org.jmol.smiles
Class SmilesBond

java.lang.Object
  extended by org.jmol.smiles.SmilesBond
All Implemented Interfaces:
JmolEdge

public class SmilesBond
extends java.lang.Object
implements JmolEdge

Bond in a SmilesMolecule


Field Summary
private  SmilesAtom atom1
           
private  SmilesAtom atom2
           
 SmilesBond[] bondsOr
           
(package private)  int bondType
           
(package private)  int index
           
(package private)  boolean isNot
           
(package private)  JmolEdge matchingBond
           
 int nBondsOr
           
 int nPrimitives
           
 SmilesBond[] primitives
           
static int TYPE_ANY
           
static int TYPE_AROMATIC
           
static int TYPE_ATROPISOMER_1
           
static int TYPE_ATROPISOMER_2
           
static int TYPE_BIO_PAIR
           
static int TYPE_BIO_SEQUENCE
           
static int TYPE_DIRECTIONAL_1
           
static int TYPE_DIRECTIONAL_2
           
static int TYPE_DOUBLE
           
static int TYPE_MULTIPLE
           
static int TYPE_NONE
           
static int TYPE_RING
           
static int TYPE_SINGLE
           
static int TYPE_TRIPLE
           
static int TYPE_UNKNOWN
           
 
Fields inherited from interface org.jmol.api.JmolEdge
BOND_AROMATIC, BOND_AROMATIC_DOUBLE, BOND_AROMATIC_MASK, BOND_AROMATIC_SINGLE, BOND_COVALENT_DOUBLE, BOND_COVALENT_MASK, BOND_COVALENT_QUADRUPLE, 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_STEREO_FAR, BOND_STEREO_MASK, BOND_STEREO_NEAR, BOND_STRUT, BOND_SULFUR_MASK
 
Constructor Summary
SmilesBond(int bondType, boolean isNot)
           
SmilesBond(SmilesAtom atom1, SmilesAtom atom2, int bondType, boolean isNot)
          SmilesBond constructor
 
Method Summary
 SmilesBond addBondOr()
           
 SmilesBond addPrimitive()
           
 SmilesAtom getAtom1()
           
 SmilesAtom getAtom2()
           
 int getAtomIndex1()
           
 int getAtomIndex2()
           
(package private) static java.lang.String getBondOrderString(int order)
           
 int getBondType()
           
static int getBondTypeFromCode(char code)
           
 int getCovalentOrder()
           
 int getIndex()
           
 int getOrder()
           
 JmolNode getOtherAtom(JmolNode atom)
           
 SmilesAtom getOtherAtom(SmilesAtom a)
           
 int getValence()
           
(package private) static boolean isBondType(char ch, boolean isSearch, boolean isBioSequence)
           
 boolean isCovalent()
           
 boolean isHydrogen()
           
(package private)  void set(int bondType, boolean isNot)
           
(package private)  void set(SmilesAtom atom1, SmilesAtom atom2)
           
 void set(SmilesBond bond)
           
(package private)  void setAtom2(SmilesAtom atom)
           
(package private)  void switchAtoms()
           
 java.lang.String toString()
           
 
Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait
 

Field Detail

TYPE_UNKNOWN

public static final int TYPE_UNKNOWN
See Also:
Constant Field Values

TYPE_NONE

public static final int TYPE_NONE
See Also:
Constant Field Values

TYPE_SINGLE

public static final int TYPE_SINGLE
See Also:
Constant Field Values

TYPE_DOUBLE

public static final int TYPE_DOUBLE
See Also:
Constant Field Values

TYPE_TRIPLE

public static final int TYPE_TRIPLE
See Also:
Constant Field Values

TYPE_AROMATIC

public static final int TYPE_AROMATIC
See Also:
Constant Field Values

TYPE_DIRECTIONAL_1

public static final int TYPE_DIRECTIONAL_1
See Also:
Constant Field Values

TYPE_DIRECTIONAL_2

public static final int TYPE_DIRECTIONAL_2
See Also:
Constant Field Values

TYPE_ATROPISOMER_1

public static final int TYPE_ATROPISOMER_1
See Also:
Constant Field Values

TYPE_ATROPISOMER_2

public static final int TYPE_ATROPISOMER_2
See Also:
Constant Field Values

TYPE_RING

public static final int TYPE_RING
See Also:
Constant Field Values

TYPE_ANY

public static final int TYPE_ANY
See Also:
Constant Field Values

TYPE_BIO_SEQUENCE

public static final int TYPE_BIO_SEQUENCE
See Also:
Constant Field Values

TYPE_BIO_PAIR

public static final int TYPE_BIO_PAIR
See Also:
Constant Field Values

TYPE_MULTIPLE

public static final int TYPE_MULTIPLE
See Also:
Constant Field Values

atom1

private SmilesAtom atom1

atom2

private SmilesAtom atom2

bondType

int bondType

index

int index

isNot

boolean isNot

matchingBond

JmolEdge matchingBond

primitives

public SmilesBond[] primitives

nPrimitives

public int nPrimitives

bondsOr

public SmilesBond[] bondsOr

nBondsOr

public int nBondsOr
Constructor Detail

SmilesBond

public SmilesBond(SmilesAtom atom1,
                  SmilesAtom atom2,
                  int bondType,
                  boolean isNot)
SmilesBond constructor

Parameters:
atom1 - First atom
atom2 - Second atom
bondType - Bond type
isNot -

SmilesBond

SmilesBond(int bondType,
           boolean isNot)
Method Detail

getBondOrderString

static java.lang.String getBondOrderString(int order)

getIndex

public int getIndex()
Specified by:
getIndex in interface JmolEdge

set

public void set(SmilesBond bond)

addBondOr

public SmilesBond addBondOr()

addPrimitive

public SmilesBond addPrimitive()

toString

public java.lang.String toString()
Overrides:
toString in class java.lang.Object

set

void set(int bondType,
         boolean isNot)

set

void set(SmilesAtom atom1,
         SmilesAtom atom2)

isBondType

static boolean isBondType(char ch,
                          boolean isSearch,
                          boolean isBioSequence)
                   throws InvalidSmilesException
Throws:
InvalidSmilesException

getBondTypeFromCode

public static int getBondTypeFromCode(char code)
Parameters:
code - Bond code
Returns:
Bond type

getAtom1

public SmilesAtom getAtom1()

getAtom2

public SmilesAtom getAtom2()

setAtom2

void setAtom2(SmilesAtom atom)

getBondType

public int getBondType()

getOtherAtom

public SmilesAtom getOtherAtom(SmilesAtom a)

getAtomIndex1

public int getAtomIndex1()
Specified by:
getAtomIndex1 in interface JmolEdge

getAtomIndex2

public int getAtomIndex2()
Specified by:
getAtomIndex2 in interface JmolEdge

getCovalentOrder

public int getCovalentOrder()
Specified by:
getCovalentOrder in interface JmolEdge

getOrder

public int getOrder()
Specified by:
getOrder in interface JmolEdge

getOtherAtom

public JmolNode getOtherAtom(JmolNode atom)
Specified by:
getOtherAtom in interface JmolEdge

isCovalent

public boolean isCovalent()
Specified by:
isCovalent in interface JmolEdge

getValence

public int getValence()

isHydrogen

public boolean isHydrogen()
Specified by:
isHydrogen in interface JmolEdge

switchAtoms

void switchAtoms()