Molecule (JChem Base API documentation (c) 1998-2021 ChemAxon Ltd.)

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

All Implemented Interfaces:

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

Direct Known Subclasses:

RgMolecule, RxnMolecule
```
@PublicAPI
public class Molecule
extends MoleculeGraph
implements chemaxon.struc.MObjectContainer
```
Molecule class. A MoleculeGraph that may also contain S-groups.

Version:

6.2 10/09/2013.

Author:

Peter Csizmadia, Andras Volford, Szabolcs Csepregi, Erika Biro

See Also:

Serialized Form

Property Summary
- Properties inherited from class chemaxon.struc.MoleculeGraph
  hasSelfReferringProperty

Nested Class Summary
- Nested classes/interfaces inherited from class chemaxon.struc.MoleculeGraph
  MoleculeGraph.ValenceCheckState

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`DEFAULT_UNGROUP` Do not ungroup and do not expand S-group's children.
`static int`	`RECURSIVE_UNGROUP` Ungroup and expand (if possible) the child S-groups.
`static int`	`RM_KEEP_LEAVINGGROUPS` Deprecated. As of Marvin 6.2, no replacement. Not supported feature.
`static int`	`RMCLEANUP_FROMSGROUPS` Remove atoms from S-groups.
`static int`	`RMCLEANUP_SGROUPATOMS` Remove S-groups of removed superatoms.
`protected static int`	`RMSG_DEFAULT` Remove S-group's children and remove S-group from its parent.
`protected static int`	`RMSG_KEEP_CHILDREN` Do not remove S-group's children.
`protected static int`	`RMSG_KEEP_MULTICENTER` Do not remove central atom of multicenter S-groups.
`protected static int`	`RMSG_KEEP_PARENT` Do not remove S-group from its parent.

Fields inherited from class chemaxon.struc.MoleculeGraph
AROM_AMBIGUOUS, AROM_BASIC, AROM_CHUCKEL, AROM_GENERAL, AROM_LOOSE, AROM_SUBSTRUCTURE, atomCount, AUTO_UNGROUP, bondCount, btab, CACHE_REMOVE_ALL, CACHE_REMOVE_AROMATAMODULE, CACHE_REMOVE_CACHEMEMORY, CACHE_REMOVE_GRINVMODULE, CACHE_REMOVE_PARITYMODULE, CACHE_REMOVE_SSSRMODULE, CACHE_REMOVE_TABS, cacheMemory, ctab, DEAROM_GENERAL, DEAROM_HUCKELCHECK, DEAROM_HUCKELCHECK_EX, DIM_MASK, FRAG_BASIC, FRAG_KEEPING_MULTICENTERS, FRAG_KEEPING_SGROUPS, FRAG_TYPE_COUNT, gearch, GRINV_DONT_STORE, GRINV_NOHYDROGEN, GRINV_OLDSTEREO, GRINV_STEREO, GRINV_USEMAPS, GRINV_VALUE_OPTIONS, grinvCC, INITIAL_CAPACITY, INVALID_LINKNODE_MESSAGE, MIN_RING_SIZE_FOR_TRANS_DB, OMIT_POSTCLEAN, orix, oriy, oriz, parentGraph, propertyContainer, RMCLEANUP_ALL, RMCLEANUP_EDGES, RMCLEANUP_FIXCOMPONENT, RMCLEANUP_MOBJECT, RMCLEANUP_NONE, RMCLEANUP_PARENTDOC, RMCLEANUP_STEREO, superGraph, theAtoms, theBonds, useOnlyFirstAtomInStereoCalculation, VALENCE_CHECK, VALENCE_CHECK_AMBIGUOUS

Fields inherited from interface chemaxon.struc.StereoConstants
ANTI, ATOMSTEREO_EITHER, ATOMSTEREO_MASK, ATOMSTEREO_NONE, ATOMSTEREO_SPECIFIC, CHIRALITY_M, CHIRALITY_MASK, CHIRALITY_P, CHIRALITY_r, CHIRALITY_R, CHIRALITY_s, CHIRALITY_S, CHIRALITYSUPPORT_ALL, CHIRALITYSUPPORT_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
`Molecule()` Construct a 2 dimensional molecule.
`Molecule(Molecule p, int na, int nb)` Construct a molecule or fragment with the specified number of atoms and bonds.
`Molecule(Molecule p, MolAtom a)` Construct a molecule consisting of a single atom (node).
`Molecule(Molecule p, MolBond b)` Construct a molecule consisting of a single bond (edge).

Method Summary

All Methods Static Methods Instance Methods Concrete Methods Deprecated Methods
Modifier and Type	Method and Description
`void`	`add(MolBond bond)` Adds a bond to the molecule.
`protected void`	`addAtom0(MolAtom node)` Adds an atom.
`protected void`	`addAtomToFragment(MolAtom atom)` Adds an atom to a fragment.
`protected void`	`addBond0(MolBond bond)` Adds a bond.
`void`	`addSgroup(Sgroup sg, boolean setparent)` Adds an S-group to this object.
`protected void`	`addSgroupClones(Molecule origparentm, Molecule origm, Molecule newm)` Adds the S-groups of a child molecule clone to the new parent molecule clone.
`protected void`	`addSgroupsOf(Molecule m)` Adds S-groups to this object and its parent.
`void`	`aromatize(int method)` Aromatizes molecule.
`void`	`aromatize(int method, boolean checkAmbiguity)` Aromatizes molecule.
`double`	`bondlength()` Calculate the regular bond length for the unified structure.
`boolean`	`canBeReactionComponent()` Tests whether an object of this class can be a reaction component.
`void`	`checkConsistency()` Deprecated. As of Marvin 5.7, no replacement. Not intended for public use, it was intended only for internal debugging.
`protected void`	`checkSgroupConsistency()` Checks the internal consisitency of S-groups.
`void`	`clear()` Clears the molecule.
`void`	`clearExtraLabels()` Clears extra atom labels.
`void`	`clearForImport(java.lang.String format)` Initializes molecule for import.
`void`	`clearObjects()`
`void`	`clearProperties()` Clears RDfile/SDfile properties.
`Molecule`	`clone()` Makes 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 and bonds of this molecule to another one.
`void`	`clonecopy(MoleculeGraph g)` Makes another molecule identical to this one.
`protected void`	`clonecopyWithoutSgroups(Molecule m)` Copies the all the contents except the S-groups into another molecule object.
`void`	`clonelesscopy(MoleculeGraph g)` Deprecated. as of Marvin 6.3. Not supported feature.
`Molecule`	`cloneMolecule()` Deprecated. as of Marvin 2014.09.01.0 use `clone()` instead
`Molecule`	`cloneMoleculeWithDocument()` Makes an identical copy of the molecule and its document.
`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`	`contractSgroups()` Contracts all S-groups.
`boolean`	`contractSgroups(int opts)` Contracts all S-groups.
`Molecule[]`	`convertToFrags()` Converts this molecule to its disconnected fragments, expanding all S-groups and keeping disconnected Multicenter S-groups in the same fragment, but ungroupping and separating fragments in all other types of S-groups.
`int`	`countExpandableContractableSgroups()` Counts the expandable and contractable S-groups.
`int`	`countOrderedComponentSgroups()` Counts the ordered component S-groups.
`protected chemaxon.struc.gearch.MoleculeGraphGearch`	`createGearch()`
`boolean`	`dearomatize()` Dearomatize molecule.
`void`	`endReuse(int n)` End reusing atoms.
`boolean`	`expandSgroups()` Expands all S-groups.
`boolean`	`expandSgroups(int opts)` Expands all S-groups.
`byte[]`	`exportToBinFormat(java.lang.String fmt)` Deprecated. As of Marvin 5.7, replaced by `MolExporter.exportToBinFormat(Molecule, String)`.
`java.lang.String`	`exportToFormat(java.lang.String fmt)` Deprecated. As of Marvin 5.7, replaced by `MolExporter.exportToFormat(Molecule, String)`.
`java.lang.Object`	`exportToObject(java.lang.String fmt)` Deprecated. As of Marvin 5.7, replaced by `MolExporter.exportToObject(Molecule, String)`.
`protected void`	`fillSelectionMolecule(SelectionMolecule s)` Adds all atoms and bonds to the specified molecule.
`Sgroup[]`	`findAllSgroupContaining(MolAtom a)` Finds all smallest S-groups containing the specified atom.
`MulticenterSgroup`	`findContainingMulticenterSgroup(MolAtom atom)` Gets the containing multicenter S-group of a multicenter atom.
`Sgroup`	`findContractableSgroup()` Finds an expanded residue.
`Sgroup`	`findExpandableSgroup()` Finds a contracted residue.
`SelectionMolecule[]`	`findFrags()` Determines the disconnected fragments and puts them into an array.
`<C extends MoleculeGraph> C[]`	`findFrags(java.lang.Class<C> cl, int fragmentationType)` Determines the disconnected fragments and puts them into an array.
`Sgroup`	`findSgroupContaining(MolAtom a)` Finds the largest S-group that contains the specified atom.
`Sgroup`	`findSgroupOf(MolAtom a)` Finds the smallest S-group related to the specified atom.
`Sgroup`	`findSmallestSgroupContaining(MolAtom a)` Finds the smallest S-group that contains the specified atom.
`protected boolean`	`fixSelfReferringProperty(MProp prop)` Fix a property containing reference to the molecule.
`protected void`	`fuse0(MoleculeGraph graph, boolean check)` Adds those atoms and bonds of a molecule graph to this one that are not already elements.
`java.util.List<MObject>`	`getAllObjects()`
`protected MolBond[]`	`getBonds(MolAtom atom)` Returns the bonds attached to the given atom.
`java.lang.String`	`getComment()` Gets the comment.
`long`	`getEndPosition()` Gets the end position of this molecule in the input file.
`protected SelectionMolecule`	`getGraphUnionAsSelection()` Gets a selection molecule containing all the atoms and bonds.
`java.lang.String`	`getId()`
`java.lang.String`	`getInputFormat()` Gets the input file format.
`protected Molecule`	`getMostSimplifiedMolecule()` Gets the simplified molecule object even if there is a parent document with other objects.
`java.lang.String`	`getName()` Gets the molecule name/title that was set by `setName(String)`.
`int`	`getObjectCount()`
`java.lang.String`	`getProperty(java.lang.String key)` Deprecated. As of Marvin 5.7, replaced by `MPropHandler.convertToString(MProp, String)`. Usage: String property = MPropHandler.convertToString(mol.properties(), key);
`int`	`getPropertyCount()` Gets the total number of RDfile/SDfile properties.
`java.lang.String`	`getPropertyKey(int i)` Gets an RDfile/SDfile property key.
`java.util.Enumeration<?>`	`getPropertyKeys()` Deprecated. As of Marvin 4.1, replaced by `properties()`.`getKeys()` and `properties()`.`getKeyEnumeration()`. One-to-one replacement is method `getKeyEnumeration()` but method `getKeys()` is simpler to use.
`java.lang.Object`	`getPropertyObject(java.lang.String key)` Gets an RDfile/SDfile property object.
`Sgroup[]`	`getRootSgroups()` Gets root s-groups (groups that are not embedded into another s-group).
`Sgroup`	`getSgroup(int i)` Gets an S-group.
`Sgroup[]`	`getSgroupArray()` Gets the array of S-groups.
`int`	`getSgroupCount()` Gets the number of S-groups.
`IteratorFactory.SgroupIterator`	`getSgroupIterator()` Returns an iterator over the s-groups in this molecule in proper sequence.
`MolAtom[]`	`getSgroupLigands()` Gets the S-group's ligands if the structure represents an S-group.
`Molecule`	`getSimplifiedMolecule()` Gets the simplified molecule object.
`Sgroup[]`	`getSortedSgroups()` Gets the sorted S-groups in parent-child order.
`long`	`getStartPosition()` Gets the starting position of this molecule in the input file.
`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`	`hasContractedSgroup()` Tests if the molecule has contracted S-groups or not.
`boolean`	`hasId(java.lang.String id)`
`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);
`int`	`indexOf(Sgroup sg)` Gets the array index of an S-group.
`boolean`	`isEmpty()` Tests whether the molecule is empty.
`boolean`	`isExpandable(int opts)` Tests if the molecule is expandable with the specified options.
`boolean`	`isGUIContracted()` Deprecated. as of Marvin 6.2 replaced by `hasContractedSgroup()`
`boolean`	`isReaction()` Checks if the structure represents a reaction or not.
`boolean`	`isSgroup()` Deprecated. As of Marvin 14.7.7, no replacement. Not supported feature.
`protected void`	`makeItSimilar(MoleculeGraph g)` Copies some properties of this molecule to the other one specified as argument.
`void`	`mergeAtoms(MolAtom that, MolAtom node)` Deprecated. As of Marvin 6.2, use `MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean)` instead.
`MoleculeGraph`	`newInstance()` Creates a new Molecule object.
`SelectionMolecule`	`newSelectionMolecule()` Creates a new SelectionMolecule object appropriate for storing selection from this molecule.
`void`	`rearrangeSgroups(int[] newIndexes)` Orders S-groups in the vector of S-groups in the given order corresponding to the given new indexes.
`void`	`removeAll()` Removes all the atoms and bonds.
`void`	`removeAllBonds()` Removes all bonds.
`protected void`	`removeAllSgroups()` Removes all S-groups.
`void`	`removeAtom(int i, int cleanupFlags)` Removes an atom and its bonds by index.
`void`	`removeAtom(MolAtom atom, int cleanupFlags)` Removes an atom and its bonds by reference.
`protected void`	`removeAtomFromChildren(Sgroup sgroup, MolAtom atom)` Removes the parameter atom from the parameter S-group and it's descendants.
`protected void`	`removeBond(int i, int cleanupFlags)` Removes a bond by index.
`protected void`	`removeBond(MolBond bond, int cleanupFlags)` Removes a bond by reference.
`void`	`removeObject(MObject mo)`
`protected void`	`removeSgroupFromList(Sgroup sg)` Removes an S-group from the sgroupVector.
`protected void`	`removeSgroupsOf(Molecule m)` Removes S-groups from this object and its parent.
`protected void`	`removeSgroupsOf(Molecule m, int rmflags)` Removes S-groups that are contained in a given molecule but not contained in another molecule.
`protected void`	`reparentSgroups(Molecule p)` Change parents of all S-groups in this molecule.
`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`	`replaceSgroup(Sgroup sgroup, Sgroup newSgroup)` Replaces an S-group with a new sgroup in the molecule.
`static java.lang.String`	`residueSymbolOf(int id)` Gets the name of a residue.
`static int`	`residueTypeOf(java.lang.String name)` Gets the residue identifier for a residue name.
`MolAtom`	`reuseAtom(int z, int i)` Reuse an atom or create a new one.
`void`	`selectAllObjects(boolean s)`
`protected void`	`setAtom0(int i, MolAtom newAtom)` Sets the atom at the specified index.
`void`	`setComment(java.lang.String s)` Sets the comment.
`void`	`setDim(int d)` Sets the dimension.
`void`	`setEndPosition(long off)` Sets the end position of this molecule in the input file.
`void`	`setGUIContracted(boolean contract)` Deprecated. as of Marvin 6.2, use `expandSgroups(int)` or `contractSgroups(int)` instead with option parameter `Expandable.LEAVE_COORDS_UNCHANGED`
`void`	`setGUIContracted(boolean contract, int opts)` Deprecated. as of Marvin 6.2, use `expandSgroups(int)` or `contractSgroups(int)` instead with option parameter `Expandable.LEAVE_COORDS_UNCHANGED`
`void`	`setId(java.lang.String id)`
`void`	`setInputFormat(java.lang.String format)` Sets the input file format.
`void`	`setName(java.lang.String s)` Sets the molecule name/title.
`void`	`setProperty(java.lang.String key, java.lang.String value)` Sets an RDfile/SDfile property.
`void`	`setPropertyObject(java.lang.String key, java.lang.Object value)` Sets an RDfile/SDfile property object.
`void`	`setSgroupParent(MolAtom a, Sgroup sg, boolean set)` Sets or unsets an S-group as a parent of an atom.
`void`	`setStartPosition(long off)` Sets the starting position of this molecule in the input file.
`void`	`sortSgroupXBonds()` Deprecated. As of Marvin 5.12, no replacement. Crossing bonds of a `SuperatomSgroup` do not need to be sorted any more. It is not advised to sort them anyway because then the indexes of bonds change in the parent molecule.
`byte[]`	`toBinFormat(java.lang.String fmt)` Deprecated. As of Marvin 5.7, replaced by `MolExporter.exportToBinFormat(Molecule, String)`.
`java.lang.String`	`toFormat(java.lang.String fmt)` Deprecated. As of Marvin 5.7, replaced by `MolExporter.exportToFormat(Molecule, String)`. To get exact replacement use: try { String out = MolExporter.exportToFormat(this, fmt); } catch (IOException e) { throw new IllegalArgumentException(e); }
`java.lang.Object`	`toObject(java.lang.String fmt)` Deprecated. As of Marvin 5.7, replaced by `MolExporter.exportToObject(Molecule, String)`.
`void`	`transform(CTransform3D t, boolean incg)` Apply a transformation matrix to the atomic coordinates and Data Sgroup coordinates.
`boolean`	`ungroupSgroup(int i)` Deprecated. as of Marvin 6.3. use `ungroupSgroup(Sgroup)` instead.
`boolean`	`ungroupSgroup(int i, int opts)` Deprecated. as of Marvin 6.3. use `ungroupSgroup(Sgroup)` instead.
`boolean`	`ungroupSgroup(Sgroup sg)` Ungroups the specified S-group and expands it if it is an Expandable S-group.
`boolean`	`ungroupSgroup(Sgroup sg, int opts)` Expand and ungroup the specified S-group.
`boolean`	`ungroupSgroups()` Expands and ungroups all S-groups.
`boolean`	`ungroupSgroups(java.util.EnumSet<SgroupType> types)` Ungroups all S-groups of the specified types in this molecule.
`boolean`	`ungroupSgroups(int type)` Deprecated. as of Marvin 6.3. use `ungroupSgroups(EnumSet)` instead.

Methods inherited from class chemaxon.struc.MoleculeGraph
add, add, addAtomsAndBondsTo, addAtomWithoutChangingIt, addBondWithoutChangingIt, addExplicitHydrogens, addExplicitHydrogens, addExplicitLonePairs, addSimpleAtomWithoutChangingIt, adjustMultiChiralFlag, aromatize, aromatize, arrangeComponents, atoms, bonds, calcCenter, calcCenter, calcDehydrogenizedGrinv, calcHeight, calcHybridization, calcOutRect, calcOutRect, calcOutRectCenter, calcOutRectCenter, calcWidth, canBeCT, canBeCT, canBeCT, checkBondConsistency, clean, clean, clearCachedInfo, clonecopyMoleculeGraphWithoutSgroups, contains, contains, createCHtab, createDehydrogenizedReadOnlyGraph, createSmolecule, dearomatize, findAtom, findAtomClone, findBasicFrags, findBond, findComponentIds, findComponentIds, findFrag, findFrag, findFragById, findFrags, findInArray, fixProperties, fuse, fuse, getAromaticAndAliphaticRings, getAtom, getAtomArray, getAtomCount, getAtomCount, getAtomicNumber, getAtomIterator, getAtomReferenceList, getBond, getBondArray, getBondCount, getBondIterator, getBondTable, getCharge, getChirality, getCSSR, getCSSRIdxesForAtoms, getCtab, getDesiredLength, getDesiredLength, getDim, getDocument, getDocumentForChild, getEnclosingCube, getExactMass, getExplicitHcount, getExplicitLonePairCount, getEZStereo, getFlags, getForefather, getFormalCharge, getFormula, getFragCount, getFragCount, getFragIds, getFreeAttachmentPoints, getGraphUnion, getGrinv, getGrinv, getGrinv, getGrinv, getGrinvCC, getGrinvOptions, getImplicitHcount, getImplicitHCount, getLigand, getLigandAtno, getLigandBondType, getLigandCount, getLocalParity, getLocation, getLock, getLonePairCount, getMass, getMaxRgroupAttachmentPointOrder, getParent, getParentDocument, getParity, getParityType, getPoints, getPossibleAttachmentPoints, getRadicalCount, getSmallestRingSizeForIdx, getSSSR, getSSSRBonds, getSSSRBondsAsBitSet, getSSSRBondSet, getSSSRBondSetInLong, getSSSRIdxesForAtoms, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getStereo2, getSubGraphCount, getSubGraphs, getSubGraphs, getTotalCharge, getValenceCheckOptions, getValenceCheckState, getValenceProperty, hasBondSet, hasExplicitLonePairs, hasExtraLabelSet, hasImplicitH, hasSelfReferringProperty, hasValenceError, hydrogenize, implicitizeHydrogens, implicitizeHydrogens, implicitizeHydrogens, incGrinvCC, incGrinvCC, incGrinvCCOnly, indexOf, indexOf, insertAtom, insertBond, insertBondInOrder, insertNullAtoms, insertNullBonds, isAbsStereo, isAcceptedSpecialLigand, isAtom, isAtomInRing, isBond, isBondParallelWith, isGrinvCCValid, isLargeMolecule, isMolecule, isMultiChiral, isolate, isolate, isOnlyFirstAtomInStereoCalculation, isQuery, isRealAtomParent, isRing, isRingBond, isSelfReference, isSimilarTo, isSymmetric, isValenceCheckEnabled, isValidLinkNode, mergeFrags, moveTo, pack, partialClean, partialClean, partialClean, properties, qpropCheck, regenBonds, regenBtab, regenCtab, regenGearch, removeAtom, removeAtom, removeBond, removeBond, removeExplicitLonePairs, removeIsolatedAtoms, removeIsolatedBonds, replaceBond, resetCtab, resetGrinvInParents, restoreCache, revalidateCoordDependentProps, saveCache, setAbsStereo, setAtom, setAtomSetSeqs, setBond, setBondSetSeqs, setChirality, setChirality, setFlags, setFlags, setGrinvCC, setGrinvOptions, setLinkNodeDefaultOuters, setLocalParity, setLocalParity, setLocation, setParity, setParity, setParity, setSupergraph, setValenceCheckEnabled, setValenceCheckOptions, setValenceCheckState, smol, sortBondsAccordingTo, stereoClean, sumConservedQuantities, toString, transform, updateDim, useOnlyFirstAtomInStereoCalculation, valenceCheck, valenceCheck

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

- Field Detail
  - RMCLEANUP_SGROUPATOMS
```
public static final int RMCLEANUP_SGROUPATOMS
```
    Remove S-groups of removed superatoms.
    
    Since:
    
    Marvin 4.1, 07/27/2006
    
    See Also:
    
    removeAtom(MolAtom, int), removeAtom(int, int), MoleculeGraph.RMCLEANUP_ALL, Constant Field Values
  - RMCLEANUP_FROMSGROUPS
```
public static final int RMCLEANUP_FROMSGROUPS
```
    Remove atoms from S-groups. The S-groups, which contain the atoms, are not removed from the molecule. The S-group removal is performed automatically only when all represented atoms were deleted from the S-group graph and the S-group graph is empty.
    
    Since:
    
    Marvin 4.1, 07/27/2006
    
    See Also:
    
    removeAtom(MolAtom, int), removeAtom(int, int), MoleculeGraph.RMCLEANUP_ALL, Constant Field Values
  - RM_KEEP_LEAVINGGROUPS
```
@Deprecated
public static final int RM_KEEP_LEAVINGGROUPS
```
    Deprecated. As of Marvin 6.2, no replacement.
    Not supported feature.
    
    Keep leaving group while removing its bond.
    
    Since:
    
    Marvin 6.2 2013.07.01.
    
    See Also:
    
    removeAtom(int, int), removeAtom(MolAtom, int), MoleculeGraph.RMCLEANUP_ALL, Constant Field Values
  - RMSG_DEFAULT
```
protected static final int RMSG_DEFAULT
```
    Remove S-group's children and remove S-group from its parent.
    
    Since:
    
    Marvin 5.0, 03/27/2007
    
    See Also:
    
    Constant Field Values
  - RMSG_KEEP_CHILDREN
```
protected static final int RMSG_KEEP_CHILDREN
```
    Do not remove S-group's children.
    
    Since:
    
    Marvin 5.0, 03/27/2007
    
    See Also:
    
    Constant Field Values
  - RMSG_KEEP_PARENT
```
protected static final int RMSG_KEEP_PARENT
```
    Do not remove S-group from its parent.
    
    Since:
    
    Marvin 5.0, 03/27/2007
    
    See Also:
    
    Constant Field Values
  - RMSG_KEEP_MULTICENTER
```
protected static final int RMSG_KEEP_MULTICENTER
```
    Do not remove central atom of multicenter S-groups.
    
    Since:
    
    Marvin 5.0, 10/22/2007
    
    See Also:
    
    Constant Field Values
  - RECURSIVE_UNGROUP
```
public static final int RECURSIVE_UNGROUP
```
    Ungroup and expand (if possible) the child S-groups.
    
    Since:
    
    Marvin 5.1, 06/05/2008
    
    See Also:
    
    Constant Field Values
  - DEFAULT_UNGROUP
```
public static final int DEFAULT_UNGROUP
```
    Do not ungroup and do not expand S-group's children.
    
    Since:
    
    Marvin 5.1, 06/05/2008
    
    See Also:
    
    Constant Field Values
- Constructor Detail
  - Molecule
```
public Molecule(Molecule 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
  - Molecule
```
public Molecule(Molecule p,
                MolAtom a)
```
    Construct a molecule consisting of a single atom (node).
    
    Parameters:
    
    p - the parent structure
    
    a - the atom
  - Molecule
```
public Molecule(Molecule p,
                MolBond b)
```
    Construct a molecule consisting of a single bond (edge).
    
    Parameters:
    
    p - the parent structure
    
    b - the bond
  - Molecule
```
public Molecule()
```
    Construct a 2 dimensional molecule.
- Method Detail
  - setDim
```
public void setDim(int d)
```
    Sets the dimension.
    
    Overrides:
    
    setDim in class MoleculeGraph
    
    Parameters:
    
    d - 0, 2, or 3
    
    See Also:
    
    MoleculeGraph.getFlags()
  - clear
```
public void clear()
```
    Clears the molecule.
    
    Overrides:
    
    clear in class MoleculeGraph
    
    See Also:
    
    MoleculeGraph.clearForImport(java.lang.String), MoleculeGraph.theAtoms
  - clearForImport
```
public void clearForImport(java.lang.String format)
```
    Initializes molecule for import.
    
    Overrides:
    
    clearForImport in class MoleculeGraph
    
    Parameters:
    
    format - input file format
    
    Since:
    
    Marvin 2.7
    
    See Also:
    
    MoleculeGraph.theBonds, MoleculeGraph.orix, MoleculeGraph.oriy, MoleculeGraph.oriz, MoleculeGraph.setFlags(int)
  - getStartPosition
```
public long getStartPosition()
```
    Gets the starting position of this molecule in the input file.
    
    Returns:
    
    the starting position
  - setStartPosition
```
public void setStartPosition(long off)
```
    Sets the starting position of this molecule in the input file.
    
    Parameters:
    
    off - the starting position
  - getEndPosition
```
public long getEndPosition()
```
    Gets the end position of this molecule in the input file.
    
    Returns:
    
    the end position
  - setEndPosition
```
public void setEndPosition(long off)
```
    Sets the end position of this molecule in the input file.
    
    Parameters:
    
    off - the end position
  - getName
```
public java.lang.String getName()
```
    Gets the molecule name/title that was set by setName(String).
    
    Specified by:
    
    getName in interface Incomplecule
    
    Overrides:
    
    getName in class MoleculeGraph
    
    Returns:
    
    the molecule name or an empty string
    
    Since:
    
    Marvin 2.7
  - setName
```
public void setName(java.lang.String s)
```
    Sets the molecule name/title.
    
    Parameters:
    
    s - the molecule name, empty string or null (null is equivalent to empty string)
    
    Since:
    
    Marvin 2.7
  - getComment
```
public java.lang.String getComment()
```
    Gets the comment.
    
    Returns:
    
    the comment or empty string
    
    Since:
    
    Marvin 2.9
  - setComment
```
public void setComment(java.lang.String s)
```
    Sets the comment.
    
    Parameters:
    
    s - the comment, empty string or null (null is equivalent to empty string)
    
    Since:
    
    Marvin 2.9
  - getId
```
public java.lang.String getId()
```
  - setId
```
public void setId(java.lang.String id)
```
  - hasId
```
public boolean hasId(java.lang.String id)
```
  - getInputFormat
```
public final java.lang.String getInputFormat()
```
    Gets the input file format. Set by the import module if the molecule is from a file.
    
    Returns:
    
    "mrv", "mol", "mol:V3", "csmol", "sdf", "cssdf", "rdf", "csrdf", "smiles", "sybyl", "mol2", "pdb", "xyz" or "cube" or "inchi" or null if not imported from any format
    
    Since:
    
    Marvin 2.7
  - setInputFormat
```
public void setInputFormat(java.lang.String format)
```
    Sets the input file format.
    
    Parameters:
    
    format - the input format
    
    Since:
    
    Marvin 2.7
    
    See Also:
    
    getInputFormat()
  - clearProperties
```
public void clearProperties()
```
    Clears RDfile/SDfile properties.
  - getPropertyCount
```
public int getPropertyCount()
```
    Gets the total number of RDfile/SDfile properties.
    
    Returns:
    
    number of properties
    
    Since:
    
    Marvin 2.7
  - getPropertyKeys
```
@Deprecated
public java.util.Enumeration<?> getPropertyKeys()
```
    Deprecated. As of Marvin 4.1, replaced by properties().getKeys() and properties().getKeyEnumeration().
    One-to-one replacement is method getKeyEnumeration() but method getKeys() is simpler to use.
  - getPropertyKey
```
public java.lang.String getPropertyKey(int i)
```
    Gets an RDfile/SDfile property key.
    
    Parameters:
    
    i - property index
    
    Returns:
    
    the property name
    
    Since:
    
    Marvin 2.7
  - getProperty
```
@Deprecated
public java.lang.String getProperty(java.lang.String key)
```
    Deprecated.
    As of Marvin 5.7, replaced by MPropHandler.convertToString(MProp, String).
    Usage:
    String property = MPropHandler.convertToString(mol.properties(), key);
    Gets an RDfile/SDfile property.
    
    Parameters:
    
    key - property name
    
    Returns:
    
    the value of the property, or null if the key is not found
  - getPropertyObject
```
public java.lang.Object getPropertyObject(java.lang.String key)
```
    Gets an RDfile/SDfile property object.
    
    Parameters:
    
    key - property name
    
    Returns:
    
    the value of the property, or null if the key is not found
    
    Since:
    
    Marvin 3.1.2
  - setProperty
```
public void setProperty(java.lang.String key,
                        java.lang.String value)
```
    Sets an RDfile/SDfile property. Setting null value removes the property.
    
    Parameters:
    
    key - the property name
    
    value - the value or null
  - setPropertyObject
```
public void setPropertyObject(java.lang.String key,
                              java.lang.Object value)
```
    Sets an RDfile/SDfile property object. Setting null value removes the property.
    
    Parameters:
    
    key - the property name
    
    value - the value or null
    
    Since:
    
    Marvin 3.1.2
  - residueTypeOf
```
public static int residueTypeOf(java.lang.String name)
```
    Gets the residue identifier for a residue name.
    
    Parameters:
    
    name - residue name
    
    Returns:
    
    the residue type
  - residueSymbolOf
```
public static java.lang.String residueSymbolOf(int id)
```
    Gets the name of a residue.
    
    Parameters:
    
    id - the residue identifier
    
    Returns:
    
    the residue symbol
  - setAtom0
```
protected void setAtom0(int i,
                        MolAtom newAtom)
```
    Sets the atom at the specified index. Overridden because Sgroups must be set correctly in RgMolecule.clone() and RxnMolecule.clone().
    
    Overrides:
    
    setAtom0 in class MoleculeGraph
    
    Parameters:
    
    i - the atom index
    
    newAtom - the atom
  - removeAtom
```
public void removeAtom(MolAtom atom,
                       int cleanupFlags)
```
    Removes an atom and its bonds by reference. This method is for internal use only. Use MoleculeGraph.removeAtom(MolAtom) instead unless you are sure what you are doing.
    
    Overrides:
    
    removeAtom in class MoleculeGraph
    
    Parameters:
    
    atom - the atom
    
    cleanupFlags - extra clean-up methods
    
    Since:
    
    Marvin 3.1
    
    See Also:
    
    MoleculeGraph.RMCLEANUP_NONE, MoleculeGraph.RMCLEANUP_ALL, MoleculeGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO, RMCLEANUP_FROMSGROUPS
  - removeAtom
```
public void removeAtom(int i,
                       int cleanupFlags)
```
    Removes an atom and its bonds by index. This method is for internal use only. Use MoleculeGraph.removeAtom(MolAtom) instead unless you are sure what you are doing.
    
    Overrides:
    
    removeAtom in class MoleculeGraph
    
    Parameters:
    
    i - the atom index
    
    cleanupFlags - extra clean-up methods
    
    Since:
    
    Marvin 3.1
    
    See Also:
    
    MoleculeGraph.RMCLEANUP_NONE, MoleculeGraph.RMCLEANUP_ALL, MoleculeGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO, RMCLEANUP_FROMSGROUPS
  - removeBond
```
protected void removeBond(MolBond bond,
                          int cleanupFlags)
```
    Removes a bond by reference.
    
    Overrides:
    
    removeBond in class MoleculeGraph
    
    Parameters:
    
    bond - the bond
    
    cleanupFlags - extra clean-up methods
    
    Since:
    
    Marvin 3.1
    
    See Also:
    
    MoleculeGraph.RMCLEANUP_NONE, MoleculeGraph.RMCLEANUP_ALL, MoleculeGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO
  - removeBond
```
protected void removeBond(int i,
                          int cleanupFlags)
```
    Removes a bond by index.
    
    Overrides:
    
    removeBond in class MoleculeGraph
    
    Parameters:
    
    i - the bond index
    
    cleanupFlags - extra clean-up methods
    
    Since:
    
    Marvin 3.1
    
    See Also:
    
    MoleculeGraph.RMCLEANUP_NONE, MoleculeGraph.RMCLEANUP_ALL, MoleculeGraph.RMCLEANUP_EDGES, MoleculeGraph.RMCLEANUP_STEREO
  - removeAllBonds
```
public void removeAllBonds()
```
    Removes all bonds.
    
    Overrides:
    
    removeAllBonds in class MoleculeGraph
  - removeAll
```
public void removeAll()
```
    Removes all the atoms and bonds.
    
    Overrides:
    
    removeAll in class MoleculeGraph
  - isEmpty
```
public boolean isEmpty()
```
    Tests whether the molecule is empty.
    
    Overrides:
    
    isEmpty in class MoleculeGraph
    
    Returns:
    
    true if the molecule graph does not contain any atoms, bonds or non-empty S-groups, false otherwise
    
    Since:
    
    Marvin 4.1.1, 09/06/2006
  - aromatize
```
public void aromatize(int method)
```
    Aromatizes molecule.
    
    Overrides:
    
    aromatize in class MoleculeGraph
    
    Parameters:
    
    method - Specifies the algorithm for aromatization.
    
    Throws:
    
    java.lang.SecurityException - cannot load module because of a security problem (firewall)
    
    See Also:
    
    MoleculeGraph.AROM_BASIC, MoleculeGraph.AROM_GENERAL, MoleculeGraph.AROM_LOOSE, Document about aromatization
  - aromatize
```
public void aromatize(int method,
                      boolean checkAmbiguity)
```
    Aromatizes molecule.
    
    Overrides:
    
    aromatize in class MoleculeGraph
    
    Parameters:
    
    method - Specifies the algorithm for aromatization.
    
    checkAmbiguity - Specifies whether ANY bonds should be considered during aromatization.
    
    Throws:
    
    java.lang.SecurityException - cannot load module because of a security problem (firewall)
    
    See Also:
    
    MoleculeGraph.AROM_BASIC, MoleculeGraph.AROM_GENERAL, MoleculeGraph.AROM_LOOSE, Document about aromatization
  - dearomatize
```
public boolean dearomatize()
```
    Dearomatize molecule.
    
    Overrides:
    
    dearomatize in class MoleculeGraph
    
    Returns:
    
    true if success, else false.
    
    Throws:
    
    java.lang.SecurityException - cannot load module because of a security problem (firewall)
  - clonecopy
```
public void clonecopy(MoleculeGraph g)
```
    Makes another molecule identical to this one.
    
    Overrides:
    
    clonecopy in class MoleculeGraph
    
    Parameters:
    
    g - the target molecule
  - fixSelfReferringProperty
```
protected boolean fixSelfReferringProperty(MProp prop)
```
    Fix a property containing reference to the molecule. Called from clonelesscopy().
    
    Overrides:
    
    fixSelfReferringProperty in class MoleculeGraph
    
    Parameters:
    
    prop - the property
    
    Since:
    
    Marvin 4.1.6, 02/14/2007
    
    See Also:
    
    MoleculeGraph.clonecopy(MoleculeGraph)
  - addSgroupClones
```
protected final void addSgroupClones(Molecule origparentm,
                                     Molecule origm,
                                     Molecule newm)
```
    Adds the S-groups of a child molecule clone to the new parent molecule clone.
    
    Parameters:
    
    origparentm - the original parent molecule
    
    origm - the original child molecule
    
    newm - the new child molecule (clone of the original)
    
    Since:
    
    Marvin 3.4
  - clonecopy
```
public void clonecopy(int[] iatoms,
                      MoleculeGraph g)
```
    Copies the specified atoms and bonds of this molecule to another one.
    
    Overrides:
    
    clonecopy in class MoleculeGraph
    
    Parameters:
    
    iatoms - array of atom indices to copy or null
    
    g - the target molecule graph
    
    Since:
    
    Marvin 5.0.2, 03/11/2008
  - clonecopyWithoutSgroups
```
protected void clonecopyWithoutSgroups(Molecule m)
```
    Copies the all the contents except the S-groups into another molecule object.
    
    Parameters:
    
    m - the target molecule
    
    Since:
    
    Marvin 3.4
  - cloneAtoms
```
protected int cloneAtoms(int[] cnodes,
                         MoleculeGraph graph)
```
    Copies the specified atoms.
    
    Overrides:
    
    cloneAtoms in class MoleculeGraph
    
    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.
  - clonelesscopy
```
@Deprecated
public void clonelesscopy(MoleculeGraph g)
```
    Deprecated. as of Marvin 6.3.
    Not supported feature.
    
    Copies to selection. Makes another molecule identical to this one, but does not clone atoms, bonds, and the properties.
    
    Overrides:
    
    clonelesscopy in class MoleculeGraph
    
    Parameters:
    
    g - the target molecule object (the selection)
  - cloneMoleculeWithDocument
```
public Molecule cloneMoleculeWithDocument()
```
    Makes an identical copy of the molecule and its document. If the molecule does not have a parent, then copies non-molecular data: graphics objects, electron flows, text boxes, atom and bond sets (color, font and thickness). Otherwise (root, rgroup, component molecule) creates a new document.
    
    Returns:
    
    the copy
    
    Since:
    
    Marvin 4.1, 01/16/2006
  - cloneMolecule
```
@Deprecated
public Molecule cloneMolecule()
```
    Deprecated. as of Marvin 2014.09.01.0 use clone() instead
    
    Makes an identical copy of the molecule. It also clones the atoms and bonds of the Molecule. Note that it does not clone the corresponding MDocument, hence the atom and bond formatting (color, font, thickness) is lost.
    
    Returns:
    
    the copy
    
    Since:
    
    Marvin 3.5.1, 11/20/2004
  - clone
```
public Molecule clone()
```
    Makes an identical copy of the molecule. It also clones the atoms and bonds of the Molecule. Note, that it does not clone the corresponding MDocument, hence the atom and bond formatting (color, font, thickness) is lost.
    
    Overrides:
    
    clone in class MoleculeGraph
    
    Returns:
    
    the copy
  - toFormat
```
@Deprecated
public final java.lang.String toFormat(java.lang.String fmt)
```
    Deprecated.
    As of Marvin 5.7, replaced by MolExporter.exportToFormat(Molecule, String).
    To get exact replacement use:
    
    try { String out = MolExporter.exportToFormat(this, fmt); } catch (IOException e) { throw new IllegalArgumentException(e); }
    Creates a string representation of the molecule. The format descriptor string can also contain export options. Format and options are separated by a colon, multiple options can be separated by commas. See the text formats and their options on the File Formats in Marvin page. Examples:
```
 s1 = mol.toFormat("mol");
 s2 = mol.toFormat("smiles:a-H"); // aromatize and remove Hydrogens
 
```
    Parameters:
    
    fmt - the format descriptor string
    
    Returns:
    
    string representation of the molecule in the specified format
    
    Throws:
    
    java.lang.IllegalArgumentException - Invalid format string.
    
    java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).
    
    See Also:
    
    toObject(java.lang.String)
  - exportToFormat
```
@Deprecated
public final java.lang.String exportToFormat(java.lang.String fmt)
                                                  throws java.io.IOException
```
    Deprecated. As of Marvin 5.7, replaced by MolExporter.exportToFormat(Molecule, String).
    
    Creates a string representation of the molecule. Similar to toFormat(String), the only difference is that export exceptions are not converted to IllegalArgumentException.
    
    Parameters:
    
    fmt - the format descriptor string
    
    Returns:
    
    string representation of the molecule in the specified format
    
    Throws:
    
    java.io.IOException
    
    MolExportException - Export error
    
    java.lang.IllegalArgumentException - Invalid format string.
    
    java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).
    
    Since:
    
    Marvin 4.0, 07/01/2005
    
    See Also:
    
    toFormat(String)
  - toBinFormat
```
@Deprecated
public final byte[] toBinFormat(java.lang.String fmt)
```
    Deprecated. As of Marvin 5.7, replaced by MolExporter.exportToBinFormat(Molecule, String).
    Creates a binary representation of the molecule. Works with all the text formats that are supported by the toFormat method, and also with the binary image formats (jpeg, msbmp, png). When creating an image, display options can also be specified in the format descriptor string. Format and options are separated by a colon, multiple options can be separated by commas. See the possible formats and their options on the File Formats in Marvin page. Examples:
```
 
 byte[] d1 = mol.toBinFormat("mol");
 byte[] d2 = mol.toBinFormat("smiles:a-H"); // aromatize and remove H
 byte[] d3 = mol.toBinFormat("png:w300,h300,b32,#00ffff00");
 byte[] d4 = mol.toBinFormat("jpeg:w300,h300,Q95,#ffff00,spacefill");
 
```
    Parameters:
    
    fmt - the format descriptor string
    
    Returns:
    
    a binary representation of the molecule in the specified format
    
    Throws:
    
    java.lang.IllegalArgumentException - Invalid format string.
    
    java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).
    
    Since:
    
    Marvin 2.7.11
    
    See Also:
    
    toObject(java.lang.String)
  - exportToBinFormat
```
@Deprecated
public final byte[] exportToBinFormat(java.lang.String fmt)
                                           throws java.io.IOException
```
    Deprecated. As of Marvin 5.7, replaced by MolExporter.exportToBinFormat(Molecule, String).
    
    Creates a binary representation of the molecule. Similar to toBinFormat(String), the only difference is that export exceptions are not converted to IllegalArgumentException.
    
    Parameters:
    
    fmt - the format descriptor string
    
    Returns:
    
    a binary representation of the molecule in the specified format
    
    Throws:
    
    MolExportException - Export error
    
    java.lang.IllegalArgumentException - Invalid format string.
    
    java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).
    
    java.io.IOException
    
    Since:
    
    Marvin 4.0, 07/01/2005
    
    See Also:
    
    toBinFormat(String)
  - toObject
```
@Deprecated
public java.lang.Object toObject(java.lang.String fmt)
```
    Deprecated. As of Marvin 5.7, replaced by MolExporter.exportToObject(Molecule, String).
    Creates a String, byte[] array or Image representation of the molecule. When creating an image, display options can also be specified in the format descriptor string. Format and options are separated by a colon, multiple options can be separated by commas. See the possible formats and their options on the File Formats in Marvin page. Examples:
```
 import java.awt.Image;
 ...
 String s1 = (String)mol.toObject("mol");
 String s2 = (String)mol.toObject("smiles:a-H"); // aromatize, remove H
 Image img = (Image)mol.toObject("image:w300,h300,#ffff00");
 byte[] d3 = (byte[])mol.toObject("png:w300,h300,b32,#00ffff00");
 byte[] d4 = (byte[])mol.toObject("jpeg:w300,h300,Q95,#ffff00,spacefill");
 
```
    Parameters:
    
    fmt - the format descriptor string
    
    Returns:
    
    a String, a byte[] array or an Image
    
    Throws:
    
    java.lang.IllegalArgumentException - Invalid format string.
    
    java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).
    
    Since:
    
    Marvin 2.8.1
    
    See Also:
    
    toFormat(java.lang.String), toBinFormat(java.lang.String)
  - exportToObject
```
@Deprecated
public java.lang.Object exportToObject(java.lang.String fmt)
                                            throws java.io.IOException
```
    Deprecated. As of Marvin 5.7, replaced by MolExporter.exportToObject(Molecule, String).
    
    Creates a String, byte[] array or Image representation of the molecule. Similar to toObject(String), the only difference is that export exceptions are not converted to IllegalArgumentException.
    
    Parameters:
    
    fmt - the format descriptor string
    
    Returns:
    
    a String, a byte[] array or an Image
    
    Throws:
    
    MolExportException - Export error
    
    java.lang.IllegalArgumentException - Invalid format string.
    
    java.lang.SecurityException - Export module cannot be loaded because of security reasons (firewall).
    
    java.io.IOException
    
    Since:
    
    Marvin 4.0, 07/01/2005
    
    See Also:
    
    toObject(String)
  - reuseAtom
```
public MolAtom reuseAtom(int z,
                         int i)
```
    Reuse an atom or create a new one. If an atom is reused, all its properties except the corners are initialized.
    
    Parameters:
    
    z - the atomic number
    
    i - the atom index
    
    Returns:
    
    the atom reference
    
    Since:
    
    Marvin 2.6
  - endReuse
```
public void endReuse(int n)
```
    End reusing atoms.
    
    Parameters:
    
    n - number of atoms
    
    Since:
    
    Marvin 2.6
  - newInstance
```
public MoleculeGraph newInstance()
```
    Creates a new Molecule object. The dimension and the origin coordinates will be the same as in the original molecule.
    
    Overrides:
    
    newInstance in class MoleculeGraph
    
    Returns:
    
    a Molecule object
  - newSelectionMolecule
```
public SelectionMolecule newSelectionMolecule()
```
    Creates a new SelectionMolecule object appropriate for storing selection from this molecule.
    
    Returns:
    
    an empty selection molecule
    
    Since:
    
    Marvin 4.1, 11/24/2005
  - makeItSimilar
```
protected void makeItSimilar(MoleculeGraph g)
```
    Copies some properties of this molecule to the other one specified as argument. Copies the input format.
    
    Overrides:
    
    makeItSimilar in class MoleculeGraph
    
    Parameters:
    
    g - the molecule to change
  - getSimplifiedMolecule
```
public final Molecule getSimplifiedMolecule()
```
    Gets the simplified molecule object. It returns this usually. In case of RgMolecule, it returns the simply modified root structure if there are no R-groups present. In this case the RgMolecule will be inconsistent. It can simplify the molecule only if there is no parent document containing other objects.
    
    Returns:
    
    the simplified molecule
    
    Since:
    
    Marvin 3.0.1
  - getMostSimplifiedMolecule
```
protected Molecule getMostSimplifiedMolecule()
```
    Gets the simplified molecule object even if there is a parent document with other objects. It returns this usually. In case of RgMolecule, it returns the root structure if there are no R-groups present.
    
    Returns:
    
    this in the default implementation
    
    Since:
    
    Marvin 4.1.13, 09/20/2007
  - isReaction
```
public boolean isReaction()
```
    Checks if the structure represents a reaction or not.
    
    Returns:
    
    false
    
    Since:
    
    Marvin 3.0
  - canBeReactionComponent
```
public boolean canBeReactionComponent()
```
    Tests whether an object of this class can be a reaction component. This implementation returns true
    
    Returns:
    
    true if it can be a reactant, product or agent, false if adding it to an RxnMolecule is not supported
    
    Since:
    
    Marvin 4.1.13, 09/19/2007
  - isSgroup
```
@Deprecated
public boolean isSgroup()
```
    Deprecated. As of Marvin 14.7.7, no replacement.
    Not supported feature.
    
    Checks if the structure represents an S-group or not.
    
    Returns:
    
    true if the structure is an S-group, false otherwise
    
    Since:
    
    Marvin 3.0
  - getSgroupLigands
```
public MolAtom[] getSgroupLigands()
```
    Gets the S-group's ligands if the structure represents an S-group.
    
    Returns:
    
    the array of ligands if the structure is an S-group with ligands, null otherwise
    
    Since:
    
    Marvin 3.0
  - findExpandableSgroup
```
public final Sgroup findExpandableSgroup()
```
    Finds a contracted residue.
    
    Returns:
    
    the S-group if found, null if all S-groups are expanded
    
    Since:
    
    Marvin 3.0
  - findContractableSgroup
```
public final Sgroup findContractableSgroup()
```
    Finds an expanded residue.
    
    Returns:
    
    the S-group if found, null if all S-groups are contracted
    
    Since:
    
    Marvin 3.0
  - getSgroupArray
```
public final Sgroup[] getSgroupArray()
```
    Gets the array of S-groups.
    Warning! Expansion or contraction of an S-group in this array may invalidate other array elements. Examples:
    - contracting a MultipleSgroup removes any embedded SuperatomSgroup except those inside the repeating unit,
    - expanding a MultipleSgroup adds n-1 new clones for each embedded SuperatomSgroup in the repeating unit.
    Returns:
    
    an array containing all the S-groups
    
    Since:
    
    Marvin 3.0
  - getSgroupCount
```
public final int getSgroupCount()
```
    Gets the number of S-groups.
    
    Returns:
    
    the number of S-groups
    
    Since:
    
    Marvin 3.0
  - countExpandableContractableSgroups
```
public final int countExpandableContractableSgroups()
```
    Counts the expandable and contractable S-groups.
    
    Returns:
    
    the number of expandable/contractable S-groups
    
    Since:
    
    Marvin 5.0, 02/28/2007
  - countOrderedComponentSgroups
```
public final int countOrderedComponentSgroups()
```
    Counts the ordered component S-groups.
    
    Returns:
    
    the number of ordered component S-groups.
    
    Since:
    
    Marvin 4.1.6, 02/28/2007
  - getSgroup
```
public final Sgroup getSgroup(int i)
```
    Gets an S-group.
    
    Parameters:
    
    i - S-group index
    
    Since:
    
    Marvin 3.0
  - getSortedSgroups
```
public final Sgroup[] getSortedSgroups()
```
    Gets the sorted S-groups in parent-child order.
    Warning! Expansion or contraction of an S-group in this array may invalidate other array elements. Examples:
    - contracting a MultipleSgroup removes any embedded SuperatomSgroup except those inside the repeating unit,
    - expanding a MultipleSgroup adds n-1 new clones for each embedded SuperatomSgroup in the repeating unit.
    Returns:
    
    array containing the S-groups
    
    Since:
    
    Marvin 3.4, 05/04/2004
  - getRootSgroups
```
public final Sgroup[] getRootSgroups()
```
    Gets root s-groups (groups that are not embedded into another s-group).
    
    Returns:
    
    array containing the root s-groups (empty array if there are no s-groups)
    
    Since:
    
    Marvin 5.3.3, 31/03/2010
  - sortSgroupXBonds
```
@Deprecated
public void sortSgroupXBonds()
```
    Deprecated. As of Marvin 5.12, no replacement.
    Crossing bonds of a SuperatomSgroup do not need to be sorted any more. It is not advised to sort them anyway because then the indexes of bonds change in the parent molecule.
    
    Sorts superatom S-group crossing bonds in attachment point number order.
    
    Since:
    
    Marvin 5.0, 12/07/2007
  - indexOf
```
public final int indexOf(Sgroup sg)
```
    Gets the array index of an S-group.
    
    Parameters:
    
    sg - the S-group
    
    Since:
    
    Marvin 3.0
  - findSgroupOf
```
public final Sgroup findSgroupOf(MolAtom a)
```
    Finds the smallest S-group related to the specified atom.
    
    Parameters:
    
    a - the atom
    
    Returns:
    
    the S-group or null if not found
    
    Since:
    
    Marvin 3.0
  - findSgroupContaining
```
public final Sgroup findSgroupContaining(MolAtom a)
```
    Finds the largest S-group that contains the specified atom.
    
    Parameters:
    
    a - the atom
    
    Returns:
    
    the S-group or null if not found
    
    Since:
    
    Marvin 3.0
  - findSmallestSgroupContaining
```
public final Sgroup findSmallestSgroupContaining(MolAtom a)
```
    Finds the smallest S-group that contains the specified atom.
    
    Parameters:
    
    a - the atom
    
    Returns:
    
    the S-group or null if not found
    
    Since:
    
    Marvin 3.4
  - findAllSgroupContaining
```
public Sgroup[] findAllSgroupContaining(MolAtom a)
```
    Finds all smallest S-groups containing the specified atom. There can be more groups containing the same atom and not embedding each other because of the data S-groups: they are not in the embedding hierarchy.
    
    Parameters:
    
    a - the atom
    
    Returns:
    
    the array of S-groups
    
    Since:
    
    Marvin 5.0.1
  - contains
```
public boolean contains(MolAtom atom)
```
    Checks if the molecule graph contains the specified atom. If the atom is not found in the graph, looks in the sgroupgraphs of contracted Expandable-Sgroups.
    
    Overrides:
    
    contains in class MoleculeGraph
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    true if the graph or an sgroupgraph contains the object, false otherwise
  - setSgroupParent
```
public void setSgroupParent(MolAtom a,
                            Sgroup sg,
                            boolean set)
```
    Sets or unsets an S-group as a parent of an atom.
    
    Parameters:
    
    a - the atom
    
    sg - the S-group
    
    set - set (true) or unset (false)
    
    Throws:
    
    java.lang.IllegalArgumentException - molecule does not contain the atom
    
    Since:
    
    Marvin 3.0
  - reparentSgroups
```
protected final void reparentSgroups(Molecule p)
```
    Change parents of all S-groups in this molecule.
    
    Parameters:
    
    p - the new parent
    
    Throws:
    
    java.lang.IllegalArgumentException - molecule does not contain the atom
    
    Since:
    
    Marvin 3.0
  - mergeAtoms
```
@Deprecated
public void mergeAtoms(MolAtom that,
                                   MolAtom node)
```
    Deprecated. As of Marvin 6.2, use MergeUtil.mergeAtoms(MolAtom, MolAtom, boolean) instead.
    
    Merges bonds of an atom with another atom, then adds the atom to the molecule.
    
    Overrides:
    
    mergeAtoms in class MoleculeGraph
    
    Parameters:
    
    that - the atom
    
    node - the other atom
  - addAtom0
```
protected void addAtom0(MolAtom node)
```
    Adds an atom.
    
    Overrides:
    
    addAtom0 in class MoleculeGraph
    
    Parameters:
    
    node - the atom reference
  - addAtomToFragment
```
protected void addAtomToFragment(MolAtom atom)
```
    Adds an atom to a fragment. S-groups are added only if all atoms are already in the molecule.
    
    Overrides:
    
    addAtomToFragment in class MoleculeGraph
    
    Parameters:
    
    atom - the atom reference
  - addBond0
```
protected void addBond0(MolBond bond)
```
    Adds a bond.
    
    Overrides:
    
    addBond0 in class MoleculeGraph
    
    Parameters:
    
    bond - the bond reference
  - fuse0
```
protected void fuse0(MoleculeGraph graph,
                     boolean check)
```
    Adds those atoms and bonds of a molecule graph to this one that are not already elements.
    
    Overrides:
    
    fuse0 in class MoleculeGraph
    
    Parameters:
    
    graph - the 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 moleclue graph is known to be disjoint from this one and this check can be safely skipped
    
    Since:
    
    Marvin 5.0
  - contractSgroups
```
public final boolean contractSgroups()
```
    Contracts all S-groups.
    
    Returns:
    
    true if the operation was successful, false if nothing changed
    
    Since:
    
    Marvin 3.0
  - contractSgroups
```
public final boolean contractSgroups(int opts)
```
    Contracts all S-groups.
    
    Parameters:
    
    opts - contraction options
    
    Returns:
    
    true if the operation was successful, false if nothing changed
    
    Since:
    
    Marvin 3.4
    
    See Also:
    
    Expandable.contract(int), Expandable.DEFAULT_OPTIONS, Expandable.LEAVE_COORDS_UNCHANGED, Expandable.NONRECURSIVE_EXPAND
  - expandSgroups
```
public final boolean expandSgroups()
```
    Expands all S-groups.
    
    Returns:
    
    true if the operation was successful, false if nothing changed
    
    Since:
    
    Marvin 3.0
    
    See Also:
    
    expandSgroups(int)
  - expandSgroups
```
public final boolean expandSgroups(int opts)
```
    Expands all S-groups.
    
    Parameters:
    
    opts - expansion options
    
    Returns:
    
    true if the operation was successful, false if nothing changed
    
    Since:
    
    Marvin 3.3
    
    See Also:
    
    Expandable.expand(int), Expandable.DEFAULT_OPTIONS, Expandable.MDL_EXPAND, Expandable.LEAVE_COORDS_UNCHANGED
  - isExpandable
```
public final boolean isExpandable(int opts)
```
    Tests if the molecule is expandable with the specified options.
    
    Parameters:
    
    opts - expansion options
    
    Returns:
    
    true if an S-group is GUI-contractable, false otherwise
    
    Since:
    
    Marvin 4.0.2, 10/26/2005
    
    See Also:
    
    Expandable.DEFAULT_OPTIONS, Expandable.LEAVE_COORDS_UNCHANGED
  - setGUIContracted
```
@Deprecated
public final void setGUIContracted(boolean contract)
```
    Deprecated. as of Marvin 6.2, use expandSgroups(int) or contractSgroups(int) instead with option parameter Expandable.LEAVE_COORDS_UNCHANGED
    S-group expansion or contraction is performed depending on the parameter contract.
    If contract is set to:
    - false, then expansion happens to the contracted groups with no coordinate generation.
    - true, then contraction is performed for those s-groups that were expanded the way that was explained in the previous point.
    Parameters:
    
    contract - true for contraction, false for expansion
    
    Since:
    
    Marvin 3.4, 05/04/2004
  - setGUIContracted
```
@Deprecated
public final void setGUIContracted(boolean contract,
                                               int opts)
```
    Deprecated. as of Marvin 6.2, use expandSgroups(int) or contractSgroups(int) instead with option parameter Expandable.LEAVE_COORDS_UNCHANGED
    S-group expansion or contraction is performed depending on the parameter contract.
    If contract is set to:
    - false, then expansion happens to the contracted groups with no coordinate generation.
    - true, then contraction is performed for those s-groups that were expanded the way that was explained in the previous point.
    Parameters:
    
    contract - true for contraction, false for expansion
    
    opts - for further expand options
    
    Since:
    
    Marvin 3.4, 05/04/2004
  - isGUIContracted
```
@Deprecated
public final boolean isGUIContracted()
```
    Deprecated. as of Marvin 6.2 replaced by hasContractedSgroup()
    
    Tests if the molecule has contracted S-groups or not.
    
    Returns:
    
    true there is at least one contracted S-group, false otherwise
    
    Since:
    
    Marvin 3.4.1, 07/26/2004
  - hasContractedSgroup
```
public boolean hasContractedSgroup()
```
    Tests if the molecule has contracted S-groups or not.
    
    Returns:
    
    true there is at least one contracted S-group, false otherwise
    
    Since:
    
    Marvin 6.2, 2013/09/25
  - ungroupSgroup
```
public final boolean ungroupSgroup(Sgroup sg)
```
    Ungroups the specified S-group and expands it if it is an Expandable S-group. Ungroups and expands the child S-groups also if they are Expandable S-groups. Calls a recursive ungroup.
    
    Parameters:
    
    sg - the S-group
    
    Returns:
    
    true if the operation was successful, false if nothing changed
    
    Since:
    
    Marvin 3.4
    
    See Also:
    
    RECURSIVE_UNGROUP, ungroupSgroup(int)
  - ungroupSgroup
```
public final boolean ungroupSgroup(Sgroup sg,
                                   int opts)
```
    Expand and ungroup the specified S-group.
    
    Parameters:
    
    sg - the S-group
    
    opts - option to specify the ungroup type
    
    Returns:
    
    true if the operation was successful, false if nothing changed
    
    Since:
    
    Marvin 5.1.2
    
    See Also:
    
    RECURSIVE_UNGROUP, DEFAULT_UNGROUP, ungroupSgroup(int, int)
  - ungroupSgroup
```
@Deprecated
public final boolean ungroupSgroup(int i)
```
    Deprecated. as of Marvin 6.3. use ungroupSgroup(Sgroup) instead.
    
    Ungroups the specified S-group and expands it if it is an Expandable S-group. Ungroups and expands the child S-groups also if they are Expandable S-groups.
    
    Parameters:
    
    i - the S-group index
    
    Returns:
    
    true if the operation was successful, false if nothing changed
    
    Since:
    
    Marvin 3.4
    
    See Also:
    
    ungroupSgroup(chemaxon.struc.Sgroup), RECURSIVE_UNGROUP
  - ungroupSgroups
```
@Deprecated
public final boolean ungroupSgroups(int type)
```
    Deprecated. as of Marvin 6.3. use ungroupSgroups(EnumSet) instead.
    
    Ungroups all S-groups of a specified type in this molecule. Performs expand before ungroup if the type is an expandable S-group type.
    
    Parameters:
    
    type - the S-group type that specifies which S-groups to ungroup.
    
    Returns:
    
    true if the operation was successful, false if nothing changed.
    
    Since:
    
    Marvin 5.2
    
    See Also:
    
    ungroupSgroup(Sgroup sg)
  - ungroupSgroups
```
public final boolean ungroupSgroups(java.util.EnumSet<SgroupType> types)
```
    Ungroups all S-groups of the specified types in this molecule. Performs expand before ungroup if a type is an expandable S-group type. NOTE that giving SgroupType.SUPERATOM as parameter will leave the SgroupType.AMINOACID typed S-groups in unchanged state while the former method (ungroupSgroups(int)) ungrouped the AminoAcidSgroups as well.
    
    Parameters:
    
    types - the S-group types that specifies which S-group types to ungroup.
    
    Returns:
    
    true if the operation was successful, false if nothing changed.
    
    Since:
    
    Marvin 6.3
    
    See Also:
    
    SgroupType
  - ungroupSgroup
```
@Deprecated
public final boolean ungroupSgroup(int i,
                                               int opts)
```
    Deprecated. as of Marvin 6.3. use ungroupSgroup(Sgroup) instead.
    
    Ungroups the specified S-group and expands it if it is an Expandable S-group. Ungroups and expands the child S-groups also if they are Expandable S-groups according to the specified option.
    
    Parameters:
    
    i - the S-group index
    
    opts - option to specify the ungroup type
    
    Returns:
    
    true if the operation was successful, false if nothing changed
    
    Since:
    
    Marvin 5.1
    
    See Also:
    
    RECURSIVE_UNGROUP, DEFAULT_UNGROUP, ungroupSgroup(chemaxon.struc.Sgroup)
  - ungroupSgroups
```
public final boolean ungroupSgroups()
```
    Expands and ungroups all S-groups.
    
    Returns:
    
    true if the operation was successful, false if nothing changed
    
    Since:
    
    Marvin 3.0
  - addSgroupsOf
```
protected final void addSgroupsOf(Molecule m)
```
    Adds S-groups to this object and its parent.
  - removeSgroupsOf
```
protected final void removeSgroupsOf(Molecule m,
                                     int rmflags)
```
    Removes S-groups that are contained in a given molecule but not contained in another molecule.
    
    Parameters:
    
    m - the molecule whose S-groups are to remove
    
    rmflags - removal flags
    
    Since:
    
    Marvin 4.1.7
    
    See Also:
    
    RMSG_DEFAULT, RMSG_KEEP_CHILDREN, RMSG_KEEP_PARENT
  - removeSgroupsOf
```
protected final void removeSgroupsOf(Molecule m)
```
    Removes S-groups from this object and its parent.
  - removeAllSgroups
```
protected void removeAllSgroups()
```
    Removes all S-groups.
  - removeSgroupFromList
```
protected void removeSgroupFromList(Sgroup sg)
```
    Removes an S-group from the sgroupVector.
    
    Since:
    
    Marvin 4.1, 07/28/2006
  - rearrangeSgroups
```
public void rearrangeSgroups(int[] newIndexes)
```
    Orders S-groups in the vector of S-groups in the given order corresponding to the given new indexes.
    
    Parameters:
    
    newIndexes - array of new S-group indexes, ith element of the array contains the new index of the ith s-group in the s-group vector
    
    Throws:
    
    java.lang.IllegalArgumentException - if newIndexes are not in the range [0..getSgroupCount()] or not all values in this range are contained.
    
    Since:
    
    Marvin 5.12, 2012.11.12.
  - addSgroup
```
public void addSgroup(Sgroup sg,
                      boolean setparent)
```
    Adds an S-group to this object.
    
    Parameters:
    
    sg - the S-group to add.
    
    setparent - if true then the parent of the S-group is set to this molecule and the S-group is removed from the old parent molecule.
    
    Since:
    
    Marvin 5.2
  - removeAtomFromChildren
```
protected void removeAtomFromChildren(Sgroup sgroup,
                                      MolAtom atom)
```
    Removes the parameter atom from the parameter S-group and it's descendants.
  - getGraphUnionAsSelection
```
protected final SelectionMolecule getGraphUnionAsSelection()
```
    Gets a selection molecule containing all the atoms and bonds. Returns the same object until the unified structure is (or might be) changed, then recreates it.
    
    Returns:
    
    a selection molecule object containing the unified structure
    
    Since:
    
    Marvin 3.0, 11/05/2002
    
    See Also:
    
    SelectionMolecule
  - bondlength
```
public double bondlength()
```
    Calculate the regular bond length for the unified structure.
    
    Overrides:
    
    bondlength in class MoleculeGraph
    
    Returns:
    
    the regular bond length
  - convertToFrags
```
public final Molecule[] convertToFrags()
```
    Converts this molecule to its disconnected fragments, expanding all S-groups and keeping disconnected Multicenter S-groups in the same fragment, but ungroupping and separating fragments in all other types of S-groups.
    Warning: Atoms are removed from the original molecule object to the created fragments, therefore the original molecule becomes inconsistent.
    
    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.
    
    Returns:
    
    array of fragments
    
    Since:
    
    Marvin 3.1
    
    See Also:
    
    MoleculeGraph.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. If not using the FRAG_KEEPING_SGROUPS option and an S-group would contain more fragments, then it won't be added to any of them, and its parent-child relations with other S-groups will be removed. Fragmentation is performed depending on fragmentation type:
    - Merge only fragmented multicenter S-groups (see MoleculeGraph.FRAG_KEEPING_MULTICENTERS)
    - Merge all types of S-groups (see MoleculeGraph.FRAG_KEEPING_SGROUPS)
    - Keep all fragments separately, do not take into account the S-groups (see MoleculeGraph.FRAG_BASIC)
    Overrides:
    
    findFrags in class MoleculeGraph
    
    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:
    
    MoleculeGraph.FRAG_BASIC, MoleculeGraph.FRAG_KEEPING_MULTICENTERS, MoleculeGraph.FRAG_KEEPING_SGROUPS
  - findFrags
```
public final SelectionMolecule[] findFrags()
```
    Determines the disconnected fragments and puts them into an array. Multicenter S-groups are kept in one fragment.
    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.
    
    Returns:
    
    array of fragments
    
    Since:
    
    Marvin 3.0
  - fillSelectionMolecule
```
protected void fillSelectionMolecule(SelectionMolecule s)
```
    Adds all atoms and bonds to the specified molecule.
    
    Parameters:
    
    s - the selection molecule
    
    Since:
    
    Marvin 3.0, 11/05/2002
  - clearExtraLabels
```
public void clearExtraLabels()
```
    Clears extra atom labels.
  - 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.
    
    Overrides:
    
    checkConsistency in class MoleculeGraph
    
    Throws:
    
    java.lang.RuntimeException - if inconsistency found
    
    Since:
    
    Marvin 5.0, 11/06/2007
  - checkSgroupConsistency
```
protected void checkSgroupConsistency()
```
    Checks the internal consisitency of S-groups.
    
    Throws:
    
    java.lang.RuntimeException - if inconsistency found
    
    Since:
    
    Marvin 5.0, 11/06/2007
  - getVisibleCoords
```
public double[] getVisibleCoords(MolAtom ma)
```
    Returns the coordinates of the given atom (contained in the molecule). If the atom is part of a contracted superatom sgroup, its coordinates may be false, so this method returns the coordinates of the corresponding sgroup atom instead.
    
    Overrides:
    
    getVisibleCoords in class MoleculeGraph
    
    Parameters:
    
    ma - The atom to be queried.
    
    Returns:
    
    The real coordinates of ma.
    
    Since:
    
    Marvin 4.0 8/07/2005
  - transform
```
public void transform(CTransform3D t,
                      boolean incg)
```
    Apply a transformation matrix to the atomic coordinates and Data Sgroup coordinates.
    
    Overrides:
    
    transform in class MoleculeGraph
    
    Parameters:
    
    t - the transformation matrix
    
    incg - graph invariants are changed (true) or not (false)
    
    Since:
    
    Marvin 4.0 2/09/2005
  - findContainingMulticenterSgroup
```
public MulticenterSgroup findContainingMulticenterSgroup(MolAtom atom)
```
    Gets the containing multicenter S-group of a multicenter atom.
    
    Parameters:
    
    atom - the multicenter atom.
    
    Returns:
    
    the containing multicenter S-group, null if none of the multicenter sgroups contains the multicenter atom.
    
    Since:
    
    Marvin 5.0 04/20/2007
    
    See Also:
    
    MulticenterSgroup, MolAtom.MULTICENTER
  - createGearch
```
protected chemaxon.struc.gearch.MoleculeGraphGearch createGearch()
```
    Overrides:
    
    createGearch in class MoleculeGraph
  - clearObjects
```
public void clearObjects()
```
    Specified by:
    
    clearObjects in interface chemaxon.struc.MObjectContainer
  - getObjectCount
```
public int getObjectCount()
```
    Specified by:
    
    getObjectCount in interface chemaxon.struc.MObjectContainer
  - removeObject
```
public void removeObject(MObject mo)
```
    Specified by:
    
    removeObject in interface chemaxon.struc.MObjectContainer
  - selectAllObjects
```
public void selectAllObjects(boolean s)
```
    Specified by:
    
    selectAllObjects in interface chemaxon.struc.MObjectContainer
  - getAllObjects
```
public java.util.List<MObject> getAllObjects()
```
    Specified by:
    
    getAllObjects in interface chemaxon.struc.MObjectContainer
  - replaceSgroup
```
public void replaceSgroup(Sgroup sgroup,
                          Sgroup newSgroup)
```
    Replaces an S-group with a new sgroup in the molecule. Sets parent - child relations of the new sgroup according to the parent - child relations of the old sgroup.
    
    Parameters:
    
    sgroup - the sgroup to replace
    
    newSgroup - the sgroup to replace with
  - 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);
    Overrides:
    
    implicitizeHydrogens0 in class MoleculeGraph
    
    Returns:
    
    true if success else false
  - 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).
    
    Overrides:
    
    add in class MoleculeGraph
    
    Parameters:
    
    bond - the bond object
  - 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. Sets the sgroup hierarchy.
    
    Overrides:
    
    replaceAtom in class MoleculeGraph
    
    Parameters:
    
    i - the index of the original atom
    
    newAtom - the atom which will replace the original
  - getBonds
```
protected MolBond[] getBonds(MolAtom atom)
```
    Returns the bonds attached to the given atom.
    
    Overrides:
    
    getBonds in class MoleculeGraph
    
    Parameters:
    
    atom - the atom
    
    Returns:
    
    the bonds attached to the given atom in this molecule
    
    Since:
    
    Marvin 6.2
  - getSgroupIterator
```
public IteratorFactory.SgroupIterator getSgroupIterator()
```
    Returns an iterator over the s-groups in this molecule in proper sequence.
    
    Returns:
    
    an iterator over the s-groups in this molecule in proper sequence
    
    Since:
    
    Marvin 6.2, 2013.09.09.
  - connectOriginalBondsToNewAtom
```
protected void connectOriginalBondsToNewAtom(MolAtom newAtom,
                                             MolAtom orig,
                                             MolBond[] bonds)
```
    Description copied from class: MoleculeGraph
    
    Sets the original connections to the new atom.
    
    Overrides:
    
    connectOriginalBondsToNewAtom in class MoleculeGraph
    
    Parameters:
    
    newAtom - the atom which replace the original
    
    orig - the original atom
    
    bonds - the original atoms bonds (before any modification)
  - hasAtomSet
```
public boolean hasAtomSet()
```
    Description copied from class: MoleculeGraph
    
    Tests whether the molecule graph has atom sets.
    
    Overrides:
    
    hasAtomSet in class MoleculeGraph
    
    Returns:
    
    true if there are atom sets, false otherwise

Class Molecule

Property Summary

Properties inherited from class chemaxon.struc.MoleculeGraph

Nested Class Summary

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

Field Summary

Fields inherited from class chemaxon.struc.MoleculeGraph

Fields inherited from interface chemaxon.struc.StereoConstants

Constructor Summary

Method Summary

Methods inherited from class chemaxon.struc.MoleculeGraph

Methods inherited from class java.lang.Object

Field Detail

RMCLEANUP_SGROUPATOMS

RMCLEANUP_FROMSGROUPS

RM_KEEP_LEAVINGGROUPS

RMSG_DEFAULT

RMSG_KEEP_CHILDREN

RMSG_KEEP_PARENT

RMSG_KEEP_MULTICENTER

RECURSIVE_UNGROUP

DEFAULT_UNGROUP

Constructor Detail

Molecule

Molecule

Molecule

Molecule

Method Detail

setDim

clear

clearForImport

getStartPosition

setStartPosition

getEndPosition

setEndPosition

getName

setName

getComment

setComment

getId

setId

hasId

getInputFormat

setInputFormat

clearProperties

getPropertyCount

getPropertyKeys

getPropertyKey

getProperty

getPropertyObject

setProperty

setPropertyObject

residueTypeOf

residueSymbolOf

setAtom0

removeAtom

removeAtom

removeBond

removeBond

removeAllBonds

removeAll

isEmpty

aromatize

aromatize

dearomatize

clonecopy

fixSelfReferringProperty

addSgroupClones

clonecopy

clonecopyWithoutSgroups

cloneAtoms

clonelesscopy

cloneMoleculeWithDocument

cloneMolecule

clone

toFormat

exportToFormat

toBinFormat

exportToBinFormat

toObject