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) 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

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(String smarts)

Retrieve an array of bit sets that match a given SMARTS

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(String smarts)

Return a bit set corresponding to a SMARTS

CIPDataSmiles

setAtomsForSmiles(Viewer vwr, 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 Details
- smiles
  
  String smiles
- nodes
  
  private Node[] nodes
Constructor Details
- CIPDataSmiles
  
  public CIPDataSmiles()
Method Details
- 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, String smiles) throws Exception
  
  Throws:
  
  Exception
- getList
  
  protected javajs.util.BS[] getList(String smarts) throws 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:
  
  Exception
- match
  
  protected javajs.util.BS match(String smarts) throws 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:
  
  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 String[] getSmilesChiralityArray()

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 Details

smiles

nodes

Constructor Details

CIPDataSmiles

Method Details

isSmiles

setAtomsForSmiles

getList

match

getBondOrder

isCis

getStereoEdge

isPositiveTorsion

findCumulativeCenter

setCoord

getSmilesChiralityArray