Package org.jmol.modelset
Class Bond
java.lang.Object
org.jmol.util.Edge
org.jmol.modelset.Bond
- All Implemented Interfaces:
SimpleEdge
- Direct Known Subclasses:
HBond
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Field Summary
FieldsModifier and TypeFieldDescriptionshort
short
static final int
int
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_MASK, BOND_RENDER_SINGLE, BOND_STEREO_EITHER, 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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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptiongetAtom
(int i) Get the respective atom, 0 or 1int
int
getCIPChirality
(boolean doCalculate) Not implemented.int
float
getOtherAtom
(Atom thisAtom) getOtherNode
(SimpleNode thisAtom) int
boolean
is
(int bondType) boolean
boolean
boolean
boolean
void
void
setCIPChirality
(int c) Not implemented.void
setMad
(short mad) void
setOrder
(int order) void
setTranslucent
(boolean isTranslucent, float translucentLevel) toString()
Methods inherited from class org.jmol.util.Edge
getArgbHbondType, getAtropismNode, getAtropismOrder, getAtropismOrder12, getBondOrderFromFloat, getBondOrderFromString, getBondOrderNameFromOrder, getBondOrderNumberFromOrder, getBondType, getCmlBondOrder, getCovalentBondOrder, getFloatEncodedInt, getPartialBondDotted, getPartialBondOrder, getPartialBondOrderFromFloatEncodedInt, isAtropism, isOrderH
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Field Details
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myVisibilityFlag
public static final int myVisibilityFlag -
atom1
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atom2
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mad
public short mad -
colix
public short colix -
shapeVisibilityFlags
public int shapeVisibilityFlags
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Constructor Details
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Bond
- Parameters:
atom1
-atom2
-order
-mad
-colix
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Method Details
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setMad
public void setMad(short mad) -
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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isPartial
public boolean isPartial() -
getEnergy
public float getEnergy() -
getValence
public int getValence() -
setTranslucent
public void setTranslucent(boolean isTranslucent, float translucentLevel) -
setOrder
public void setOrder(int order) -
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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getOtherAtom
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is
public boolean is(int bondType) -
getOtherNode
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setAtropisomerOptions
public void setAtropisomerOptions() -
getCIPChirality
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
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getAtom
Description copied from interface:SimpleEdge
Get the respective atom, 0 or 1- Returns:
- SimpleNode
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isCovalentNotPartial0
public boolean isCovalentNotPartial0()
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