Package org.jmol.symmetry
Class CIPDataSmiles
java.lang.Object
org.jmol.symmetry.CIPData
org.jmol.symmetry.CIPDataSmiles
A subclass that allows Jmol processing of SMILES using
"...smiles...".find("SMILES","chirality")
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Field Summary
FieldsFields 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
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionprivate SmilesAtom
(package private) int
getBondOrder
(SimpleEdge bond) protected javajs.util.BS[]
Retrieve an array of bit sets that match a given SMARTSString[]
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 identifierprotected javajs.util.BS
Return a bit set corresponding to a SMARTSsetAtomsForSmiles
(Viewer vwr, String smiles) (package private) boolean
setCoord
(SimpleNode atom, CIPChirality.CIPAtom[] atoms) set the coordinate -- SMILES onlyMethods inherited from class org.jmol.symmetry.CIPData
checkHandedness, couldBeChiralAlkene, couldBeChiralAtom, getEneKekule, getRootTrackerResult, getTrigonality, init, isTracker, set, setRule6Full, track
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Field Details
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smiles
String smiles -
nodes
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Constructor Details
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CIPDataSmiles
public CIPDataSmiles()
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Method Details
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isSmiles
boolean isSmiles()Description copied from class:CIPData
Subclass identifier -
setAtomsForSmiles
- Throws:
Exception
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getList
Description copied from class:CIPData
Retrieve an array of bit sets that match a given SMARTS -
match
Description copied from class:CIPData
Return a bit set corresponding to a SMARTS -
getBondOrder
- Overrides:
getBondOrder
in classCIPData
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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. -
getStereoEdge
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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 classCIPData
- Parameters:
a
-b
-c
-d
-- Returns:
- true if torsion angle is
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findCumulativeCenter
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setCoord
Description copied from class:CIPData
set the coordinate -- SMILES only -
getSmilesChiralityArray
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