Package org.jmol.symmetry
Class CIPDataSmiles
- java.lang.Object
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- org.jmol.symmetry.CIPData
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- org.jmol.symmetry.CIPDataSmiles
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public class CIPDataSmiles extends CIPData
A subclass that allows Jmol processing of SMILES using "...smiles...".find("SMILES","chirality")
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Field Summary
Fields Modifier and Type Field Description private Node[]
nodes
(package private) String
smiles
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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
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Constructor Summary
Constructors Constructor Description CIPDataSmiles()
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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(String smarts)
Retrieve an array of bit sets that match a given SMARTSString[]
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 identifierprotected javajs.util.BS
match(String smarts)
Return a bit set corresponding to a SMARTSCIPDataSmiles
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
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Method Detail
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isSmiles
boolean isSmiles()
Description copied from class:CIPData
Subclass identifier
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setAtomsForSmiles
public CIPDataSmiles setAtomsForSmiles(Viewer vwr, String smiles) throws Exception
- Throws:
Exception
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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
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match
protected javajs.util.BS match(String smarts) throws Exception
Description copied from class:CIPData
Return a bit set corresponding to a SMARTS
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getBondOrder
int getBondOrder(SimpleEdge bond)
- 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.
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getStereoEdge
private int getStereoEdge(SimpleNode atom, SimpleNode winner)
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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
private SmilesAtom findCumulativeCenter(CIPChirality.CIPAtom a, CIPChirality.CIPAtom a2)
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setCoord
boolean setCoord(SimpleNode atom, CIPChirality.CIPAtom[] atoms)
Description copied from class:CIPData
set the coordinate -- SMILES only
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getSmilesChiralityArray
public String[] getSmilesChiralityArray()
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