org.jmol.api

Interface SmilesMatcherInterface

All Known Implementing Classes:

SmilesMatcher

public interface SmilesMatcherInterface

Method Summary

Modifier and Type	Method and Description
int	areEqual(java.lang.String smiles1, java.lang.String smiles2)
BS[]	find(java.lang.String pattern, java.lang.String smiles, boolean isSmarts, boolean firstMatchOnly)
int[][]	getCorrelationMaps(java.lang.String pattern, Node[] atoms, int ac, BS bsSelected, boolean isSmarts, boolean firstMatchOnly)
java.lang.String	getLastException()
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, BS bsSelected, boolean asBioSmiles, boolean bioAllowUnmatchedRings, boolean bioAddCrossLinks, java.lang.String bioComment, boolean explicitH)
BS	getSubstructureSet(java.lang.String pattern, Node[] atoms, int ac, BS bsSelected, boolean isSmarts, boolean firstMatchOnly)
BS[]	getSubstructureSetArray(java.lang.String pattern, Node[] atoms, int ac, BS bsSelected, BS bsAromatic, boolean isSmarts, boolean firstMatchOnly)
void	getSubstructureSets(java.lang.String[] smarts, Node[] atoms, int ac, int flags, BS bsSelected, javajs.util.Lst<BS> bitSets, javajs.util.Lst<BS>[] vRings)
java.lang.String	reverseChirality(java.lang.String smiles)

Method Detail

getLastException

java.lang.String getLastException()

areEqual

int areEqual(java.lang.String smiles1,
             java.lang.String smiles2)
      throws java.lang.Exception

Throws:

java.lang.Exception

find

BS[] find(java.lang.String pattern,
          java.lang.String smiles,
          boolean isSmarts,
          boolean firstMatchOnly)
   throws java.lang.Exception

Throws:

java.lang.Exception

getSubstructureSet

BS getSubstructureSet(java.lang.String pattern,
                      Node[] atoms,
                      int ac,
                      BS bsSelected,
                      boolean isSmarts,
                      boolean firstMatchOnly)
               throws java.lang.Exception

Throws:

java.lang.Exception

getSubstructureSetArray

BS[] getSubstructureSetArray(java.lang.String pattern,
                             Node[] atoms,
                             int ac,
                             BS bsSelected,
                             BS bsAromatic,
                             boolean isSmarts,
                             boolean firstMatchOnly)
                      throws java.lang.Exception

Throws:

java.lang.Exception

getCorrelationMaps

int[][] getCorrelationMaps(java.lang.String pattern,
                           Node[] atoms,
                           int ac,
                           BS bsSelected,
                           boolean isSmarts,
                           boolean firstMatchOnly)
                    throws java.lang.Exception

Throws:

java.lang.Exception

getMolecularFormula

java.lang.String getMolecularFormula(java.lang.String pattern,
                                     boolean isSearch)
                              throws java.lang.Exception

Throws:

java.lang.Exception

getSmiles

java.lang.String getSmiles(Node[] atoms,
                           int ac,
                           BS bsSelected,
                           boolean asBioSmiles,
                           boolean bioAllowUnmatchedRings,
                           boolean bioAddCrossLinks,
                           java.lang.String bioComment,
                           boolean explicitH)
                    throws java.lang.Exception

Throws:

java.lang.Exception

getRelationship

java.lang.String getRelationship(java.lang.String smiles1,
                                 java.lang.String smiles2)
                          throws java.lang.Exception

Throws:

java.lang.Exception

reverseChirality

java.lang.String reverseChirality(java.lang.String smiles)
                           throws java.lang.Exception

Throws:

java.lang.Exception

getSubstructureSets

void getSubstructureSets(java.lang.String[] smarts,
                         Node[] atoms,
                         int ac,
                         int flags,
                         BS bsSelected,
                         javajs.util.Lst<BS> bitSets,
                         javajs.util.Lst<BS>[] vRings)
                  throws java.lang.Exception

Throws:

java.lang.Exception