org.jmol.modelset

Class Bond

java.lang.Object

org.jmol.modelset.Bond

All Implemented Interfaces:

JmolEdge

Direct Known Subclasses:

HBond

public class Bond
extends java.lang.Object
implements JmolEdge

Nested Class Summary

Nested Classes

Modifier and Type	Class and Description
static class	Bond.BondSet

Field Summary

Fields

Modifier and Type	Field and Description
(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

Constructors

Constructor and Description
Bond(Atom atom1, Atom atom2, int order, short mad, short colix)

Method Summary

Methods

Modifier and Type	Method and Description
(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