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starfish.chemistry
Class Atom

java.lang.Object
  extended by starfish.chemistry.Atom
All Implemented Interfaces:
java.io.Serializable
public class Atom
extends java.lang.Object
implements java.io.Serializable

See Also:
Serialized Form

Field Summary
 int aNum
           
 float bondLength
           
 java.util.Vector bonds
           
 int canonValue
           
 float charge
           
 SpatialSet defaultSpatialSet
           
 float dihedralAngle
           
static int DISPLAY
           
 Entity entity
           
 java.util.ArrayList<AtomEquivalency> equivAtoms
           
 float fcharge
           
 java.lang.String forceFieldCode
           
 int iAtom
           
 int irpIndex
           
 java.lang.String label
           
static int LABEL
           
 double mass
           
 java.lang.String name
           
 Atom next
           
 byte nonHydrogens
           
 byte nPiBonds
           
static double NULL_PPM
           
 Atom parent
           
 Atom previous
           
 float radius
           
 Atom rotGroup
           
 Atom rotUnit
           
static int SELECT
           
 java.lang.String stereoStr
           
static int SUPER
           
 java.lang.String type
           
 float valanceAngle
           
 float value
           
 
Constructor Summary
Atom(AtomParser atomParse)
           
Atom(AtomParser atomParse, java.lang.String setName)
           
Atom(java.lang.String name)
           
Atom(java.lang.String name, java.lang.String setName)
           
Atom(java.lang.String name, java.lang.String aType, java.lang.String setName)
           
 
Method Summary
 void add(java.lang.String name, java.lang.String elementName, int order)
           
static int addBond(Atom atom1, Atom atom2, int order)
           
static int addBond(Atom atom1, Atom atom2, int order, int stereo)
           
 void addBond(Bond bond)
           
static Point3 avgAtom(java.util.Vector selected)
           
static Point3 avgAtom(java.util.Vector selected, int structureNum)
           
static double calcAngle(Point3 pt1, Point3 pt2, Point3 pt3)
           
static int calcBond(Atom atom1, Atom atom2, int order)
           
static int calcBond(Atom atom1, Atom atom2, int order, int stereo)
           
static double calcDihedral(Point3 pt1, Point3 pt2, Point3 pt3, Point3 pt4)
           
static double calcDistance(Point3 pt1, Point3 pt2)
           
static double calcWeightedDistance(SpatialSetGroup spg1, SpatialSetGroup spg2, int iStruct, double expNum)
           
 void dumpCoords(tcl.lang.Interp interp)
           
 int getAtomicNumber()
           
 float getBFactor()
           
 float getBlue()
           
 int getBMRBAmbiguity()
           
 java.util.Vector getChildren()
           
 java.util.Vector getConnected()
           
 SpatialSet getDefaultSpatialSet()
           
static void getDistances(SpatialSetGroup spg1, SpatialSetGroup spg2, int iStruct, java.util.ArrayList<java.lang.Double> dArray)
           
static java.lang.String getElementName(int eNum)
           
 byte getElementNumber()
           
static byte getElementNumber(java.lang.String elemName)
           
 Entity getEntity()
           
 void getEquivalency(tcl.lang.Interp interp)
           
 java.lang.String getEquivIndices()
           
 float getFormalCharge()
           
 java.lang.String getFullName()
           
 float getGreen()
           
 java.lang.String getName()
           
 float getOccupancy()
           
 Atom getParent()
           
 Atom[] getPartners(int targetANum, int shells)
           
 Point3 getPoint()
           
 Point3 getPoint(int i)
           
 Point3 getPoint(java.lang.String setName, int i)
           
 boolean getPointValidity(java.lang.String setName, int i)
           
 PPMv getPPM(int i)
           
 PPMv getPPM(java.lang.String setName, int i)
           
 boolean getProperty(int propIndex)
           
 boolean getProperty(java.lang.String setName, int propIndex)
           
 java.lang.String getPseudoName(int level)
           
 float getRed()
           
 starfish.datasets.peaks.ResonanceSet getResonanceSet()
           
 int getSelected()
           
 int getSelected(java.lang.String setName)
           
 java.lang.String getShortName()
           
 SpatialSet getSpatialSet(java.lang.String spatialSetName)
           
 int getStereo()
           
 java.lang.String getType()
           
 boolean isMethyl()
           
 boolean isMethylene()
           
 java.lang.String ppmToString(tcl.lang.Interp interp, int iStruct, int iAtom)
           
 java.lang.String ppmToString(tcl.lang.Interp interp, SpatialSet spatialSet, int iStruct, int iAtom)
           
 java.lang.String ppmToString(tcl.lang.Interp interp, java.lang.String setName, int iStruct, int iAtom)
           
 java.lang.String ppmToXMLString(tcl.lang.Interp interp, int iStruct, int iAtom)
           
 java.lang.String ppmToXMLString(tcl.lang.Interp interp, SpatialSet spatialSet, int iPPM, int iAtom)
           
 java.lang.String ppmToXMLString(tcl.lang.Interp interp, java.lang.String setName, int iStruct, int iAtom)
           
 void remove()
           
 void removeBonds()
           
 void removeBondTo(Atom atom)
           
static void resetLastAtom()
           
 double rmsAtom()
           
 double rmsAtom(SpatialSet spatialSet)
           
 double rmsAtom(java.lang.String setName)
           
 void setAtomicNumber(int num)
           
 void setAtomicNumber(java.lang.String name)
           
 void setBFactor(float bfactor)
           
 void setBFactor(java.lang.String setName, float bfactor)
           
 void setBlue(float blue)
           
 void setColor(float red, float green, float blue)
           
 void setColorByType()
           
 void setDefaultSpatialSet(java.lang.String name)
           
 void setDisplayStatus(int value)
           
 void setFormalCharge(float charge)
           
 void setGreen(float green)
           
 void setLabelStatus(int value)
           
 void setName(java.lang.String name)
           
 void setOccupancy(float occupancy)
           
 void setOccupancy(java.lang.String setName, float occupancy)
           
 void setPointValidity(int i, boolean validity)
           
 void setPointValidity(java.lang.String setName, int i, boolean validity)
           
 void setPPMValidity(int i, boolean validity)
           
 void setPPMValidity(java.lang.String setName, int i, boolean validity)
           
 void setProperty(int propIndex)
           
 void setProperty(java.lang.String setName, int propIndex)
           
 void setRed(float red)
           
 void setResonanceSet(starfish.datasets.peaks.ResonanceSet resonanceSet)
           
 void setSelected(int value)
           
 void setStereo(int stereo)
           
 void setType(java.lang.String name)
           
 void unsetProperty(int propIndex)
           
 void unsetProperty(java.lang.String setName, int propIndex)
           
static double volume(org.apache.commons.math.geometry.Vector3D a, org.apache.commons.math.geometry.Vector3D b, org.apache.commons.math.geometry.Vector3D c, org.apache.commons.math.geometry.Vector3D d)
           
 java.lang.String xyzToFFDString(tcl.lang.Interp interp, SpatialSet spatialSet, int iStruct, int iAtom, java.lang.String resNum)
           
 java.lang.String xyzToString(tcl.lang.Interp interp, int iStruct, int iAtom)
           
 java.lang.String xyzToString(tcl.lang.Interp interp, SpatialSet spatialSet, int iStruct, int iAtom)
           
 java.lang.String xyzToString(tcl.lang.Interp interp, java.lang.String setName, int iStruct, int iAtom)
           
 java.lang.String xyzToXMLString(tcl.lang.Interp interp, int iStruct, int iAtom)
           
 java.lang.String xyzToXMLString(tcl.lang.Interp interp, SpatialSet spatialSet, int iStruct, int iAtom)
           
 java.lang.String xyzToXMLString(tcl.lang.Interp interp, java.lang.String setName, int iStruct, int iAtom)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

SELECT

public static final int SELECT
See Also:
Constant Field Values

DISPLAY

public static final int DISPLAY
See Also:
Constant Field Values

SUPER

public static final int SUPER
See Also:
Constant Field Values

LABEL

public static final int LABEL
See Also:
Constant Field Values

NULL_PPM

public static final double NULL_PPM
See Also:
Constant Field Values

iAtom

public int iAtom

parent

public Atom parent

name

public java.lang.String name

type

public java.lang.String type

label

public java.lang.String label

entity

public Entity entity

bonds

public java.util.Vector bonds

previous

public Atom previous

next

public Atom next

mass

public double mass

nPiBonds

public byte nPiBonds

nonHydrogens

public byte nonHydrogens

charge

public float charge

fcharge

public float fcharge

bondLength

public float bondLength

valanceAngle

public float valanceAngle

dihedralAngle

public float dihedralAngle

stereoStr

public java.lang.String stereoStr

radius

public float radius

aNum

public int aNum

forceFieldCode

public java.lang.String forceFieldCode

value

public float value

equivAtoms

public java.util.ArrayList<AtomEquivalency> equivAtoms

defaultSpatialSet

public SpatialSet defaultSpatialSet

irpIndex

public int irpIndex

rotUnit

public Atom rotUnit

rotGroup

public Atom rotGroup

canonValue

public int canonValue
Constructor Detail

Atom

public Atom(AtomParser atomParse)

Atom

public Atom(AtomParser atomParse,
            java.lang.String setName)

Atom

public Atom(java.lang.String name,
            java.lang.String setName)

Atom

public Atom(java.lang.String name)

Atom

public Atom(java.lang.String name,
            java.lang.String aType,
            java.lang.String setName)
Method Detail

add

public void add(java.lang.String name,
                java.lang.String elementName,
                int order)

remove

public void remove()

removeBonds

public void removeBonds()

removeBondTo

public void removeBondTo(Atom atom)

getConnected

public java.util.Vector getConnected()

setName

public void setName(java.lang.String name)

setType

public void setType(java.lang.String name)

getType

public java.lang.String getType()

getAtomicNumber

public int getAtomicNumber()

setAtomicNumber

public void setAtomicNumber(int num)

setAtomicNumber

public void setAtomicNumber(java.lang.String name)

setDefaultSpatialSet

public void setDefaultSpatialSet(java.lang.String name)

getDefaultSpatialSet

public SpatialSet getDefaultSpatialSet()

getName

public java.lang.String getName()

getShortName

public java.lang.String getShortName()

getEntity

public Entity getEntity()

getFullName

public java.lang.String getFullName()

addBond

public void addBond(Bond bond)

getSpatialSet

public SpatialSet getSpatialSet(java.lang.String spatialSetName)

setResonanceSet

public void setResonanceSet(starfish.datasets.peaks.ResonanceSet resonanceSet)

getResonanceSet

public starfish.datasets.peaks.ResonanceSet getResonanceSet()

setSelected

public void setSelected(int value)

getSelected

public int getSelected()

getSelected

public int getSelected(java.lang.String setName)

setDisplayStatus

public void setDisplayStatus(int value)

setLabelStatus

public void setLabelStatus(int value)

setColorByType

public void setColorByType()

setColor

public void setColor(float red,
                     float green,
                     float blue)

setRed

public void setRed(float red)

setGreen

public void setGreen(float green)

setBlue

public void setBlue(float blue)

getRed

public float getRed()

getGreen

public float getGreen()

getBlue

public float getBlue()

getPoint

public Point3 getPoint()

getPoint

public Point3 getPoint(int i)

getPoint

public Point3 getPoint(java.lang.String setName,
                       int i)

dumpCoords

public void dumpCoords(tcl.lang.Interp interp)
                throws tcl.lang.TclException
Throws:
tcl.lang.TclException

setPointValidity

public void setPointValidity(int i,
                             boolean validity)

setPointValidity

public void setPointValidity(java.lang.String setName,
                             int i,
                             boolean validity)

getPointValidity

public boolean getPointValidity(java.lang.String setName,
                                int i)

getPPM

public PPMv getPPM(int i)

getPPM

public PPMv getPPM(java.lang.String setName,
                   int i)

setPPMValidity

public void setPPMValidity(int i,
                           boolean validity)

setPPMValidity

public void setPPMValidity(java.lang.String setName,
                           int i,
                           boolean validity)

setBFactor

public void setBFactor(float bfactor)

getBFactor

public float getBFactor()

setBFactor

public void setBFactor(java.lang.String setName,
                       float bfactor)

getOccupancy

public float getOccupancy()

setOccupancy

public void setOccupancy(float occupancy)

setOccupancy

public void setOccupancy(java.lang.String setName,
                         float occupancy)

setProperty

public void setProperty(int propIndex)

setProperty

public void setProperty(java.lang.String setName,
                        int propIndex)

unsetProperty

public void unsetProperty(int propIndex)

unsetProperty

public void unsetProperty(java.lang.String setName,
                          int propIndex)

getProperty

public boolean getProperty(int propIndex)

getProperty

public boolean getProperty(java.lang.String setName,
                           int propIndex)

calcDistance

public static double calcDistance(Point3 pt1,
                                  Point3 pt2)

calcAngle

public static double calcAngle(Point3 pt1,
                               Point3 pt2,
                               Point3 pt3)

volume

public static double volume(org.apache.commons.math.geometry.Vector3D a,
                            org.apache.commons.math.geometry.Vector3D b,
                            org.apache.commons.math.geometry.Vector3D c,
                            org.apache.commons.math.geometry.Vector3D d)

calcDihedral

public static double calcDihedral(Point3 pt1,
                                  Point3 pt2,
                                  Point3 pt3,
                                  Point3 pt4)

calcWeightedDistance

public static double calcWeightedDistance(SpatialSetGroup spg1,
                                          SpatialSetGroup spg2,
                                          int iStruct,
                                          double expNum)

getDistances

public static void getDistances(SpatialSetGroup spg1,
                                SpatialSetGroup spg2,
                                int iStruct,
                                java.util.ArrayList<java.lang.Double> dArray)

avgAtom

public static Point3 avgAtom(java.util.Vector selected)

avgAtom

public static Point3 avgAtom(java.util.Vector selected,
                             int structureNum)

rmsAtom

public double rmsAtom()

rmsAtom

public double rmsAtom(java.lang.String setName)

rmsAtom

public double rmsAtom(SpatialSet spatialSet)

xyzToString

public java.lang.String xyzToString(tcl.lang.Interp interp,
                                    int iStruct,
                                    int iAtom)
                             throws tcl.lang.TclException
Throws:
tcl.lang.TclException

xyzToString

public java.lang.String xyzToString(tcl.lang.Interp interp,
                                    java.lang.String setName,
                                    int iStruct,
                                    int iAtom)
                             throws tcl.lang.TclException
Throws:
tcl.lang.TclException

xyzToString

public java.lang.String xyzToString(tcl.lang.Interp interp,
                                    SpatialSet spatialSet,
                                    int iStruct,
                                    int iAtom)
                             throws tcl.lang.TclException
Throws:
tcl.lang.TclException

xyzToFFDString

public java.lang.String xyzToFFDString(tcl.lang.Interp interp,
                                       SpatialSet spatialSet,
                                       int iStruct,
                                       int iAtom,
                                       java.lang.String resNum)
                                throws tcl.lang.TclException
Throws:
tcl.lang.TclException

ppmToString

public java.lang.String ppmToString(tcl.lang.Interp interp,
                                    int iStruct,
                                    int iAtom)
                             throws tcl.lang.TclException
Throws:
tcl.lang.TclException

ppmToString

public java.lang.String ppmToString(tcl.lang.Interp interp,
                                    java.lang.String setName,
                                    int iStruct,
                                    int iAtom)
                             throws tcl.lang.TclException
Throws:
tcl.lang.TclException

ppmToString

public java.lang.String ppmToString(tcl.lang.Interp interp,
                                    SpatialSet spatialSet,
                                    int iStruct,
                                    int iAtom)
                             throws tcl.lang.TclException
Throws:
tcl.lang.TclException

xyzToXMLString

public java.lang.String xyzToXMLString(tcl.lang.Interp interp,
                                       int iStruct,
                                       int iAtom)
                                throws tcl.lang.TclException
Throws:
tcl.lang.TclException

xyzToXMLString

public java.lang.String xyzToXMLString(tcl.lang.Interp interp,
                                       java.lang.String setName,
                                       int iStruct,
                                       int iAtom)
                                throws tcl.lang.TclException
Throws:
tcl.lang.TclException

xyzToXMLString

public java.lang.String xyzToXMLString(tcl.lang.Interp interp,
                                       SpatialSet spatialSet,
                                       int iStruct,
                                       int iAtom)
                                throws tcl.lang.TclException
Throws:
tcl.lang.TclException

ppmToXMLString

public java.lang.String ppmToXMLString(tcl.lang.Interp interp,
                                       int iStruct,
                                       int iAtom)
                                throws tcl.lang.TclException
Throws:
tcl.lang.TclException

ppmToXMLString

public java.lang.String ppmToXMLString(tcl.lang.Interp interp,
                                       java.lang.String setName,
                                       int iStruct,
                                       int iAtom)
                                throws tcl.lang.TclException
Throws:
tcl.lang.TclException

ppmToXMLString

public java.lang.String ppmToXMLString(tcl.lang.Interp interp,
                                       SpatialSet spatialSet,
                                       int iPPM,
                                       int iAtom)
                                throws tcl.lang.TclException
Throws:
tcl.lang.TclException

getParent

public Atom getParent()

getChildren

public java.util.Vector getChildren()

calcBond

public static int calcBond(Atom atom1,
                           Atom atom2,
                           int order)

calcBond

public static int calcBond(Atom atom1,
                           Atom atom2,
                           int order,
                           int stereo)

addBond

public static int addBond(Atom atom1,
                          Atom atom2,
                          int order)

addBond

public static int addBond(Atom atom1,
                          Atom atom2,
                          int order,
                          int stereo)

getElementName

public static java.lang.String getElementName(int eNum)

getElementNumber

public byte getElementNumber()

getElementNumber

public static byte getElementNumber(java.lang.String elemName)

resetLastAtom

public static void resetLastAtom()

getStereo

public int getStereo()

setStereo

public void setStereo(int stereo)

setFormalCharge

public void setFormalCharge(float charge)

getFormalCharge

public float getFormalCharge()

getEquivalency

public void getEquivalency(tcl.lang.Interp interp)
                    throws tcl.lang.TclException
Throws:
tcl.lang.TclException

isMethyl

public boolean isMethyl()

getPartners

public Atom[] getPartners(int targetANum,
                          int shells)

isMethylene

public boolean isMethylene()

getBMRBAmbiguity

public int getBMRBAmbiguity()

getEquivIndices

public java.lang.String getEquivIndices()

getPseudoName

public java.lang.String getPseudoName(int level)
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