Package org.jmol.modelset
Class Bond
- java.lang.Object
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- org.jmol.util.Edge
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- org.jmol.modelset.Bond
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- All Implemented Interfaces:
SimpleEdge
- Direct Known Subclasses:
HBond
public class Bond extends Edge
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Field Summary
Fields Modifier and Type Field Description Atom
atom1
Atom
atom2
short
colix
short
mad
static int
myVisibilityFlag
int
shapeVisibilityFlags
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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
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Method Summary
All Methods Instance Methods Concrete Methods Modifier and Type Method 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()
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Methods inherited from class org.jmol.util.Edge
getArgbHbondType, getAtropismNode, getAtropismOrder, getAtropismOrder12, getBondOrderFromFloat, getBondOrderFromString, getBondOrderNameFromOrder, getBondOrderNumberFromOrder, getCmlBondOrder, getCovalentBondOrder, getPartialBondDotted, getPartialBondOrder, isAtropism, isOrderH
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Method Detail
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setMad
public void setMad(short mad)
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setShapeVisibility
void setShapeVisibility(boolean isVisible)
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getIdentity
public java.lang.String getIdentity()
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isCovalent
public boolean isCovalent()
- Specified by:
isCovalent
in interfaceSimpleEdge
- Specified by:
isCovalent
in classEdge
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isHydrogen
public boolean isHydrogen()
- Specified by:
isHydrogen
in classEdge
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isStereo
boolean isStereo()
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isPartial
boolean isPartial()
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isAromatic
boolean isAromatic()
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getEnergy
public float getEnergy()
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getValence
public int getValence()
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deleteAtomReferences
void deleteAtomReferences()
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setTranslucent
public void setTranslucent(boolean isTranslucent, float translucentLevel)
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setOrder
public void setOrder(int order)
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getAtomIndex1
public int getAtomIndex1()
- Specified by:
getAtomIndex1
in classEdge
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getAtomIndex2
public int getAtomIndex2()
- Specified by:
getAtomIndex2
in classEdge
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getCovalentOrder
public int getCovalentOrder()
- Specified by:
getCovalentOrder
in interfaceSimpleEdge
- Specified by:
getCovalentOrder
in classEdge
- Returns:
- the bond order 1-4 if it is covalent, or 0 if not.
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is
public boolean is(int bondType)
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getOtherNode
public SimpleNode getOtherNode(SimpleNode thisAtom)
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setAtropisomerOptions
public void setAtropisomerOptions(javajs.util.BS bsA, javajs.util.BS bsB)
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getCIPChirality
public java.lang.String getCIPChirality(boolean doCalculate)
Not implemented.- Overrides:
getCIPChirality
in classEdge
- Parameters:
doCalculate
-- Returns:
- "" or "Z" or "E"
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setCIPChirality
public void setCIPChirality(int c)
Not implemented.- Overrides:
setCIPChirality
in classEdge
- Parameters:
c
- [0:unknown; 1: Z; 2: E; 3: none]
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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