Package org.jmol.smiles
Class SmilesBond
java.lang.Object
org.jmol.util.Edge
org.jmol.smiles.SmilesBond
- All Implemented Interfaces:
SimpleEdge
Bond in a SmilesMolecule
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Field Summary
FieldsModifier and TypeFieldDescriptionboolean
static final int
static final int
static final int
static final int
static final int
static final int
static final int
Fields inherited from class org.jmol.util.Edge
BOND_AROMATIC, BOND_AROMATIC_DOUBLE, BOND_AROMATIC_MASK, BOND_AROMATIC_SINGLE, BOND_COVALENT_DOUBLE, BOND_COVALENT_MASK, BOND_COVALENT_QUADRUPLE, BOND_COVALENT_QUINTUPLE, BOND_COVALENT_sextuple, 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_PYMOL_MULT, BOND_PYMOL_NOMULT, BOND_RENDER_MASK, BOND_RENDER_SINGLE, BOND_STEREO_EITHER, BOND_STEREO_FAR, BOND_STEREO_MASK, BOND_STEREO_NEAR, BOND_STRUT, BOND_SULFUR_MASK, index, order, TYPE_ATROPISOMER, TYPE_ATROPISOMER_REV
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Constructor Summary
ConstructorsConstructorDescriptionSmilesBond
(SmilesAtom atom1, SmilesAtom atom2, int bondType, boolean isNot) SmilesBond constructor -
Method Summary
Modifier and TypeMethodDescriptiongetAtom
(int i) Get the respective atom, 0 or 1getAtom1()
int
int
int
getOtherNode
(SimpleNode atom) int
int
boolean
boolean
boolean
void
set2
(int bondType, boolean isNot) setPrimitive
(int i) toString()
Methods inherited from class org.jmol.util.Edge
getArgbHbondType, getAtropismNode, getAtropismOrder, getAtropismOrder12, getBondOrderFromFloat, getBondOrderFromString, getBondOrderNameFromOrder, getBondOrderNumberFromOrder, getBondType, getCIPChirality, getCmlBondOrder, getCovalentBondOrder, getFloatEncodedInt, getPartialBondDotted, getPartialBondOrder, getPartialBondOrderFromFloatEncodedInt, isAtropism, isOrderH, setCIPChirality
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Field Details
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TYPE_UNKNOWN
public static final int TYPE_UNKNOWN- See Also:
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TYPE_NONE
public static final int TYPE_NONE- See Also:
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TYPE_AROMATIC
public static final int TYPE_AROMATIC- See Also:
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TYPE_RING
public static final int TYPE_RING- See Also:
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TYPE_ANY
public static final int TYPE_ANY- See Also:
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TYPE_BIO_SEQUENCE
public static final int TYPE_BIO_SEQUENCE- See Also:
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TYPE_BIO_CROSSLINK
public static final int TYPE_BIO_CROSSLINK- See Also:
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isChain
public boolean isChain
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Constructor Details
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SmilesBond
SmilesBond constructor- Parameters:
atom1
- First atomatom2
- Second atombondType
- Bond typeisNot
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Method Details
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getAtom1
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setPrimitive
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toString
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set2
public void set2(int bondType, boolean isNot) -
getValence
public int getValence() -
getOtherAtom
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getAtomIndex1
public int getAtomIndex1()- Specified by:
getAtomIndex1
in classEdge
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getAtomIndex2
public int getAtomIndex2()- Specified by:
getAtomIndex2
in classEdge
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getCovalentOrder
public int getCovalentOrder()- Specified by:
getCovalentOrder
in interfaceSimpleEdge
- Specified by:
getCovalentOrder
in classEdge
- Returns:
- the bond order 1-4 if it is covalent, or 0 if not.
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getOtherNode
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isCovalent
public boolean isCovalent()- Specified by:
isCovalent
in interfaceSimpleEdge
- Specified by:
isCovalent
in classEdge
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isPartial
public boolean isPartial() -
isHydrogen
public boolean isHydrogen()- Specified by:
isHydrogen
in classEdge
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getRealCovalentOrder
public int getRealCovalentOrder() -
getMatchingBond
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getAtom
Description copied from interface:SimpleEdge
Get the respective atom, 0 or 1- Returns:
- SimpleNode
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