public class SmilesBond extends JmolEdge
Modifier and Type | Field and Description |
---|---|
private SmilesAtom |
atom1 |
private SmilesAtom |
atom2 |
SmilesBond[] |
bondsOr |
(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 |
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, FLAG_AROMATIC_DEFINED, FLAG_AROMATIC_DOUBLE, FLAG_AROMATIC_STRICT, FLAG_IGNORE_STEREOCHEMISTRY, FLAG_NO_AROMATIC, index, order
Constructor and Description |
---|
SmilesBond(int bondType,
boolean isNot) |
SmilesBond(SmilesAtom atom1,
SmilesAtom atom2,
int bondType,
boolean isNot)
SmilesBond constructor
|
Modifier and Type | Method and Description |
---|---|
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() |
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() |
getArgbHbondType, getBondOrderFromFloat, getBondOrderFromString, getBondOrderNameFromOrder, getBondOrderNumberFromOrder, getCmlBondOrder, getCovalentBondOrder, getPartialBondDotted, getPartialBondOrder
public static final int TYPE_UNKNOWN
public static final int TYPE_NONE
public static final int TYPE_SINGLE
public static final int TYPE_DOUBLE
public static final int TYPE_TRIPLE
public static final int TYPE_AROMATIC
public static final int TYPE_DIRECTIONAL_1
public static final int TYPE_DIRECTIONAL_2
public static final int TYPE_ATROPISOMER_1
public static final int TYPE_ATROPISOMER_2
public static final int TYPE_RING
public static final int TYPE_ANY
public static final int TYPE_BIO_SEQUENCE
public static final int TYPE_BIO_PAIR
public static final int TYPE_MULTIPLE
private SmilesAtom atom1
private SmilesAtom atom2
boolean isNot
JmolEdge matchingBond
public SmilesBond[] primitives
public int nPrimitives
public SmilesBond[] bondsOr
public int nBondsOr
public SmilesBond(SmilesAtom atom1, SmilesAtom atom2, int bondType, boolean isNot)
atom1
- First atomatom2
- Second atombondType
- Bond typeisNot
- SmilesBond(int bondType, boolean isNot)
static java.lang.String getBondOrderString(int order)
public void set(SmilesBond bond)
public SmilesBond addBondOr()
public SmilesBond addPrimitive()
public java.lang.String toString()
toString
in class java.lang.Object
void set(int bondType, boolean isNot)
void set(SmilesAtom atom1, SmilesAtom atom2)
static boolean isBondType(char ch, boolean isSearch, boolean isBioSequence) throws InvalidSmilesException
InvalidSmilesException
public static int getBondTypeFromCode(char code)
code
- Bond codepublic SmilesAtom getAtom1()
public SmilesAtom getAtom2()
void setAtom2(SmilesAtom atom)
public int getBondType()
public SmilesAtom getOtherAtom(SmilesAtom a)
public int getAtomIndex1()
getAtomIndex1
in class JmolEdge
public int getAtomIndex2()
getAtomIndex2
in class JmolEdge
public int getCovalentOrder()
getCovalentOrder
in class JmolEdge
public JmolNode getOtherAtom(JmolNode atom)
getOtherAtom
in class JmolEdge
public boolean isCovalent()
isCovalent
in class JmolEdge
public int getValence()
public boolean isHydrogen()
isHydrogen
in class JmolEdge
void switchAtoms()