Package org.jmol.scriptext
Class SmilesExt
- java.lang.Object
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- org.jmol.scriptext.SmilesExt
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public class SmilesExt extends java.lang.Object
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Field Summary
Fields Modifier and Type Field Description private ScriptEval
e
private SmilesMatcherInterface
sm
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Constructor Summary
Constructors Constructor Description SmilesExt()
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Method Summary
All Methods Static Methods Instance Methods Concrete Methods Modifier and Type Method Description float[]
getFlexFitList(javajs.util.BS bs1, javajs.util.BS bs2, java.lang.String smiles1, boolean isSmarts)
float
getSmilesCorrelation(javajs.util.BS bsA, javajs.util.BS bsB, java.lang.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.java.lang.Object
getSmilesMatches(java.lang.String pattern, java.lang.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)
SmilesExt
init(java.lang.Object se)
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Field Detail
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e
private ScriptEval e
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sm
private SmilesMatcherInterface sm
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Method Detail
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init
public SmilesExt init(java.lang.Object se)
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getSmilesCorrelation
public float getSmilesCorrelation(javajs.util.BS bsA, javajs.util.BS bsB, java.lang.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 java.lang.Object getSmilesMatches(java.lang.String pattern, java.lang.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, java.lang.String smiles1, boolean isSmarts) throws ScriptException
- Throws:
ScriptException
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getTorsions
private static void getTorsions(Atom[] atoms, int[][] bondMap, float[][] diff, int pt)
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