TanimotoSimilarityButton

    Calculate Similarity score

    
    /*
    * Find Similarity Value
    *
    *
    * Usage:
    * 1. Run your Similarity Query
    * 2. Run button script
    *
    * The button script expects that SIMILARITY search 
    * and Tanimoto metric is used. If you want to use different 
    * metric, please see all available 
    * https://docs.chemaxon.com/display/docs/Functions+by+Categories#dissimilarity_functions
    *
    * @author David Pech <dpech@chemaxon.com>
    */
    import com.im.df.api.*
    import com.im.df.api.chem.DissimilarityCalculator
    import chemaxon.struc.Molecule
    import chemaxon.jep.*
    import chemaxon.jep.context.MolContext
    import chemaxon.formats.MolImporter;
     
    import chemaxon.sss.search.JChemSearchOptions;
    import chemaxon.standardizer.Standardizer;
    import com.im.df.api.capabilities.JChemEntityCapability;
    init = { widget ->
    }
    destroy = { widget ->
    }
    evaluate = { widget ->
        def ety = dataTree.rootVertex.entity // assumes you have reference to the data tree
        def edp = ety.schema.dataProvider.getEntityDataProvider(ety)
        def molFld = ety.fields.items.find { it.name == 'Structure' } // find the structure field
        def rs = ety.schema.dataProvider.getDefaultResultSet(dataTree, false, DFEnvironmentRO.DEV_NULL) // find the ResultSet
        def rootVS = rs.getVertexState(dataTree.rootVertex) // obtain the VertexState
     
        // define the entity Capability so that we can sniff out the query paramenters
        JChemEntityCapability entityCap = DIFUtilities.findCapability(ety, JChemEntityCapability.class);
     
        // obtain the query paramenters from last used query
        boolean isReaction = false
        int bitCount = entityCap.getNumberOfOnes();
        int bondCount = entityCap.getNumberOfEdges();
        int fpLengthInBits = entityCap.getNumberOfInts() * 32;
     
        MarvinStructure queryStructure; // define empty query structure (will be defined in the cycle below)
     
        // obtain the query structure from last used query parameters
            List<DFTermExpression> expressions = DIFUtilities.findSimpleFieldUsagesInQuery(rs.getLastExecutedQuery(), molFld);
            for (DFTermExpression dFTermExpression : expressions) {
                DFOperator operator = dFTermExpression.getOperator();
                if (operator instanceof Operators.StructureOperator) {
                    boolean caseInsensitive = (Boolean) dFTermExpression.getOptions()
                            .get(LegacyConstants.CASE_INSENSITIVE_SEARCH);
                    List<DFTerm> operands = dFTermExpression.getOperands();
                    for (DFTerm dFTerm : operands) {
                        if (dFTerm instanceof DFTermValue && ((DFTermValue) dFTerm).getValue() instanceof MarvinStructure) {
                            queryStructure = ((DFTermValue) dFTerm).getValue(); // assign the query structure value to a variable
                        }
                    }
                }
            }
     
        List ids = rootVS.getSelectedRowsIds() // get the selected IDs
        if (ids.size == 1) {
            Map rows = rootVS.getData(ids, DFEnvironmentRO.DEV_NULL) // get the data
            Map row = rows[ids[0]] // get the first and only row
            MarvinStructure mol = row[molFld.id] // Get the Structure. Its a com.im.df.api.chem.MarvinStructure instance
            Molecule cxnMol = mol.getNative() // obtain the chemaxon.struc.Molecule instance
    
            // set other needed parameters for the calculation
            JChemSearchOptions jcso = new JChemSearchOptions(JChemSearchOptions.SIMILARITY); // set SIMILARITY search type
            jcso.setDissimilarityMetric("TANIMOTO"); // use TANIMOTO metric
            Molecule query = queryStructure.getNative() // obtain the chemaxon.struct.Molecule instance and set it as query
            Standardizer noSt = new Standardizer("<StandardizerConfiguration><Actions></Actions></StandardizerConfiguration>")
     
            // create Dissimilarity calculator with all needed paramenters
            DissimilarityCalculator dissimilarity = new DissimilarityCalculator(isReaction, query, jcso, bitCount, bondCount, fpLengthInBits, noSt);
            def dissimilarityValue = dissimilarity.computeDissimilarity(cxnMol) // caluclate Disimilarity score for selected molecule
            def similarityValue = 1 - dissimilarityValue // calculate the Similarity value
     
            println "Similarity Value is ${similarityValue}"
     
    
        } else {
            println "bad selection"
        }
    }
    on_change = { widget, button ->
    
    }