Package org.jmol.smiles
Class SmilesBond
- java.lang.Object
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- org.jmol.util.Edge
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- org.jmol.smiles.SmilesBond
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public class SmilesBond extends Edge
Bond in a SmilesMolecule
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Field Summary
Fields Modifier and Type Field Description private static java.lang.String
ALL_BONDS
(package private) SmilesAtom
atom1
(package private) SmilesAtom
atom2
(package private) int[]
atropType
(package private) SmilesBond[]
bondsOr
boolean
isChain
(package private) boolean
isConnection
(package private) boolean
isNot
(package private) Edge
matchingBond
(package private) int
nBondsOr
(package private) int
nPrimitives
private SmilesBond[]
primitives
private static java.lang.String
SMILES_BONDS
static int
TYPE_ANY
static int
TYPE_AROMATIC
static int
TYPE_BIO_CROSSLINK
static int
TYPE_BIO_SEQUENCE
static int
TYPE_NONE
static int
TYPE_RING
static int
TYPE_UNKNOWN
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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_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_SINGLE, 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
Constructors Constructor Description SmilesBond(SmilesAtom atom1, SmilesAtom atom2, int bondType, boolean isNot)
SmilesBond constructor
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description (package private) SmilesBond
addBondOr()
(package private) SmilesBond
addPrimitive()
int
getAtomIndex1()
int
getAtomIndex2()
(package private) static java.lang.String
getBondOrderString(int order)
(package private) int
getBondType()
(package private) static int
getBondTypeFromCode(char code)
int
getCovalentOrder()
(package private) SmilesAtom
getOtherAtom(SmilesAtom a)
Node
getOtherAtomNode(Node atom)
(package private) int
getValence()
(package private) static int
isBondType(char ch, boolean isSearch, boolean isBioSequence)
boolean
isCovalent()
(package private) boolean
isFromPreviousTo(SmilesAtom atom)
Check to see if this is the bond to the previous atomboolean
isHydrogen()
(package private) void
set(SmilesBond bond)
(package private) void
set2(int bondType, boolean isNot)
(package private) void
set2a(SmilesAtom a1, SmilesAtom a2)
(package private) void
setAtom2(SmilesAtom atom, SmilesSearch molecule)
from parse ring(package private) void
setAtropType(int nn)
SmilesBond
setPrimitive(int i)
(package private) void
switchAtoms()
Ensure that atom ordering is proper.java.lang.String
toString()
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Methods inherited from class org.jmol.util.Edge
getArgbHbondType, getAtropismNode, getAtropismOrder, getAtropismOrder12, getBondOrderFromFloat, getBondOrderFromString, getBondOrderNameFromOrder, getBondOrderNumberFromOrder, getCmlBondOrder, getCovalentBondOrder, getPartialBondDotted, getPartialBondOrder, isAtropism, isOrderH
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Field Detail
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TYPE_UNKNOWN
public static final int TYPE_UNKNOWN
- See Also:
- Constant Field Values
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TYPE_NONE
public static final int TYPE_NONE
- See Also:
- Constant Field Values
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TYPE_AROMATIC
public static final int TYPE_AROMATIC
- See Also:
- Constant Field Values
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TYPE_RING
public static final int TYPE_RING
- See Also:
- Constant Field Values
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TYPE_ANY
public static final int TYPE_ANY
- See Also:
- Constant Field Values
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TYPE_BIO_SEQUENCE
public static final int TYPE_BIO_SEQUENCE
- See Also:
- Constant Field Values
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TYPE_BIO_CROSSLINK
public static final int TYPE_BIO_CROSSLINK
- See Also:
- Constant Field Values
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ALL_BONDS
private static final java.lang.String ALL_BONDS
- See Also:
- Constant Field Values
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SMILES_BONDS
private static final java.lang.String SMILES_BONDS
- See Also:
- Constant Field Values
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atom1
SmilesAtom atom1
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atom2
SmilesAtom atom2
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isNot
boolean isNot
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matchingBond
Edge matchingBond
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primitives
private SmilesBond[] primitives
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nPrimitives
int nPrimitives
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bondsOr
SmilesBond[] bondsOr
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nBondsOr
int nBondsOr
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isConnection
boolean isConnection
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atropType
int[] atropType
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isChain
public boolean isChain
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Constructor Detail
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SmilesBond
SmilesBond(SmilesAtom atom1, SmilesAtom atom2, int bondType, boolean isNot)
SmilesBond constructor- Parameters:
atom1
- First atomatom2
- Second atombondType
- Bond typeisNot
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Method Detail
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getBondOrderString
static java.lang.String getBondOrderString(int order)
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getBondTypeFromCode
static int getBondTypeFromCode(char code)
- Parameters:
code
- Bond code- Returns:
- Bond type
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set
void set(SmilesBond bond)
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setAtropType
void setAtropType(int nn)
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setPrimitive
public SmilesBond setPrimitive(int i)
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addBondOr
SmilesBond addBondOr()
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addPrimitive
SmilesBond addPrimitive()
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toString
public java.lang.String toString()
- Overrides:
toString
in classjava.lang.Object
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set2
void set2(int bondType, boolean isNot)
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set2a
void set2a(SmilesAtom a1, SmilesAtom a2)
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setAtom2
void setAtom2(SmilesAtom atom, SmilesSearch molecule)
from parse ring- Parameters:
atom
-molecule
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isFromPreviousTo
boolean isFromPreviousTo(SmilesAtom atom)
Check to see if this is the bond to the previous atom- Parameters:
atom
-- Returns:
- TRUE if other atom is previous atom
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isBondType
static int isBondType(char ch, boolean isSearch, boolean isBioSequence) throws InvalidSmilesException
- Throws:
InvalidSmilesException
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getBondType
int getBondType()
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getValence
int getValence()
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getOtherAtom
SmilesAtom getOtherAtom(SmilesAtom a)
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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 classEdge
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getOtherAtomNode
public Node getOtherAtomNode(Node atom)
- Specified by:
getOtherAtomNode
in classEdge
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isCovalent
public boolean isCovalent()
- Specified by:
isCovalent
in classEdge
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isHydrogen
public boolean isHydrogen()
- Specified by:
isHydrogen
in classEdge
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switchAtoms
void switchAtoms()
Ensure that atom ordering is proper. possibly not fully tested
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