java.lang.Object
- org.jmol.util.Edge
- - org.jmol.modelset.Bond

All Implemented Interfaces:

SimpleEdge

Direct Known Subclasses:

HBond
```
public class Bond
extends Edge
```

Field Summary

Fields
Modifier and Type Field Description

Atom atom1

Atom atom2

short colix

short mad

static int myVisibilityFlag

int shapeVisibilityFlags
- Fields inherited from class org.jmol.util.Edge
  BOND_AROMATIC, BOND_AROMATIC_DOUBLE, BOND_AROMATIC_MASK, BOND_AROMATIC_SINGLE, BOND_COVALENT_DOUBLE, BOND_COVALENT_MASK, BOND_COVALENT_QUADRUPLE, BOND_COVALENT_QUINTUPLE, BOND_COVALENT_sextuple, 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_NOMULT, BOND_RENDER_SINGLE, BOND_STEREO_FAR, BOND_STEREO_MASK, BOND_STEREO_NEAR, BOND_STRUT, BOND_SULFUR_MASK, index, order, TYPE_ATROPISOMER, TYPE_ATROPISOMER_REV

Constructor Summary

Constructors
Constructor Description

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

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`(package private) void`	`deleteAtomReferences()`
`SimpleNode`	`getAtom(int i)`	Get the respective atom, 0 or 1
`int`	`getAtomIndex1()`
`int`	`getAtomIndex2()`
`java.lang.String`	`getCIPChirality(boolean doCalculate)`	Not implemented.
`int`	`getCovalentOrder()`
`float`	`getEnergy()`
`java.lang.String`	`getIdentity()`
`Atom`	`getOtherAtom(Atom thisAtom)`
`SimpleNode`	`getOtherNode(SimpleNode thisAtom)`
`int`	`getValence()`
`boolean`	`is(int bondType)`
`(package private) boolean`	`isAromatic()`
`boolean`	`isCovalent()`
`boolean`	`isHydrogen()`
`(package private) boolean`	`isPartial()`
`(package private) boolean`	`isStereo()`
`void`	`setAtropisomerOptions(javajs.util.BS bsA, javajs.util.BS bsB)`
`void`	`setCIPChirality(int c)`	Not implemented.
`void`	`setMad(short mad)`
`void`	`setOrder(int order)`
`(package private) void`	`setShapeVisibility(boolean isVisible)`
`void`	`setTranslucent(boolean isTranslucent, float translucentLevel)`
`java.lang.String`	`toString()`

Methods inherited from class org.jmol.util.Edge
getArgbHbondType, getAtropismNode, getAtropismOrder, getAtropismOrder12, getBondOrderFromFloat, getBondOrderFromString, getBondOrderNameFromOrder, getBondOrderNumberFromOrder, getBondType, getCmlBondOrder, getCovalentBondOrder, getPartialBondDotted, getPartialBondOrder, isAtropism, isOrderH

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait

Field Detail

myVisibilityFlag

public static final int myVisibilityFlag

atom1
```
public Atom atom1
```

atom2
```
public Atom atom2
```

mad
```
public short mad
```

colix
```
public short colix
```

shapeVisibilityFlags
```
public int shapeVisibilityFlags
```

Constructor Detail

Bond

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

Parameters:: atom1 -; atom2 -; order -; mad -; colix -

Method Detail

setMad
```
public void setMad(short mad)
```

setShapeVisibility

void setShapeVisibility(boolean isVisible)

getIdentity
```
public java.lang.String getIdentity()
```

isCovalent
```
public boolean isCovalent()
```
Specified by:

isCovalent in interface SimpleEdge

Specified by:

isCovalent in class Edge

isHydrogen
```
public boolean isHydrogen()
```
Specified by:

isHydrogen in class Edge

isStereo
```
boolean isStereo()
```

isPartial
```
boolean isPartial()
```

isAromatic
```
boolean isAromatic()
```

getEnergy
```
public float getEnergy()
```

getValence
```
public int getValence()
```

deleteAtomReferences
```
void deleteAtomReferences()
```

setTranslucent

public void setTranslucent(boolean isTranslucent,
                           float translucentLevel)

setOrder
```
public void setOrder(int order)
```

getAtomIndex1
```
public int getAtomIndex1()
```
Specified by:

getAtomIndex1 in class Edge

getAtomIndex2
```
public int getAtomIndex2()
```
Specified by:

getAtomIndex2 in class Edge

getCovalentOrder
```
public int getCovalentOrder()
```
Specified by:

getCovalentOrder in interface SimpleEdge

Specified by:

getCovalentOrder in class Edge

Returns:

the bond order 1-4 if it is covalent, or 0 if not.

getOtherAtom

public Atom getOtherAtom(Atom thisAtom)

is
```
public boolean is(int bondType)
```

getOtherNode

public SimpleNode getOtherNode(SimpleNode thisAtom)

setAtropisomerOptions

public void setAtropisomerOptions(javajs.util.BS bsA,
                                  javajs.util.BS bsB)

getCIPChirality
```
public java.lang.String getCIPChirality(boolean doCalculate)
```
Not implemented.

Overrides:

getCIPChirality in class Edge

Parameters:

doCalculate -

Returns:

"" or "Z" or "E"

setCIPChirality
```
public void setCIPChirality(int c)
```
Not implemented.

Overrides:

setCIPChirality in class Edge

Parameters:

c - [0:unknown; 1: Z; 2: E; 3: none]

toString
```
public java.lang.String toString()
```
Overrides:

toString in class java.lang.Object

getAtom
```
public SimpleNode getAtom(int i)
```
Description copied from interface: SimpleEdge

Get the respective atom, 0 or 1

Returns:

SimpleNode

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

Class Bond

Field Summary

Fields inherited from class org.jmol.util.Edge

Constructor Summary

Method Summary

Methods inherited from class org.jmol.util.Edge

Methods inherited from class java.lang.Object

Field Detail

myVisibilityFlag

atom1

atom2

mad

colix

shapeVisibilityFlags

Constructor Detail

Bond

Method Detail

setMad

setShapeVisibility

getIdentity

isCovalent

isHydrogen

isStereo

isPartial

isAromatic

getEnergy

getValence

deleteAtomReferences

setTranslucent

setOrder

getAtomIndex1

getAtomIndex2

getCovalentOrder

getOtherAtom

is

getOtherNode

setAtropisomerOptions

getCIPChirality

setCIPChirality

toString

getAtom