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, isOrderH
public 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 SimpleEdge
isCovalent
in class Edge
public boolean isHydrogen()
isHydrogen
in class Edge
boolean 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 Edge
public int getAtomIndex2()
getAtomIndex2
in class Edge
public int getCovalentOrder()
getCovalentOrder
in interface SimpleEdge
getCovalentOrder
in class Edge
public 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 Edge
doCalculate
- public void setCIPChirality(int c)
setCIPChirality
in class Edge
c
- [0:unknown; 1: Z; 2: E; 3: none]public java.lang.String toString()
toString
in class java.lang.Object