From: Egon W. <eg...@us...> - 2004-03-03 13:29:54
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Update of /cvsroot/cdk/cdk/src/org/openscience/cdk/isomorphism In directory sc8-pr-cvs1.sourceforge.net:/tmp/cvs-serv10109/src/org/openscience/cdk/isomorphism Modified Files: UniversalIsomorphismTester.java Log Message: More tweaks to the architecture. Result: The old UniversalIsomorphismTester is maintained, but *does* allow querying with QueryAtomContainer (see new test). However, the latter is not used yet, that will come in a moment. Index: UniversalIsomorphismTester.java =================================================================== RCS file: /cvsroot/cdk/cdk/src/org/openscience/cdk/isomorphism/UniversalIsomorphismTester.java,v retrieving revision 1.14 retrieving revision 1.15 diff -u -r1.14 -r1.15 --- UniversalIsomorphismTester.java 16 Feb 2004 13:39:03 -0000 1.14 +++ UniversalIsomorphismTester.java 3 Mar 2004 13:09:27 -0000 1.15 @@ -56,18 +56,20 @@ import org.openscience.cdk.tools.ChemModelManipulator; /** - * This class implements a multipurpose structure comparaison tool. + * This class implements a multipurpose structure comparison tool. * It allows to find maximal common substructure, find the * mapping of a substructure in another structure, and the mapping of - * 2 isomorph structure. - * Structure comparaison may be associated to bond constraints + * two isomorphic structures. + * + * <p>Structure comparison may be associated to bond constraints * (mandatory bonds, e.g. scaffolds, reaction cores,...) on each source graph. * The constraint flexibility allows a number of interesting queries. * The substructure analysis relies on the RGraph generic class (see: RGraph) * This class implements the link between the RGraph model and the * the CDK model in this way the RGraph remains independant and may be used * in other contexts. - * This algorithm derives from the algorithm described in "Machine Learning of + * + * <p>This algorithm derives from the algorithm described in "Machine Learning of * of generic Reactions : 3. An efficient Algorithm for Maximal Common * Substructure determination" C. Tonnelier, Ph. Jauffret, T. Hanser * and G. Kaufmann. Tetrahedron Vol. 3, No 6, pp. 351-358, 1990. @@ -75,7 +77,7 @@ * de m???hodes de synth???e ???partir d'exemples". Universit???Louis Pasteur * STRASBOURG 1993. * - * < FONT COLOR="#FF0000"> + * <p><FONT COLOR="#FF0000"> * warning : As a result of the adjacency perception used in this algorithm * there is a single limitation : cyclopropane and isobutane are seen as isomorph * This is due to the fact that these two compounds are the only ones where @@ -88,7 +90,7 @@ * not the same (3 != 4) and in most case this will be already * screened out by a fingerprint based filtering. * It is possible to add a special treatment for these special query. - * < /FONT> + * </FONT> * * * @author Stephane Werner from IXELIS ma...@ix... @@ -96,10 +98,10 @@ * @cdk.require java1.4 */ public class UniversalIsomorphismTester { + final static int ID1 = 0; final static int ID2 = 1; - /////////////////////////////////////////////////////////////////////////// // Query Methods // |