org.jmol.modelset
Class HBond

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

public class HBond
extends Bond


Nested Class Summary
 
Nested classes/interfaces inherited from class org.jmol.modelset.Bond
Bond.BondSet
 
Field Summary
(package private)  float energy
           
private  byte paletteID
           
private static double QConst
           
 
Fields inherited from class org.jmol.modelset.Bond
atom1, atom2, colix, index, mad, myVisibilityFlag, order, 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
HBond(Atom atom1, Atom atom2, int order, float energy)
           
HBond(Atom atom1, Atom atom2, int order, short mad, short colix, float energy)
           
 
Method Summary
 float getEnergy()
           
static int getEnergy(double distAH, double distCH, double distCD, double distAD)
           
 byte getPaletteId()
           
 void setPaletteID(byte paletteID)
           
 
Methods inherited from class org.jmol.modelset.Bond
deleteAtomReferences, getAtom1, getAtom2, getAtomIndex1, getAtomIndex2, getColix, getColix1, getColix2, getCovalentOrder, getIdentity, getIndex, getMad, getOrder, getOrderName, getOrderNumberAsString, getOtherAtom, getOtherAtom, getRadius, getShapeVisibilityFlags, getValence, is, isAromatic, isCovalent, isHydrogen, isHydrogen, isPartial, isStereo, isTranslucent, setColix, setIndex, setMad, setOrder, setShapeVisibility, setShapeVisibilityFlags, setTranslucent
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

energy

float energy

paletteID

private byte paletteID

QConst

private static final double QConst
See Also:
Constant Field Values
Constructor Detail

HBond

public HBond(Atom atom1,
             Atom atom2,
             int order,
             short mad,
             short colix,
             float energy)

HBond

public HBond(Atom atom1,
             Atom atom2,
             int order,
             float energy)
Method Detail

getEnergy

public float getEnergy()
Overrides:
getEnergy in class Bond

getPaletteId

public byte getPaletteId()

setPaletteID

public void setPaletteID(byte paletteID)
Overrides:
setPaletteID in class Bond

getEnergy

public static final int getEnergy(double distAH,
                                  double distCH,
                                  double distCD,
                                  double distAD)
Parameters:
distAH -
distCH -
distCD -
distAD -
Returns:
cal/mol