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

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chemaxon.struc
Class MolAtom

java.lang.Object
  chemaxon.struc.CNode
      chemaxon.struc.MolAtom

All Implemented Interfaces:: java.lang.Cloneable, java.io.Serializable, StereoConstants

Direct Known Subclasses:: SgroupAtom

public class MolAtom
extends CNode
implements StereoConstants

Atom object and the properties of the elements. Atom objects are identified by their reference values.

Version:: 4.1.1, 09/01/2006
Author:: Peter Csizmadia, Ferenc Csizmadia, Gabor Bartha, Tamas Vertse, Szabolcs Csepregi, Erika Biro, Szilveszter Juhos
See Also:: Serialized Form

Field Summary
`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`	`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` Attachment point on first and second site.
`static int`	`ATTACH1` Attachment point on first site.
`static int`	`ATTACH2` Attachment point on second site.
`static int`	`CHARGED_H` Include charged Hydrogen atom(s).
`static int`	`ELEMENT_COUNT` Number of elements in the periodic system
`static int`	`EMPTY` Empty atom type.
`static int`	`FIX_CHARGE` The charge is fix if this flag is set.
`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 lonely pair.
`static int`	`MAPPED_H` Mapped Hydrogen atom(s).
`static int`	`NOTLIST` "Atomic number" of the exclusive atom list.
`static int`	`PSEUDO` "Atomic number" of a pseudoatom.
`static int`	`RAD_COUNT_MASK` Radical's free electron count bits in flags.
`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 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_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`	`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`	`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.
`static int`	`VALCHK_ATTACH` Deprecated. as of Marvin 3.5, attachment points are always checked
`static int`	`VALENCE_CHECKED` Valence checked if this flag is set.
`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 class chemaxon.struc.CNode

edges, nedges

Fields inherited from interface chemaxon.struc.StereoConstants

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

Constructor Summary
`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
`protected void`	`add(CEdge b)` Add an edge if it had not been already added.
`void`	`bondweights(double[] w, CTransform3D t)` Calculates the average of the bond unit vectors pointing out of this atom.
`void`	`clear()` Clear query properties, charge, and hcount.
`void`	`clearExtraLabel()` Clears the extra label.
`void`	`clearQProps()` Clears query props.
`java.lang.Object`	`clone()` Clones the atom.
`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(java.lang.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.
`java.lang.String`	`getAliasstr()` Gets the alias string or pseudo atom type string for pseudo atoms.
`int`	`getAtno()` Gets the atomic number.
`int`	`getAtomMap()` Gets the atom-atom mapping number.
`java.lang.String`	`getAtomSymbol(int opts, int aflags, int[] lcenter, CTransform3D preTransform)` Gets the string representation of the atom symbol.
`int`	`getAttach()` Gets attachment point information.
`MolBond`	`getBond(int i)` Gets the i-th bond.
`int`	`getBondCount()` Gets the number of bonds/ligands.
`int`	`getCharge()` Gets the charge.
`static int`	`getColumn(int z)` The column or group of an element in the periodic system.
`int`	`getExplicitHcount()` Gets number of hydrogen connections.
`java.lang.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).
`int`	`getExtraLabelSetSeq()`
`int`	`getFlags()` Gets flags.
`int`	`getHybridizationState()` Gets the hybridization state.
`int`	`getImplicitHcount()` Gets the number of implicit hydrogens attached.
`int`	`getLinkNodeOuterAtom(int idx)` Gets the index of one of the link node's outer neighbour atom.
`int[]`	`getList()` Gets the atom list.
`DPoint3`	`getLocation()` Gets the coordinates.
`void`	`getLocation(DPoint3 p)` Gets the coordinates.
`double`	`getMass()` Gets the atomic weight.
`int`	`getMassno()` Gets the mass number.
`int`	`getMaxRepetitions()` Gets the maximum number of repetitions for a link node.
`int`	`getMinRepetitions()` Gets the minimum number of repetitions for a link node.
`int`	`getNonQueryImplicitHcount()` Gets the number of implicit hydrogens attached.
`int`	`getPreferredLabelDir(CTransform3D pretr, int h)` Gets the preferred direction for an additional label.
`java.lang.Object`	`getQProp(java.lang.String name)` Gets a query property.
`int`	`getQPropAsInt(java.lang.String name)` Gets a query property as an integer.
`int[]`	`getQPropMinMax(java.lang.String name)` Gets the minimum and maximum possible values of a query property.
`java.lang.String[]`	`getQPropNames()` Gets the names of query properties with non-null values.
`java.util.Set`	`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.
`java.lang.String`	`getQueryLabel()` Gets the string representation of the query atom
`java.lang.String`	`getQuerystr()` Gets the query properties.
`int`	`getRadical()` Gets the radical value.
`int`	`getRadicalCount()` Gets the number of free electrons.
`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.
`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.
`java.lang.String`	`getSymbol()` Gets the element symbol.
`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.
`boolean`	`hasQProps()` Does it have query properties?
`boolean`	`hasQueryBonds()` Tests whether the atom has query bonds ("ANY" bonds).
`boolean`	`hasSMARTSProps()` Tests whether it is a SMARTS query atom.
`boolean`	`hasSMARTSPropsExcluding(java.lang.String exclude)` Tests whether it is a SMARTS query atom.
`boolean`	`hasValenceError()` Determines if this atom has a valence error.
`boolean`	`hasWedgedBond()` Tests whether the atom has a wedged bond.
`boolean`	`haveEqualProperties(CNode node)` Tests if two atoms have the same properties.
`int`	`incQProp(java.lang.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.
`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`	`isAmbigousStereo()` Check if the atom has ambiguous stereo wedge configuration.
`boolean`	`isArrowEnd()` Tests if this is an arrow endpoint.
`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()` Is it a mappable atom?
`boolean`	`isNobleGas()` Is it a noble gas?
`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
`static java.lang.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(java.lang.String e)` Gets the atomic number of an element.
`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.
`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.
`void`	`qpropCheck()` Query property checking.
`protected void`	`removeEdge(int i)` Removes a bond.
`static java.lang.String`	`residueSymbolOf(int id)` Gets the name of a residue.
`static int`	`residueTypeOf(java.lang.String name)` Gets the residue identifier for a residue name.
`void`	`set(MolAtom atom)` Set all atom properties except the coordinates.
`void`	`setAliasstr(java.lang.String s)` Sets the alias string or pseudo atom type string for pseudo atoms.
`void`	`setAtno(int z)` Sets the atomic number.
`void`	`setAtomMap(int map)` Sets the atom-atom mapping number.
`void`	`setAttach(int a)` Sets attachment point information.
`void`	`setAttach(int a, Sgroup sg)` Sets attachment point information for an S-group attachment atom.
`void`	`setCharge(int q)` Sets the charge.
`void`	`setCorners(double xnw, double ynw, double xse, double yse)` Used internally by MolPainter.
`void`	`setExtraLabel(java.lang.String s)` Sets the extra atom label (also called atom value): "label" or "label1\|label2".
`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(java.lang.String sym)` Sets the special atom symbol and the atomic weight for deuterium or tricium.
`void`	`setHybridizationState(int h)` Sets the hybridization state.
`void`	`setImplicitHcount(int h)` Sets the number of implicit hydrogens.
`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 neighbour atom.
`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`	`setMassnoIfKnown(java.lang.String sym)` Deprecated. as of Marvin 4.1, replaced by `setForSpecIsotopeSymbol(String)`
`void`	`setMaxRepetitions(int r)` Sets the maximum number of repetitions for a link node.
`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(java.lang.String name, int v)` Sets a query property as an integer.
`void`	`setQProp(java.lang.String name, java.lang.Object v)` Sets a query property.
`void`	`setQueryAromaticity(int x)` Sets the aromatic/aliphatic query property.
`void`	`setQuerystr(java.lang.String s)` Assigns the query properties string to this atom while setting all necessary atom and query properties.
`void`	`setQuerystr(java.lang.String s, int options)` Assigns the query properties string to this atom while setting all necessary atom and query properties.
`void`	`setRadical(int r)` 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`	`setSelected(boolean sel)` Selects or unselects this atom.
`void`	`setSetSeq(int id)` Sets the atom set sequence number.
`void`	`setSMARTS(java.lang.String s)` Sets SMARTS query string data.
`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.
`static java.lang.String`	`symbolOf(int z)` Gets the element symbol for the specified atomic number.
`java.lang.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.
`void`	`valenceCheck(int opts)` Valence checking.

Methods inherited from class chemaxon.struc.CNode

getEdge, getEdgeCount, getEdgeTo, getLigand, getLigandIndex, getLock, getParent, haveSimilarEdges, indexOf, isBoundTo, pack, removeAllEdges, removeEdge, setNode1, setNode2, sringsize

Methods inherited from class java.lang.Object

equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

VALCHK_ATTACH

public static final int VALCHK_ATTACH

Deprecated. as of Marvin 3.5, attachment points are always checked

Valence checking option: attachment points must be checked too.

Since:: Marvin 3.4
See Also:: valenceCheck(int), Constant Field Values

LONELY_H

public static final int LONELY_H

Include lonely Hydrogen atom(s).

Since:: Marvin 3.1
See Also:: MoleculeGraph.implicitizeHydrogens(int), Constant Field Values

ISOTOPE_H

public static final int ISOTOPE_H

Include Hydrogen isotope(s).

Since:: Marvin 3.1
See Also:: MoleculeGraph.implicitizeHydrogens(int), Constant Field Values

CHARGED_H

public static final int CHARGED_H

Include charged Hydrogen atom(s).

Since:: Marvin 3.1
See Also:: MoleculeGraph.implicitizeHydrogens(int), Constant Field Values

RADICAL_H

public static final int RADICAL_H

Include radical Hydrogen atom(s).

Since:: Marvin 3.1
See Also:: MoleculeGraph.implicitizeHydrogens(int), Constant Field Values

MAPPED_H

public static final int MAPPED_H

Mapped Hydrogen atom(s).

Since:: Marvin 3.1
See Also:: MoleculeGraph.implicitizeHydrogens(int), Constant Field Values

WEDGED_H

public static final int WEDGED_H

Hydrogen atom(s) with wedge bonds.

Since:: Marvin 4.0
See Also:: MoleculeGraph.implicitizeHydrogens(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:: MoleculeGraph.implicitizeHydrogens(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 lonely pair.

See Also:: Constant Field Values

ANY

public static final int ANY

"Atomic number" of the any atom A.

See Also:: Constant Field Values

HETERO

public static final int HETERO

"Atomic number" of the hetero any atom Q.

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

ATOM_TYPE_COUNT

public static final int ATOM_TYPE_COUNT

Number of atom types in the elements array

See Also:: Constant Field Values

ATOM_TYPE_MAX

public static final int ATOM_TYPE_MAX

Maximum atom number.

See Also:: Constant Field Values

VALENCE_CHECKED

public static final int VALENCE_CHECKED

Valence checked if this flag is set.

See Also:: getFlags(), Constant Field Values

FIX_CHARGE

public static final int FIX_CHARGE

The charge is fix if this flag is set.

See Also:: getFlags(), 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.

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.

See Also:: getHybridizationState(), Constant Field Values

HS_SP3

public static final int HS_SP3

SP3 hybridization state.

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.

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

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

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

ATTACH1

public static final int ATTACH1

Attachment point on first site.

Since:: Marvin 3.1
See Also:: getAttach(), Constant Field Values

ATTACH2

public static final int ATTACH2

Attachment point on second site.

Since:: Marvin 3.1
See Also:: getAttach(), Constant Field Values

ATTACH_BOTH

public static final int ATTACH_BOTH

Attachment point on first and second site.

Since:: Marvin 3.1
See Also:: getAttach(), 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

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.
Parameters:: zZ - the atomic number; x - the x coordinate; y - the y coordinate; z - the z coordinate

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.
Parameters:: z - the atomic number

Method Detail

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 java.lang.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.

Parameters:: z - the atomic number

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

public void setForSpecIsotopeSymbol(java.lang.String sym)

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

setMassnoIfKnown

public void setMassnoIfKnown(java.lang.String sym)

Deprecated. as of Marvin 4.1, replaced by setForSpecIsotopeSymbol(String)

Sets the atomic weight for deuterium or tricium.

Parameters:: sym - the atom symbol

getMass

public double getMass()

Gets the atomic weight.

Returns:: the atomic weight

isNobleGas

public boolean isNobleGas()

Is it a noble gas?

Returns:: true if noble gas, false otherwise

isMappable

public boolean isMappable()

Is it a mappable atom?

Returns:: true if it is a real mappable atom, false if it 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

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.

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:: java.lang.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.

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

public int getRadical()

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

setRadical

public void setRadical(int r)

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

getRadicalCount

public int getRadicalCount()

Gets the number of free electrons.

Returns:: the number of free electrons
Since:: Marvin 3.0

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 java.lang.Object getQProp(java.lang.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(java.lang.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(java.lang.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(java.lang.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(java.lang.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(java.lang.String name,
                     java.lang.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(java.lang.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 java.lang.String[] getQPropNames()

Gets the names of query properties with non-null values.

Since:: Marvin 4.1, 03/21/2006

getQPropNameSet

public java.util.Set 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:: 0, AROMATIC, ALIPHATIC or AROMATIC_OR_ALIPHATIC
Since:: Marvin 3.3

setQueryAromaticity

public void setQueryAromaticity(int x)

Sets the aromatic/aliphatic query property.

Parameters:: x - 0, 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

public int getAttach()

Gets attachment point information.

Returns:: 0 (not an attachment point), ATTACH1 (first), ATTACH2 (second) or ATTACH_BOTH (both)

setAttach

public void setAttach(int a)

Sets attachment point information.

Parameters:: a - 0 (not an attachment point), ATTACH1 (first), ATTACH2 (second) or ATTACH_BOTH (both)

setAttach

public void setAttach(int a,
                      Sgroup sg)

Sets attachment point information for an S-group attachment atom.

Parameters:: a - 0 (not an attachment point), ATTACH1 (first), ATTACH2 (second) or ATTACH_BOTH (both); sg - the parent S-group or null
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(java.lang.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 java.lang.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 node.

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 node.

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 neighbour atom. (Outer: not repeating.)

Parameters:: idx - Which outer atom (0 or 1)
Returns:: The specified outer atom (as available through getLigand() or -1 if not set.
Since:: Marvin 4.0 12/22/2004
See Also:: CNode.getLigand(int)

setLinkNodeOuterAtom

public void setLinkNodeOuterAtom(int idx,
                                 int outer)

Sets one of the link node's outer neighbour atom. (Outer: not repeating.)

Parameters:: idx - Which outer atom (0 or 1); outer - The outer neighbour atom index (as used with getLigand() ) or -1 if clearing.
Since:: Marvin 4.0 12/22/2004
See Also:: CNode.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

isArrowEnd

public final boolean isArrowEnd()

Tests if this is an arrow endpoint.

Returns:: true if this is an arrow endpoint, false otherwise
Since:: Marvin 2.9, 08/06/2001
See Also:: MolBond.isArrow()

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 java.lang.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 java.lang.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).

Returns:: true if it is a query atom, false otherwise

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, non-isotope, neutral, non-radical, non-mapped 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 or mapped 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, MoleculeGraph.implicitizeHydrogens(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

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

public final boolean hasSMARTSProps()

Tests whether it is a SMARTS query atom.

Returns:: true if it has SMARTS properties, false otherwise

hasSMARTSPropsExcluding

public final boolean hasSMARTSPropsExcluding(java.lang.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

public void setSMARTS(java.lang.String s)
               throws java.lang.SecurityException

Sets SMARTS query string data.

Parameters:: s - the SMARTS string
Throws:: java.lang.SecurityException - the SmilesImport cannot be loaded, possibly because of a misconfigured firewall

getQuerystr

public java.lang.String getQuerystr()

Gets the query properties.

Returns:: the query string

setQuerystr

public void setQuerystr(java.lang.String s)

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

public void setQuerystr(java.lang.String s,
                        int options)

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

setAliasstr

public void setAliasstr(java.lang.String s)

Sets the alias string or pseudo atom type string for pseudo atoms.

Parameters:: s - the alias
See Also:: isPseudo()

getAliasstr

public java.lang.String getAliasstr()

Gets the alias string or pseudo atom type string for pseudo atoms.

Returns:: the alias
See Also:: isPseudo()

setExtraLabel

public void setExtraLabel(java.lang.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)

getExtraLabel

public java.lang.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

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 java.lang.Object clone()

Clones the atom. The bonds are not cloned: their references do not change.

Specified by:: clone in class CNode

Returns:: the clone

toString

public java.lang.String toString()

Overrides Object.toString() to ease debugging.

Overrides:: toString in class CNode

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

public static int numOf(java.lang.String e)

Gets the atomic number of an element.

Parameters:: e - the element name
Returns:: the atomic number or zero if not found

symbolOf

public static java.lang.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

nameOf

public static java.lang.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 unstable, 2 if naturally occuring

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, 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.

See Also:: hasValenceError(), getImplicitHcount()

valenceCheck

public void valenceCheck(int opts)

Valence checking. Determines if there is a valence error. Calculates implicit hydrogen atoms.

Parameters:: opts - valence checking options
Since:: Marvin 3.4
See Also:: VALCHK_ATTACH

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

getFlags

public int getFlags()

Gets flags. Flags contain the selected (1 bit), valenceError (1 bit), explicitCharge (1 bit), parity (3 bit), R/S (2 bit), hybridization state (3 bit), atom map (10 bit) 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()

Determines if this atom has a valence error. (Set by method valenceCheck().)

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 void add(CEdge b)

Add an edge if it had not been already added. Also runs valence checking if charge and implicit hydogens were previously set this way.

Overrides:: add in class CNode

Parameters:: b - the edge to add

removeEdge

protected void removeEdge(int i)

Removes a bond. Also runs valence checking if charge and implicit hydogens were previously set this way.

Overrides:: removeEdge in class CNode

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(CNode node)

Tests if two atoms have the same properties. Atom coordinates, the "selected" property and the number of implicit hydrogens are not taken into account.

Overrides:: haveEqualProperties in class CNode

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

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)

isAmbigousStereo

public boolean isAmbigousStereo()

Check if the atom has ambiguous stereo wedge configuration. If 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.

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

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chemaxon.struc Class MolAtom

VALCHK_ATTACH

LONELY_H

ISOTOPE_H

CHARGED_H

RADICAL_H

MAPPED_H

WEDGED_H

HCONNECTED_H

ELEMENT_COUNT

EMPTY

LIST

NOTLIST

LP

ANY

HETERO

RGROUP

SGROUP

PSEUDO

ATOM_TYPE_COUNT

ATOM_TYPE_MAX

VALENCE_CHECKED

FIX_CHARGE

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

AAMAP_MAX

AAMAP_OFF

AAMAP_MASK

SETSEQ_MAX

RESTYPE_MAX

RESSEQ_MAX

RXNSTEREO_NONE

RXNSTEREO_INVERSION

RXNSTEREO_RETENTION

AROMATIC

ALIPHATIC

AROMATIC_OR_ALIPHATIC

ATTACH1

ATTACH2

ATTACH_BOTH

SMARTS_H_DAYLIGHT_COMP_MODE

SMARTS_H_MARVIN_COMP_MODE

LDIR_RIGHT

LDIR_LEFT

LDIR_ABOVE

LDIR_BELOW

SYM_SQBRACKETS

SYM_IMPLH

SYM_EXPLH

SYM_NEUTRAL

SYM_SMARTS

SYM_MOLEX

xCoordinate

yCoordinate

zCoordinate

RADICAL_CHAR

MolAtom

MolAtom

MolAtom

getBondCount

getBond

getRealBondCount

set

getX

setX

getY

chemaxon.struc
Class MolAtom