Package org.jmol.api

Interface SmilesMatcherInterface

All Known Implementing Classes:

SmilesMatcher

public interface SmilesMatcherInterface

Method Summary

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)

Method Detail

areEqual

int areEqual(String smiles1,
             String smiles2)
      throws Exception

Throws:

Exception

find

int[][] find(String pattern,
             String smiles,
             int flags)
      throws Exception

Throws:

Exception

getLastException

String getLastException()

getMolecularFormula

String getMolecularFormula(String pattern,
                           boolean isSearch)
                    throws Exception

Throws:

Exception

getRelationship

String getRelationship(String smiles1,
                       String smiles2)
                throws Exception

Throws:

Exception

reverseChirality

String reverseChirality(String smiles)
                 throws Exception

Throws:

Exception

polyhedronToSmiles

String polyhedronToSmiles(Node center,
                          int[][] faces,
                          int atomCount,
                          javajs.util.P3[] points,
                          int flags,
                          String details)
                   throws Exception

Throws:

Exception

getSubstructureSet

javajs.util.BS getSubstructureSet(String pattern,
                                  Node[] atoms,
                                  int ac,
                                  javajs.util.BS bsSelected,
                                  int flags)
                           throws Exception

Throws:

Exception

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

getCorrelationMaps

int[][] getCorrelationMaps(String pattern,
                           Node[] atoms,
                           int ac,
                           javajs.util.BS bsSelected,
                           int flags)
                    throws Exception

Throws:

Exception

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

getSmiles

String getSmiles(Node[] atoms,
                 int ac,
                 javajs.util.BS bsSelected,
                 String bioComment,
                 int flags)
          throws Exception

Throws:

Exception

cleanSmiles

String cleanSmiles(String smiles)

getMapForJME

int[][] getMapForJME(String jme,
                     Atom[] at,
                     javajs.util.BS bsAtoms)

getAtoms

Node[] getAtoms(String target)
         throws Exception

Throws:

Exception