net.sf.jniinchi
Class JniInchiAtom

java.lang.Object
  net.sf.jniinchi.JniInchiAtom

public class JniInchiAtom
extends Object

Encapsulates properties of InChI Atom. See inchi_api.h.

Author:

Sam Adams

Field Summary

protected static int

ISOTOPIC_SHIFT_FLAG Indicates relative rather than absolute isotopic mass.

Constructor Summary

JniInchiAtom(double x, double y, double z, String el)
Create new atom.

JniInchiAtom(String el)
Convenience method to create a new atom with zero coordinates.

Method Summary

void	debug() Outputs information on atom, for debugging purposes.
int	getCharge() Returns charge on atom.
String	getDebugString() Generates string representation of information on atom, for debugging purposes.
String	getElementType() Returns chemical element symbol of atom.
int	getImplicitDeuterium() Returns number of implicit deuteriums (2H) on atom.
int	getImplicitH() Returns number of implicit hydrogens on atom.
int	getImplicitProtium() Returns number of implicit protiums (1H) on atom.
int	getImplicitTritium() Returns number of implicit tritiums (3H) on atom.
int	getIsotopicMass() Returns isotopic mass of atom.
INCHI_RADICAL	getRadical() Returns radical state of atom.
double	getX() Returns atom's X-coordinate.
double	getY() Returns atom's Y-coordinate.
double	getZ() Returns atom's Z-coordinate.
void	setCharge(int charge) Sets charge on atom.
void	setImplicitDeuterium(int n) Sets number of implicit deuterium (2H) on atom.
void	setImplicitH(int n) Sets number of implicit hydrogens on atom.
void	setImplicitProtium(int n) Sets number of implicit protium (1H) on atom.
void	setImplicitTritium(int n) Sets number of implicit tritium (3H) on atom.
void	setIsotopicMass(int mass) Sets isotopic mass.
void	setIsotopicMassShift(int shift) Sets isotopic mass, relative to standard mass.
void	setRadical(INCHI_RADICAL radical) Sets radical status of atom.

Methods inherited from class java.lang.Object

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

Field Detail

ISOTOPIC_SHIFT_FLAG

protected static final int ISOTOPIC_SHIFT_FLAG

Indicates relative rather than absolute isotopic mass. Value from inchi_api.h.

See Also:

Constant Field Values

Constructor Detail

JniInchiAtom

public JniInchiAtom(double x,
                    double y,
                    double z,
                    String el)

Create new atom.

Coordinates and element symbol must be set (unknown coordinates/dimensions should be set to zero). All other parameters are initialised to default values:

Num Implicit H = 0
Num Implicit 1H = 0
Num Implicit 2H = 0
Num Implicit 3H = 0
Isotopic mass = 0 (non isotopic)
Radical status = NONE (radical status not defined)

Parameters:

x - x-coordinate

y - y-coordinate

z - z-coordinate

el - Chemical element symbol

Throws:

NullPointerException - - if the element symbol is null.

JniInchiAtom

public JniInchiAtom(String el)

Convenience method to create a new atom with zero coordinates.

Parameters:

el -

Method Detail

setCharge

public void setCharge(int charge)

Sets charge on atom.

Parameters:

charge -

setRadical

public void setRadical(INCHI_RADICAL radical)

Sets radical status of atom.

Parameters:

radical -

setIsotopicMass

public void setIsotopicMass(int mass)

Sets isotopic mass. If set to 0, non-isotopic.

Parameters:

mass - Isotopic mass

setIsotopicMassShift

public void setIsotopicMassShift(int shift)

Sets isotopic mass, relative to standard mass.

Parameters:

shift - Isotopic mass minus average atomic mass

setImplicitH

public void setImplicitH(int n)

Sets number of implicit hydrogens on atom. If set to -1, InChI will add implicit H automatically.

Parameters:

n - Number of implicit hydrogen

setImplicitProtium

public void setImplicitProtium(int n)

Sets number of implicit protium (1H) on atom.

Parameters:

n - Number of implicit protium

setImplicitDeuterium

public void setImplicitDeuterium(int n)

Sets number of implicit deuterium (2H) on atom.

Parameters:

n - Number of implicit deuterium

setImplicitTritium

public void setImplicitTritium(int n)

Sets number of implicit tritium (3H) on atom.

Parameters:

n - Number of implicit tritium

getElementType

public String getElementType()

Returns chemical element symbol of atom.

Returns:

getCharge

public int getCharge()

Returns charge on atom.

Returns:

getRadical

public INCHI_RADICAL getRadical()

Returns radical state of atom.

Returns:

getX

public double getX()

Returns atom's X-coordinate.

Returns:

getY

public double getY()

Returns atom's Y-coordinate.

Returns:

getZ

public double getZ()

Returns atom's Z-coordinate.

Returns:

getImplicitH

public int getImplicitH()

Returns number of implicit hydrogens on atom.

Returns:

getImplicitProtium

public int getImplicitProtium()

Returns number of implicit protiums (1H) on atom.

Returns:

getImplicitDeuterium

public int getImplicitDeuterium()

Returns number of implicit deuteriums (2H) on atom.

Returns:

getImplicitTritium

public int getImplicitTritium()

Returns number of implicit tritiums (3H) on atom.

Returns:

getIsotopicMass

public int getIsotopicMass()

Returns isotopic mass of atom.

Returns:

getDebugString

public String getDebugString()

Generates string representation of information on atom, for debugging purposes.

debug

public void debug()

Outputs information on atom, for debugging purposes.