// Counts the number of MetaPrint2D predicted metabolization sites. // // See DOI: 10.1186/1471-2105-11-362 // load the Novartis malaria data set mols = cdk.loadMolecules("/OxfordAdmet2010/malaria box/Novartis_GNF-Pf.sdf.out") for (block=0; block<65; block++) { // blocks of 100 items; size of above file is 6511 structures // it's up to the user to manually do the last 11 :) list = cdk.createMoleculeList() for (i =0; i<100; i++) list.add(mols.get(block*100 + i)); results = metaprint2d.calculate(list) iter = results.keySet().iterator() while (iter.hasNext()) { mol = iter.next(); container = mol.getAtomContainer() js.print(container.getProperty("CAS_NO")) reds = 0 greens = 0 oranges = 0 mp = results.get(mol) for (i=0; i= 0.66) { reds++ } // ratios used in Bioclipse 2.4 else if (ratio >= 0.33) { oranges++ } else if (ratio >= 0.15) { greens++ } } js.say(" r,o,g: " + reds + "," + oranges + "," + greens) } "" }