MolAtom (Marvin API documentation (c) 1998-2004 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 valees.

Version:: 3.3, 11/29/2003
Author:: Peter Csizmadia, Ferenc Csizmadia, Gabor Bartha, Tamas Vertse
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 int the elements array
`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`	`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`	`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`	`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`	`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.
`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`	`VALENCE_CHECKED` Valence checked if this flag is set.
`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`	`clearCalcstr()`
`java.lang.Object`	`clone()` Clones the atom.
`protected void`	`copy(CNode node)` Make a copy of this 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.
`static int`	`electronegOf(int z)` Gets 10 times the electronegativity value for the specified element.
`java.lang.String`	`getAliasstr()` Gets the alias string.
`int`	`getAtno()` Gets the atomic number.
`java.lang.String`	`getAtomLabels(boolean showAtnums, int atomIndex, boolean showMap, int[] ranks)` Gets the string representation of the atom labels.
`int`	`getAtomMap()` Gets the atom-atom mapping number.
`java.lang.String`	`getAtomSymbol(int style, 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`	`getCalcrgb(int i)` Gets the calculation result color: (alpha<<24 + red<<16 + green<<8 + blue).
`long`	`getCalcrgbs()` Gets the calculation result color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).
`java.lang.String`	`getCalcstr()` Gets the calculation result string: "result" or "result1\|result2".
`int`	`getCharge()` Gets the charge.
`int`	`getExplicitHcount()` Gets number of hydrogen connections.
`int`	`getFlags()` Gets flags.
`int`	`getHybridizationState()` Gets the hybridization state.
`int`	`getImplicitHcount()` Gets the number of implicit hydrogens attached.
`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.
`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`	`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`	`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 index.
`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.
`int`	`getStereoGroupType()` Gets the stereochemical group type.
`java.lang.String`	`getSymbol()` Gets the element symbol.
`int`	`getValence()` Gets the valence.
`double`	`getX()` Gets the X coordinate.
`double`	`getY()` Gets the Y coordinate.
`double`	`getZ()` Gets the Z coordinate.
`boolean`	`hasAromaticBond()` True if the atom has aromatic bond.
`boolean`	`hasQProps()` Does it have query properties?
`boolean`	`hasQueryBonds()` True if the atom has query bonds ("ANY" bonds).
`boolean`	`hasSMARTSProps()` Is it a SMARTS query atom?
`boolean`	`hasSMARTSPropsExcluding(java.lang.String exclude)` Is it a SMARTS query atom?
`boolean`	`hasValenceError()` Determines if this atom has a valence error.
`boolean`	`insideLabel(double x, double y)` Determine if the specified point is inside the atom label.
`static int`	`ionChargeOf(int z)` Gets the ion charge.
`boolean`	`isArrowEnd()` Returns true if this is an arrow endpoint.
`boolean`	`isImplicitizableH(int f)` Determine if the hydrogen atom is implicitizable or not.
`boolean`	`isNobleGas()` Is it a noble gas?
`static int`	`isotopeType(int z, int a)` Gets the type of an isotope.
`boolean`	`isPseudo()` True if the atom is a pseudo atom.
`boolean`	`isQProp()` Determine wether is a query property or not
`boolean`	`isQuery()` Is it 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()` Determines if this atom is selected.
`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`	`setAliasstr(java.lang.String s)` Sets the alias string.
`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`	`setCalcrgbs(long rgbs)` Sets the calculation color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).
`void`	`setCalcstr(java.lang.String s)` Sets the calculation result string: "result" or "result1\|result2".
`void`	`setCharge(int q)` Sets the charge.
`void`	`setCorners(double xnw, double ynw, double xse, double yse)` Used internally by MolPainter.
`void`	`setFlags(int f)` Sets the flags.
`void`	`setFlags(int f, int mask)` Sets the flags.
`void`	`setHybridizationState(int h)` Sets the hybridization state.
`void`	`setImplicitHcount(int h)` Sets the number of implicit hydrogens.
`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)` Sets the atomic weight for deuterium or tricium.
`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)` Sets the query properties string.
`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 index.
`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`	`setStereoGroupNumber(int n)` Sets the stereochemical group number.
`void`	`setStereoGroupType(int t)` Sets the stereochemical group type.
`void`	`setValenceError(boolean v)` Sets or clears the valence error flag.
`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(int style, int aflags, CTransform3D preTransform, int[] lcenter)` Deprecated. as of Marvin 3.0, replaced by getAtomSymbol and getAtomLabels
`int`	`twicesumbonds(boolean countH, boolean all2)` Calculates the sum of bond orders.
`void`	`valenceCheck()` Valence checking.

Methods inherited from class chemaxon.struc.CNode

getEdge, getEdgeCount, getLigand, getLock, getParent, indexOf, isBoundTo, pack, removeAllEdges, removeEdge, setNode1, setNode2, sringsize, toString

Methods inherited from class java.lang.Object

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

Field Detail

LONELY_H

public static final int LONELY_H

Include lonely Hydrogen atom(s).

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

ISOTOPE_H

public static final int ISOTOPE_H

Include Hydrogen isotope(s).

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

CHARGED_H

public static final int CHARGED_H

Include charged Hydrogen atom(s).

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

RADICAL_H

public static final int RADICAL_H

Include radical Hydrogen atom(s).

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

MAPPED_H

public static final int MAPPED_H

Mapped Hydrogen atom(s).

Since:: 3.1
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

ATOM_TYPE_COUNT

public static final int ATOM_TYPE_COUNT

Number of atom types int the elements array

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. Not implemented.

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.

See Also:: setRgroup(int), Constant Field Values

RAD_OFF

public static final int RAD_OFF

Radical value offset in flags.

Since:: 3.0
See Also:: Constant Field Values

RAD_MASK

public static final int RAD_MASK

Radical value bits in flags.

Since:: 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:: 3.0
See Also:: Constant Field Values

RAD1

public static final int RAD1

Monovalent radical center.

Since:: 3.0
See Also:: Constant Field Values

RAD2

public static final int RAD2

Divalent radical center.

Since:: 3.0
See Also:: Constant Field Values

RAD2_SINGLET

public static final int RAD2_SINGLET

Divalent radical center with singlet electronic configuration.

Since:: 3.0
See Also:: Constant Field Values

RAD2_TRIPLET

public static final int RAD2_TRIPLET

Divalent radical center with triplet electronic configuration.

Since:: 3.0
See Also:: Constant Field Values

RAD3

public static final int RAD3

Trivalent radical center.

Since:: 3.0
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:: 3.0
See Also:: setSetSeq(int), Constant Field Values

RESTYPE_MAX

public static final int RESTYPE_MAX

Maximum residue type is currently 63.

Since:: 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:: 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:: 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:: 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:: 3.0
See Also:: Constant Field Values

AROMATIC

public static final int AROMATIC

Aromatic query atom.

Since:: 3.3
See Also:: getQueryAromaticity(), Constant Field Values

ALIPHATIC

public static final int ALIPHATIC

Aliphatic query atom.

Since:: 3.3
See Also:: getQueryAromaticity(), Constant Field Values

AROMATIC_OR_ALIPHATIC

public static final int AROMATIC_OR_ALIPHATIC

Aromatic or aliphatic query atom.

Since:: 3.3
See Also:: getQueryAromaticity(), Constant Field Values

ATTACH1

public static final int ATTACH1

Attachment point on first site.

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

ATTACH2

public static final int ATTACH2

Attachment point on second site.

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

ATTACH_BOTH

public static final int ATTACH_BOTH

Attachment point on first and second site.

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

xCoordinate

protected transient double xCoordinate

X coordinate.

yCoordinate

protected transient double yCoordinate

Y coordinate.

zCoordinate

protected transient double zCoordinate

Z coordinate.

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:: 3.0

getBond

public final MolBond getBond(int i)

Gets the i-th bond.

Parameters:: i - bond index
Returns:: the bond object
Since:: 3.0

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

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.

Returns:: the symbol

getAtno

public 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

setMassnoIfKnown

public void setMassnoIfKnown(java.lang.String sym)

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

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.

Returns:: the implicit hydrogen count or the number of query hydrogens

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

getCharge

public int getCharge()

Gets the charge.

Returns:: the charge

setCharge

public void setCharge(int q)

Sets the charge.

Parameters:: q - the charge

getRadical

public int getRadical()

Gets the radical value.

Returns:: the radical value
Since:: 3.0
See Also:: RAD1, RAD2, RAD2_SINGLET, RAD2_TRIPLET, RAD3

setRadical

public void setRadical(int r)

Sets the radical value.

Parameters:: r - the radical value
Since:: 3.0
See Also:: RAD1, RAD2, RAD2_SINGLET, RAD2_TRIPLET, RAD3

getRadicalCount

public int getRadicalCount()

Gets the number of free electrons.

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

getValence

public int getValence()

Gets the valence. The valence is the sum of bond orders plus the number of query hydrogen atoms. Non-query, implicit hydrogens are not counted.

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

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
"v": number of bonds including bonds to implied H's
"R": number of rings: 256 = R = ring atom
"r": smallest ring size
"a": deprecated, use getQueryAromaticity() instead

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.

Parameters:: name - the property name
Returns:: the value of the property or -1 if not set
See Also:: getQProp(java.lang.String)

setQProp

public void setQProp(java.lang.String name,
                     java.lang.Object v)

Sets a query property.

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.

Parameters:: name - the property name; v - the value

getQueryAromaticity

public int getQueryAromaticity()

Gets the aromatic/aliphatic query property.

Returns:: 0, AROMATIC, ALIPHATIC or AROMATIC_OR_ALIPHATIC
Since:: 3.3

setQueryAromaticity

public void setQueryAromaticity(int x)

Sets the aromatic/aliphatic query property.

Parameters:: x - 0, AROMATIC, ALIPHATIC or AROMATIC_OR_ALIPHATIC
Since:: 3.3

getRgroup

public int getRgroup()

Gets the R-group index.

Returns:: a number between 1 and 32

setRgroup

public void setRgroup(int r)

Sets the R-group index.

Parameters:: r - Rgroup number, between 1 and 32
See Also:: 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.

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

getHybridizationState

public int getHybridizationState()

Gets the hybridization state.

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

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:: 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:: 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:: 3.1.3

setResidueAtomId

public void setResidueAtomId(int id)

Sets the residue atom identifier.

Returns:: the residue atom identifier
Since:: 3.1.3

isArrowEnd

public final boolean isArrowEnd()

Returns true if this is an arrow endpoint.

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

toString

public java.lang.String toString(int style,
                                 int aflags,
                                 CTransform3D preTransform,
                                 int[] lcenter)

Deprecated. as of Marvin 3.0, replaced by getAtomSymbol and getAtomLabels

Make a string representation in the specified style.

Parameters:: style - normal (0), show hydrogen count (1), SMARTS string with total H count(2), show total hydrogen count (3), don't show mapping (4), or force SMARTS query string (5).; 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

getAtomSymbol

public java.lang.String getAtomSymbol(int style,
                                      int aflags,
                                      int[] lcenter,
                                      CTransform3D preTransform)

Gets the string representation of the atom symbol.

Parameters:: style - normal (0), show hydrogen count (1), SMARTS string with total H count(2), show total hydrogen count (3), don't show mapping (4), or force SMARTS query string (5).; 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:: 3.0

getAtomLabels

public java.lang.String getAtomLabels(boolean showAtnums,
                                      int atomIndex,
                                      boolean showMap,
                                      int[] ranks)

Gets the string representation of the atom labels.

Parameters:: showAtnums - display atom number; atomIndex - display atom index; showMap - display atom mapping; ranks - if not null display graph invariant esle not
Returns:: the string representation
Since:: 3.0

getQueryLabel

public java.lang.String getQueryLabel()

Gets the string representation of the query atom

Returns:: the string representation
Since:: 3.0

isQuery

public final boolean isQuery()

Is it a query atom?

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

isQProp

public boolean isQProp()

Determine wether is a query property or not

Returns:: true if query property false if not

isImplicitizableH

public boolean isImplicitizableH(int f)

Determine if 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:: 3.1
See Also:: LONELY_H, ISOTOPE_H, CHARGED_H, RADICAL_H, MAPPED_H, MoleculeGraph.implicitizeHydrogens(int)

isPseudo

public boolean isPseudo()

True if the atom is a pseudo atom. Currently pseudo atoms are ANY atoms having an alias enclosed in single quotes.

Returns:: true if the atom is a pseudo atom, false otherwise
Since:: 3.3

hasAromaticBond

public final boolean hasAromaticBond()

True if the atom has aromatic bond.

Returns:: true if it has query bonds, false otherwise

hasQueryBonds

public final boolean hasQueryBonds()

True if the atom has query bonds ("ANY" bonds).

Returns:: true if it has query bonds, false otherwise

hasSMARTSProps

public final boolean hasSMARTSProps()

Is it a SMARTS query atom?

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

hasSMARTSPropsExcluding

public final boolean hasSMARTSPropsExcluding(java.lang.String exclude)

Is it a SMARTS query atom?

Parameters:: exclude - list of SMARTS properties to exclude
Returns:: true if it has SMARTS properties, false otherwise
Since:: 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)

Sets the query properties string.

Parameters:: s - the query string

setAliasstr

public void setAliasstr(java.lang.String s)

Sets the alias string.

Parameters:: s - the alias

getAliasstr

public java.lang.String getAliasstr()

Gets the alias string.

Returns:: the alias

setCalcstr

public void setCalcstr(java.lang.String s)

Sets the calculation result string: "result" or "result1|result2".

setCalcrgbs

public void setCalcrgbs(long rgbs)

Sets the calculation color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).

Parameters:: rgbs - the calculation color(s)

getCalcstr

public java.lang.String getCalcstr()

Gets the calculation result string: "result" or "result1|result2".

Returns:: the calcstr

getCalcrgbs

public long getCalcrgbs()

Gets the calculation result color(s): lower 32 bits and upper 32 bits as (alpha<<24 + red<<16 + green<<8 + blue).

Returns:: the calcrgbs

getCalcrgb

public int getCalcrgb(int i)

Gets the calculation result color: (alpha<<24 + red<<16 + green<<8 + blue).

Parameters:: i - is the result index (0 or 1)
Returns:: the calcrgb

clearCalcstr

public void clearCalcstr()

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:: 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

insideLabel

public boolean insideLabel(double x,
                           double y)

Determine if 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 oxidateon state

negOxOf

public static int negOxOf(int z)

Gets the negative oxidation number.

Parameters:: z - the atomic number
Returns:: the negative oxidation number
Since:: 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:: 2.7

ionChargeOf

public static int ionChargeOf(int z)

Gets the ion charge.

Parameters:: z - the atomic number
Returns:: the charge
Since:: 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:: 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 sum of bond orders.

Parameters:: countH - also count bonds to explicit hydrogen atoms; all2 - calculate (two times) the number of bonds instead of the sum of bond orders
Returns:: two times the sum

qpropCheck

public void qpropCheck()

Query property checking.

valenceCheck

public void valenceCheck()

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

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()

Determines if this atom is selected.

Returns:: true if selected, false otherwise
Since:: 2.9.12

setSelected

public void setSelected(boolean sel)

Selects or unselects this atom.

Parameters:: sel - true to select, false to unselect
Since:: 2.9.12

hasValenceError

public boolean hasValenceError()

Determines if this atom has a valence error.

Returns:: true in case of error, false otherwise
Since:: 2.9.12

setValenceError

public void setValenceError(boolean v)

Sets or clears the valence error flag.

Parameters:: v - true to set, false to unset
Since:: 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.

Returns:: the stereochemical group type
Since:: 3.1.4
See Also:: StereoConstants.STGRP_NONE, StereoConstants.STGRP_ABS, StereoConstants.STGRP_OR, StereoConstants.STGRP_AND

setStereoGroupType

public void setStereoGroupType(int t)

Sets the stereochemical group type.

Parameters:: t - the stereochemical group type
Since:: 3.1.4
See Also:: getStereoGroupType()

getStereoGroupNumber

public int getStereoGroupNumber()

Gets the stereochemical group number.

Returns:: the stereochemical group number (positive integer)
Since:: 3.1.4
See Also:: getStereoGroupType(), StereoConstants.STGRP_OR, StereoConstants.STGRP_AND

setStereoGroupNumber

public void setStereoGroupNumber(int n)

Sets the stereochemical group number.

Parameters:: n - the stereochemical group number (positive integer)
Since:: 3.1.4
See Also:: getStereoGroupNumber()

copy

protected void copy(CNode node)

Make a copy of this atom.

Parameters:: node - the target atom

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)

countAllAtoms

protected int countAllAtoms()

Counts all atoms represented by this atom.

Returns:: 1
Since:: 3.0

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chemaxon.struc Class MolAtom

LONELY_H

ISOTOPE_H

CHARGED_H

RADICAL_H

MAPPED_H

ELEMENT_COUNT

ATOM_TYPE_COUNT

EMPTY

LIST

NOTLIST

LP

ANY

HETERO

RGROUP

SGROUP

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

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

xCoordinate

yCoordinate

zCoordinate

MolAtom

MolAtom

MolAtom

getBondCount

getBond

getX

setX

getY

setY

getZ

setZ

setXY

setXYZ

getLocation

getLocation

setLocation

getSymbol

getAtno

setAtno

getMassno

setMassno

setMassnoIfKnown

getMass

isNobleGas

getRelativeNegativity

getImplicitHcount

setImplicitHcount

getCharge

setCharge

getRadical

chemaxon.struc
Class MolAtom