org.jmol.modelset
Class Bond

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

public class Bond
extends java.lang.Object
implements JmolEdge


Nested Class Summary
static class Bond.BondSet
           
 
Field Summary
(package private)  Atom atom1
           
(package private)  Atom atom2
           
(package private)  short colix
           
(package private)  int index
           
(package private)  short mad
           
(package private) static int myVisibilityFlag
           
(package private)  int order
           
(package private)  int shapeVisibilityFlags
           
 
Fields inherited from interface org.jmol.api.JmolEdge
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
 
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()
           
 int getIndex()
           
 short getMad()
           
 int getOrder()
           
(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(int shapeVisibilityFlag, boolean isVisible)
           
 void setShapeVisibilityFlags(int shapeVisibilityFlags)
           
 void setTranslucent(boolean isTranslucent, float translucentLevel)
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

atom1

Atom atom1

atom2

Atom atom2

order

int order

mad

short mad

colix

short colix

index

int index

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()

getIndex

public int getIndex()
Specified by:
getIndex in interface JmolEdge

getShapeVisibilityFlags

public int getShapeVisibilityFlags()

getIdentity

public java.lang.String getIdentity()

isCovalent

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

isHydrogen

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

isHydrogen

public static boolean isHydrogen(int order)

isStereo

boolean isStereo()

isPartial

boolean isPartial()

isAromatic

boolean isAromatic()

setPaletteID

public void setPaletteID(byte pid)

getEnergy

public float getEnergy()

getValence

int getValence()

deleteAtomReferences

void deleteAtomReferences()

setMad

public void setMad(short mad)

setShapeVisibility

final void setShapeVisibility(int shapeVisibilityFlag,
                              boolean isVisible)

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 interface JmolEdge

getAtomIndex2

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

getRadius

float getRadius()

getOrder

public int getOrder()
Specified by:
getOrder in interface JmolEdge

getCovalentOrder

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

getOrderName

java.lang.String getOrderName()

getOrderNumberAsString

java.lang.String getOrderNumberAsString()

getColix1

short getColix1()

getColix2

short getColix2()

getOtherAtom

public Atom getOtherAtom(Atom thisAtom)

setShapeVisibilityFlags

public void setShapeVisibilityFlags(int shapeVisibilityFlags)

setIndex

public void setIndex(int i)

is

public boolean is(int bondType)

getOtherAtom

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