org.jmol.util
Class JmolEdge

java.lang.Object
  extended by org.jmol.util.JmolEdge
Direct Known Subclasses:
Bond, SmilesBond

public abstract class JmolEdge
extends java.lang.Object


Nested Class Summary
private static class JmolEdge.EnumBondOrder
           
 
Field Summary
static int[] argbsHbondType
           
static int BOND_AROMATIC
           
static int BOND_AROMATIC_DOUBLE
           
static int BOND_AROMATIC_MASK
           
static int BOND_AROMATIC_SINGLE
           
static int BOND_COVALENT_DOUBLE
           
static int BOND_COVALENT_MASK
           
static int BOND_COVALENT_QUADRUPLE
           
static int BOND_COVALENT_SINGLE
           
static int BOND_COVALENT_TRIPLE
           
static int BOND_H_CALC
           
static int BOND_H_CALC_MASK
           
static int BOND_H_MINUS_3
           
static int BOND_H_MINUS_4
           
static int BOND_H_NUCLEOTIDE
           
static int BOND_H_PLUS_2
           
static int BOND_H_PLUS_3
           
static int BOND_H_PLUS_4
           
static int BOND_H_PLUS_5
           
static int BOND_H_REGULAR
           
static int BOND_HBOND_SHIFT
           
static int BOND_HYDROGEN_MASK
           
static int BOND_NEW
           
static int BOND_ORDER_ANY
           
static int BOND_ORDER_NULL
           
static int BOND_ORDER_UNSPECIFIED
           
static int BOND_PARTIAL_MASK
           
static int BOND_PARTIAL01
           
static int BOND_PARTIAL12
           
static int BOND_PARTIAL23
           
static int BOND_PARTIAL32
           
static int BOND_STEREO_FAR
           
static int BOND_STEREO_MASK
          Extended Bond Definition Types
static int BOND_STEREO_NEAR
           
static int BOND_STRUT
           
static int BOND_SULFUR_MASK
           
 int index
           
 int order
           
 
Constructor Summary
JmolEdge()
           
 
Method Summary
static int getArgbHbondType(int order)
           
abstract  int getAtomIndex1()
           
abstract  int getAtomIndex2()
           
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 command
static java.lang.String getCmlBondOrder(int order)
           
protected static int getCovalentBondOrder(int order)
           
abstract  int getCovalentOrder()
           
abstract  JmolNode getOtherAtom(JmolNode atom)
           
static int getPartialBondDotted(int order)
           
static int getPartialBondOrder(int order)
           
abstract  boolean isCovalent()
           
abstract  boolean isHydrogen()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait
 

Field Detail

BOND_STEREO_MASK

public static final int BOND_STEREO_MASK
Extended Bond Definition Types

See Also:
Constant Field Values

BOND_STEREO_NEAR

public static final int BOND_STEREO_NEAR
See Also:
Constant Field Values

BOND_STEREO_FAR

public static final int BOND_STEREO_FAR
See Also:
Constant Field Values

BOND_AROMATIC_MASK

public static final int BOND_AROMATIC_MASK
See Also:
Constant Field Values

BOND_AROMATIC_SINGLE

public static final int BOND_AROMATIC_SINGLE
See Also:
Constant Field Values

BOND_AROMATIC_DOUBLE

public static final int BOND_AROMATIC_DOUBLE
See Also:
Constant Field Values

BOND_AROMATIC

public static final int BOND_AROMATIC
See Also:
Constant Field Values

BOND_SULFUR_MASK

public static final int BOND_SULFUR_MASK
See Also:
Constant Field Values

BOND_PARTIAL_MASK

public static final int BOND_PARTIAL_MASK
See Also:
Constant Field Values

BOND_PARTIAL01

public static final int BOND_PARTIAL01
See Also:
Constant Field Values

BOND_PARTIAL12

public static final int BOND_PARTIAL12
See Also:
Constant Field Values

BOND_PARTIAL23

public static final int BOND_PARTIAL23
See Also:
Constant Field Values

BOND_PARTIAL32

public static final int BOND_PARTIAL32
See Also:
Constant Field Values

BOND_COVALENT_MASK

public static final int BOND_COVALENT_MASK
See Also:
Constant Field Values

BOND_COVALENT_SINGLE

public static final int BOND_COVALENT_SINGLE
See Also:
Constant Field Values

BOND_COVALENT_DOUBLE

public static final int BOND_COVALENT_DOUBLE
See Also:
Constant Field Values

BOND_COVALENT_TRIPLE

public static final int BOND_COVALENT_TRIPLE
See Also:
Constant Field Values

BOND_COVALENT_QUADRUPLE

public static final int BOND_COVALENT_QUADRUPLE
See Also:
Constant Field Values

BOND_ORDER_UNSPECIFIED

public static final int BOND_ORDER_UNSPECIFIED
See Also:
Constant Field Values

BOND_ORDER_ANY

public static final int BOND_ORDER_ANY
See Also:
Constant Field Values

BOND_ORDER_NULL

public static final int BOND_ORDER_NULL
See Also:
Constant Field Values

BOND_NEW

public static final int BOND_NEW
See Also:
Constant Field Values

BOND_STRUT

public static final int BOND_STRUT
See Also:
Constant Field Values

BOND_HBOND_SHIFT

public static final int BOND_HBOND_SHIFT
See Also:
Constant Field Values

BOND_HYDROGEN_MASK

public static final int BOND_HYDROGEN_MASK
See Also:
Constant Field Values

BOND_H_REGULAR

public static final int BOND_H_REGULAR
See Also:
Constant Field Values

BOND_H_CALC_MASK

public static final int BOND_H_CALC_MASK
See Also:
Constant Field Values

BOND_H_CALC

public static final int BOND_H_CALC
See Also:
Constant Field Values

BOND_H_PLUS_2

public static final int BOND_H_PLUS_2
See Also:
Constant Field Values

BOND_H_PLUS_3

public static final int BOND_H_PLUS_3
See Also:
Constant Field Values

BOND_H_PLUS_4

public static final int BOND_H_PLUS_4
See Also:
Constant Field Values

BOND_H_PLUS_5

public static final int BOND_H_PLUS_5
See Also:
Constant Field Values

BOND_H_MINUS_3

public static final int BOND_H_MINUS_3
See Also:
Constant Field Values

BOND_H_MINUS_4

public static final int BOND_H_MINUS_4
See Also:
Constant Field Values

BOND_H_NUCLEOTIDE

public static final int BOND_H_NUCLEOTIDE
See Also:
Constant Field Values

argbsHbondType

public static final int[] argbsHbondType

index

public int index

order

public int order
Constructor Detail

JmolEdge

public JmolEdge()
Method Detail

getAtomIndex1

public abstract int getAtomIndex1()

getAtomIndex2

public abstract int getAtomIndex2()

getCovalentOrder

public abstract int getCovalentOrder()

getOtherAtom

public abstract JmolNode getOtherAtom(JmolNode atom)

isCovalent

public abstract boolean isCovalent()

isHydrogen

public abstract boolean isHydrogen()

getArgbHbondType

public static int getArgbHbondType(int order)

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

getCmlBondOrder

public static final java.lang.String getCmlBondOrder(int order)

getBondOrderNameFromOrder

public static final java.lang.String getBondOrderNameFromOrder(int order)

getPartialBondDotted

public static final int getPartialBondDotted(int order)

getPartialBondOrder

public static final int getPartialBondOrder(int order)

getCovalentBondOrder

protected static final int getCovalentBondOrder(int order)

getBondOrderFromFloat

public static final int getBondOrderFromFloat(float fOrder)

getBondOrderFromString

public static int getBondOrderFromString(java.lang.String name)