org.jmol.modelset

Class HBond

java.lang.Object

org.jmol.util.JmolEdge

org.jmol.modelset.Bond

org.jmol.modelset.HBond

public class HBond
extends Bond

Nested Class Summary

Nested classes/interfaces inherited from class org.jmol.modelset.Bond

Bond.BondSet

Field Summary

Fields

Modifier and Type	Field and Description
(package private) float	energy
private byte	paletteID
private static double	QConst

Fields inherited from class org.jmol.modelset.Bond

atom1, atom2, colix, mad, myVisibilityFlag, 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

Constructors

Constructor and Description
HBond(Atom atom1, Atom atom2, int order, float energy)
HBond(Atom atom1, Atom atom2, int order, short mad, short colix, float energy)

Method Summary

Methods

Modifier and Type	Method and Description
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, getMad, getOrderName, getOrderNumberAsString, getOtherAtom, getOtherAtom, getRadius, getShapeVisibilityFlags, getValence, is, isAromatic, isCovalent, isHydrogen, isHydrogen, isPartial, isStereo, isTranslucent, setColix, setIndex, setMad, setOrder, setShapeVisibility, setShapeVisibilityFlags, setTranslucent, 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

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