java.lang.Object
- org.jmol.symmetry.CIPData
- - org.jmol.symmetry.CIPDataSmiles

```
public class CIPDataSmiles
extends CIPData
```
A subclass that allows Jmol processing of SMILES using "...smiles...".find("SMILES","chirality")

Field Summary

Fields
Modifier and Type Field Description

private Node[] nodes

(package private) java.lang.String smiles
- Fields inherited from class org.jmol.symmetry.CIPData
  atoms, bsAromatic, bsAtoms, bsAtropisomeric, bsAzacyclic, bsEnes, bsHelixM, bsHelixP, bsKekuleAmbiguous, bsMolecule, bsNegativeAromatic, bsXAromatic, lstSmallRings, testRule6Full, TRIGONALITY_MIN, vNorm, vTemp, vwr

Constructor Summary

Constructors
Constructor Description

CIPDataSmiles()

Method Summary

All Methods Instance Methods Concrete Methods
Modifier and Type	Method	Description
`private SmilesAtom`	`findCumulativeCenter(CIPChirality.CIPAtom a, CIPChirality.CIPAtom a2)`
`(package private) int`	`getBondOrder(SimpleEdge bond)`
`protected javajs.util.BS[]`	`getList(java.lang.String smarts)`	Retrieve an array of bit sets that match a given SMARTS
`java.lang.String[]`	`getSmilesChiralityArray()`
`private int`	`getStereoEdge(SimpleNode atom, SimpleNode winner)`
`(package private) int`	`isCis(CIPChirality.CIPAtom a, CIPChirality.CIPAtom b, CIPChirality.CIPAtom c, CIPChirality.CIPAtom d)`	Check cis vs.
`(package private) int`	`isPositiveTorsion(CIPChirality.CIPAtom a, CIPChirality.CIPAtom b, CIPChirality.CIPAtom c, CIPChirality.CIPAtom d)`	Checks the torsion angle and returns true if it is positive
`(package private) boolean`	`isSmiles()`	Subclass identifier
`protected javajs.util.BS`	`match(java.lang.String smarts)`	Return a bit set corresponding to a SMARTS
`CIPDataSmiles`	`setAtomsForSmiles(Viewer vwr, java.lang.String smiles)`
`(package private) boolean`	`setCoord(SimpleNode atom, CIPChirality.CIPAtom[] atoms)`	set the coordinate -- SMILES only

Methods inherited from class org.jmol.symmetry.CIPData
checkHandedness, couldBeChiralAlkene, couldBeChiralAtom, getEneKekule, getRootTrackerResult, getTrigonality, init, isTracker, set, setRule6Full, track

Methods inherited from class java.lang.Object
clone, equals, finalize, getClass, hashCode, notify, notifyAll, toString, wait, wait, wait

Field Detail

smiles
```
java.lang.String smiles
```

nodes
```
private Node[] nodes
```

Constructor Detail
- CIPDataSmiles
```
public CIPDataSmiles()
```

Method Detail

isSmiles
```
boolean isSmiles()
```
Description copied from class: CIPData

Subclass identifier

Overrides:

isSmiles in class CIPData

Returns:

true for CIPDataSmiles

setAtomsForSmiles

public CIPDataSmiles setAtomsForSmiles(Viewer vwr,
                                       java.lang.String smiles)
                                throws java.lang.Exception

Throws:: java.lang.Exception

getList
```
protected javajs.util.BS[] getList(java.lang.String smarts)
                            throws java.lang.Exception
```
Description copied from class: CIPData

Retrieve an array of bit sets that match a given SMARTS

Overrides:

getList in class CIPData

Returns:

array of matching bit sets

Throws:

java.lang.Exception

match
```
protected javajs.util.BS match(java.lang.String smarts)
                        throws java.lang.Exception
```
Description copied from class: CIPData

Return a bit set corresponding to a SMARTS

Overrides:

match in class CIPData

Returns:

bit set matching this SMARTS

Throws:

java.lang.Exception

getBondOrder
```
int getBondOrder(SimpleEdge bond)
```
Overrides:

getBondOrder in class CIPData

isCis

int isCis(CIPChirality.CIPAtom a,
          CIPChirality.CIPAtom b,
          CIPChirality.CIPAtom c,
          CIPChirality.CIPAtom d)

Check cis vs. trans nature of a--b==c--d.

Overrides:: isCis in class CIPData
Parameters:: a -; b -; c -; d -
Returns:: true if this is a cis relationship

getStereoEdge

private int getStereoEdge(SimpleNode atom,
                          SimpleNode winner)

isPositiveTorsion

int isPositiveTorsion(CIPChirality.CIPAtom a,
                      CIPChirality.CIPAtom b,
                      CIPChirality.CIPAtom c,
                      CIPChirality.CIPAtom d)

Checks the torsion angle and returns true if it is positive

Overrides:: isPositiveTorsion in class CIPData
Parameters:: a -; b -; c -; d -
Returns:: true if torsion angle is

findCumulativeCenter

private SmilesAtom findCumulativeCenter(CIPChirality.CIPAtom a,
                                        CIPChirality.CIPAtom a2)

setCoord
```
boolean setCoord(SimpleNode atom,
                 CIPChirality.CIPAtom[] atoms)
```
Description copied from class: CIPData

set the coordinate -- SMILES only

Overrides:

setCoord in class CIPData

Returns:

true if coordinate is able to be set

getSmilesChiralityArray

public java.lang.String[] getSmilesChiralityArray()

Modifier and Type	Field	Description
`private Node[]`	`nodes`
`(package private) java.lang.String`	`smiles`

Class CIPDataSmiles

Field Summary

Fields inherited from class org.jmol.symmetry.CIPData

Constructor Summary

Method Summary

Methods inherited from class org.jmol.symmetry.CIPData

Methods inherited from class java.lang.Object

Field Detail

smiles

nodes

Constructor Detail

CIPDataSmiles

Method Detail

isSmiles

setAtomsForSmiles

getList

match

getBondOrder

isCis

getStereoEdge

isPositiveTorsion

findCumulativeCenter

setCoord

getSmilesChiralityArray