Package org.jmol.api
Interface SmilesMatcherInterface
- All Known Implementing Classes:
SmilesMatcher
public interface SmilesMatcherInterface
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Method Summary
Modifier and TypeMethodDescriptionint
cleanSmiles
(String smiles) int[][]
Node[]
int[][]
getCorrelationMaps
(String pattern, Node[] atoms, int ac, javajs.util.BS bsSelected, int flags) 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) getMolecularFormula
(String pattern, boolean isSearch) getRelationship
(String smiles1, String smiles2) 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) polyhedronToSmiles
(Node center, int[][] faces, int atomCount, javajs.util.P3[] points, int flags, String details) reverseChirality
(String smiles)
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Method Details
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areEqual
- Throws:
Exception
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find
- Throws:
Exception
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getLastException
String getLastException() -
getMolecularFormula
- Throws:
Exception
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getRelationship
- Throws:
Exception
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reverseChirality
- 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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cleanSmiles
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getMapForJME
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getAtoms
- Throws:
Exception
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