org.jmol.modelset

Class Bond

java.lang.Object

org.jmol.util.Edge

org.jmol.modelset.Bond

Direct Known Subclasses:

HBond

public class Bond
extends Edge

Field Summary

Fields

Modifier and Type	Field and Description
Atom	atom1
Atom	atom2
short	colix
short	mad
static int	myVisibilityFlag
int	shapeVisibilityFlags

Fields inherited from class org.jmol.util.Edge

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_PYMOL_MULT, BOND_PYMOL_SINGLE, BOND_STEREO_FAR, BOND_STEREO_MASK, BOND_STEREO_NEAR, BOND_STRUT, BOND_SULFUR_MASK, FLAG_AROMATIC_DEFINED, FLAG_AROMATIC_DOUBLE, FLAG_AROMATIC_STRICT, FLAG_IGNORE_STEREOCHEMISTRY, FLAG_NO_AROMATIC, index, order

Constructor Summary

Constructors

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

Method Summary

Modifier and Type	Method and Description
(package private) void	deleteAtomReferences()
Atom	getAtom1()
Atom	getAtom2()
int	getAtomIndex1()
int	getAtomIndex2()
(package private) short	getColix1()
(package private) short	getColix2()
int	getCovalentOrder()
float	getEnergy()
java.lang.String	getIdentity()
(package private) java.lang.String	getOrderName()
(package private) java.lang.String	getOrderNumberAsString()
Atom	getOtherAtom(Atom thisAtom)
Node	getOtherAtomNode(Node thisAtom)
(package private) float	getRadius()
int	getShapeVisibilityFlags()
int	getValence()
boolean	is(int bondType)
(package private) boolean	isAromatic()
boolean	isCovalent()
boolean	isHydrogen()
static boolean	isOrderH(int order)
(package private) boolean	isPartial()
(package private) boolean	isPymolStyle()
(package private) boolean	isStereo()
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.Edge

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

public Atom atom1

atom2

public Atom atom2

mad

public short mad

colix

public short colix

shapeVisibilityFlags

public int shapeVisibilityFlags

myVisibilityFlag

public static final int myVisibilityFlag

Constructor Detail

Bond

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

Method Detail

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 Edge

isHydrogen

public boolean isHydrogen()

Specified by:

isHydrogen in class Edge

isOrderH

public static boolean isOrderH(int order)

isStereo

boolean isStereo()

isPartial

boolean isPartial()

isAromatic

boolean isAromatic()

isPymolStyle

boolean isPymolStyle()

setPaletteID

public void setPaletteID(byte pid)

Parameters:

pid -

getEnergy

public float getEnergy()

getValence

public int getValence()

deleteAtomReferences

void deleteAtomReferences()

setColix

public void setColix(short colix)

setTranslucent

public void setTranslucent(boolean isTranslucent,
                           float translucentLevel)

setOrder

public void setOrder(int order)

getAtom1

public Atom getAtom1()

getAtom2

public Atom getAtom2()

getAtomIndex1

public int getAtomIndex1()

Specified by:

getAtomIndex1 in class Edge

getAtomIndex2

public int getAtomIndex2()

Specified by:

getAtomIndex2 in class Edge

getRadius

float getRadius()

getCovalentOrder

public int getCovalentOrder()

Specified by:

getCovalentOrder in class Edge

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)

getOtherAtomNode

public Node getOtherAtomNode(Node thisAtom)

Specified by:

getOtherAtomNode in class Edge

toString

public java.lang.String toString()

Overrides:

toString in class java.lang.Object