public class CIPDataSmiles extends CIPData
| Modifier and Type | Field and Description |
|---|---|
private Node[] |
nodes |
(package private) java.lang.String |
smiles |
atoms, bsAromatic, bsAtoms, bsAtropisomeric, bsAzacyclic, bsEnes, bsHelixM, bsHelixP, bsKekuleAmbiguous, bsMolecule, bsNegativeAromatic, bsXAromatic, lstSmallRings, testRule6Full, TRIGONALITY_MIN, vNorm, vTemp, vwr| Constructor and Description |
|---|
CIPDataSmiles() |
| Modifier and Type | Method and 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
|
checkHandedness, couldBeChiralAlkene, couldBeChiralAtom, getEneKekule, getRootTrackerResult, getTrigonality, init, isTracker, set, setRule6Full, trackjava.lang.String smiles
private Node[] nodes
boolean isSmiles()
CIPDatapublic CIPDataSmiles setAtomsForSmiles(Viewer vwr, java.lang.String smiles) throws java.lang.Exception
java.lang.Exceptionprotected javajs.util.BS[] getList(java.lang.String smarts)
throws java.lang.Exception
CIPDataprotected javajs.util.BS match(java.lang.String smarts)
throws java.lang.Exception
CIPDataint getBondOrder(SimpleEdge bond)
getBondOrder in class CIPDataint isCis(CIPChirality.CIPAtom a, CIPChirality.CIPAtom b, CIPChirality.CIPAtom c, CIPChirality.CIPAtom d)
private int getStereoEdge(SimpleNode atom, SimpleNode winner)
int isPositiveTorsion(CIPChirality.CIPAtom a, CIPChirality.CIPAtom b, CIPChirality.CIPAtom c, CIPChirality.CIPAtom d)
isPositiveTorsion in class CIPDataa - b - c - d - private SmilesAtom findCumulativeCenter(CIPChirality.CIPAtom a, CIPChirality.CIPAtom a2)
boolean setCoord(SimpleNode atom, CIPChirality.CIPAtom[] atoms)
CIPDatapublic java.lang.String[] getSmilesChiralityArray()