Package org.jmol.util
Class Edge
- java.lang.Object
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- org.jmol.util.Edge
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- All Implemented Interfaces:
SimpleEdge
- Direct Known Subclasses:
Bond
,SmilesBond
public abstract class Edge extends java.lang.Object implements SimpleEdge
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Nested Class Summary
Nested Classes Modifier and Type Class Description private static class
Edge.EnumBondOrder
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Field Summary
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Constructor Summary
Constructors Constructor Description Edge()
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Method Summary
All Methods Static Methods Instance Methods Abstract Methods Concrete Methods Modifier and Type Method Description static int
getArgbHbondType(int order)
abstract int
getAtomIndex1()
abstract int
getAtomIndex2()
private static int
getAtropismCode(int order)
static Node
getAtropismNode(int order, Node a1, boolean isFirst)
static int
getAtropismOrder(int nn, int mm)
static int
getAtropismOrder12(int nnmm)
static int
getBondOrderFromFloat(float fOrder)
static int
getBondOrderFromString(java.lang.String name)
static java.lang.String
getBondOrderNameFromOrder(int order)
static java.lang.String
getBondOrderNumberFromOrder(int order)
used for formatting labels and in the connect PARTIAL commandint
getBondType()
Get the order of the bond.java.lang.String
getCIPChirality(boolean doCalculate)
static java.lang.String
getCmlBondOrder(int order)
protected static int
getCovalentBondOrder(int order)
abstract int
getCovalentOrder()
static int
getPartialBondDotted(int order)
static int
getPartialBondOrder(int order)
static boolean
isAtropism(int order)
abstract boolean
isCovalent()
abstract boolean
isHydrogen()
static boolean
isOrderH(int order)
void
setCIPChirality(int c)
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Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
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Methods inherited from interface org.jmol.util.SimpleEdge
getAtom, getOtherNode
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Field Detail
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BOND_RENDER_SINGLE
public static final int BOND_RENDER_SINGLE
Extended Bond Definition Types Originally these were short 16-bit values- See Also:
- Constant Field Values
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TYPE_ATROPISOMER
public static final int TYPE_ATROPISOMER
- See Also:
- Constant Field Values
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TYPE_ATROPISOMER_REV
public static final int TYPE_ATROPISOMER_REV
- See Also:
- Constant Field Values
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ATROPISOMER_SHIFT
private static final int ATROPISOMER_SHIFT
- See Also:
- Constant Field Values
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BOND_STEREO_MASK
public static final int BOND_STEREO_MASK
- See Also:
- Constant Field Values
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BOND_STEREO_NEAR
public static final int BOND_STEREO_NEAR
- See Also:
- Constant Field Values
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BOND_STEREO_FAR
public static final int BOND_STEREO_FAR
- See Also:
- Constant Field Values
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BOND_AROMATIC_MASK
public static final int BOND_AROMATIC_MASK
- See Also:
- Constant Field Values
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BOND_AROMATIC_SINGLE
public static final int BOND_AROMATIC_SINGLE
- See Also:
- Constant Field Values
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BOND_AROMATIC_DOUBLE
public static final int BOND_AROMATIC_DOUBLE
- See Also:
- Constant Field Values
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BOND_AROMATIC
public static final int BOND_AROMATIC
- See Also:
- Constant Field Values
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BOND_SULFUR_MASK
public static final int BOND_SULFUR_MASK
- See Also:
- Constant Field Values
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BOND_PARTIAL_MASK
public static final int BOND_PARTIAL_MASK
- See Also:
- Constant Field Values
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BOND_PARTIAL01
public static final int BOND_PARTIAL01
- See Also:
- Constant Field Values
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BOND_PARTIAL12
public static final int BOND_PARTIAL12
- See Also:
- Constant Field Values
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BOND_PARTIAL23
public static final int BOND_PARTIAL23
- See Also:
- Constant Field Values
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BOND_PARTIAL32
public static final int BOND_PARTIAL32
- See Also:
- Constant Field Values
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BOND_COVALENT_MASK
public static final int BOND_COVALENT_MASK
- See Also:
- Constant Field Values
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BOND_COVALENT_SINGLE
public static final int BOND_COVALENT_SINGLE
- See Also:
- Constant Field Values
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BOND_COVALENT_DOUBLE
public static final int BOND_COVALENT_DOUBLE
- See Also:
- Constant Field Values
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BOND_COVALENT_TRIPLE
public static final int BOND_COVALENT_TRIPLE
- See Also:
- Constant Field Values
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BOND_COVALENT_QUADRUPLE
public static final int BOND_COVALENT_QUADRUPLE
- See Also:
- Constant Field Values
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BOND_COVALENT_QUINTUPLE
public static final int BOND_COVALENT_QUINTUPLE
- See Also:
- Constant Field Values
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BOND_COVALENT_sextuple
public static final int BOND_COVALENT_sextuple
- See Also:
- Constant Field Values
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BOND_ORDER_UNSPECIFIED
public static final int BOND_ORDER_UNSPECIFIED
- See Also:
- Constant Field Values
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BOND_ORDER_ANY
public static final int BOND_ORDER_ANY
- See Also:
- Constant Field Values
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BOND_ORDER_NULL
public static final int BOND_ORDER_NULL
- See Also:
- Constant Field Values
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BOND_STRUT
public static final int BOND_STRUT
- See Also:
- Constant Field Values
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BOND_PYMOL_NOMULT
public static final int BOND_PYMOL_NOMULT
- See Also:
- Constant Field Values
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BOND_PYMOL_MULT
public static final int BOND_PYMOL_MULT
- See Also:
- Constant Field Values
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BOND_NEW
public static final int BOND_NEW
- See Also:
- Constant Field Values
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BOND_HBOND_SHIFT
public static final int BOND_HBOND_SHIFT
- See Also:
- Constant Field Values
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BOND_HYDROGEN_MASK
public static final int BOND_HYDROGEN_MASK
- See Also:
- Constant Field Values
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BOND_H_REGULAR
public static final int BOND_H_REGULAR
- See Also:
- Constant Field Values
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BOND_H_CALC_MASK
public static final int BOND_H_CALC_MASK
- See Also:
- Constant Field Values
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BOND_H_CALC
public static final int BOND_H_CALC
- See Also:
- Constant Field Values
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BOND_H_PLUS_2
public static final int BOND_H_PLUS_2
- See Also:
- Constant Field Values
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BOND_H_PLUS_3
public static final int BOND_H_PLUS_3
- See Also:
- Constant Field Values
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BOND_H_PLUS_4
public static final int BOND_H_PLUS_4
- See Also:
- Constant Field Values
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BOND_H_PLUS_5
public static final int BOND_H_PLUS_5
- See Also:
- Constant Field Values
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BOND_H_MINUS_3
public static final int BOND_H_MINUS_3
- See Also:
- Constant Field Values
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BOND_H_MINUS_4
public static final int BOND_H_MINUS_4
- See Also:
- Constant Field Values
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BOND_H_NUCLEOTIDE
public static final int BOND_H_NUCLEOTIDE
- See Also:
- Constant Field Values
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argbsHbondType
private static final int[] argbsHbondType
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index
public int index
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order
public int order
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Method Detail
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getAtomIndex1
public abstract int getAtomIndex1()
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getAtomIndex2
public abstract int getAtomIndex2()
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getCovalentOrder
public abstract int getCovalentOrder()
- Specified by:
getCovalentOrder
in interfaceSimpleEdge
- Returns:
- the bond order 1-4 if it is covalent, or 0 if not.
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isCovalent
public abstract boolean isCovalent()
- Specified by:
isCovalent
in interfaceSimpleEdge
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isHydrogen
public abstract boolean isHydrogen()
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getArgbHbondType
public static int getArgbHbondType(int order)
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getBondOrderNumberFromOrder
public static final java.lang.String getBondOrderNumberFromOrder(int order)
used for formatting labels and in the connect PARTIAL command- Parameters:
order
-- Returns:
- a string representation to preserve float n.m
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getCmlBondOrder
public static final java.lang.String getCmlBondOrder(int order)
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getBondOrderNameFromOrder
public static final java.lang.String getBondOrderNameFromOrder(int order)
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getAtropismOrder
public static int getAtropismOrder(int nn, int mm)
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getAtropismOrder12
public static int getAtropismOrder12(int nnmm)
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getAtropismCode
private static int getAtropismCode(int order)
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isAtropism
public static boolean isAtropism(int order)
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isOrderH
public static boolean isOrderH(int order)
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getPartialBondDotted
public static final int getPartialBondDotted(int order)
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getPartialBondOrder
public static final int getPartialBondOrder(int order)
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getCovalentBondOrder
protected static final int getCovalentBondOrder(int order)
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getBondOrderFromFloat
public static final int getBondOrderFromFloat(float fOrder)
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getBondOrderFromString
public static int getBondOrderFromString(java.lang.String name)
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getBondType
public int getBondType()
Description copied from interface:SimpleEdge
Get the order of the bond. This could be covalent order, but also could be NEAR, FAR, etc.- Specified by:
getBondType
in interfaceSimpleEdge
- Returns:
- order
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setCIPChirality
public void setCIPChirality(int c)
- Parameters:
c
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getCIPChirality
public java.lang.String getCIPChirality(boolean doCalculate)
- Parameters:
doCalculate
-- Returns:
- CIP chirality label
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