public class Bond extends Edge
| Modifier and Type | Field and Description |
|---|---|
Atom |
atom1 |
Atom |
atom2 |
short |
colix |
short |
mad |
static int |
myVisibilityFlag |
int |
shapeVisibilityFlags |
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 and Description |
|---|
Bond(Atom atom1,
Atom atom2,
int order,
short mad,
short colix) |
| Modifier and Type | Method and Description |
|---|---|
(package private) void |
deleteAtomReferences() |
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() |
getArgbHbondType, getAtropismNode, getAtropismOrder, getAtropismOrder12, getBondOrderFromFloat, getBondOrderFromString, getBondOrderNameFromOrder, getBondOrderNumberFromOrder, getCmlBondOrder, getCovalentBondOrder, getPartialBondDotted, getPartialBondOrder, isAtropism, isOrderHpublic static final int myVisibilityFlag
public Atom atom1
public Atom atom2
public short mad
public short colix
public int shapeVisibilityFlags
public void setMad(short mad)
void setShapeVisibility(boolean isVisible)
public java.lang.String getIdentity()
public boolean isCovalent()
isCovalent in interface SimpleEdgeisCovalent in class Edgepublic boolean isHydrogen()
isHydrogen in class Edgeboolean isStereo()
boolean isPartial()
boolean isAromatic()
public float getEnergy()
public int getValence()
void deleteAtomReferences()
public void setTranslucent(boolean isTranslucent,
float translucentLevel)
public void setOrder(int order)
public int getAtomIndex1()
getAtomIndex1 in class Edgepublic int getAtomIndex2()
getAtomIndex2 in class Edgepublic int getCovalentOrder()
getCovalentOrder in interface SimpleEdgegetCovalentOrder in class Edgepublic boolean is(int bondType)
public SimpleNode getOtherNode(SimpleNode thisAtom)
public void setAtropisomerOptions(javajs.util.BS bsA,
javajs.util.BS bsB)
public java.lang.String getCIPChirality(boolean doCalculate)
getCIPChirality in class EdgedoCalculate - public void setCIPChirality(int c)
setCIPChirality in class Edgec - [0:unknown; 1: Z; 2: E; 3: none]public java.lang.String toString()
toString in class java.lang.Object