOptions(false, true));
             
```
Enables or disables valence check on atoms of the molecule graph, depending on the value of the parameter state. Full valence check means that the valence check is called for all atoms in this molecule graph when needed. When ambiguous aromatic atoms are ignored then these kind of atoms are not checked, their implicit Hydrogen count is not set, they remain untouched.
The possibility to ignore Nitrogen-like aromatic atoms is added for speedup reasons because for these atoms implicit Hydrogens can be stored (e.g. in cxsmiles format).
Valence check is enabled initially by default.

Parameters:

state - determines which atoms will be checked in the following calls of valenceCheck()

Since:

Marvin 5.9

See Also:

getValenceCheckState(), valenceCheck()

getValenceCheckState

@Deprecated
public MoleculeGraph.ValenceCheckState getValenceCheckState()

Deprecated. As of Marvin 6.0, replaced by getValenceCheckOptions() and isValenceCheckEnabled().
Usage:

 // Same as getValenceCheckState() == ValenceCheckState.OFF:
 isValenceCheckEnabled() == true;
 // Same as getValenceCheckState() == ValenceCheckState.AMBIGUOUS_AROMATIC_ATOMS_IGNORED:
 getValenceCheckOptions.isLocalAromatic() == true;
 // Same as getValenceCheckState() == ValenceCheckState.FULL:
 getValenceCheckOptions.isLocalAromatic() == false;

Returns:: the valence check state

setValenceCheckOptions
```
public void setValenceCheckOptions(ValenceCheckOptions options)
```
Sets the options for valence checking. To just enable/disable valence check in the molecule use setValenceCheckEnabled(boolean). Calling this function with a not null parameter automatically enables the valence check.

Parameters:

options - the new valence check options

Since:

Marvin 6.0

See Also:

ValenceCheckOptions

getValenceCheckOptions
```
public ValenceCheckOptions getValenceCheckOptions()
```
Returns the options for valence checking. To see if the valence check is enabled on the molecule use isValenceCheckEnabled()

Returns:

the valence check options

Since:

Marvin 6.0

See Also:

ValenceCheckOptions

isLargeMolecule
```
public boolean isLargeMolecule()
```
Returns true if large molecule (number of atoms exceeds 1000).

Returns:

true if large molecule

getFreeAttachmentPoints
```
public int getFreeAttachmentPoints(MolAtom atom)
```
Specified by:

getFreeAttachmentPoints in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>

Since:

Marvin 5.11

getPossibleAttachmentPoints
```
@Deprecated
protected int getPossibleAttachmentPoints(MolAtom molAtom)
```
Deprecated.
As of Marvin 6.0, replaced by SuperatomSgroup.getAttachmentPointOrders(MolAtom) and MolAtom.getAttachParentSgroup().
Usage:
```
 SuperatomSgroup group = (SuperatomSgroup)molAtom.getAttachParentSgroup());
 List<Integer> orders = group.getAttachmentPointOrders(molAtom);
             
```
Calculates the possible attachment point value for an atom based on the attachment point settings of the atom.

Parameters:

molAtom - the atom to calculate the possible attachment point value for

Returns:

the calculated attachment point value

Since:

Marvin 5.10

See Also:

MolAtom.getAttach()

getAtomReferenceList
```
public java.util.List<MolAtom> getAtomReferenceList()
```
Deprecated. Use atoms() instead.

Since:

Marvin 5.11

getLigandCount
```
public int getLigandCount(MolAtom atom)
```
Specified by:

getLigandCount in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>

Since:

Marvin 5.11

getLigand
```
public MolAtom getLigand(MolAtom atom,
                         int n)
```
Specified by:

getLigand in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>

Since:

Marvin 5.11

getLigandBondType
```
public chemaxon.struc.BondType getLigandBondType(MolAtom atom,
                                                 int i)
```
Specified by:

getLigandBondType in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>

Since:

Marvin 5.11

getLigandAtno
```
public int getLigandAtno(MolAtom atom,
                         int n)
```
Specified by:

getLigandAtno in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>

Since:

Marvin 5.11

getCharge
```
public int getCharge(MolAtom atom)
```
Specified by:

getCharge in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>

Since:

Marvin 5.11

getAtomicNumber
```
public int getAtomicNumber(MolAtom atom)
```
Specified by:

getAtomicNumber in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>

Since:

Marvin 5.11

getRadicalCount
```
public int getRadicalCount(MolAtom atom)
```
Specified by:

getRadicalCount in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>

Since:

Marvin 5.11

getValenceProperty
```
public int getValenceProperty(MolAtom atom)
```
Specified by:

getValenceProperty in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>

Since:

Marvin 5.11

getImplicitHCount
```
public int getImplicitHCount(MolAtom atom)
```
Specified by:

getImplicitHCount in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>

Since:

Marvin 5.11

isAtomInRing
```
public boolean isAtomInRing(MolAtom atom)
```
Specified by:

isAtomInRing in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>

Since:

Marvin 5.11

isAcceptedSpecialLigand
```
public boolean isAcceptedSpecialLigand(MolAtom atom)
```
Specified by:

isAcceptedSpecialLigand in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>

Since:

Marvin 5.11

isBondParallelWith
```
protected boolean isBondParallelWith(MolBond b)
```
Checks if there is a bond parallel (having same endpoints) with the given bond in this MoleculeGraph.

Parameters:

b - bond

Returns:

true if there is a bond parallel with the given bond else false

replaceAtom
```
public void replaceAtom(int i,
                        MolAtom newAtom)
```
Replaces the atom on the given index with the parameter atom and removes the parameter atom from its original parent molecule if needed.

Parameters:

i - the index of the original atom

newAtom - the atom which will replace the original

connectOriginalBondsToNewAtom

protected void connectOriginalBondsToNewAtom(MolAtom newAtom,
                                             MolAtom orig,
                                             MolBond[] bonds)

Sets the original connections to the new atom.

Parameters:: newAtom - the atom which replace the original; orig - the original atom; bonds - the original atoms bonds (before any modification)

getAtomIterator
```
public IteratorFactory.AtomIterator getAtomIterator()
```
Returns an iterator over the atoms in this molecule in proper sequence.

Returns:

an iterator over the atoms in this molecule in proper sequencer

Since:

Marvin 6.2, 2013.09.09.

getBondIterator
```
public IteratorFactory.BondIterator getBondIterator()
```
Returns an iterator over the bonds in this molecule in proper sequence.

Returns:

an iterator over the bonds in this molecule in proper sequence

Since:

Marvin 6.2, 2013.09.09.

setSupergraph
```
protected void setSupergraph(MoleculeGraph molecule)
```
Sets the given molecule as the supergraph of this graph.

Parameters:

molecule - the molecule

Since:

Marvin 14.7.7, Jul 2, 2014

atoms
```
public final java.util.List<MolAtom> atoms()
```
Provides a list view of the atoms in the molecule. It is a dynamic view, which follows every change of the molecule structure. However, you must not add or remove atoms and bonds during iteration.

Specified by:

atoms in interface chemaxon.core.calculations.valencecheck.MoleculeWithValence<MolAtom>

Returns:

a dynamic list view of the atoms

bonds
```
public final java.util.List<MolBond> bonds()
```
Provides a list view of the bonds in the molecule. It is a dynamic view, which follows every change of the molecule structure. However, you must not add or remove atoms and bonds during iteration.

Returns:

a dynamic list view of the bonds

fixProperties
```
public void fixProperties()
```
Delegates to tracker's fixProperties().

Class MoleculeGraph

Property Summary

Nested Class Summary

Field Summary

Fields inherited from interface chemaxon.struc.StereoConstants

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Property Detail

hasSelfReferring

Field Detail

INITIAL_CAPACITY

AROM_BASIC

AROM_GENERAL

AROM_LOOSE

AROM_SUBSTRUCTURE

AROM_AMBIGUOUS

AROM_CHUCKEL

DEAROM_GENERAL

DEAROM_HUCKELCHECK

DEAROM_HUCKELCHECK_EX

INVALID_LINKNODE_MESSAGE

DIM_MASK

AUTO_UNGROUP

VALENCE_CHECK

VALENCE_CHECK_AMBIGUOUS

RMCLEANUP_NONE

RMCLEANUP_FIXCOMPONENT

RMCLEANUP_ALL

RMCLEANUP_EDGES

CACHE_REMOVE_ALL

CACHE_REMOVE_CACHEMEMORY

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

CACHE_REMOVE_TABS

MIN_RING_SIZE_FOR_TRANS_DB

OMIT_POSTCLEAN

FRAG_BASIC

FRAG_KEEPING_MULTICENTERS

FRAG_KEEPING_SGROUPS

FRAG_TYPE_COUNT

superGraph

parentGraph

theAtoms

atomCount

theBonds

bondCount

orix

oriy

oriz

grinvCC

cacheMemory

ctab

btab

gearch

propertyContainer

useOnlyFirstAtomInStereoCalculation

Constructor Detail

MoleculeGraph

MoleculeGraph

Method Detail

getParent

getForefather

getLock

add

add

add

addAtom0

addAtomWithoutChangingIt