Package org.jmol.api
Interface SmilesMatcherInterface
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- All Known Implementing Classes:
SmilesMatcher
public interface SmilesMatcherInterface
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Method Summary
All Methods Instance Methods Abstract Methods Modifier and Type Method Description int
areEqual(java.lang.String smiles1, java.lang.String smiles2)
java.lang.String
cleanSmiles(java.lang.String smiles)
int[][]
find(java.lang.String pattern, java.lang.String smiles, int flags)
Node[]
getAtoms(java.lang.String target)
int[][]
getCorrelationMaps(java.lang.String pattern, Node[] atoms, int ac, javajs.util.BS bsSelected, int flags)
java.lang.String
getLastException()
int[][]
getMapForJME(java.lang.String jme, Atom[] at, javajs.util.BS bsAtoms)
void
getMMFF94AtomTypes(java.lang.String[] smarts, Node[] atoms, int ac, javajs.util.BS bsSelected, javajs.util.Lst<javajs.util.BS> bitSets, javajs.util.Lst<javajs.util.BS>[] vRings)
java.lang.String
getMolecularFormula(java.lang.String pattern, boolean isSearch)
java.lang.String
getRelationship(java.lang.String smiles1, java.lang.String smiles2)
java.lang.String
getSmiles(Node[] atoms, int ac, javajs.util.BS bsSelected, java.lang.String bioComment, int flags)
javajs.util.BS
getSubstructureSet(java.lang.String pattern, Node[] atoms, int ac, javajs.util.BS bsSelected, int flags)
javajs.util.BS[]
getSubstructureSetArray(java.lang.String pattern, Node[] atoms, int ac, javajs.util.BS bsSelected, javajs.util.BS bsAromatic, int flags)
java.lang.String
polyhedronToSmiles(Node center, int[][] faces, int atomCount, javajs.util.P3[] points, int flags, java.lang.String details)
java.lang.String
reverseChirality(java.lang.String smiles)
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Method Detail
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areEqual
int areEqual(java.lang.String smiles1, java.lang.String smiles2) throws java.lang.Exception
- Throws:
java.lang.Exception
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find
int[][] find(java.lang.String pattern, java.lang.String smiles, int flags) throws java.lang.Exception
- Throws:
java.lang.Exception
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getLastException
java.lang.String getLastException()
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getMolecularFormula
java.lang.String getMolecularFormula(java.lang.String pattern, boolean isSearch) throws java.lang.Exception
- Throws:
java.lang.Exception
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getRelationship
java.lang.String getRelationship(java.lang.String smiles1, java.lang.String smiles2) throws java.lang.Exception
- Throws:
java.lang.Exception
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reverseChirality
java.lang.String reverseChirality(java.lang.String smiles) throws java.lang.Exception
- Throws:
java.lang.Exception
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polyhedronToSmiles
java.lang.String polyhedronToSmiles(Node center, int[][] faces, int atomCount, javajs.util.P3[] points, int flags, java.lang.String details) throws java.lang.Exception
- Throws:
java.lang.Exception
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getSubstructureSet
javajs.util.BS getSubstructureSet(java.lang.String pattern, Node[] atoms, int ac, javajs.util.BS bsSelected, int flags) throws java.lang.Exception
- Throws:
java.lang.Exception
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getSubstructureSetArray
javajs.util.BS[] getSubstructureSetArray(java.lang.String pattern, Node[] atoms, int ac, javajs.util.BS bsSelected, javajs.util.BS bsAromatic, int flags) throws java.lang.Exception
- Throws:
java.lang.Exception
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getCorrelationMaps
int[][] getCorrelationMaps(java.lang.String pattern, Node[] atoms, int ac, javajs.util.BS bsSelected, int flags) throws java.lang.Exception
- Throws:
java.lang.Exception
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getMMFF94AtomTypes
void getMMFF94AtomTypes(java.lang.String[] smarts, Node[] atoms, int ac, javajs.util.BS bsSelected, javajs.util.Lst<javajs.util.BS> bitSets, javajs.util.Lst<javajs.util.BS>[] vRings) throws java.lang.Exception
- Throws:
java.lang.Exception
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getSmiles
java.lang.String getSmiles(Node[] atoms, int ac, javajs.util.BS bsSelected, java.lang.String bioComment, int flags) throws java.lang.Exception
- Throws:
java.lang.Exception
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cleanSmiles
java.lang.String cleanSmiles(java.lang.String smiles)
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getMapForJME
int[][] getMapForJME(java.lang.String jme, Atom[] at, javajs.util.BS bsAtoms)
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getAtoms
Node[] getAtoms(java.lang.String target) throws java.lang.Exception
- Throws:
java.lang.Exception
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