org.jmol.modelset
Class Bond

java.lang.Object
  extended by org.jmol.util.JmolEdge
      extended by org.jmol.modelset.Bond
Direct Known Subclasses:
HBond

public class Bond
extends JmolEdge


Nested Class Summary
static class Bond.BondSet
           
 
Field Summary
(package private)  Atom atom1
           
(package private)  Atom atom2
           
(package private)  short colix
           
(package private)  short mad
           
(package private) static int myVisibilityFlag
           
(package private)  int shapeVisibilityFlags
           
 
Fields inherited from class org.jmol.util.JmolEdge
argbsHbondType, BOND_AROMATIC, BOND_AROMATIC_DOUBLE, BOND_AROMATIC_MASK, BOND_AROMATIC_SINGLE, BOND_COVALENT_DOUBLE, BOND_COVALENT_MASK, BOND_COVALENT_QUADRUPLE, BOND_COVALENT_SINGLE, BOND_COVALENT_TRIPLE, BOND_H_CALC, BOND_H_CALC_MASK, BOND_H_MINUS_3, BOND_H_MINUS_4, BOND_H_NUCLEOTIDE, BOND_H_PLUS_2, BOND_H_PLUS_3, BOND_H_PLUS_4, BOND_H_PLUS_5, BOND_H_REGULAR, BOND_HBOND_SHIFT, BOND_HYDROGEN_MASK, BOND_NEW, BOND_ORDER_ANY, BOND_ORDER_NULL, BOND_ORDER_UNSPECIFIED, BOND_PARTIAL_MASK, BOND_PARTIAL01, BOND_PARTIAL12, BOND_PARTIAL23, BOND_PARTIAL32, BOND_STEREO_FAR, BOND_STEREO_MASK, BOND_STEREO_NEAR, BOND_STRUT, BOND_SULFUR_MASK, index, order
 
Constructor Summary
Bond(Atom atom1, Atom atom2, int order, short mad, short colix)
           
 
Method Summary
(package private)  void deleteAtomReferences()
           
 Atom getAtom1()
           
 Atom getAtom2()
           
 int getAtomIndex1()
           
 int getAtomIndex2()
           
 short getColix()
           
(package private)  short getColix1()
           
(package private)  short getColix2()
           
 int getCovalentOrder()
           
 float getEnergy()
           
 java.lang.String getIdentity()
           
 short getMad()
           
(package private)  java.lang.String getOrderName()
           
(package private)  java.lang.String getOrderNumberAsString()
           
 Atom getOtherAtom(Atom thisAtom)
           
 JmolNode getOtherAtom(JmolNode thisAtom)
           
(package private)  float getRadius()
           
 int getShapeVisibilityFlags()
           
(package private)  int getValence()
           
 boolean is(int bondType)
           
(package private)  boolean isAromatic()
           
 boolean isCovalent()
           
 boolean isHydrogen()
           
static boolean isHydrogen(int order)
           
(package private)  boolean isPartial()
           
(package private)  boolean isStereo()
           
(package private)  boolean isTranslucent()
           
 void setColix(short colix)
           
 void setIndex(int i)
           
 void setMad(short mad)
           
 void setOrder(int order)
           
 void setPaletteID(byte pid)
           
(package private)  void setShapeVisibility(boolean isVisible)
           
 void setShapeVisibilityFlags(int shapeVisibilityFlags)
           
 void setTranslucent(boolean isTranslucent, float translucentLevel)
           
 java.lang.String toString()
           
 
Methods inherited from class org.jmol.util.JmolEdge
getArgbHbondType, getBondOrderFromFloat, getBondOrderFromString, getBondOrderNameFromOrder, getBondOrderNumberFromOrder, getCmlBondOrder, getCovalentBondOrder, getPartialBondDotted, getPartialBondOrder
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

atom1

Atom atom1

atom2

Atom atom2

mad

short mad

colix

short colix

shapeVisibilityFlags

int shapeVisibilityFlags

myVisibilityFlag

static final int myVisibilityFlag
Constructor Detail

Bond

public Bond(Atom atom1,
            Atom atom2,
            int order,
            short mad,
            short colix)
Method Detail

getMad

public short getMad()

getColix

public short getColix()

setMad

public void setMad(short mad)

setShapeVisibilityFlags

public void setShapeVisibilityFlags(int shapeVisibilityFlags)

getShapeVisibilityFlags

public int getShapeVisibilityFlags()

setShapeVisibility

void setShapeVisibility(boolean isVisible)

getIdentity

public java.lang.String getIdentity()

isCovalent

public boolean isCovalent()
Specified by:
isCovalent in class JmolEdge

isHydrogen

public boolean isHydrogen()
Specified by:
isHydrogen in class JmolEdge

isHydrogen

public static boolean isHydrogen(int order)

isStereo

boolean isStereo()

isPartial

boolean isPartial()

isAromatic

boolean isAromatic()

setPaletteID

public void setPaletteID(byte pid)
Parameters:
pid -

getEnergy

public float getEnergy()

getValence

int getValence()

deleteAtomReferences

void deleteAtomReferences()

setColix

public void setColix(short colix)

setTranslucent

public void setTranslucent(boolean isTranslucent,
                           float translucentLevel)

isTranslucent

boolean isTranslucent()

setOrder

public void setOrder(int order)

getAtom1

public Atom getAtom1()

getAtom2

public Atom getAtom2()

getAtomIndex1

public int getAtomIndex1()
Specified by:
getAtomIndex1 in class JmolEdge

getAtomIndex2

public int getAtomIndex2()
Specified by:
getAtomIndex2 in class JmolEdge

getRadius

float getRadius()

getCovalentOrder

public int getCovalentOrder()
Specified by:
getCovalentOrder in class JmolEdge

getOrderName

java.lang.String getOrderName()

getOrderNumberAsString

java.lang.String getOrderNumberAsString()

getColix1

short getColix1()

getColix2

short getColix2()

getOtherAtom

public Atom getOtherAtom(Atom thisAtom)

setIndex

public void setIndex(int i)

is

public boolean is(int bondType)

getOtherAtom

public JmolNode getOtherAtom(JmolNode thisAtom)
Specified by:
getOtherAtom in class JmolEdge

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object