MolAtom (Marvin API documentation (c) 1998-2014 ChemAxon Ltd.)

java.lang.Object
- chemaxon.struc.MolAtom

All Implemented Interfaces:

StereoConstants, Serializable

Direct Known Subclasses:

SgroupAtom
```
public class MolAtom
extends Object
implements StereoConstants, Serializable
```
Atom object and the properties of the elements. Atom objects are identified by their reference values. Atom object can contain general properties (property value - property key pairs). The following methods are available to handle general atom properties:
- propertySet()
- propertyKeySet()
- removeProperty(String key)
- containsPropertyKey(String key)
- propertyCount()
- getProperty(String key)
- putProperty(String key, Object value)
- clearProperties()
Version:

5.3, 09/26/2009

Author:

Peter Csizmadia, Ferenc Csizmadia, Gabor Bartha, Tamas Vertse, Szabolcs Csepregi, Erika Biro, Szilveszter Juhos

See Also:
Serialized Form

Field Summary

Fields
Modifier and Type	Field and Description
`static int`	`AAMAP_MASK` Atom map mask in flags.
`static int`	`AAMAP_MAX` Maximum atom-atom mapping number.
`static int`	`AAMAP_OFF` Atom map offset in flags.
`static int`	`ALIPHATIC` Aliphatic query atom.
`static int`	`ALL_H` Include any Hydrogen atom.
`static int`	`ANY` "Atomic number" of the any atom A.
`static int`	`AROMATIC` Aromatic query atom.
`static int`	`AROMATIC_OR_ALIPHATIC` Aromatic or aliphatic query atom.
`static int`	`ATOM_TYPE_COUNT` Number of atom types in the elements array
`static int`	`ATOM_TYPE_MAX` Maximum atom number.
`static int`	`ATTACH_BOTH` S-group attachment point on first and second site.
`static int`	`ATTACH_NONE` There is no S-group attachment point setting on this atom.
`static int`	`ATTACH_UNKNOWN` S-group attachment point information
`static int`	`ATTACH1` S-group attachment point on first site.
`static int`	`ATTACH2` S-group attachment point on second site.
`protected int`	`bondCount` Number of bonds.
`static int`	`BRIDGEHEAD_H` Hydrogen atom which is connected to a bridgehead atom.
`static int`	`CHARGED_H` Include charged Hydrogen atom(s).
`static int`	`CTSPECIFIC_H` Deprecated. As of Marvin 5.11 Graph invariants are checked by default when calculating CIS/TRANS stereo, so this option is out of use.
`static int`	`ELEMENT_COUNT` Number of elements in the periodic system
`static int`	`EMPTY` Empty atom type.
`static int`	`FIX_CHARGE` Valence checking will replace radicals with charges if this flag is set.
`static int`	`HBONDED_H` Hydrogen atom wtih a `MolBond.HYDROGEN` bond on it.
`static int`	`HCONNECTED_H` Hydrogen atom(s) connected to another hydrogen only.
`static int`	`HETERO` "Atomic number" of the hetero any atom Q.
`static int`	`HS_S` S hybridization state.
`static int`	`HS_SP` SP hybridization state.
`static int`	`HS_SP2` SP2 hybridization state.
`static int`	`HS_SP3` SP3 hybridization state.
`static int`	`HS_UNKNOWN` Unknown hybridization state.
`static int`	`ISOTOPE_H` Include Hydrogen isotope(s).
`static int`	`LDIR_ABOVE` Implicit Hydrogen(s) are above the element symbol.
`static int`	`LDIR_BELOW` Implicit Hydrogen(s) are below the element symbol.
`static int`	`LDIR_LEFT` Implicit Hydrogen(s) are left to element symbol.
`static int`	`LDIR_RIGHT` Implicit Hydrogen(s) are right to element symbol.
`static int`	`LIST` "Atomic number" of the inclusive atom list.
`static int`	`LONELY_H` Include lonely Hydrogen atom(s).
`static int`	`LP` "Atomic number" of the lone pair.
`static int`	`MAPPED_H` Mapped Hydrogen atom(s).
`static int`	`MULTICENTER` "Atomic number" of a central atom of a MulticenterSgroup.
`static int`	`NOTLIST` "Atomic number" of the exclusive atom list.
`static int`	`POLYMERENDGROUP_H` Hydrogen atom which have a neighbor that is in an Sgroup (not DataSgroup or SuperatomSgroup) and the H is not in the same sgroup should be kept.
`static int`	`PSEUDO` "Atomic number" of a pseudoatom.
`static int`	`RAD_COUNT_MASK` Radical's free electron count bits in flags for valid radical values.
`static int`	`RAD_MASK` Radical value bits in flags.
`static int`	`RAD_OFF` Radical value offset in flags.
`static int`	`RAD1` Monovalent radical center.
`static int`	`RAD2` Divalent radical center.
`static int`	`RAD2_SINGLET` Divalent radical center with singlet electronic configuration.
`static int`	`RAD2_TRIPLET` Divalent radical center with triplet electronic configuration.
`static int`	`RAD3` Trivalent radical center.
`static int`	`RAD3_DOUBLET` Trivalent radical center with doublet electronic configuration.
`static int`	`RAD3_QUARTET` Trivalent radical center with quartet electronic configuration.
`static int`	`RAD4` Invalid value for radical center for students.
`static char`	`RADICAL_CHAR`
`static int`	`RADICAL_H` Include radical Hydrogen atom(s).
`static int`	`RESSEQ_MAX` Maximum residue sequence number is currently 8191.
`static int`	`RESTYPE_MAX` Maximum residue type is currently 63.
`static int`	`RGROUP` "Atomic number" of the Rgroup query "atom".
`static int`	`RGROUP_ATTACHMENT` "Atomic number" of an ordered R-group attachment point.
`static int`	`RGROUP_MAX` Maximum R-group index (32767).
`static int`	`RXNSTEREO_INVERSION` The stereo configuration of the atom is inverted during the reaction.
`static int`	`RXNSTEREO_NONE` The stereo configuration of the atom is not considered during the reaction.
`static int`	`RXNSTEREO_RETENTION` The stereo configuration of the atom is retained during the reaction.
`static int`	`SETSEQ_MAX` Maximum atom set sequence number is currently 63.
`static int`	`SGROUP` "Atomic number" of an Sgroup.
`static int`	`SGROUP_H` Hydrogen atom which is the only atom in an Sgroup.
`static int`	`SGROUPEND_H` Hydrogen atom which have a neighbor that is in a SuperatomSgroup.
`static int`	`SMARTS_H_DAYLIGHT_COMP_MODE` Option flag to express daylight-type smarts atom parsing of H.
`static int`	`SMARTS_H_MARVIN_COMP_MODE` Option flag to express marvin-pre-3.5-type smarts atom parsing of H.
`static int`	`STAR` "Atomic number" of the star atom.
`static int`	`SYM_CX` Atom symbol string for CxSMILES export.
`static int`	`SYM_EXPLH` Atom symbol string contains explicit H count if this flag is set.
`static int`	`SYM_IMPLH` Atom symbol string contains implicit H count is shown flag is set.
`static int`	`SYM_MOLEX` Atom symbol string for Molfile export.
`static int`	`SYM_NEUTRAL` Atom symbol string does not contain the charge if this flag is set.
`static int`	`SYM_SMARTS` Atom symbol string for SMILES export.
`static int`	`SYM_SQBRACKETS` Atom symbol is shown in square brackets if this flag is set.
`protected MolBond[]`	`theBonds` The bonds.
`static int`	`UNSPECIFIED_AROMATICITY` Atom aromaticity is not specified explicitly.
`static int`	`VALENCE_CHECKED` Valence checked if this flag is set.
`static int`	`VALENCE_ERROR` The atom has valence error if this flag is set.
`static int`	`VALENCEERROR_H` Hydrogen atom(s) connected to an atom which have valence error.
`static int`	`WEDGED_H` Hydrogen atom(s) with wedge bonds.
`protected double`	`xCoordinate` X coordinate.
`protected double`	`yCoordinate` Y coordinate.
`protected double`	`zCoordinate` Z coordinate.

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

Constructor Summary

Constructors
Constructor and Description
`MolAtom(double x, double y)` Construct a carbon atom at the specified location.
`MolAtom(int z)` Construct an atom of the specified type at the origin.
`MolAtom(int zZ, double x, double y, double z)` Construct an atom.

Method Summary

Methods
Modifier and Type	Method and Description
`protected boolean`	`add(MolBond b)` Add a bond if it had not been already added.
`MolAtom`	`addRgroupAttachmentPoint(int order, int bondtype)` Attaches a new R-group attachment point to this atom by a bond of a specified type.
`void`	`bondweights(double[] w, CTransform3D t)` Calculates the average of the bond unit vectors pointing out of this atom.
`static boolean`	`checkAtno(int z)` Check if the given atomic number is positive and less then atomic type maximum value.
`void`	`clear()` Clear query properties, charge, and hcount.
`void`	`clearExtraLabel()` Clears the extra label.
`void`	`clearProperties()` Removes all properties from this atom.
`void`	`clearQProps()` Clears query props.
`MolAtom`	`clone()` Clones the atom.
`boolean`	`containsPropertyKey(String key)` Returns true if this atom has a mapping for the specified property key.
`protected int`	`countAllAtoms()` Counts all atoms represented by this atom.
`static double`	`covalentRadiusOf(int z, int t)` Gets the covalent radius in C-C bond length units.
`int`	`decQProp(String name)` Decrements the value of a query property.
`int`	`decValenceProp()` Decrements the value of the valence property.
`static int`	`electronegOf(int z)` Gets 10 times the electronegativity value for the specified element.
`boolean`	`equals(Object other)` Two `MolAtom`s are equal if they are the same reference.
`String`	`getAliasstr()` Gets the alias string or pseudo atom type string for pseudo atoms.
`int`	`getAtno()` Gets the atomic number.
`static int`	`getAtomicNumber(String element)` Deprecated. As of Marvin 5.9, replaced by a similar method `PeriodicSystem.findAtomicNumber(String)`. The recommended method does not work for symbol not representing a chemical element (e.g. R-atom, any atom), as this method should not have worked on them either.
`int`	`getAtomMap()` Gets the atom-atom mapping number.
`String`	`getAtomSymbol(int opts, int aflags, int[] lcenter, CTransform3D preTransform)` Gets the string representation of the atom symbol.
`int`	`getAttach()` Deprecated. as of Marvin 6.0 replaced by `SuperatomSgroup.getAttachmentPointOrders(MolAtom)`. If the atom takes place in a Superatom S-group then it's attachment point orders can be reached through the Superatom S-group.
`int`	`getAttachFromExtraAtomProp()` Gets the attachment information stored in the extra atom properties
`Sgroup`	`getAttachParentSgroup()` Gets the smallest containing sgroup which can have the attachment point information of this atom.
`chemaxon.struc.BicycloStereoDescriptor[]`	`getBicycloStereo()` Gets the previously stored bicyclo stereo information of this atom.
`MolBond`	`getBond(int i)` Gets the i-th bond.
`MolBond[]`	`getBondArray()` Gets the bonds connected to this atom.
`int`	`getBondCount()` Gets the number of bonds/ligands.
`MolBond`	`getBondTo(MolAtom other)` Finds the bond that connects this atom to another atom.
`int`	`getCharge()` Gets the charge.
`static int`	`getColumn(int z)` The column or group of an element in the periodic system.
`int`	`getElectronProp()` Returns the number of lone pairs on this atom.
`int`	`getExplicitHcount()` Gets number of hydrogen connections.
`String`	`getExtraLabel()` Gets the label string (also called atom value): "result" or "result1\|result2".
`long`	`getExtraLabelColor()` Gets the extra label color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).
`int`	`getExtraLabelColor(int i)` Gets the extra label color: (alpha<<24 + red<<16 + green<<8 + blue).
`static int`	`getExtraLabelColor(long rgbs, int i)` Gets extra label color from composed color value.
`int`	`getExtraLabelSetSeq()`
`int`	`getFlags()` Gets flags.
`int`	`getHybridizationState()` Gets the hybridization state.
`int`	`getImplicitHcount()` Gets the number of implicit hydrogens attached.
`int`	`getImplicitHCount(boolean runVCIfNeeded)` Gets the implicit Hydrogen count of the atom.
`MolAtom`	`getLigand(int i)` Gets the i-th ligand of this atom.
`int`	`getLigandIndex(MolAtom atom)` Returns the index of the specified ligand in this atom.
`int`	`getLigandOrder(MolAtom ligand)` Gets the order of a specified ligand.
`MolAtom[]`	`getLigands()` Returns the atoms connected to this atom by a bond.
`int`	`getLinkNodeOuterAtom(int idx)` Gets the index of one of the link node's outer neighbor atoms.
`int[]`	`getList()` Gets the atom list.
`DPoint3`	`getLocation()` Gets the coordinates.
`void`	`getLocation(DPoint3 p)` Gets the coordinates.
`protected Object`	`getLock()` Get lock object for synchronization.
`int`	`getLonePairCount()` Returns the automatically calculated lone pair count of this atom.
`double`	`getMass()` Gets the atomic weight.
`int`	`getMassno()` Gets the mass number.
`int`	`getMaxRepetitions()` Gets the maximum number of repetitions for a link atom.
`int`	`getMinRepetitions()` Gets the minimum number of repetitions for a link node.
`int`	`getNonQueryImplicitHcount()` Gets the number of implicit hydrogens attached.
`MoleculeGraph`	`getParent()` Return the molecule graph that contains this atom.
`int`	`getPreferredLabelDir(CTransform3D pretr, int h)` Gets the preferred direction for an additional label.
`Object`	`getProperty(String key)` Returns the property value to which the specified property key is mapped at this atom, or null if this atom has no mapping for this property key.
`Object`	`getQProp(String name)` Gets a query property.
`int`	`getQPropAsInt(String name)` Gets a query property as an integer.
`int[]`	`getQPropMinMax(String name)` Gets the minimum and maximum possible values of a query property.
`String[]`	`getQPropNames()` Gets the names of query properties with non-null values.
`Set<String>`	`getQPropNameSet()` Gets the names of query properties with non-null values, or null if no query properties are set.
`int`	`getQueryAromaticity()` Gets the aromatic/aliphatic query property.
`String`	`getQueryLabel()` Gets the string representation of the query atom
`String`	`getQuerystr()` Deprecated. As of release 5.7, replaced by `getQueryString()`
`String`	`getQueryString()` Returns s the query string assigned to this atom.
`int`	`getRadical()` Deprecated. as of Marvin 6.2. use `getRadicalValue()` instead
`int`	`getRadicalCount()` Gets the number of free electrons.
`AtomProperty.Radical`	`getRadicalValue()` Gets the `AtomProperty.Radical` enum value that represents the radical of the atom.
`int`	`getReactionStereo()` Gets the reaction stereo property describing how the stereo configuration of the atom changes during the reaction.
`int`	`getRealBondCount()` Gets the number of bonds connected to "real" atoms.
`int`	`getRelativeNegativity()` Check negativity compared to the neighbors.
`int`	`getResidueAtomId()` Gets the residue atom identifier.
`int`	`getResidueSeq()` Gets the residue sequence number.
`int`	`getResidueType()` Gets the residue type.
`int`	`getRgroup()` Gets the R-group ID.
`int`	`getRgroupAttachmentPointOrder()` Gets the attachment point order of an R-group attachment point.
`static int`	`getRow(int z)` The row or or period of an element in the periodic system.
`int`	`getSetSeq()` Gets the atom set sequence number.
`boolean`	`getStereoCare()` Reports double bond stereo care information on the connected bonds.
`int`	`getStereoGroupNumber()` Gets the stereochemical group number for AND and OR groups of the enhanced stereo representation.
`int`	`getStereoGroupType()` Gets the stereochemical group type for the enhanced stereo representation.
`String`	`getSymbol()` Gets the element symbol.
`Object`	`getTemporaryObject(String key)` Gets a temporary object.
`int`	`getValence()` Gets the valence.
`int`	`getValenceProp()` Gets the valence property.
`int[]`	`getValencePropMinMax()` Gets the minimum and maximum possible values of the valence property.
`double`	`getX()` Gets the X coordinate.
`double`	`getY()` Gets the Y coordinate.
`double`	`getZ()` Gets the Z coordinate.
`boolean`	`hasAromaticBond()` Tests whether the atom has aromatic bonds.
`int`	`hashCode()` Returns the hash code of the atom.
`boolean`	`hasQProps()` Does it have query properties?
`boolean`	`hasQueryBonds()` Tests whether the atom has query bonds ("ANY" bonds).
`boolean`	`hasSMARTSProps()` Deprecated. As of release 5.7, replaced by `SmartsAtomQuerifier.hasSMARTSProps(MolAtom atom)`
`boolean`	`hasSMARTSPropsExcluding(String exclude)` Deprecated. As of release 5.7, replaced by `SmartsAtomQuerifier.hasSMARTSPropsExcluding(MolAtom atom, String exclude)`
`boolean`	`hasValenceError()` Returns previously set valence error.
`boolean`	`hasWedgedBond()` Tests whether the atom has a wedged bond.
`boolean`	`haveEqualProperties(MolAtom a)` Tests if two atoms have the same properties.
`boolean`	`haveSimilarBonds(MolAtom a)` Checks if two atoms have similar bonds.
`int`	`incQProp(String name)` Increments the value of a query property.
`int`	`incQueryAromaticity()` Increments the value of the query aromaticity property.
`int`	`incValenceProp()` Increments the value of the valence property.
`int`	`indexOf(MolBond bond)` Returns the index of the specified bond in this atom.
`protected int`	`indexOfReferenced(MolBond bond)` Returns the index of the referenced bond in this atom.
`protected void`	`insertBond(int i, MolBond bond)` Inserts a bond at a specified index.
`boolean`	`insideLabel(double x, double y)` Tests whether the specified point is inside the atom label.
`static int`	`ionChargeOf(int z)` Gets the ion charge.
`boolean`	`isAmbiguousStereo()` Check if the atom has ambiguous stereo wedge configuration.
`static boolean`	`isAromaticSMILESSubset(int atno)` Is the atom can be aromatic according to the daylight specification: Only atoms on the following list can be considered aromatic: C, N, O, P, S, As, Se, and * (wildcard).
`boolean`	`isBoundTo(MolAtom other)` Checks if this MolAtom is connected to another one or not.
`boolean`	`isGeneric()` Tests whether the atom is a generic atom.
`boolean`	`isImplicitizableH(int f)` Tests whether the hydrogen atom is implicitizable or not.
`boolean`	`isLinkNode()` The atom is a link node if the maximum number of repetitions is nonzero.
`boolean`	`isMappable()` Checks if this atom it a mappable.
`static int`	`isotopeType(int z, int a)` Gets the type of an isotope.
`boolean`	`isPseudo()` Tests whether if the atom is a pseudo atom.
`boolean`	`isQProp()` Tests whether this object represents a query property.
`boolean`	`isQuery()` Tests whether it is a query atom.
`static boolean`	`isSameParityClass(int i1, int i2, int i3, int i4, int j1, int j2, int j3, int j4)` Calculates if chirality centers in the structure and the query belong to the same parity class.
`boolean`	`isSelected()` Tests whether this atom is selected.
`boolean`	`isSpecIsotopeSymbolPreferred()` Tests whether special symbol is used.
`boolean`	`isSpecIsotopeSymbolUsed()` Tests whether special symbol is used.
`boolean`	`isTerminalAtom()` Determines whether it is a terminal atom or not.
`static int`	`maxAbsOxStateOf(int z)` Gets the oxidation state that has the maximum absolute value
`void`	`moveCorners(double diffx, double diffy)` Translates the coordinates of the atom label.
`static String`	`nameOf(int z)` Gets the name of the specified element.
`static double`	`naturalWeightOf(int z)` Gets the natural weight of the element.
`static int`	`negOxOf(int z)` Gets the negative oxidation number.
`static int`	`numOf(String e)` Deprecated. As of Marvin 5.9, replaced by a similar method `PeriodicSystem.findAtomicNumber(String)`. The recommended method does not work for symbol that does not represent a chemical element (e.g. R-atom, any atom), as this method should not have worked on them either.
`static int`	`numoxstatesOf(int z)` Gets the number of oxidation states for the specified element.
`static int`	`oxstateOf(int z, int k)` Gets the oxidation states.
`void`	`pack()` Reduce memory usage.
`static int`	`paritySign(int a, int b, int c, int d)` Calculates the sign of the parity for the specified indexes.
`static int`	`posOxOf(int z)` Gets the smallest positive oxidation number.
`int`	`propertyCount()` Returns the number of property (property key - property value) mappings of this atom.
`Set<String>`	`propertyKeySet()` Returns a set view of the property keys of this atom.
`Set<Map.Entry<String,Object>>`	`propertySet()` Returns a collection view of the properties (property key - property value mappings) of this atom.
`void`	`putProperty(String key, Object value)` Associates the specified value with the specified key at this atom.
`void`	`qpropCheck()` Query property checking.
`protected void`	`removeAllBonds()` Removes all bonds.
`protected void`	`removeAllBonds(boolean clearFromAttachmentPoints)` Removes all bonds.
`protected void`	`removeBond(int i)` Removes a bond.
`protected void`	`removeBond(int i, boolean clearFromAttachmentPoints)` Removes a bond.
`protected void`	`removeBond(MolBond bond)` Removes a bond by reference.
`protected void`	`removeBond(MolBond bond, boolean clearFromAttachmentPoints)` Removes a bond by reference.
`Object`	`removeProperty(String key)` Removes the mapping for this property key from this atom if present.
`static String`	`residueSymbolOf(int id)` Gets the name of a residue.
`static int`	`residueTypeOf(String name)` Gets the residue identifier for a residue name.
`void`	`set(MolAtom atom)` Set all atom properties except the coordinates.
`void`	`setAliasstr(String s)` Sets the alias string or pseudo atom type string for pseudo atoms.
`void`	`setAtno(int z)` Sets the atomic number.
`protected static void`	`setAtom1(MolBond bond, MolAtom newatom)` Sets the first atom of a bond.
`protected static void`	`setAtom2(MolBond bond, MolAtom newatom)` Sets the second atom of a bond.
`void`	`setAtomMap(int map)` Sets the atom-atom mapping number.
`void`	`setAttach(int a)` Deprecated. as of Marvin 6.0, replaced by `SuperatomSgroup.addAttachmentPoint(MolAtom)`, or `SuperatomSgroup.addAttachmentPoint(MolAtom, int)`.
`void`	`setAttach(int newOrder, Sgroup sg)` Deprecated. as of Marvin 6.0, replaced by `SuperatomSgroup.addAttachmentPoint(MolAtom)`, or `SuperatomSgroup.addAttachmentPoint(MolAtom, int)`.
`void`	`setAttachParentSgroup(Sgroup sgroup)` Sets the attach parent s-group information to the extra atom properties
`void`	`setBicycloStereo(chemaxon.struc.BicycloStereoDescriptor[] descriptors)` Registers the bicyclo stereo information for this atom.
`void`	`setCharge(int q)` Sets the charge.
`void`	`setCorners(double xnw, double ynw, double xse, double yse)` Used internally by MolPainter.
`void`	`setElectronProp(int eProp)` Sets the number of lone pairs.
`void`	`setExtraLabel(String s)` Sets the extra atom label (also called atom value): "label" or "label1\|label2".
`void`	`setExtraLabelColor(int rgb1, int rgb2)` Sets the extra label colors: lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).
`void`	`setExtraLabelColor(long rgbs)` Sets the extra label color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).
`void`	`setExtraLabelSetSeq(int id)`
`void`	`setFlags(int f)` Sets the flags.
`void`	`setFlags(int f, int mask)` Sets the flags.
`void`	`setForSpecIsotopeSymbol(String sym)` Deprecated. as of Marvin 6.3. use `setSpecIsotopeSymbolPreferred(boolean)` and `setMassno(int)` instead.
`void`	`setHybridizationState(int h)` Sets the hybridization state.
`void`	`setImplicitHBasedOnValence(chemaxon.core.calculations.valencecheck.Valence v)` Deprecated. as of Marvin 6.0.1, exists only for internal usage Usage: Internal usage only.
`void`	`setImplicitHcount(int h)` Sets the number of implicit hydrogens.
`protected void`	`setIsValenceCheckNeeded(boolean isValenceCheckNeeded)` Sets the boolean value if `isValenceCheckNeeded`.
`boolean`	`setLigandOrder(int order, MolAtom ligand)` Sets the order of a specified ligand.
`void`	`setLinkNodeDefaultOuters()` Sets link node outer atoms to default values, if they are not set yet.
`void`	`setLinkNodeOuterAtom(int idx, int outer)` Sets one of the link node's outer neighbor atoms.
`void`	`setList(int[] l)` Sets the list elements.
`void`	`setList(int[] l, int n)` Sets the list elements.
`void`	`setLocation(DPoint3 p)` Sets the coordinates.
`void`	`setMassno(int a)` Sets the mass number.
`void`	`setMaxRepetitions(int r)` Sets the maximum number of repetitions for a link atom.
`void`	`setMinRepetitions(int r)` Sets the minimum number of repetitions for a link node.
`void`	`setNonQueryImplicitHcount(int h)` Sets the number of non-query implicit hydrogens attached.
`void`	`setQProp(String name, int v)` Sets a query property as an integer.
`void`	`setQProp(String name, Object v)` Sets a query property.
`void`	`setQueryAromaticity(int x)` Sets the aromatic/aliphatic query property.
`void`	`setQuerystr(String s)` Deprecated. As of release 5.7, replaced by `SmartsAtomQuerifier.setQuerystr(MolAtom atom, String s)` and `setQueryString(String)`.
`void`	`setQuerystr(String s, int options)` Deprecated. As of release 5.7, replaced by `SmartsAtomQuerifier.setQuerystr(MolAtom atom, String s, int options)` and `setQueryString(String)`.
`void`	`setQueryString(String queryString)` Assigns the query string to this atom.
`void`	`setRadical(int r)` Deprecated. as of Marvin 6.2. Use `setRadicalValue(AtomProperty.Radical)` instead.
`void`	`setRadicalValue(AtomProperty.Radical radical)` Sets the radical value.
`void`	`setReactionStereo(int r)` Sets the reaction stereo property describing how the stereo configuration of the atom changes during the reaction.
`void`	`setResidueAtomId(int id)` Sets the residue atom identifier.
`void`	`setResidueSeq(int n)` Sets the residue sequence number.
`void`	`setResidueType(int t)` Sets the residue type.
`void`	`setRgroup(int r)` Sets the R-group ID.
`void`	`setRgroupAttachmentPointOrder(int order)` Sets the attachment point order of an R-group attachment point.
`void`	`setSelected(boolean sel)` Selects or unselects this atom.
`void`	`setSetSeq(int id)` Sets the atom set sequence number.
`void`	`setSMARTS(String s)` Deprecated. As of release 5.7, replaced by `SmartsAtomQuerifier.setSMARTS(MolAtom atom, String s)`
`void`	`setSpecIsotopeSymbolPreferred(boolean v)` Sets special isotope symbol usage preference.
`void`	`setStereoGroupNumber(int n)` Sets the stereochemical group number for AND and OR groups of the enhanced stereo representation.
`void`	`setStereoGroupType(int t)` Sets the stereochemical group type for enhanced stereo representation.
`void`	`setValenceError(boolean v)` Sets or clears the valence error flag.
`void`	`setValenceProp(int v)` Sets the valence property.
`void`	`setX(double x)` Sets the X coordinate.
`void`	`setXY(double x, double y)` Sets the x and y coordinates.
`void`	`setXYZ(double x, double y, double z)` Sets the coordinates.
`void`	`setY(double y)` Sets the Y coordinate.
`void`	`setZ(double z)` Sets the Z coordinate.
`int`	`sringsize()` Calculate the size of smallest ring containing this atom.
`void`	`storeTemporaryObject(String key, Object val)` Stores an object temporarily.
`static String`	`symbolOf(int z)` Gets the element symbol for the specified atomic number.
`static String`	`symbolOf(int z, int a)` Gets the special element symbol for the specified atomic and mass numbers.
`String`	`toString()` Overrides Object.toString() to ease debugging.
`void`	`transform(CTransform3D t, boolean incg)` Apply a transformation matrix to the coordinates.
`int`	`twicesumbonds(boolean countH, boolean all2)` Calculates the total number of bonding electrons, excluding implicit hydrogens.
`void`	`valenceCheck()` Valence checking.

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

- Field Detail
  - LONELY_H
```
public static final int LONELY_H
```
    Include lonely Hydrogen atom(s). It is not possible to convert these Hydrogen atom to implicit one, so in this case the Hydrogen atom simply is removed.
    
    Since:
    
    Marvin 3.1
    
    See Also:
    Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int), Constant Field Values
  - ISOTOPE_H
```
public static final int ISOTOPE_H
```
    Include Hydrogen isotope(s).
    
    Since:
    
    Marvin 3.1
    
    See Also:
    Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int), Constant Field Values
  - CHARGED_H
```
public static final int CHARGED_H
```
    Include charged Hydrogen atom(s).
    
    Since:
    
    Marvin 3.1
    
    See Also:
    Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int), Constant Field Values
  - RADICAL_H
```
public static final int RADICAL_H
```
    Include radical Hydrogen atom(s).
    
    Since:
    
    Marvin 3.1
    
    See Also:
    Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int), Constant Field Values
  - MAPPED_H
```
public static final int MAPPED_H
```
    Mapped Hydrogen atom(s).
    
    Since:
    
    Marvin 3.1
    
    See Also:
    Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int), Constant Field Values
  - WEDGED_H
```
public static final int WEDGED_H
```
    Hydrogen atom(s) with wedge bonds.
    
    Since:
    
    Marvin 4.0
    
    See Also:
    Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int), Constant Field Values
  - HCONNECTED_H
```
public static final int HCONNECTED_H
```
    Hydrogen atom(s) connected to another hydrogen only.
    
    Since:
    
    Marvin 4.0
    
    See Also:
    Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int), Constant Field Values
  - CTSPECIFIC_H
```
@Deprecated
public static final int CTSPECIFIC_H
```
    Deprecated. As of Marvin 5.11
    Graph invariants are checked by default when calculating CIS/TRANS stereo, so this option is out of use.
    
    Hydrogen atom connecting alone to one side of a double bond with specified CIS or TRANS stereo information. The removal of this atom would abolish the stereo information at the neighboring double bond.
    
    Since:
    
    Marvin 5.0
    
    See Also:
    Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int), Constant Field Values
  - POLYMERENDGROUP_H
```
public static final int POLYMERENDGROUP_H
```
    Hydrogen atom which have a neighbor that is in an Sgroup (not DataSgroup or SuperatomSgroup) and the H is not in the same sgroup should be kept. The removal of this atom would spoil the sgroup meaning in case of polymers.
    
    Since:
    
    Marvin 5.2.3 09/06/2009
    
    See Also:
    Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int), Constant Field Values
  - SGROUPEND_H
```
public static final int SGROUPEND_H
```
    Hydrogen atom which have a neighbor that is in a SuperatomSgroup. and the H is not in the same sgroup should be kept. The removal of this atom would result in sgroup attachment point.
    
    Since:
    
    Marvin 5.8.1 01/25/2012
    
    See Also:
    Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int), Constant Field Values
  - VALENCEERROR_H
```
public static final int VALENCEERROR_H
```
    Hydrogen atom(s) connected to an atom which have valence error. The removal of this atom would result in loss of implicit Hydrogen atom count after valenceCheck call. (ValenceCheck modifies the implicit Hydrogen atom count to chemically valid value.)
    
    Since:
    
    Marvin 5.9.1 03/12/2012
    
    See Also:
    Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int), Constant Field Values
  - SGROUP_H
```
public static final int SGROUP_H
```
    Hydrogen atom which is the only atom in an Sgroup.
    
    Since:
    
    Marvin 5.10 05/11/2012
    
    See Also:
    Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int), Constant Field Values
  - BRIDGEHEAD_H
```
public static final int BRIDGEHEAD_H
```
    Hydrogen atom which is connected to a bridgehead atom.
    
    Since:
    
    Marvin 5.11 08/01/2012
    
    See Also:
    Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int), Constant Field Values
  - HBONDED_H
```
public static final int HBONDED_H
```
    Hydrogen atom wtih a MolBond.HYDROGEN bond on it.
    
    Since:
    
    Marvin 6.1 15/07/2013
    
    See Also:
    Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int), Constant Field Values
  - ALL_H
```
public static final int ALL_H
```
    Include any Hydrogen atom.
    
    Since:
    
    Marvin 4.1.3, 11/09/2006
    
    See Also:
    Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int), Constant Field Values
  - ELEMENT_COUNT
```
public static final int ELEMENT_COUNT
```
    Number of elements in the periodic system
    
    See Also:
    Constant Field Values
  - EMPTY
```
public static final int EMPTY
```
    Empty atom type. Useful for bond drawing.
    
    See Also:
    Constant Field Values
  - LIST
```
public static final int LIST
```
    "Atomic number" of the inclusive atom list.
    
    See Also:
    Constant Field Values
  - NOTLIST
```
public static final int NOTLIST
```
    "Atomic number" of the exclusive atom list.
    
    See Also:
    Constant Field Values
  - LP
```
public static final int LP
```
    "Atomic number" of the lone pair.
    
    See Also:
    Constant Field Values
  - ANY
```
public static final int ANY
```
    "Atomic number" of the any atom A. Represents any atom except hydrogen.
    
    See Also:
    Constant Field Values
  - HETERO
```
public static final int HETERO
```
    "Atomic number" of the hetero any atom Q.
    
    See Also:
    Constant Field Values
  - STAR
```
public static final int STAR
```
    "Atomic number" of the star atom. Star atoms represent unknown or unspecified end groups. For more information on star atoms, see
    
    See Also:
    , , Constant Field Values
  - RGROUP
```
public static final int RGROUP
```
    "Atomic number" of the Rgroup query "atom".
    
    See Also:
    Constant Field Values
  - SGROUP
```
public static final int SGROUP
```
    "Atomic number" of an Sgroup.
    
    See Also:
    Constant Field Values
  - PSEUDO
```
public static final int PSEUDO
```
    "Atomic number" of a pseudoatom. The atom type string of a pseudo atom can be obtained by the getAliasstr() method.
    
    Since:
    
    Marvin 3.5, 07/22/2004
    
    See Also:
    getAliasstr(), setAliasstr(String), isPseudo(), Constant Field Values
  - MULTICENTER
```
public static final int MULTICENTER
```
    "Atomic number" of a central atom of a MulticenterSgroup.
    
    Since:
    
    Marvin 5.0, 01/05/2007
    
    See Also:
    Constant Field Values
  - RGROUP_ATTACHMENT
```
public static final int RGROUP_ATTACHMENT
```
    "Atomic number" of an ordered R-group attachment point.
    
    Since:
    
    Marvin 5.4, 20/07/2010
    
    See Also:
    setRgroupAttachmentPointOrder(int order), getRgroupAttachmentPointOrder(), Constant Field Values
  - ATOM_TYPE_MAX
```
public static final int ATOM_TYPE_MAX
```
    Maximum atom number.
    
    See Also:
    Constant Field Values
  - ATOM_TYPE_COUNT
```
public static final int ATOM_TYPE_COUNT
```
    Number of atom types in the elements array
    
    See Also:
    Constant Field Values
  - HS_UNKNOWN
```
public static final int HS_UNKNOWN
```
    Unknown hybridization state.
    
    See Also:
    getHybridizationState(), Constant Field Values
  - HS_S
```
public static final int HS_S
```
    S hybridization state. Line configuration.
    
    See Also:
    getHybridizationState(), Constant Field Values
  - HS_SP
```
public static final int HS_SP
```
    SP hybridization state.
    
    See Also:
    getHybridizationState(), Constant Field Values
  - HS_SP2
```
public static final int HS_SP2
```
    SP2 hybridization state. Planar configuration.
    
    See Also:
    getHybridizationState(), Constant Field Values
  - HS_SP3
```
public static final int HS_SP3
```
    SP3 hybridization state. Tetrahedral configuration.
    
    See Also:
    getHybridizationState(), Constant Field Values
  - RGROUP_MAX
```
public static final int RGROUP_MAX
```
    Maximum R-group index (32767).
    
    See Also:
    setRgroup(int), Constant Field Values
  - RAD_OFF
```
public static final int RAD_OFF
```
    Radical value offset in flags.
    
    Since:
    
    Marvin 3.0
    
    See Also:
    Constant Field Values
  - RAD_MASK
```
public static final int RAD_MASK
```
    Radical value bits in flags.
    
    Since:
    
    Marvin 3.0
    
    See Also:
    Constant Field Values
  - RAD_COUNT_MASK
```
public static final int RAD_COUNT_MASK
```
    Radical's free electron count bits in flags for valid radical values.
    
    Since:
    
    Marvin 3.0
    
    See Also:
    Constant Field Values
  - RAD1
```
public static final int RAD1
```
    Monovalent radical center.
    
    Since:
    
    Marvin 3.0
    
    See Also:
    Constant Field Values
  - RAD2
```
public static final int RAD2
```
    Divalent radical center.
    
    Since:
    
    Marvin 3.0
    
    See Also:
    Constant Field Values
  - RAD2_SINGLET
```
public static final int RAD2_SINGLET
```
    Divalent radical center with singlet electronic configuration.
    
    Since:
    
    Marvin 3.0
    
    See Also:
    Constant Field Values
  - RAD2_TRIPLET
```
public static final int RAD2_TRIPLET
```
    Divalent radical center with triplet electronic configuration.
    
    Since:
    
    Marvin 3.0
    
    See Also:
    Constant Field Values
  - RAD3
```
public static final int RAD3
```
    Trivalent radical center.
    
    Since:
    
    Marvin 3.0
    
    See Also:
    Constant Field Values
  - RAD3_DOUBLET
```
public static final int RAD3_DOUBLET
```
    Trivalent radical center with doublet electronic configuration.
    
    Since:
    
    Marvin 4.0.2, 08/22/2005
    
    See Also:
    Constant Field Values
  - RAD3_QUARTET
```
public static final int RAD3_QUARTET
```
    Trivalent radical center with quartet electronic configuration.
    
    Since:
    
    Marvin 4.0.2, 08/22/2005
    
    See Also:
    Constant Field Values
  - RAD4
```
public static final int RAD4
```
    Invalid value for radical center for students.
    
    Since:
    
    Marvin 5.8
    
    See Also:
    Constant Field Values
  - AAMAP_MAX
```
public static final int AAMAP_MAX
```
    Maximum atom-atom mapping number.
    
    See Also:
    setAtomMap(int), Constant Field Values
  - AAMAP_OFF
```
public static final int AAMAP_OFF
```
    Atom map offset in flags.
    
    See Also:
    Constant Field Values
  - AAMAP_MASK
```
public static final int AAMAP_MASK
```
    Atom map mask in flags.
    
    See Also:
    getAtomMap(), getFlags(), Constant Field Values
  - SETSEQ_MAX
```
public static final int SETSEQ_MAX
```
    Maximum atom set sequence number is currently 63.
    
    Since:
    
    Marvin 3.0
    
    See Also:
    setSetSeq(int), Constant Field Values
  - RESTYPE_MAX
```
public static final int RESTYPE_MAX
```
    Maximum residue type is currently 63.
    
    Since:
    
    Marvin 3.0
    
    See Also:
    setResidueType(int), Constant Field Values
  - RESSEQ_MAX
```
public static final int RESSEQ_MAX
```
    Maximum residue sequence number is currently 8191.
    
    Since:
    
    Marvin 3.0
    
    See Also:
    setResidueSeq(int), Constant Field Values
  - RXNSTEREO_NONE
```
public static final int RXNSTEREO_NONE
```
    The stereo configuration of the atom is not considered during the reaction.
    
    Since:
    
    Marvin 3.0
    
    See Also:
    Constant Field Values
  - RXNSTEREO_INVERSION
```
public static final int RXNSTEREO_INVERSION
```
    The stereo configuration of the atom is inverted during the reaction.
    
    Since:
    
    Marvin 3.0
    
    See Also:
    Constant Field Values
  - RXNSTEREO_RETENTION
```
public static final int RXNSTEREO_RETENTION
```
    The stereo configuration of the atom is retained during the reaction.
    
    Since:
    
    Marvin 3.0
    
    See Also:
    Constant Field Values
  - UNSPECIFIED_AROMATICITY
```
public static final int UNSPECIFIED_AROMATICITY
```
    Atom aromaticity is not specified explicitly.
    
    Since:
    
    Marvin 3.3
    
    See Also:
    getQueryAromaticity(), Constant Field Values
  - AROMATIC
```
public static final int AROMATIC
```
    Aromatic query atom.
    
    Since:
    
    Marvin 3.3
    
    See Also:
    getQueryAromaticity(), Constant Field Values
  - ALIPHATIC
```
public static final int ALIPHATIC
```
    Aliphatic query atom.
    
    Since:
    
    Marvin 3.3
    
    See Also:
    getQueryAromaticity(), Constant Field Values
  - AROMATIC_OR_ALIPHATIC
```
public static final int AROMATIC_OR_ALIPHATIC
```
    Aromatic or aliphatic query atom.
    
    Since:
    
    Marvin 3.3
    
    See Also:
    getQueryAromaticity(), Constant Field Values
  - ATTACH_NONE
```
public static final int ATTACH_NONE
```
    There is no S-group attachment point setting on this atom.
    
    Since:
    
    Marvin 5.11
    
    See Also:
    getAttach(), Constant Field Values
  - ATTACH1
```
public static final int ATTACH1
```
    S-group attachment point on first site.
    
    Since:
    
    Marvin 3.1
    
    See Also:
    getAttach(), Constant Field Values
  - ATTACH2
```
public static final int ATTACH2
```
    S-group attachment point on second site.
    
    Since:
    
    Marvin 3.1
    
    See Also:
    getAttach(), Constant Field Values
  - ATTACH_BOTH
```
public static final int ATTACH_BOTH
```
    S-group attachment point on first and second site.
    
    Since:
    
    Marvin 3.1
    
    See Also:
    getAttach(), Constant Field Values
  - ATTACH_UNKNOWN
```
public static final int ATTACH_UNKNOWN
```
    S-group attachment point information
    
    See Also:
    SuperatomSgroup.getAttachmentPointOrders(MolAtom), Constant Field Values
  - SMARTS_H_DAYLIGHT_COMP_MODE
```
public static final int SMARTS_H_DAYLIGHT_COMP_MODE
```
    Option flag to express daylight-type smarts atom parsing of H. ("H" is only considered H atom in this special case: [<isotope>H<charge><map>].
    
    Since:
    
    Marvin 3.5
    
    See Also:
    setQuerystr(String, int), Constant Field Values
  - SMARTS_H_MARVIN_COMP_MODE
```
public static final int SMARTS_H_MARVIN_COMP_MODE
```
    Option flag to express marvin-pre-3.5-type smarts atom parsing of H. ("H" is considered H atom when no atom type expression is preceding it in the atom expression.)
    
    Since:
    
    Marvin 3.5
    
    See Also:
    setQuerystr(String, int), Constant Field Values
  - LDIR_RIGHT
```
public static final int LDIR_RIGHT
```
    Implicit Hydrogen(s) are right to element symbol.
    
    Since:
    
    Marvin 4.0, 02/16/2005
    
    See Also:
    Constant Field Values
  - LDIR_LEFT
```
public static final int LDIR_LEFT
```
    Implicit Hydrogen(s) are left to element symbol.
    
    Since:
    
    Marvin 4.0, 02/16/2005
    
    See Also:
    Constant Field Values
  - LDIR_ABOVE
```
public static final int LDIR_ABOVE
```
    Implicit Hydrogen(s) are above the element symbol.
    
    Since:
    
    Marvin 4.0, 02/16/2005
    
    See Also:
    Constant Field Values
  - LDIR_BELOW
```
public static final int LDIR_BELOW
```
    Implicit Hydrogen(s) are below the element symbol.
    
    Since:
    
    Marvin 4.0, 02/16/2005
    
    See Also:
    Constant Field Values
  - SYM_SQBRACKETS
```
public static final int SYM_SQBRACKETS
```
    Atom symbol is shown in square brackets if this flag is set.
    
    Since:
    
    Marvin 4.0, 05/10/2005
    
    See Also:
    getAtomSymbol(int, int, int[], CTransform3D), Constant Field Values
  - SYM_IMPLH
```
public static final int SYM_IMPLH
```
    Atom symbol string contains implicit H count is shown flag is set.
    
    Since:
    
    Marvin 4.0, 05/10/2005
    
    See Also:
    getAtomSymbol(int, int, int[], CTransform3D), Constant Field Values
  - SYM_EXPLH
```
public static final int SYM_EXPLH
```
    Atom symbol string contains explicit H count if this flag is set.
    
    Since:
    
    Marvin 4.0, 05/10/2005
    
    See Also:
    getAtomSymbol(int, int, int[], CTransform3D), Constant Field Values
  - SYM_NEUTRAL
```
public static final int SYM_NEUTRAL
```
    Atom symbol string does not contain the charge if this flag is set.
    
    Since:
    
    Marvin 4.0, 05/10/2005
    
    See Also:
    getAtomSymbol(int, int, int[], CTransform3D), Constant Field Values
  - SYM_SMARTS
```
public static final int SYM_SMARTS
```
    Atom symbol string for SMILES export. Forces SMARTS query string. Only meaningful if SYM_SQBRACKETS is also set.
    
    Since:
    
    Marvin 4.0, 05/10/2005
    
    See Also:
    getAtomSymbol(int, int, int[], CTransform3D), Constant Field Values
  - SYM_MOLEX
```
public static final int SYM_MOLEX
```
    Atom symbol string for Molfile export. SMARTS string with A/a property shown always. Only meaningful if SYM_SQBRACKETS is also set.
    
    Since:
    
    Marvin 4.0, 05/10/2005
    
    See Also:
    getAtomSymbol(int, int, int[], CTransform3D), Constant Field Values
  - SYM_CX
```
public static final int SYM_CX
```
    Atom symbol string for CxSMILES export. CxSMILES string may contain aromatic boron atom which is written as 'b'. Only meaningful if SYM_SQBRACKETS is also set.
    
    Since:
    
    Marvin 5.2.1, 09/03/2009
    
    See Also:
    getAtomSymbol(int, int, int[], CTransform3D), Constant Field Values
  - VALENCE_CHECKED
```
public static final int VALENCE_CHECKED
```
    Valence checked if this flag is set.
    
    See Also:
    getFlags(), Constant Field Values
  - VALENCE_ERROR
```
public static final int VALENCE_ERROR
```
    The atom has valence error if this flag is set.
    
    See Also:
    getFlags(), Constant Field Values
  - FIX_CHARGE
```
public static final int FIX_CHARGE
```
    Valence checking will replace radicals with charges if this flag is set.
    
    See Also:
    getFlags(), Constant Field Values
  - bondCount
```
protected transient int bondCount
```
    Number of bonds.
  - theBonds
```
protected transient MolBond[] theBonds
```
    The bonds.
  - xCoordinate
```
protected transient double xCoordinate
```
    X coordinate.
  - yCoordinate
```
protected transient double yCoordinate
```
    Y coordinate.
  - zCoordinate
```
protected transient double zCoordinate
```
    Z coordinate.
  - RADICAL_CHAR
```
public static final char RADICAL_CHAR
```
- Constructor Detail
  - MolAtom
```
public MolAtom(int zZ,
       double x,
       double y,
       double z)
```
    Construct an atom. Given atomic number is not checked for speed consideration. Use checkAtno(int) to check whether the atomic number is valid.
    
    Parameters:
    zZ - the atomic number
    x - the x coordinate
    y - the y coordinate
    z - the z coordinate
    See Also:
    checkAtno(int)
  - MolAtom
```
public MolAtom(double x,
       double y)
```
    Construct a carbon atom at the specified location.
    
    Parameters:
    x - the x coordinate
    y - the y coordinate
  - MolAtom
```
public MolAtom(int z)
```
    Construct an atom of the specified type at the origin. Given atomic number is not checked for speed consideration. Use checkAtno(int) to check whether the atomic number is valid.
    
    Parameters:
    z - the atomic number
    See Also:
    checkAtno(int)
- Method Detail
  - getParent
```
public final MoleculeGraph getParent()
```
    Return the molecule graph that contains this atom.
    
    Returns:
    the parent graph
  - indexOf
```
public int indexOf(MolBond bond)
```
    Returns the index of the specified bond in this atom. This method uses MolBond.equals() for the bond comparison.
    
    Parameters:
    bond - bond reference
    
    Returns:
    the bond index
    See Also:
    Object.equals(Object)
  - indexOfReferenced
```
protected final int indexOfReferenced(MolBond bond)
```
    Returns the index of the referenced bond in this atom. This method uses == for the bond comparison!
    
    Parameters:
    bond -
    
    Returns:
    the index of the referenced bond in this atom
  - getLigands
```
public final MolAtom[] getLigands()
```
    Returns the atoms connected to this atom by a bond.
    
    Returns:
    the array of connected (ligand) atoms
    Since:
    
    Marvin 5.3.3
    
    See Also:
    getLigand(int)
  - getLigand
```
public final MolAtom getLigand(int i)
```
    Gets the i-th ligand of this atom.
    
    Parameters:
    i - bond index
    
    Returns:
    the atom at the other end of the bond
    Since:
    
    Marvin 2.6
  - getLigandIndex
```
public final int getLigandIndex(MolAtom atom)
```
    Returns the index of the specified ligand in this atom.
    
    Parameters:
    atom - the other atom
    
    Returns:
    the connecting ligand index or -1 if not connected.
    Since:
    
    Marvin 4.0 12/22/2004
    
    See Also:
    getLigand(int)
  - getBondTo
```
public final MolBond getBondTo(MolAtom other)
```
    Finds the bond that connects this atom to another atom.
    
    Parameters:
    other - the other atom
    
    Returns:
    the connecting bond or null
    Since:
    
    Marvin 5.3, 04/30/2009
    
    See Also:
    isBoundTo(MolAtom)
  - isBoundTo
```
public final boolean isBoundTo(MolAtom other)
```
    Checks if this MolAtom is connected to another one or not.
    
    Parameters:
    other - the other atom
    
    Returns:
    true if the two atomss are connected with a bond, false otherwise
    See Also:
    getBondTo(MolAtom)
  - sringsize
```
public final int sringsize()
```
    Calculate the size of smallest ring containing this atom. Coordinative bonds are used in ring traversal but Hydrogen bonds are not.
    
    Returns:
    the SRS or Integer.MAX_VALUE if ring not found
  - getLock
```
protected final Object getLock()
```
    Get lock object for synchronization.
    
    Returns:
    reference to the top parent graph
  - setAtom1
```
protected static void setAtom1(MolBond bond,
            MolAtom newatom)
```
    Sets the first atom of a bond. Use it from derived classes.
    
    Parameters:
    bond - the bond
    newatom - the new atom value
  - setAtom2
```
protected static void setAtom2(MolBond bond,
            MolAtom newatom)
```
    Sets the second atom of a bond. Use it from derived classes.
    
    Parameters:
    bond - the bond
    newatom - the new atom value
  - haveSimilarBonds
```
public boolean haveSimilarBonds(MolAtom a)
```
    Checks if two atoms have similar bonds. Two atoms have similar bonds if for each bond bi of the first atom, there is a corresponding bond bj of the other atom with "equal properties".
    
    Returns:
    true if they have similar bonds, false otherwise
    Since:
    
    Marvin 5.3, 04/30/2009
    
    See Also:
    MolBond.haveEqualProperties(MolBond)
  - getBondCount
```
public final int getBondCount()
```
    Gets the number of bonds/ligands.
    
    Returns:
    the number of bonds
    Since:
    
    Marvin 3.0
  - getBond
```
public final MolBond getBond(int i)
```
    Gets the i-th bond.
    
    Parameters:
    i - bond index
    
    Returns:
    the bond object
    Since:
    
    Marvin 3.0
  - getRealBondCount
```
public final int getRealBondCount()
```
    Gets the number of bonds connected to "real" atoms. An LP node is not a real atom.
    
    Returns:
    the number of bonds
    Since:
    
    Marvin 3.5
  - set
```
public void set(MolAtom atom)
```
    Set all atom properties except the coordinates.
    
    Parameters:
    atom - the source atom
    Since:
    
    Marvin 4.1, 01/01/2006
  - getX
```
public double getX()
```
    Gets the X coordinate.
    
    Returns:
    the x coordinate in Angstroms
  - setX
```
public void setX(double x)
```
    Sets the X coordinate.
    
    Parameters:
    x - the x coordinate in Angstroms
  - getY
```
public double getY()
```
    Gets the Y coordinate.
    
    Returns:
    the y coordinate in Angstroms
  - setY
```
public void setY(double y)
```
    Sets the Y coordinate.
    
    Parameters:
    y - the y coordinate in Angstroms
  - getZ
```
public double getZ()
```
    Gets the Z coordinate.
    
    Returns:
    the z coordinate in Angstroms
  - setZ
```
public void setZ(double z)
```
    Sets the Z coordinate.
    
    Parameters:
    z - the z coordinate in Angstroms
  - setXY
```
public void setXY(double x,
         double y)
```
    Sets the x and y coordinates.
    
    Parameters:
    x - the x coordinate in Angstroms
    y - the y coordinate in Angstroms
  - setXYZ
```
public void setXYZ(double x,
          double y,
          double z)
```
    Sets the coordinates.
    
    Parameters:
    x - the x coordinate in Angstroms
    y - the y coordinate in Angstroms
    z - the z coordinate in Angstroms
  - getLocation
```
public final DPoint3 getLocation()
```
    Gets the coordinates.
    
    Returns:
    the location
  - getLocation
```
public final void getLocation(DPoint3 p)
```
    Gets the coordinates.
    
    Parameters:
    p - object that will store the location
  - setLocation
```
public void setLocation(DPoint3 p)
```
    Sets the coordinates.
    
    Parameters:
    p - the location
  - transform
```
public void transform(CTransform3D t,
             boolean incg)
```
    Apply a transformation matrix to the coordinates.
    
    Parameters:
    t - the transformation matrix
    incg - graph invariants are changed (true) or not (false)
    Since:
    
    Marvin 4.0.2, 10/26/2005
  - getSymbol
```
public String getSymbol()
```
    Gets the element symbol. The symbol is the same as the MDL codename for special atom types: "L" for LIST and NOTLIST. For pseudo atoms, the atom alias string is returned in TeX-like format for subscripts and superscripts.
    
    Returns:
    the symbol
  - getAtno
```
public final int getAtno()
```
    Gets the atomic number.
    
    Returns:
    the atomic number
  - setAtno
```
public void setAtno(int z)
```
    Sets the atomic number. Given atomic number is not checked for speed consideration. Use checkAtno(int) to check whether the the atomic number is valid.
    
    Parameters:
    z - the atomic number
    See Also:
    checkAtno(int)
  - checkAtno
```
public static boolean checkAtno(int z)
```
    Check if the given atomic number is positive and less then atomic type maximum value.
    
    Parameters:
    z - atomic number
    
    Returns:
    true if the given number is valid.
    See Also:
    ATOM_TYPE_COUNT
  - getMassno
```
public int getMassno()
```
    Gets the mass number. In the case of an element it returns 0, because it is a mix of isotopes having different mass numbers.
    
    Returns:
    the mass number, or zero if not specified
  - setMassno
```
public void setMassno(int a)
```
    Sets the mass number.
    
    Parameters:
    a - the mass number or zero
  - setForSpecIsotopeSymbol
```
@Deprecated
public void setForSpecIsotopeSymbol(String sym)
```
    Deprecated. as of Marvin 6.3. use setSpecIsotopeSymbolPreferred(boolean) and setMassno(int) instead.
    
    Sets the special atom symbol and the atomic weight for deuterium or tricium. No operation for other element types.
    
    Parameters:
    sym - the atom symbol
    Since:
    
    Marvin 4.1, 11/05/2005
  - getMass
```
public double getMass()
```
    Gets the atomic weight.
    
    Returns:
    the atomic weight
  - isMappable
```
public boolean isMappable()
```
    Checks if this atom it a mappable. Since Marvin 5.0 all atoms except Lone Electron Pairs are mappeble.
    
    Returns:
    true if map index can be assigned to the atom false if atom is a lone pair
    Since:
    
    Marvin 3.4, 06/23/2004
  - getRelativeNegativity
```
public int getRelativeNegativity()
```
    Check negativity compared to the neighbors.
    
    Returns:
    -1 if the atom is more electronegative than its neighbors, 1 if the neighbors are more electronegative, 0 if it has negative and positive neighbors also or or the neighbors have the same e.n. as the atom
  - setIsValenceCheckNeeded
```
protected void setIsValenceCheckNeeded(boolean isValenceCheckNeeded)
```
    Sets the boolean value if isValenceCheckNeeded.
    
    Since:
    
    6.0.1.
  - getImplicitHCount
```
public int getImplicitHCount(boolean runVCIfNeeded)
```
    Gets the implicit Hydrogen count of the atom. If there has been some valence changing modification since the latest valence check call then with calling the method with true parameter it will perform valence checking on this atom.
    
    Parameters:
    runVCIfNeeded -
    
    Returns:
    the implicit hydrogen count or the number of query hydrogens
    Since:
    
    Marvin 6.0.1. 2013.06.12.
  - getImplicitHcount
```
public int getImplicitHcount()
```
    Gets the number of implicit hydrogens attached. This information may not be accurate if some manipulation has been made on the molecule. In this case, use valenceCheck() before this method or call getImplicitHCount(boolean) instead. The result is always a non-negative number.
    
    Returns:
    the implicit hydrogen count or the number of query hydrogens
    See Also:
    valenceCheck()
  - setImplicitHcount
```
public void setImplicitHcount(int h)
```
    Sets the number of implicit hydrogens. Also removes the "H" query property.
    
    Parameters:
    h - the number of implicit hydrogens
    
    Throws:
    
    IllegalArgumentException - negative h value specified
  - getNonQueryImplicitHcount
```
public int getNonQueryImplicitHcount()
```
    Gets the number of implicit hydrogens attached.
    
    Returns:
    the implicit hydrogen count, not including the query H count.
  - setNonQueryImplicitHcount
```
public void setNonQueryImplicitHcount(int h)
```
    Sets the number of non-query implicit hydrogens attached.
    
    Parameters:
    h - the implicit hydrogen count, not including the query H count.
    Since:
    
    Marvin 3.5.9, 07/12/2005
  - getCharge
```
public int getCharge()
```
    Gets the charge.
    
    Returns:
    the charge
  - setCharge
```
public void setCharge(int q)
```
    Sets the charge. This function does not call valence checking to set implicit Hydrogen count due to charge change.
    
    Parameters:
    q - the charge
  - getColumn
```
public static int getColumn(int z)
```
    The column or group of an element in the periodic system.
    
    Parameters:
    z - atomic number (protons)
    
    Returns:
    column of the given atom (0 for unknown)
    Since:
    
    Marvin 4.1
  - getRadical
```
@Deprecated
public int getRadical()
```
    Deprecated. as of Marvin 6.2. use getRadicalValue() instead
    
    Gets the radical value.
    
    Returns:
    the radical value
    Since:
    
    Marvin 3.0
    
    See Also:
    RAD1, RAD2, RAD2_SINGLET, RAD2_TRIPLET, RAD3, RAD3_DOUBLET, RAD3_QUARTET, RAD4
  - getRadicalValue
```
public AtomProperty.Radical getRadicalValue()
```
    Gets the AtomProperty.Radical enum value that represents the radical of the atom.
    
    Returns:
    the enum value of the radical
  - setRadical
```
@Deprecated
public void setRadical(int r)
```
    Deprecated. as of Marvin 6.2. Use setRadicalValue(AtomProperty.Radical) instead.
    
    Sets the radical value.
    
    Parameters:
    r - the radical value
    Since:
    
    Marvin 3.0
    
    See Also:
    RAD1, RAD2, RAD2_SINGLET, RAD2_TRIPLET, RAD3, RAD3_DOUBLET, RAD3_QUARTET, RAD4
  - setRadicalValue
```
public void setRadicalValue(AtomProperty.Radical radical)
```
    Sets the radical value.
    
    Parameters:
    radical - the new radical
    Since:
    
    Marvin 6.2. 2013/11/07
    
    See Also:
    AtomProperty.Radical
  - getRadicalCount
```
public int getRadicalCount()
```
    Gets the number of free electrons.
    
    Returns:
    the number of free electrons
    Since:
    
    Marvin 3.0
    
    See Also:
    RAD1, RAD2, RAD3, RAD4
  - getRow
```
public static int getRow(int z)
```
    The row or or period of an element in the periodic system.
    
    Parameters:
    z - atomic number (protons)
    
    Returns:
    column of the atom (0 for unknown types)
    Since:
    
    Marvin 4.1
  - getValencePropMinMax
```
public int[] getValencePropMinMax()
```
    Gets the minimum and maximum possible values of the valence property.
    
    Returns:
    two-element array containing the minimum and maximum values
    Since:
    
    Marvin 4.1, 03/23/2006
  - getValenceProp
```
public int getValenceProp()
```
    Gets the valence property.
    
    Returns:
    the valence or -1 if not set
    Since:
    
    Marvin 3.5, 09/04/2004
  - setValenceProp
```
public void setValenceProp(int v)
```
    Sets the valence property.
    
    Parameters:
    v - the valence or -1 to unset
    Since:
    
    Marvin 3.5, 09/04/2004
  - incValenceProp
```
public int incValenceProp()
```
    Increments the value of the valence property.
    
    Returns:
    the new value
    Since:
    
    Marvin 4.1, 03/23/2006
  - decValenceProp
```
public int decValenceProp()
```
    Decrements the value of the valence property.
    
    Returns:
    the new value
    Since:
    
    Marvin 4.1, 03/23/2006
  - getValence
```
public int getValence()
```
    Gets the valence. If valence is set as a property, returns that. Otherwise the valence is the sum of bond orders plus the number of implicit hydrogens or query hydrogen atoms.
    
    Returns:
    the valence
  - getExplicitHcount
```
public int getExplicitHcount()
```
    Gets number of hydrogen connections.
    
    Returns:
    the number of H connections
  - hasQProps
```
public boolean hasQProps()
```
    Does it have query properties?
    
    Returns:
    true if it has query properties, false otherwise
    See Also:
    isQuery()
  - getQProp
```
public Object getQProp(String name)
```
    Gets a query property.
    - "H": query hydrogens connected
    - "X": number of connections including bonds to implied H's
    - "D": number of explicit connections
    - "R": number of rings: [R] (ring atom) is represented by value 256
    - "h": number of implicit hydrogens
    - "r": smallest ring size: [r] (ring atom) is represented by value 256
    - "a": deprecated, use getQueryAromaticity() instead
    - "c": component number
    - "s": substitution count: -1 = off, -2 = s*, 0 = s0, 1 = s1, etc.
    - "u": unsaturated atom: 1 = on
    - "rb": ring bond count: -1 = off, -2 = rbc*, 0 = rbc0, 1 = rbc1, etc.
    For a meaning of the above properties, see The JChem Query Guide
    Parameters:
    name - the property name
    
    Returns:
    the value of the property or null if not set
  - getQPropAsInt
```
public int getQPropAsInt(String name)
```
    Gets a query property as an integer.
    - "H": query hydrogens connected
    - "X": number of connections including bonds to implied H's
    - "D": number of explicit connections
    - "R": number of rings: [R] (ring atom) is represented by value 256
    - "h": number of implicit hydrogens
    - "r": smallest ring size: [r] (ring atom) is represented by value 256
    - "a": deprecated, use getQueryAromaticity() instead
    - "c": component number
    - "s": substitution count: -1 = off, -2 = s*, 0 = s0, 1 = s1, etc.
    - "u": unsaturated atom: 1 = on
    - "rb": ring bond count: -1 = off, -2 = rbc*, 0 = rbc0, 1 = rbc1, etc.
    For a meaning of the above properties, see The JChem Query Guide
    Parameters:
    name - the property name
    
    Returns:
    the value of the property or -1 if not set
    See Also:
    getQProp(java.lang.String)
  - getQPropMinMax
```
public int[] getQPropMinMax(String name)
```
    Gets the minimum and maximum possible values of a query property.
    
    Parameters:
    name - the query property abbreviation
    
    Returns:
    two-element array containing the minimum and the maximum value
    Since:
    
    Marvin 4.1, 03/22/2006
  - incQProp
```
public int incQProp(String name)
```
    Increments the value of a query property.
    
    Parameters:
    name - the query property abbreviation
    
    Returns:
    the new value
    Since:
    
    Marvin 4.1, 03/22/2006
  - decQProp
```
public int decQProp(String name)
```
    Decrements the value of a query property.
    
    Parameters:
    name - the query property abbreviation
    
    Returns:
    the new value
    Since:
    
    Marvin 4.1, 03/22/2006
  - setQProp
```
public void setQProp(String name,
            Object v)
```
    Sets a query property.
    - "H": query hydrogens connected
    - "X": number of connections including bonds to implied H's
    - "D": number of explicit connections
    - "R": number of rings: [R] (ring atom) is represented by value 256
    - "h": number of implicit hydrogens
    - "r": smallest ring size: [r] (ring atom) is represented by value 256
    - "a": deprecated, use getQueryAromaticity() instead
    - "c": component number
    - "s": substitution count: -1 = off, -2 = s*, 0 = s0, 1 = s1, etc.
    - "u": unsaturated atom: 1 = on
    - "rb": ring bond count: -1 = off, -2 = rbc*, 0 = rbc0, 1 = rbc1, etc.
    For a meaning of the above properties, see The JChem Query Guide
    Parameters:
    name - the property name
    v - the value
    See Also:
    getQProp(java.lang.String)
  - setQProp
```
public void setQProp(String name,
            int v)
```
    Sets a query property as an integer.
    - "H": query hydrogens connected
    - "X": number of connections including bonds to implied H's
    - "D": number of explicit connections
    - "R": number of rings: [R] (ring atom) is represented by value 256
    - "h": number of implicit hydrogens
    - "r": smallest ring size: [r] (ring atom) is represented by value 256
    - "a": deprecated, use getQueryAromaticity() instead
    - "c": component number
    - "s": substitution count: -1 = off, -2 = s*, 0 = s0, 1 = s1, etc.
    - "u": unsaturated atom: 1 = on
    - "rb": ring bond count: -1 = off, -2 = rbc*, 0 = rbc0, 1 = rbc1, etc.
    The value -1 has special meaning, it removes the property.
    For a meaning of the above properties, see The JChem Query Guide
    Parameters:
    name - the property name
    v - the value or -1
  - clearQProps
```
public void clearQProps()
```
    Clears query props.
    
    Since:
    
    Marvin 3.4
  - getQPropNames
```
public String[] getQPropNames()
```
    Gets the names of query properties with non-null values.
    
    Since:
    
    Marvin 4.1, 03/21/2006
  - getQPropNameSet
```
public Set<String> getQPropNameSet()
```
    Gets the names of query properties with non-null values, or null if no query properties are set.
    
    Since:
    
    Marvin 4.1, 05/10/2006
  - getQueryAromaticity
```
public int getQueryAromaticity()
```
    Gets the aromatic/aliphatic query property.
    
    Returns:
    UNSPECIFIED_AROMATICITY, AROMATIC, ALIPHATIC or AROMATIC_OR_ALIPHATIC
    Since:
    
    Marvin 3.3
  - setQueryAromaticity
```
public void setQueryAromaticity(int x)
```
    Sets the aromatic/aliphatic query property.
    
    Parameters:
    x - UNSPECIFIED_AROMATICITY, AROMATIC, ALIPHATIC or AROMATIC_OR_ALIPHATIC
    Since:
    
    Marvin 3.3
  - incQueryAromaticity
```
public int incQueryAromaticity()
```
    Increments the value of the query aromaticity property.
    
    Returns:
    the new value
    Since:
    
    Marvin 4.1, 03/23/2006
  - getRgroup
```
public int getRgroup()
```
    Gets the R-group ID.
    
    Returns:
    Rgroup number, between 0 and RGROUP_MAX
  - setRgroup
```
public void setRgroup(int r)
```
    Sets the R-group ID.
    
    Parameters:
    r - Rgroup number, between 0 and RGROUP_MAX
  - getAttach
```
@Deprecated
public int getAttach()
```
    Deprecated. as of Marvin 6.0 replaced by SuperatomSgroup.getAttachmentPointOrders(MolAtom).
    If the atom takes place in a Superatom S-group then it's attachment point orders can be reached through the Superatom S-group.
    
    Gets the S-group attachment point information.
    
    Returns:
    ATTACH_NONE (not an S-group attachment point), ATTACH1 (first), ATTACH2 (second), ATTACH_BOTH (both), or ATTACH_UNKNOWN if the attachment information can not be specified. This last one basicly happens when the atom takes place in a newly built SuperatomSgroup and has more than two attachment points.
  - getAttachFromExtraAtomProp
```
public int getAttachFromExtraAtomProp()
```
    Gets the attachment information stored in the extra atom properties
    
    Returns:
    the attachment point information
  - setAttach
```
@Deprecated
public void setAttach(int a)
```
    Deprecated. as of Marvin 6.0, replaced by SuperatomSgroup.addAttachmentPoint(MolAtom), or SuperatomSgroup.addAttachmentPoint(MolAtom, int).
    
    Sets the S-group attachment point information.
    
    Parameters:
    a - ATTACH_NONE (not an S-group attachment point), ATTACH1 (first), ATTACH2 (second) or ATTACH_BOTH (both)
  - setAttach
```
@Deprecated
public void setAttach(int newOrder,
                        Sgroup sg)
```
    Deprecated. as of Marvin 6.0, replaced by SuperatomSgroup.addAttachmentPoint(MolAtom), or SuperatomSgroup.addAttachmentPoint(MolAtom, int).
    
    Sets the S-group attachment point information for an S-group attachment atom.
    
    Parameters:
    newOrder - ATTACH_NONE (not an S-group attachment point), ATTACH1 (first), ATTACH2 (second) or ATTACH_BOTH (both)
    sg - the parent S-group or null
    Since:
    
    Marvin 3.5, 10/11/2004
  - setAttachParentSgroup
```
public void setAttachParentSgroup(Sgroup sgroup)
```
    Sets the attach parent s-group information to the extra atom properties
    
    Parameters:
    sgroup -
  - getAttachParentSgroup
```
public Sgroup getAttachParentSgroup()
```
    Gets the smallest containing sgroup which can have the attachment point information of this atom.
    
    Returns:
    the parent sgroup or null if the atom is not in an sgroup
    Since:
    
    Marvin 3.5, 10/11/2004
  - getHybridizationState
```
public int getHybridizationState()
```
    Gets the hybridization state. The hybridization state value is not updated automatically when a molecule is loaded or modified. This ensures that the hybridization state set by setHybridizationState(int) is not overwritten accidentally. \br To calculate and set the hybridization state for this and all other atoms in a moecule call MoleculeGraph.calcHybridization().
    
    Returns:
    the hybridization state
    See Also:
    HS_UNKNOWN, HS_S, HS_SP, HS_SP2, HS_SP3
  - setHybridizationState
```
public void setHybridizationState(int h)
```
    Sets the hybridization state.
    
    Parameters:
    h - the hybridization state
    See Also:
    getHybridizationState()
  - getAtomMap
```
public int getAtomMap()
```
    Gets the atom-atom mapping number.
    
    Returns:
    the map value (positive integer) or 0
  - setAtomMap
```
public void setAtomMap(int map)
```
    Sets the atom-atom mapping number.
    
    Parameters:
    map - the map value (positive integer) or 0
    See Also:
    AAMAP_MAX
  - getSetSeq
```
public int getSetSeq()
```
    Gets the atom set sequence number.
    
    Returns:
    a number between 0 and SETSEQ_MAX
    See Also:
    SETSEQ_MAX
  - setSetSeq
```
public void setSetSeq(int id)
```
    Sets the atom set sequence number.
    
    Parameters:
    id - a number between 0 and SETSEQ_MAX
    See Also:
    SETSEQ_MAX
  - setExtraLabelSetSeq
```
public void setExtraLabelSetSeq(int id)
```
  - getExtraLabelSetSeq
```
public int getExtraLabelSetSeq()
```
  - residueTypeOf
```
public static int residueTypeOf(String name)
```
    Gets the residue identifier for a residue name.
    
    Parameters:
    name - residue name
    
    Returns:
    the residue type
    Since:
    
    Marvin 3.1.4
  - residueSymbolOf
```
public static String residueSymbolOf(int id)
```
    Gets the name of a residue.
    
    Parameters:
    id - the residue identifier
    
    Returns:
    the residue symbol
    Since:
    
    Marvin 3.1.4
  - getResidueType
```
public int getResidueType()
```
    Gets the residue type.
    
    Returns:
    the residue type
    See Also:
    RESTYPE_MAX
  - setResidueType
```
public void setResidueType(int t)
```
    Sets the residue type.
    
    Parameters:
    t - the residue type
    See Also:
    RESTYPE_MAX
  - getResidueSeq
```
public int getResidueSeq()
```
    Gets the residue sequence number.
    
    Returns:
    the residue sequence number
    See Also:
    RESSEQ_MAX
  - setResidueSeq
```
public void setResidueSeq(int n)
```
    Sets the residue sequence number.
    
    Parameters:
    n - the residue sequence number
    See Also:
    RESSEQ_MAX
  - getResidueAtomId
```
public int getResidueAtomId()
```
    Gets the residue atom identifier. Atoms in amino acids and nucleic acids are identified uniquely by the atom symbol and the residue atom identifier.
    
    Returns:
    the residue atom identifier
    Since:
    
    Marvin 3.1.3
  - setResidueAtomId
```
public void setResidueAtomId(int id)
```
    Sets the residue atom identifier.
    
    Parameters:
    id - the residue atom identifier
    Since:
    
    Marvin 3.1.3
  - getMinRepetitions
```
public int getMinRepetitions()
```
    Gets the minimum number of repetitions for a link node.
    
    Returns:
    the minimum number of repetitions
    Since:
    
    Marvin 3.5, 07/22/2004
  - setMinRepetitions
```
public void setMinRepetitions(int r)
```
    Sets the minimum number of repetitions for a link node.
    
    Parameters:
    r - the minimum number of repetitions
    Since:
    
    Marvin 3.5, 07/22/2004
  - getMaxRepetitions
```
public int getMaxRepetitions()
```
    Gets the maximum number of repetitions for a link atom.
    
    Returns:
    the maximum number of repetitions
    Since:
    
    Marvin 3.5, 07/22/2004
  - setMaxRepetitions
```
public void setMaxRepetitions(int r)
```
    Sets the maximum number of repetitions for a link atom.
    
    Parameters:
    r - the maximum number of repetitions
    Since:
    
    Marvin 3.5, 07/22/2004
  - getLinkNodeOuterAtom
```
public int getLinkNodeOuterAtom(int idx)
```
    Gets the index of one of the link node's outer neighbor atoms. (Outer: not repeating.)
    
    Parameters:
    idx - Which outer atom (0 or 1)
    
    Returns:
    The specified outer atom index (as used with getLigand()) or -1 if not set.
    Since:
    
    Marvin 4.0 12/22/2004
    
    See Also:
    getLigand(int)
  - setLinkNodeOuterAtom
```
public void setLinkNodeOuterAtom(int idx,
                        int outer)
```
    Sets one of the link node's outer neighbor atoms. (Outer: not repeating.)
    
    Parameters:
    idx - Which outer atom (0 or 1)
    outer - The outer neighbor atom index (as used with getLigand()) or -1 if clearing.
    Since:
    
    Marvin 4.0 12/22/2004
    
    See Also:
    getLigand(int)
  - isLinkNode
```
public boolean isLinkNode()
```
    The atom is a link node if the maximum number of repetitions is nonzero.
    
    Returns:
    if the maximum number of repetitions is nonzero
    Since:
    
    Marvin 3.5, 07/22/2004
  - bondweights
```
public void bondweights(double[] w,
               CTransform3D t)
```
    Calculates the average of the bond unit vectors pointing out of this atom. The result is not a unit vector.
    
    Parameters:
    w - 3-element array that will contain the resulting vector
    t - the rotation matrix
  - getAtomSymbol
```
public String getAtomSymbol(int opts,
                   int aflags,
                   int[] lcenter,
                   CTransform3D preTransform)
```
    Gets the string representation of the atom symbol.
    
    Parameters:
    opts - combination of SYM_* flags
    aflags - atom flags
    preTransform - viewing transformation
    lcenter - if not null, then its first two element (index 0-1) will will be set to the index and the length of the element symbol substring in the returned string, the element at at index 2 will be set to +1 if the H label is above, -1 if below the element symbol or 0 otherwise
    
    Returns:
    the string representation
    Since:
    
    Marvin 3.0
    
    See Also:
    SYM_SQBRACKETS, SYM_IMPLH, SYM_EXPLH, SYM_NEUTRAL, SYM_SMARTS, SYM_MOLEX
  - getQueryLabel
```
public String getQueryLabel()
```
    Gets the string representation of the query atom
    
    Returns:
    the string representation
    Since:
    
    Marvin 3.0
  - getPreferredLabelDir
```
public int getPreferredLabelDir(CTransform3D pretr,
                       int h)
```
    Gets the preferred direction for an additional label.
    
    Parameters:
    pretr - viewing transformation
    h - hydrogen count for hydrogen label display, 0 otherwise
    
    Returns:
    LDIR_RIGHT, LDIR_LEFT, LDIR_ABOVE or LDIR_BELOW
    Since:
    
    4.0, 02/16/2005
  - isQuery
```
public final boolean isQuery()
```
    Tests whether it is a query atom. (Has a query atom type or query property or query string):
    - link node atom
    - any atom
    - hetero atom
    - list atom
    - not list atom
    - rgroup atom
    - known query properties: H,X,R,r,a,s,u,h,D,c,rb
    For a meaning of the above properties, see The JChem Query Guide
    Returns:
    true if it is a query atom, false otherwise
    See Also:
    isLinkNode(), ANY, HETERO, LIST, NOTLIST, RGROUP
  - isQProp
```
public boolean isQProp()
```
    Tests whether this object represents a query property.
    
    Returns:
    true if it is a query property, false otherwise
    Since:
    
    Marvin 3.0, 11/08/2002
  - isImplicitizableH
```
public boolean isImplicitizableH(int f)
```
    Tests whether the hydrogen atom is implicitizable or not. Only bound (to non-Hydrogen atom and with no H-bond), non-isotope, neutral, non-radical, non-mapped, non-CIS/TRANS important H atoms are implicitizable by default (0 argument). If the argument is nonzero, then the return value can be true for lonely, isotope, charged, radical, mapped or CIS/TRANS Important H atoms also.
    
    Parameters:
    f - flags specifying special H atom types to include
    
    Returns:
    true if the hydrogen is implicitizable, false otherwise
    Since:
    
    Marvin 3.1
    
    See Also:
    LONELY_H, ISOTOPE_H, CHARGED_H, RADICAL_H, MAPPED_H, WEDGED_H, HCONNECTED_H, HBONDED_H, CTSPECIFIC_H, VALENCEERROR_H, Hydrogenize.convertExplicitHToImplicit(MoleculeGraph, int)
  - isPseudo
```
public boolean isPseudo()
```
    Tests whether if the atom is a pseudo atom. To create a pseudo atom, set atom number (setAtno(int)) to PSEUDO and set the pseudo atom type string by setAliasstr(String).
    
    Returns:
    true if the atom is a pseudo atom, false otherwise
    Since:
    
    Marvin 3.3
    
    See Also:
    getAliasstr(), PSEUDO
  - isGeneric
```
public boolean isGeneric()
```
    Tests whether the atom is a generic atom. To create a generic atom, set atom number (setAtno(int)) to PSEUDO and set the pseudo atom type string by setAliasstr(String) to one of the following:
    - "AH" : Any atom including H
    - "QH" : Any atom except C
    - "M" : Any metal
    - "MH" : Any metal or H
    - "X" : Any halogen
    - "XH" : Any halogen or H
    .
    Returns:
    true if the atom is a ganaric atom, false otherwise
    Since:
    
    Marvin 5.0
    
    See Also:
    getAliasstr(), PSEUDO
  - hasWedgedBond
```
public final boolean hasWedgedBond()
```
    Tests whether the atom has a wedged bond.
    
    Returns:
    true if it has a wedged bond, false otherwise
    Since:
    
    4.0
  - hasAromaticBond
```
public final boolean hasAromaticBond()
```
    Tests whether the atom has aromatic bonds.
    
    Returns:
    true if it has aromatic bonds, false otherwise
  - hasQueryBonds
```
public final boolean hasQueryBonds()
```
    Tests whether the atom has query bonds ("ANY" bonds).
    
    Returns:
    true if it has query bonds, false otherwise
  - hasSMARTSProps
```
@Deprecated
public final boolean hasSMARTSProps()
```
    Deprecated. As of release 5.7, replaced by SmartsAtomQuerifier.hasSMARTSProps(MolAtom atom)
    
    Tests whether it is a SMARTS query atom.
    
    Returns:
    true if it has SMARTS properties, false otherwise
  - hasSMARTSPropsExcluding
```
@Deprecated
public final boolean hasSMARTSPropsExcluding(String exclude)
```
    Deprecated. As of release 5.7, replaced by SmartsAtomQuerifier.hasSMARTSPropsExcluding(MolAtom atom, String exclude)
    
    Tests whether it is a SMARTS query atom.
    
    Parameters:
    exclude - list of SMARTS properties to exclude
    
    Returns:
    true if it has SMARTS properties, false otherwise
    Since:
    
    Marvin 3.1.2
  - setSMARTS
```
@Deprecated
public void setSMARTS(String s)
               throws SecurityException
```
    Deprecated. As of release 5.7, replaced by SmartsAtomQuerifier.setSMARTS(MolAtom atom, String s)
    
    Sets SMARTS query string data.
    
    Parameters:
    s - the SMARTS string
    
    Throws:
    
    SecurityException - the SmilesImport cannot be loaded, possibly because of a misconfigured firewall
  - getQuerystr
```
@Deprecated
public String getQuerystr()
```
    Deprecated. As of release 5.7, replaced by getQueryString()
    
    Gets the query properties.
    
    Returns:
    the query string
  - setQuerystr
```
@Deprecated
public void setQuerystr(String s)
```
    Deprecated. As of release 5.7, replaced by SmartsAtomQuerifier.setQuerystr(MolAtom atom, String s) and setQueryString(String).
    
    Assigns the query properties string to this atom while setting all necessary atom and query properties. This is done through SmartsAtomQuerifier which parses the query string. For this reason this operation may be relatively costly. The remaining part of the query string (which could not be represented/assigned) is set to queryStr.
    
    Parameters:
    s - the query string
  - setQuerystr
```
@Deprecated
public void setQuerystr(String s,
                          int options)
```
    Deprecated. As of release 5.7, replaced by SmartsAtomQuerifier.setQuerystr(MolAtom atom, String s, int options) and setQueryString(String).
    
    Assigns the query properties string to this atom while setting all necessary atom and query properties. This is done through SmartsAtomQuerifier which parses the query string. For this reason this operation may be relatively costly. The remaining part of the query string (which could not be represented/assigned) is set to queryStr.
    In daylight smarts H is only considered as H atom when the atom expression has the syntax [<mass>H<charge><map>] (mass, charge and map are optional). If options is SMARTS_H_MARVIN_COMP_MODE and "H" is not in the form [<mass>H<charge><map>] then it may be interpreted as Hydrogen atom, not total H count! It is neccesary for backward compatibility.
    
    Parameters:
    s - the query string
    options - Possible values: SMARTS_H_MARVIN_COMP_MODE or SMARTS_H_DAYLIGHT_COMP_MODE. Instead of using this option, we recommend using unambiguous smarts queries: #1 for H atom and H1 for H count 1.
    Since:
    
    Marvin 3.5
    
    See Also:
    SMARTS_H_DAYLIGHT_COMP_MODE, SMARTS_H_MARVIN_COMP_MODE
  - setQueryString
```
public void setQueryString(String queryString)
```
    Assigns the query string to this atom.
    
    Parameters:
    queryString - the query properties string to be assigned.
    See Also:
    getQueryString()
  - getQueryString
```
public String getQueryString()
```
    Returns s the query string assigned to this atom.
    
    Returns:
    the query string
    See Also:
    setQueryString(String)
  - setAliasstr
```
public void setAliasstr(String s)
```
    Sets the alias string or pseudo atom type string for pseudo atoms.
    
    Parameters:
    s - the alias
    See Also:
    isPseudo()
  - getAliasstr
```
public String getAliasstr()
```
    Gets the alias string or pseudo atom type string for pseudo atoms.
    
    Returns:
    the alias
    See Also:
    isPseudo()
  - setExtraLabel
```
public void setExtraLabel(String s)
```
    Sets the extra atom label (also called atom value): "label" or "label1|label2". In general, any user label can be set by this method.
    
    Parameters:
    s - the atom label
  - setExtraLabelColor
```
public void setExtraLabelColor(long rgbs)
```
    Sets the extra label color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).
    
    Parameters:
    rgbs - the color(s)
    See Also:
    setExtraLabel(String), setExtraLabelColor(int, int)
  - setExtraLabelColor
```
public void setExtraLabelColor(int rgb1,
                      int rgb2)
```
    Sets the extra label colors: lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).
    
    Parameters:
    rgb1 - the lower 32 bits
    rgb2 - the upper 32 bits
    Since:
    
    Marvin 5.1.2
    
    See Also:
    setExtraLabel(String), setExtraLabelColor(long)
  - getExtraLabel
```
public String getExtraLabel()
```
    Gets the label string (also called atom value): "result" or "result1|result2".
    
    Returns:
    the label
  - getExtraLabelColor
```
public long getExtraLabelColor()
```
    Gets the extra label color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).
    
    Returns:
    the label color(s)
  - getExtraLabelColor
```
public int getExtraLabelColor(int i)
```
    Gets the extra label color: (alpha<<24 + red<<16 + green<<8 + blue).
    
    Parameters:
    i - is the result index (0 or 1)
    
    Returns:
    the label color
  - getExtraLabelColor
```
public static int getExtraLabelColor(long rgbs,
                     int i)
```
    Gets extra label color from composed color value.
    
    Parameters:
    rgbs - the composed color value
    i - is the result index (0 for first color, 1 for second color)
    
    Returns:
    the label color
    Since:
    
    Marvin 5.1.2
    
    See Also:
    getExtraLabelColor()
  - clearExtraLabel
```
public void clearExtraLabel()
```
    Clears the extra label.
  - getList
```
public int[] getList()
```
    Gets the atom list.
    
    Returns:
    the list
  - setList
```
public void setList(int[] l,
           int n)
```
    Sets the list elements.
    
    Parameters:
    l - the list
    n - number of elements to set
  - setList
```
public void setList(int[] l)
```
    Sets the list elements.
    
    Parameters:
    l - the list
  - getReactionStereo
```
public int getReactionStereo()
```
    Gets the reaction stereo property describing how the stereo configuration of the atom changes during the reaction.
    
    Returns:
    the reaction stereo property
    See Also:
    RXNSTEREO_NONE, RXNSTEREO_INVERSION, RXNSTEREO_RETENTION
  - setReactionStereo
```
public void setReactionStereo(int r)
```
    Sets the reaction stereo property describing how the stereo configuration of the atom changes during the reaction.
    
    Parameters:
    r - the reaction stereo property
    Since:
    
    Marvin 3.0
    
    See Also:
    RXNSTEREO_NONE, RXNSTEREO_INVERSION, RXNSTEREO_RETENTION
  - clear
```
public void clear()
```
    Clear query properties, charge, and hcount.
  - clone
```
public MolAtom clone()
```
    Clones the atom.
    
    These are not cloned:
    - Bonds: their references do not change.
    - Parent molecule: will be set to null.
    - MDocument: Although the atomset information is cloned, when the cloned atom is taken to another MDocument, the format (color, font type) will be lost.
    Overrides:
    
    clone in class Object
    
    Returns:
    the clone
  - toString
```
public String toString()
```
    Overrides Object.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.
    
    Overrides:
    
    toString in class Object
    
    Returns:
    a string representation of the object
    Since:
    
    3.5.2, 12/16/2004
  - insideLabel
```
public boolean insideLabel(double x,
                  double y)
```
    Tests whether the specified point is inside the atom label.
    
    Parameters:
    x - the x coordinate
    y - the y coordinate
    
    Returns:
    true if inside, false if outside
  - numOf
```
@Deprecated
public static int numOf(String e)
```
    Deprecated. As of Marvin 5.9, replaced by a similar method PeriodicSystem.findAtomicNumber(String).
    The recommended method does not work for symbol that does not represent a chemical element (e.g. R-atom, any atom), as this method should not have worked on them either.
    
    Gets the atomic number of an element.
    
    Parameters:
    e - the element name
    
    Returns:
    the atomic number or zero if not found
  - getAtomicNumber
```
@Deprecated
public static int getAtomicNumber(String element)
```
    Deprecated. As of Marvin 5.9, replaced by a similar method PeriodicSystem.findAtomicNumber(String).
    The recommended method does not work for symbol not representing a chemical element (e.g. R-atom, any atom), as this method should not have worked on them either.
    
    Gets the atomic number of an element.
    
    Parameters:
    element - the element name
    
    Returns:
    the atomic number
    
    Throws:
    
    IllegalArgumentException - if element does not correspond to a chemical element.
  - symbolOf
```
public static String symbolOf(int z)
```
    Gets the element symbol for the specified atomic number. The symbol is the same as the MDL codename for special atom types: "L" for LIST and NOTLIST.
    
    Parameters:
    z - the atomic number
    
    Returns:
    the symbol
  - symbolOf
```
public static String symbolOf(int z,
              int a)
```
    Gets the special element symbol for the specified atomic and mass numbers. For Hydrogen, it can return "D" or "T" for the isotopes. Otherwise, the symbol is the same as the MDL codename for special atom types: "L" for LIST and NOTLIST.
    
    Parameters:
    z - the atomic number
    a - the mass number
    
    Returns:
    the symbol
    Since:
    
    Marvin 5.0, 10/12/2007
  - nameOf
```
public static String nameOf(int z)
```
    Gets the name of the specified element.
    
    Parameters:
    z - the atomic number
    
    Returns:
    the name
  - electronegOf
```
public static int electronegOf(int z)
```
    Gets 10 times the electronegativity value for the specified element.
    
    Parameters:
    z - the atomic number
    
    Returns:
    the electronegativity
  - numoxstatesOf
```
public static int numoxstatesOf(int z)
```
    Gets the number of oxidation states for the specified element.
    
    Parameters:
    z - the atomic number
    
    Returns:
    the number of states
  - oxstateOf
```
public static int oxstateOf(int z,
            int k)
```
    Gets the oxidation states.
    
    Parameters:
    z - the atomic number
    k - the oxidation state index
    
    Returns:
    the oxidation state
  - maxAbsOxStateOf
```
public static int maxAbsOxStateOf(int z)
```
    Gets the oxidation state that has the maximum absolute value
    
    Parameters:
    z - the atomic number
    
    Returns:
    absolute value of the oxidation state
    Since:
    
    Marvin 4.1
  - negOxOf
```
public static int negOxOf(int z)
```
    Gets the negative oxidation number.
    
    Parameters:
    z - the atomic number
    
    Returns:
    the negative oxidation number
    Since:
    
    Marvin 2.7
  - posOxOf
```
public static int posOxOf(int z)
```
    Gets the smallest positive oxidation number.
    
    Parameters:
    z - the atomic number
    
    Returns:
    the smallest positive oxidation number
    Since:
    
    Marvin 2.7
  - ionChargeOf
```
public static int ionChargeOf(int z)
```
    Gets the ion charge.
    
    Parameters:
    z - the atomic number
    
    Returns:
    the charge
    Since:
    
    Marvin 2.7
  - covalentRadiusOf
```
public static double covalentRadiusOf(int z,
                      int t)
```
    Gets the covalent radius in C-C bond length units.
    
    Parameters:
    z - the atomic number
    t - the bond type (1, 2, 3)
    
    Returns:
    the covalent radius
    Since:
    
    Marvin 2.7
  - naturalWeightOf
```
public static double naturalWeightOf(int z)
```
    Gets the natural weight of the element. WARNING: This method does not return the exact value.
    
    Parameters:
    z - the atomic number
    
    Returns:
    the weight
  - isotopeType
```
public static int isotopeType(int z,
              int a)
```
    Gets the type of an isotope.
    
    Parameters:
    z - atomic number
    a - mass number
    
    Returns:
    0 if nonexistent, 1 if non-naturally occurring, 2 if naturally occurring
  - twicesumbonds
```
public int twicesumbonds(boolean countH,
                boolean all2)
```
    Calculates the total number of bonding electrons, excluding implicit hydrogens. The number of electrons is 2 for single bond, 4 for double and 6 for triple. For other bond types, the following values are used: 3 for AROMATIC in most cases. 2 for AROMATIC for the following atoms:
    - N, P and C- with 3 aromatic bonds
    - N, P, C+ and C- with 2 aromatic bonds and an implicit H
    - O, S ,Se ,Te with 2 aromatic bonds
    2 for ANY and SINGLE_OR_AROMATIC, 3 for SINGLE_OR_DOUBLE, 4 for DOUBLE_OR_AROMATIC.
    Parameters:
    countH - bonds to explicit hydrogen atoms are counted if true, not counted if false
    all2 - use the value 2 for each bond (independently of type) if true
    
    Returns:
    the sum of bond values
  - qpropCheck
```
public void qpropCheck()
```
    Query property checking.
  - valenceCheck
```
public void valenceCheck()
```
    Valence checking. During this check implicit hydrogens are calculated and the valence error flag is set in case of error. If in parent molecule the valence check is disabled than the check is not performed. The same applies if valence check is disabled for aromatic Nitrogen-like atoms and this atom is this kind of atom.
    
    See Also:
    hasValenceError(), getImplicitHcount(), MoleculeGraph.setValenceCheckOptions(ValenceCheckOptions), MoleculeGraph.getValenceCheckOptions()
  - setCorners
```
public void setCorners(double xnw,
              double ynw,
              double xse,
              double yse)
```
    Used internally by MolPainter.
    
    Parameters:
    xnw - north-west corner x
    ynw - north-west corner y
    xse - south-east corner x
    yse - south-east corner y
  - moveCorners
```
public void moveCorners(double diffx,
               double diffy)
```
    Translates the coordinates of the atom label.
    
    Parameters:
    diffx - translates the x values of the corners by this value.
    diffy - translates the y values of the corners by this value.
  - getFlags
```
public int getFlags()
```
    Gets flags. Flags contain the parity (3 bits), chirality (R/S, 2 bits), atomStereo (2 bits), hybridization state (3 bits), radical (4 bit), valenceChecked (1 bit), valenceError (1 bit), explicitCharge (1 bit), selected (1 bit) and atom map (10 bits) fields.
    
    Returns:
    the flags
    See Also:
    StereoConstants.PARITY_MASK, StereoConstants.CHIRALITY_MASK, StereoConstants.ATOMSTEREO_MASK
  - setFlags
```
public void setFlags(int f)
```
    Sets the flags.
    
    Parameters:
    f - new flags
  - setFlags
```
public void setFlags(int f,
            int mask)
```
    Sets the flags.
    
    Parameters:
    f - new flags
    mask - bits to set in flags
  - isSelected
```
public boolean isSelected()
```
    Tests whether this atom is selected.
    
    Returns:
    true if selected, false otherwise
    Since:
    
    Marvin 2.9.12
  - setSelected
```
public void setSelected(boolean sel)
```
    Selects or unselects this atom.
    
    Parameters:
    sel - true to select, false to unselect
    Since:
    
    Marvin 2.9.12
  - hasValenceError
```
public boolean hasValenceError()
```
    Returns previously set valence error. Valence error can be detected by valenceCheck() method.
    
    Returns:
    true in case of error, false otherwise
    Since:
    
    Marvin 2.9.12
    
    See Also:
    valenceCheck()
  - setValenceError
```
public void setValenceError(boolean v)
```
    Sets or clears the valence error flag.
    
    Parameters:
    v - true to set, false to unset
    Since:
    
    Marvin 2.9.12
  - getStereoCare
```
public boolean getStereoCare()
```
    Reports double bond stereo care information on the connected bonds.
    
    Returns:
    True if there is -at least- one bond with stereo care box on, false else.
    See Also:
    MolBond.getFlags(), MolBond.setFlags(int)
  - getStereoGroupType
```
public int getStereoGroupType()
```
    Gets the stereochemical group type for the enhanced stereo representation. (Type is one of NONE, ABS, OR, AND.)
    
    Returns:
    the stereochemical group type for the enhanced stereo representation.
    Since:
    
    Marvin 3.1.4
    
    See Also:
    StereoConstants.STGRP_NONE, StereoConstants.STGRP_ABS, StereoConstants.STGRP_OR, StereoConstants.STGRP_AND, getStereoGroupType(), Enhanced Stereo section of the JChem Query Guide
  - setStereoGroupType
```
public void setStereoGroupType(int t)
```
    Sets the stereochemical group type for enhanced stereo representation.
    
    Parameters:
    t - the stereochemical group type
    Since:
    
    Marvin 3.1.4
    
    See Also:
    getStereoGroupType(), StereoConstants.STGRP_NONE, StereoConstants.STGRP_ABS, StereoConstants.STGRP_OR, StereoConstants.STGRP_AND, getStereoGroupType(), Enhanced Stereo section of the JChem Query Guide
  - getStereoGroupNumber
```
public int getStereoGroupNumber()
```
    Gets the stereochemical group number for AND and OR groups of the enhanced stereo representation.
    
    Returns:
    the stereochemical group number (positive integer)
    Since:
    
    Marvin 3.1.4
    
    See Also:
    getStereoGroupType(), StereoConstants.STGRP_OR, StereoConstants.STGRP_AND, Enhanced Stereo section of the JChem Query Guide
  - setStereoGroupNumber
```
public void setStereoGroupNumber(int n)
```
    Sets the stereochemical group number for AND and OR groups of the enhanced stereo representation.
    
    Parameters:
    n - the stereochemical group number (positive integer)
    Since:
    
    Marvin 3.1.4
    
    See Also:
    getStereoGroupNumber(), getStereoGroupType(), StereoConstants.STGRP_OR, StereoConstants.STGRP_AND, Enhanced Stereo section of the JChem Query Guide
  - isSpecIsotopeSymbolUsed
```
public boolean isSpecIsotopeSymbolUsed()
```
    Tests whether special symbol is used. The special symbols are D and T for Hydrogen isotopes.
    
    Returns:
    true if special symbol is used, false otherwise
    Since:
    
    Marvin 4.1, 11/05/2005
  - isSpecIsotopeSymbolPreferred
```
public boolean isSpecIsotopeSymbolPreferred()
```
    Tests whether special symbol is used. The special symbols are D and T for Hydrogen isotopes.
    
    Returns:
    true if special symbol is used, false otherwise
    Since:
    
    Marvin 4.1, 11/05/2005
  - setSpecIsotopeSymbolPreferred
```
public void setSpecIsotopeSymbolPreferred(boolean v)
```
    Sets special isotope symbol usage preference. The special symbols are D and T for Hydrogen isotopes.
    
    Parameters:
    v - true if special symbol is used, false otherwise
    Since:
    
    Marvin 4.1, 11/05/2005
  - add
```
protected boolean add(MolBond b)
```
    Add a bond if it had not been already added. Also runs valence checking if charge and implicit hydogens were previously set this way.
    
    Parameters:
    b - the bond to add
    
    Returns:
    true if valence check needed
  - pack
```
public void pack()
```
    Reduce memory usage.
  - removeAllBonds
```
protected void removeAllBonds()
```
    Removes all bonds.
  - removeAllBonds
```
protected void removeAllBonds(boolean clearFromAttachmentPoints)
```
    Removes all bonds.
  - removeBond
```
protected void removeBond(MolBond bond)
```
    Removes a bond by reference.
    
    Parameters:
    bond - bond reference to remove
  - removeBond
```
protected void removeBond(MolBond bond,
              boolean clearFromAttachmentPoints)
```
    Removes a bond by reference.
    
    Parameters:
    bond - bond reference to remove
  - removeBond
```
protected void removeBond(int i)
```
    Removes a bond. Also runs valence checking if charge and implicit hydogens were previously set this way.
    
    Parameters:
    i - bond index
  - removeBond
```
protected void removeBond(int i,
              boolean clearFromAttachmentPoints)
```
    Removes a bond. Also runs valence checking if charge and implicit hydogens were previously set this way.
    
    Parameters:
    i - bond index
  - paritySign
```
public static int paritySign(int a,
             int b,
             int c,
             int d)
```
    Calculates the sign of the parity for the specified indexes.
    
    Parameters:
    a - first atom index
    b - second atom index
    c - third atom index
    d - fourth atom index
    
    Returns:
    +1, -1, or 0 (if two or more indexes equal)
  - isSameParityClass
```
public static boolean isSameParityClass(int i1,
                        int i2,
                        int i3,
                        int i4,
                        int j1,
                        int j2,
                        int j3,
                        int j4)
```
    Calculates if chirality centers in the structure and the query belong to the same parity class. i1, ..., i4 are indexes of neighbors in the structure. j1, ..., j4 are indexes of corresponding neighbors in the query. In the case of explicit H the index has to be set to Integer.MAX_VALUE. In the case of implicit H i4 (or j4) has to be set to Integer.MAX_VALUE.
    
    See Also:
    paritySign(int, int, int, int)
  - isTerminalAtom
```
public boolean isTerminalAtom()
```
    Determines whether it is a terminal atom or not.
    
    Returns:
    True if terminal atom, else false.
    Since:
    
    Marvin 3.4
  - haveEqualProperties
```
public boolean haveEqualProperties(MolAtom a)
```
    Tests if two atoms have the same properties. Atom coordinates, the "selected" property and the number of implicit hydrogens are not taken into account.
    
    Returns:
    true if they have the same properties, false otherwise
    Since:
    
    Marvin 3.4.1, 07/06/2004
  - countAllAtoms
```
protected int countAllAtoms()
```
    Counts all atoms represented by this atom.
    
    Returns:
    1
    Since:
    
    Marvin 3.0
  - getLonePairCount
```
public int getLonePairCount()
```
    Returns the automatically calculated lone pair count of this atom.
    
    Returns:
    the number of the calculated lone pairs if the atom is part of a MoleculeGaph -1 otherwise
    Since:
    
    Marvin 5.1.5
  - getElectronProp
```
public int getElectronProp()
```
    Returns the number of lone pairs on this atom.
    Returns:
    the number of lone pairs
    
    a value between 0 and 4: this has the meaning that the atom has this number of lone pairs. For example: after calling setElectronProperty(3), 3 lone pairs will belong to the atom.
    The number of lone pairs is not set when the returned value is less then 0.
  - setElectronProp
```
public void setElectronProp(int eProp)
```
    Sets the number of lone pairs.
    
    Parameters:
    eProp - the number of lone pairs
  - storeTemporaryObject
```
public void storeTemporaryObject(String key,
                        Object val)
```
    Stores an object temporarily. The stored object is not cloned and not serialized. This method may be used to store lone pair coordinates when drawing them. Then the electron flow arrow can start from a stored point.
    
    Parameters:
    key - key to the object
    val - the object
    Since:
    
    Marvin 5.3, 09/13/2009
  - getTemporaryObject
```
public Object getTemporaryObject(String key)
```
    Gets a temporary object.
    
    Parameters:
    key - key to the object
    
    Returns:
    the object
    Since:
    
    Marvin 5.3, 09/13/2009
  - setLinkNodeDefaultOuters
```
public void setLinkNodeDefaultOuters()
```
    Sets link node outer atoms to default values, if they are not set yet. Does not check if it is a valid link node configuration.
    
    Since:
    
    Marvin 4.0 12/27/2004
    
    See Also:
    setLinkNodeOuterAtom(int, int), MoleculeGraph.setLinkNodeDefaultOuters(MolAtom)
  - isAmbiguousStereo
```
public boolean isAmbiguousStereo()
```
    Check if the atom has ambiguous stereo wedge configuration. If the molecule is 2D and the atom has one hashed or bold bond (starting from this atom, indicating one configuration) and one squiggly bond (starting also from this atom, indicating two configuration) than the atom has ambiguous stereo configuration. Or if the molecule is 2D and the atom parity cannot be determined from the given wedges. Or if the molecule is in 3D but the atom has wedge or hash neighbors.
    
    Returns:
    true if the atom stereo configuration is ambiguous, else false.
    Since:
    
    Marvin 4.1 01/06/2006
    
    See Also:
    MolBond.UP, MolBond.DOWN, MolBond.STEREO1_MASK
  - isAromaticSMILESSubset
```
public static final boolean isAromaticSMILESSubset(int atno)
```
    Is the atom can be aromatic according to the daylight specification: Only atoms on the following list can be considered aromatic: C, N, O, P, S, As, Se, and * (wildcard).
    
    Parameters:
    atno - atomic number
    
    Returns:
    true if the atom is the member of the aromatic subset.
    Since:
    
    Marvin 5.2 11/06/2008
  - propertySet
```
public Set<Map.Entry<String,Object>> propertySet()
```
    Returns a collection view of the properties (property key - property value mappings) of this atom. Each element in the returned collection is a Map.Entry. Changes to the properties are reflected in the collection, and vice-versa. The collection supports element removal, which removes the corresponding property from this, via the Iterator.remove, Collection.remove, removeAll, retainAll, and clear operations. It does not support the add or addAll operations.
    
    Returns:
    a collection view of the properties of this atom.
    Since:
    
    Marvin 5.4
  - propertyKeySet
```
public Set<String> propertyKeySet()
```
    Returns a set view of the property keys of this atom. Changes to the properties of this atom are reflected in the set, and vice-versa. The set supports element removal, which removes the corresponding property from this atom, via the Iterator.remove, Set.remove, removeAll, retainAll, and clear operations. It does not support the add or addAll operations.
    
    Returns:
    set view of the property keys of this atom.
    Since:
    
    Marvin 5.4
  - containsPropertyKey
```
public boolean containsPropertyKey(String key)
```
    Returns true if this atom has a mapping for the specified property key.
    
    Parameters:
    key - the property key which is to be searched for.
    
    Returns:
    true if this map contains a mapping for the specified property key.
    Since:
    
    Marvin 5.4
  - removeProperty
```
public Object removeProperty(String key)
```
    Removes the mapping for this property key from this atom if present.
    
    Parameters:
    key - property key whose mapping is to be removed from the atom.
    
    Returns:
    previous poperty value associated with specified property key, or null if there was no mapping for property key. A null return can also indicate that the property mapping previously associated null with the specified property key.
    Since:
    
    Marvin 5.4
  - propertyCount
```
public int propertyCount()
```
    Returns the number of property (property key - property value) mappings of this atom.
    
    Returns:
    the number of property mappings of this atom.
    Since:
    
    Marvin 5.4
  - getProperty
```
public Object getProperty(String key)
```
    Returns the property value to which the specified property key is mapped at this atom, or null if this atom has no mapping for this property key. A return value of null does not necessarily indicate that the atom has no mapping for the property key; it is also possible that the atom explicitly maps the property key to null. The containsKey method may be used to distinguish these two cases.
    
    Parameters:
    key - the property key whose associated property value is to be returned.
    
    Returns:
    the property value to which this atom maps the specified property key, or null if the atom has no mapping for this property key.
    Since:
    
    Marvin 5.4
  - putProperty
```
public void putProperty(String key,
               Object value)
```
    Associates the specified value with the specified key at this atom. If this atom previously had a mapping for this property key, the old property value is replaced.
    
    Parameters:
    key - property key with which the specified value is to be associated
    value - property value to be associated with the specified property key.
    Since:
    
    Marvin 5.4
  - clearProperties
```
public void clearProperties()
```
    Removes all properties from this atom.
    
    Since:
    
    Marvin 5.4
  - setRgroupAttachmentPointOrder
```
public void setRgroupAttachmentPointOrder(int order)
```
    Sets the attachment point order of an R-group attachment point.
    
    Parameters:
    order - the attachment point order to set
    Since:
    
    Marvin 5.4
    
    See Also:
    RGROUP_ATTACHMENT, getRgroupAttachmentPointOrder()
  - getRgroupAttachmentPointOrder
```
public int getRgroupAttachmentPointOrder()
```
    Gets the attachment point order of an R-group attachment point.
    
    Returns:
    the attachment point order
    Since:
    
    Marvin 5.4
    
    See Also:
    RGROUP_ATTACHMENT, setRgroupAttachmentPointOrder(int order)
  - addRgroupAttachmentPoint
```
public MolAtom addRgroupAttachmentPoint(int order,
                               int bondtype)
```
    Attaches a new R-group attachment point to this atom by a bond of a specified type. The new R-group attachment point and the new bond are added to the parent molecule of this atom. The atom must have a parent.
    
    Parameters:
    order - the order of the R-group attachment point, order should be greater than 0.
    bondtype - the type of the new bond to add
    
    Returns:
    the added R-group attachment point or null if the atom has no parent.
    Since:
    
    Marvin 5.4
    
    See Also:
    RGROUP_ATTACHMENT, setRgroupAttachmentPointOrder(int order)
  - insertBond
```
protected void insertBond(int i,
              MolBond bond)
```
    Inserts a bond at a specified index.
    
    Parameters:
    i - the index where to insert the bond
    bond - the bond reference to insert
    Since:
    
    Marvin 5.4, 08/21/2010
  - getLigandOrder
```
public int getLigandOrder(MolAtom ligand)
```
    Gets the order of a specified ligand.
    
    Parameters:
    ligand - the ligand
    
    Returns:
    the order of the ligand
    Since:
    
    Marvin 5.4, 08/21/2010
  - setLigandOrder
```
public boolean setLigandOrder(int order,
                     MolAtom ligand)
```
    Sets the order of a specified ligand.
    
    Parameters:
    order - the order to set, order should be greater than 0.
    ligand - the ligand to set the order on
    
    Returns:
    true if the order is successfully set, false otherwise when the ligand is not an existing ligand of this atom or the order is bigger than the number of ligands.
    Since:
    
    Marvin 5.4, 08/21/2010
  - getBicycloStereo
```
public chemaxon.struc.BicycloStereoDescriptor[] getBicycloStereo()
```
    Gets the previously stored bicyclo stereo information of this atom.
    
    Returns:
    the array of bicyclo stereo descriptors. Returns null if this atom has no stereo descriptor.
    Since:
    
    Marvin 5.5, 03/23/2011
  - setBicycloStereo
```
public void setBicycloStereo(chemaxon.struc.BicycloStereoDescriptor[] descriptors)
```
    Registers the bicyclo stereo information for this atom.
    
    Parameters:
    descriptors - the array of bicyclo stereo descriptors
    Since:
    
    Marvin 5.5, 03/23/2011
  - setImplicitHBasedOnValence
```
@Deprecated
public void setImplicitHBasedOnValence(chemaxon.core.calculations.valencecheck.Valence v)
```
    Deprecated. as of Marvin 6.0.1, exists only for internal usage
    Usage:
    Internal usage only.
    Parameters:
    v -
  - getBondArray
```
public MolBond[] getBondArray()
```
    Gets the bonds connected to this atom.
    
    Returns:
    the array of bonds.
    Since:
    
    Marvin 6.0.1., 04/29/2013
  - hashCode
```
public int hashCode()
```
    Returns the hash code of the atom. It is calculated to be the count of the MolAtom objects instantiated until the instantiation of this MolAtom. (Invariant for the whole life of the MolAtom.
    
    Overrides:
    
    hashCode in class Object
    
    Returns:
    the count of the instantiated MolAtoms until the instantiation of this MolAtom.
  - equals
```
public boolean equals(Object other)
```
    Two MolAtoms are equal if they are the same reference.
    
    Overrides:
    
    equals in class Object
    
    Returns:
    true if the references are the same, false otherwise

Class MolAtom

Field Summary

Fields inherited from interface chemaxon.struc.StereoConstants

Constructor Summary

Method Summary

Methods inherited from class java.lang.Object

Field Detail

LONELY_H

ISOTOPE_H

CHARGED_H

RADICAL_H

MAPPED_H

WEDGED_H

HCONNECTED_H

CTSPECIFIC_H

POLYMERENDGROUP_H

SGROUPEND_H

VALENCEERROR_H

SGROUP_H

BRIDGEHEAD_H

HBONDED_H

ALL_H

ELEMENT_COUNT

EMPTY

LIST

NOTLIST

LP

ANY

HETERO

STAR

RGROUP

SGROUP

PSEUDO

MULTICENTER

RGROUP_ATTACHMENT

ATOM_TYPE_MAX

ATOM_TYPE_COUNT

HS_UNKNOWN

HS_S

HS_SP

HS_SP2

HS_SP3

RGROUP_MAX

RAD_OFF

RAD_MASK

RAD_COUNT_MASK

RAD1

RAD2

RAD2_SINGLET

RAD2_TRIPLET

RAD3

RAD3_DOUBLET

RAD3_QUARTET

RAD4

AAMAP_MAX

AAMAP_OFF

AAMAP_MASK

SETSEQ_MAX

RESTYPE_MAX

RESSEQ_MAX

RXNSTEREO_NONE

RXNSTEREO_INVERSION

RXNSTEREO_RETENTION

UNSPECIFIED_AROMATICITY

AROMATIC

ALIPHATIC

AROMATIC_OR_ALIPHATIC

ATTACH_NONE

ATTACH1

ATTACH2

ATTACH_BOTH

ATTACH_UNKNOWN

SMARTS_H_DAYLIGHT_COMP_MODE

SMARTS_H_MARVIN_COMP_MODE

LDIR_RIGHT

LDIR_LEFT

LDIR_ABOVE

LDIR_BELOW

SYM_SQBRACKETS

SYM_IMPLH