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) compileSearchTarget
(Node[] atoms, int atomCount, BS bitSet) compileSmartsPattern
(String pattern) int[][]
Node[]
int[][]
getCorrelationMaps
(String pattern, Node[] atoms, int ac, BS bsSelected, int flags) int[][]
getMapForJME
(String jme, Atom[] at, BS bsAtoms) void
getMMFF94AtomTypes
(String[] smarts, Node[] atoms, int ac, BS bsSelected, Lst<BS> bitSets, Lst<BS>[] vRings) getMolecularFormula
(String pattern, boolean isSearch, boolean isEmpirical) getRelationship
(String smiles1, String smiles2) getSmilesFromJME
(String jmeFile) getSubstructureSet
(Object pattern, Object target, int ac, BS bsSelected, int flags) BS[]
getSubstructureSetArray
(String pattern, Node[] atoms, int ac, BS bsSelected, BS bsAromatic, int flags) int[]
hasStructure
(String smarts, String[] smilesSet, int flags) polyhedronToSmiles
(Node center, int[][] faces, int atomCount, 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, P3[] points, int flags, String details) throws Exception - Throws:
Exception
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getSubstructureSet
BS getSubstructureSet(Object pattern, Object target, int ac, BS bsSelected, int flags) throws Exception - Throws:
Exception
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getSubstructureSetArray
BS[] getSubstructureSetArray(String pattern, Node[] atoms, int ac, BS bsSelected, BS bsAromatic, int flags) throws Exception - Throws:
Exception
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getCorrelationMaps
int[][] getCorrelationMaps(String pattern, Node[] atoms, int ac, BS bsSelected, int flags) throws Exception - Throws:
Exception
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getMMFF94AtomTypes
void getMMFF94AtomTypes(String[] smarts, Node[] atoms, int ac, BS bsSelected, Lst<BS> bitSets, Lst<BS>[] vRings) throws Exception - Throws:
Exception
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getSmiles
String getSmiles(Node[] atoms, int ac, 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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getSmilesFromJME
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hasStructure
- Throws:
Exception
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compileSmartsPattern
- Throws:
Exception
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compileSearchTarget
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