public class SmilesBond extends Edge
Modifier and Type | Field and Description |
---|---|
private static 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 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 |
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
Constructor and Description |
---|
SmilesBond(SmilesAtom atom1,
SmilesAtom atom2,
int bondType,
boolean isNot)
SmilesBond constructor
|
Modifier and Type | Method and Description |
---|---|
(package private) SmilesBond |
addBondOr() |
(package private) SmilesBond |
addPrimitive() |
int |
getAtomIndex1() |
int |
getAtomIndex2() |
(package private) static 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 atom
|
boolean |
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.
|
String |
toString() |
getArgbHbondType, getAtropismNode, getAtropismOrder, getAtropismOrder12, getBondOrderFromFloat, getBondOrderFromString, getBondOrderNameFromOrder, getBondOrderNumberFromOrder, getCmlBondOrder, getCovalentBondOrder, getPartialBondDotted, getPartialBondOrder, isAtropism, isOrderH
public static final int TYPE_UNKNOWN
public static final int TYPE_NONE
public static final int TYPE_AROMATIC
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_CROSSLINK
private static final String ALL_BONDS
private static final String SMILES_BONDS
SmilesAtom atom1
SmilesAtom atom2
boolean isNot
Edge matchingBond
private SmilesBond[] primitives
int nPrimitives
SmilesBond[] bondsOr
int nBondsOr
boolean isConnection
int[] atropType
public boolean isChain
SmilesBond(SmilesAtom atom1, SmilesAtom atom2, int bondType, boolean isNot)
atom1
- First atomatom2
- Second atombondType
- Bond typeisNot
- static String getBondOrderString(int order)
static int getBondTypeFromCode(char code)
code
- Bond codevoid set(SmilesBond bond)
void setAtropType(int nn)
public SmilesBond setPrimitive(int i)
SmilesBond addBondOr()
SmilesBond addPrimitive()
void set2(int bondType, boolean isNot)
void set2a(SmilesAtom a1, SmilesAtom a2)
void setAtom2(SmilesAtom atom, SmilesSearch molecule)
atom
- molecule
- boolean isFromPreviousTo(SmilesAtom atom)
atom
- static int isBondType(char ch, boolean isSearch, boolean isBioSequence) throws InvalidSmilesException
InvalidSmilesException
int getBondType()
int getValence()
SmilesAtom getOtherAtom(SmilesAtom a)
public int getAtomIndex1()
getAtomIndex1
in class Edge
public int getAtomIndex2()
getAtomIndex2
in class Edge
public int getCovalentOrder()
getCovalentOrder
in class Edge
public Node getOtherAtomNode(Node atom)
getOtherAtomNode
in class Edge
public boolean isCovalent()
isCovalent
in class Edge
public boolean isHydrogen()
isHydrogen
in class Edge
void switchAtoms()