public class CIPDataSmiles extends CIPData
Modifier and Type | Field and Description |
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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 |
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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, track
java.lang.String smiles
private Node[] nodes
boolean isSmiles()
CIPData
public CIPDataSmiles setAtomsForSmiles(Viewer vwr, java.lang.String smiles) throws java.lang.Exception
java.lang.Exception
protected javajs.util.BS[] getList(java.lang.String smarts) throws java.lang.Exception
CIPData
protected javajs.util.BS match(java.lang.String smarts) throws java.lang.Exception
CIPData
int getBondOrder(SimpleEdge bond)
getBondOrder
in class CIPData
int 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 CIPData
a
- b
- c
- d
- private SmilesAtom findCumulativeCenter(CIPChirality.CIPAtom a, CIPChirality.CIPAtom a2)
boolean setCoord(SimpleNode atom, CIPChirality.CIPAtom[] atoms)
CIPData
public java.lang.String[] getSmilesChiralityArray()