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(String smiles1, String smiles2)
String
cleanSmiles(String smiles)
int[][]
find(String pattern, String smiles, int flags)
Node[]
getAtoms(String target)
int[][]
getCorrelationMaps(String pattern, Node[] atoms, int ac, javajs.util.BS bsSelected, int flags)
String
getLastException()
int[][]
getMapForJME(String jme, Atom[] at, javajs.util.BS bsAtoms)
void
getMMFF94AtomTypes(String[] smarts, Node[] atoms, int ac, javajs.util.BS bsSelected, javajs.util.Lst<javajs.util.BS> bitSets, javajs.util.Lst<javajs.util.BS>[] vRings)
String
getMolecularFormula(String pattern, boolean isSearch)
String
getRelationship(String smiles1, String smiles2)
String
getSmiles(Node[] atoms, int ac, javajs.util.BS bsSelected, String bioComment, int flags)
javajs.util.BS
getSubstructureSet(String pattern, Node[] atoms, int ac, javajs.util.BS bsSelected, int flags)
javajs.util.BS[]
getSubstructureSetArray(String pattern, Node[] atoms, int ac, javajs.util.BS bsSelected, javajs.util.BS bsAromatic, int flags)
String
polyhedronToSmiles(Node center, int[][] faces, int atomCount, javajs.util.P3[] points, int flags, String details)
String
reverseChirality(String smiles)
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Method Detail
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getLastException
String getLastException()
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getMolecularFormula
String getMolecularFormula(String pattern, boolean isSearch) throws Exception
- Throws:
Exception
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getRelationship
String getRelationship(String smiles1, String smiles2) throws Exception
- Throws:
Exception
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polyhedronToSmiles
String polyhedronToSmiles(Node center, int[][] faces, int atomCount, javajs.util.P3[] points, int flags, String details) throws Exception
- Throws:
Exception
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getSubstructureSet
javajs.util.BS getSubstructureSet(String pattern, Node[] atoms, int ac, javajs.util.BS bsSelected, int flags) throws Exception
- Throws:
Exception
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getSubstructureSetArray
javajs.util.BS[] getSubstructureSetArray(String pattern, Node[] atoms, int ac, javajs.util.BS bsSelected, javajs.util.BS bsAromatic, int flags) throws Exception
- Throws:
Exception
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getCorrelationMaps
int[][] getCorrelationMaps(String pattern, Node[] atoms, int ac, javajs.util.BS bsSelected, int flags) throws Exception
- Throws:
Exception
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getMMFF94AtomTypes
void getMMFF94AtomTypes(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 Exception
- Throws:
Exception
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getSmiles
String getSmiles(Node[] atoms, int ac, javajs.util.BS bsSelected, String bioComment, int flags) throws Exception
- Throws:
Exception
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