Package org.jmol.scriptext
Class SmilesExt
java.lang.Object
org.jmol.scriptext.SmilesExt
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Field Summary
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Constructor Summary
Constructors -
Method Summary
Modifier and TypeMethodDescriptionfloat[]
getFlexFitList
(javajs.util.BS bs1, javajs.util.BS bs2, String smiles1, boolean isSmarts) float
getSmilesCorrelation
(javajs.util.BS bsA, javajs.util.BS bsB, String smiles, javajs.util.Lst<javajs.util.P3> ptsA, javajs.util.Lst<javajs.util.P3> ptsB, javajs.util.M4 m4, javajs.util.Lst<javajs.util.BS> vReturn, boolean asMap, int[][] mapSet, javajs.util.P3 center, boolean bestMap, int flags) The major interface to org.jmol.smiles, this method allows for a wide variety of correlation functionality.getSmilesMatches
(String pattern, String smiles, javajs.util.BS bsSelected, javajs.util.BS bsMatch3D, int flags, boolean asOneBitset, boolean firstMatchOnly) private static void
getTorsions
(Atom[] atoms, int[][] bondMap, float[][] diff, int pt) float
mapPolyhedra
(int i1, int i2, boolean isSmiles, javajs.util.M4 m)
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Field Details
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e
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Constructor Details
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SmilesExt
public SmilesExt()
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Method Details
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init
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getSmilesCorrelation
public float getSmilesCorrelation(javajs.util.BS bsA, javajs.util.BS bsB, String smiles, javajs.util.Lst<javajs.util.P3> ptsA, javajs.util.Lst<javajs.util.P3> ptsB, javajs.util.M4 m4, javajs.util.Lst<javajs.util.BS> vReturn, boolean asMap, int[][] mapSet, javajs.util.P3 center, boolean bestMap, int flags) throws ScriptException The major interface to org.jmol.smiles, this method allows for a wide variety of correlation functionality.- Parameters:
bsA
-bsB
-smiles
-ptsA
-ptsB
-m4
-vReturn
-asMap
-mapSet
-center
-bestMap
-flags
-- Returns:
- standard deviation
- Throws:
ScriptException
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getSmilesMatches
public Object getSmilesMatches(String pattern, String smiles, javajs.util.BS bsSelected, javajs.util.BS bsMatch3D, int flags, boolean asOneBitset, boolean firstMatchOnly) throws ScriptException - Parameters:
pattern
- esmiles
-bsSelected
-bsMatch3D
-flags
-asOneBitset
-firstMatchOnly
-- Returns:
- Object
- Throws:
ScriptException
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getFlexFitList
public float[] getFlexFitList(javajs.util.BS bs1, javajs.util.BS bs2, String smiles1, boolean isSmarts) throws ScriptException - Throws:
ScriptException
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getTorsions
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mapPolyhedra
public float mapPolyhedra(int i1, int i2, boolean isSmiles, javajs.util.M4 m) throws ScriptException - Throws:
ScriptException
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