Days #3 and #4 of the CDK Workshop have been\nquite busy indeed, and I have not been able to summarize them so far. After a rather interesting day #2 ,\nthe third day was the last one with scheduled presentations. Kai Hartmann showed how he used the CDK in his systems\nbiology research, and contributed the code he wrote to predict Gibbs energies based on fragment contributions.\nMiguel Rojas showed his MS prediction work, which is based on the CDK too.
\n\nMuch of the rest of day and Thursday continued on the work started yesterday: making the 3D structure builder a\nsingleton class, and applying and testing an optimization for the AllRingsFinder to address\nmolecules like Choloyl-CoA . The trick\nbasically consists of applying the all rings finding algorithm to isolated systems only. The effect is\nconsiderable: the total computation time for Choloyl-CoA decreases by a 93 fold! We found that the\nfingerprints used in the template library for the 3D structure builder are outdated, and Christoph worked\non updating that, which required searching into old archives to find the tool to do just this.
\n\nBecause the above performance fix did not fix the current slow SMILES parsing, Kai looked at the\nDeduceBondOrderTool which is the slow component, and optimized the used algorithm by reusing determined\nmolecular ring systems. Nevertheless, on users requests, a time out mechanism is now available for SMILES\nparsing. Additionally, several of the bugs found on the second workshop day have been fixed. Meanwhile,\nI was distracted by other things. For example, fixing Bioclipse bugs for\nthe version 1.0.1 released yesterday.\nThe SENECA tool is not forgotten too, and last weekend I made some good progress with it,\nwhich Christoph blogged about.