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

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chemaxon.struc
Class MolAtom

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

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

Direct Known Subclasses:: SgroupAtom

public class MolAtom
extends CNode
implements StereoConstants
extends CNode
implements StereoConstants

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

Version:: 5.1.1, 08/28/2008
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`	`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` 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`	`CTSPECIFIC_H` Hydrogen atom connecting alone to one side of a double bond with specified CIS or TRANS stereo information.
`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`	`MULTICENTER` "Atomic number" of a central atom of a MulticenterSgroup.
`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`	`getElectronProp()` Returns the number of lone pairs or radical state set on this atom.
`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).
`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`	`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`	`isAmbiguousStereo()` Check if the atom has ambiguous stereo wedge configuration.
`boolean`	`isArrowEnd()` Tests if this is an arrow endpoint.
`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.
`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
`void`	`moveCorners(double diffx, double diffy)` Translates the coordinates of the atom label.
`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`	`setElectronProp(int eProp)` Sets the number of lone pairs or radical state.
`void`	`setExtraLabel(java.lang.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(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.
`static java.lang.String`	`symbolOf(int z, int a)` Gets the special element symbol for the specified atomic and mass numbers.
`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

CTSPECIFIC_H

public static final int CTSPECIFIC_H

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 neighbouring double bond.

Since:: Marvin 5.0
See Also:: MoleculeGraph.implicitizeHydrogens(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:: 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

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

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. 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.

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:

chemaxon.struc Class MolAtom