Package net.sf.jniinchi
Class JniInchiAtom
- java.lang.Object
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- net.sf.jniinchi.JniInchiAtom
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public class JniInchiAtom extends java.lang.Object
Encapsulates properties of InChI Atom. See inchi_api.h.
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Field Summary
Fields Modifier and Type Field Description private int
charge
Charge on atom.private java.lang.String
elname
Chemical element symbol eg C, O, Fe, Hg.private int
implicitD
Number of implicit deuteriums (isotopic 2-H) on atom.private int
implicitH
Number of implicit hydrogens on atom.private int
implicitP
Number of implicit protiums (isotopic 1-H) on atom.private int
implicitT
Number of implicit tritiums (isotopic 3-H) on atom.private int
isotopic_mass
Mass of isotope.protected static int
ISOTOPIC_SHIFT_FLAG
Indicates relative rather than absolute isotopic mass.private INCHI_RADICAL
radical
Radical status of atom.private double
x
Atom x-coordinate.private double
y
Atom y-coordinate.private double
z
Atom z-coordinate.
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Constructor Summary
Constructors Constructor Description JniInchiAtom(double x, double y, double z, java.lang.String el)
Create new atom.JniInchiAtom(java.lang.String el)
Convenience method to create a new atom with zero coordinates.
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method Description void
debug()
Outputs information on atom, for debugging purposes.int
getCharge()
Returns charge on atom.java.lang.String
getDebugString()
Generates string representation of information on atom, for debugging purposes.java.lang.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.(package private) int
getInchiRadical()
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.(package private) void
setInchiRadical(int radical)
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.
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Field Detail
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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
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x
private double x
Atom x-coordinate.
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y
private double y
Atom y-coordinate.
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z
private double z
Atom z-coordinate.
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elname
private java.lang.String elname
Chemical element symbol eg C, O, Fe, Hg.
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implicitH
private int implicitH
Number of implicit hydrogens on atom. If set to -1, InChI will add implicit H automatically.
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implicitP
private int implicitP
Number of implicit protiums (isotopic 1-H) on atom.
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implicitD
private int implicitD
Number of implicit deuteriums (isotopic 2-H) on atom.
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implicitT
private int implicitT
Number of implicit tritiums (isotopic 3-H) on atom.
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isotopic_mass
private int isotopic_mass
Mass of isotope. If set to 0, no isotopic mass set; otherwise, isotopic mass, or ISOTOPIC_SHIFT_FLAG + (mass - average atomic mass).
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radical
private INCHI_RADICAL radical
Radical status of atom.
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charge
private int charge
Charge on atom.
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Constructor Detail
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JniInchiAtom
public JniInchiAtom(double x, double y, double z, java.lang.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-coordinatey
- y-coordinatez
- z-coordinateel
- Chemical element symbol- Throws:
java.lang.NullPointerException
- - if the element symbol is null.
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JniInchiAtom
public JniInchiAtom(java.lang.String el)
Convenience method to create a new atom with zero coordinates.- Parameters:
el
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Method Detail
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setCharge
public void setCharge(int charge)
Sets charge on atom.- Parameters:
charge
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setRadical
public void setRadical(INCHI_RADICAL radical)
Sets radical status of atom.- Parameters:
radical
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setIsotopicMass
public void setIsotopicMass(int mass)
Sets isotopic mass. If set to 0, non-isotopic.- Parameters:
mass
- Isotopic mass
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setIsotopicMassShift
public void setIsotopicMassShift(int shift)
Sets isotopic mass, relative to standard mass.- Parameters:
shift
- Isotopic mass minus average atomic mass
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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
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setImplicitProtium
public void setImplicitProtium(int n)
Sets number of implicit protium (1H) on atom.- Parameters:
n
- Number of implicit protium
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setImplicitDeuterium
public void setImplicitDeuterium(int n)
Sets number of implicit deuterium (2H) on atom.- Parameters:
n
- Number of implicit deuterium
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setImplicitTritium
public void setImplicitTritium(int n)
Sets number of implicit tritium (3H) on atom.- Parameters:
n
- Number of implicit tritium
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getElementType
public java.lang.String getElementType()
Returns chemical element symbol of atom.- Returns:
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getCharge
public int getCharge()
Returns charge on atom.- Returns:
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getRadical
public INCHI_RADICAL getRadical()
Returns radical state of atom.- Returns:
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getX
public double getX()
Returns atom's X-coordinate.- Returns:
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getY
public double getY()
Returns atom's Y-coordinate.- Returns:
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getZ
public double getZ()
Returns atom's Z-coordinate.- Returns:
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getImplicitH
public int getImplicitH()
Returns number of implicit hydrogens on atom.- Returns:
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getImplicitProtium
public int getImplicitProtium()
Returns number of implicit protiums (1H) on atom.- Returns:
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getImplicitDeuterium
public int getImplicitDeuterium()
Returns number of implicit deuteriums (2H) on atom.- Returns:
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getImplicitTritium
public int getImplicitTritium()
Returns number of implicit tritiums (3H) on atom.- Returns:
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getIsotopicMass
public int getIsotopicMass()
Returns isotopic mass of atom.- Returns:
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getInchiRadical
int getInchiRadical()
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setInchiRadical
void setInchiRadical(int radical)
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getDebugString
public java.lang.String getDebugString()
Generates string representation of information on atom, for debugging purposes.
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debug
public void debug()
Outputs information on atom, for debugging purposes.
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