org.jmol.smiles
Class SmilesBond
java.lang.Object
org.jmol.util.JmolEdge
org.jmol.smiles.SmilesBond
public class SmilesBond
- extends JmolEdge
Bond in a SmilesMolecule
Fields inherited from class org.jmol.util.JmolEdge |
argbsHbondType, 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, index, order |
Methods inherited from class java.lang.Object |
clone, equals, finalize, getClass, hashCode, notify, notifyAll, wait, wait, wait |
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
isNot
boolean isNot
matchingBond
JmolEdge matchingBond
primitives
public SmilesBond[] primitives
nPrimitives
public int nPrimitives
bondsOr
public SmilesBond[] bondsOr
nBondsOr
public int nBondsOr
SmilesBond
public SmilesBond(SmilesAtom atom1,
SmilesAtom atom2,
int bondType,
boolean isNot)
- SmilesBond constructor
- Parameters:
atom1
- First atomatom2
- Second atombondType
- Bond typeisNot
-
SmilesBond
SmilesBond(int bondType,
boolean isNot)
getBondOrderString
static java.lang.String getBondOrderString(int order)
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 class JmolEdge
getAtomIndex2
public int getAtomIndex2()
- Specified by:
getAtomIndex2
in class JmolEdge
getCovalentOrder
public int getCovalentOrder()
- Specified by:
getCovalentOrder
in class JmolEdge
getOtherAtom
public JmolNode getOtherAtom(JmolNode atom)
- Specified by:
getOtherAtom
in class JmolEdge
isCovalent
public boolean isCovalent()
- Specified by:
isCovalent
in class JmolEdge
getValence
public int getValence()
isHydrogen
public boolean isHydrogen()
- Specified by:
isHydrogen
in class JmolEdge
switchAtoms
void switchAtoms()