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Ah OK, I see ;) This I don't know, sorry. I have implemented a de novo design tool based on rdkit that made heavy use of the smarts matching accessed via Python. From my experience the substructure matching will probably not be the performance bottleneck (depending on how sophisticated your scoring functions is, of course). Something you might want to consider regarding the performance of SMARTS queries is the SMARTS themselves. This is a quote from the daylight page http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html: Efficiency Considerations The Daylight 4.x SMARTS Toolkit provides a function, dt_smarts_opt(), which automatically optimizes a SMARTS by reordering, expanding, and/or consolidating atom and bond expressions. Programs which use this feature (e.g. the Merlin program) can be expected to be near optimal in terms of the time used to search typical organic structures. When this optimization method is not used, there are some things which can be done to facilitate efficient (fast) searching operations using SMARTS. It is important to recognize that SMARTS target strings are processed in strictly left-to-right order. For this reason, substantial gains in speed can be achieved by following these guidelines:
I understand that the SMARTS you want to use have already been designed, and of course what is stated by daylight refers to the their implementation. But (a) I think it applies to the rdkit implementation as well (please correct me if I'm wrong here, Greg) and (b) in case performance is really critical this could be another point to look at. Best, Markus On 04/25/2013 04:13 PM, Nicholas Firth wrote: Hi Markus, --
Markus Hartenfeller Chemoinformatics Specialist Molecular Health GmbH Belfortstr. 2 69115 Heidelberg Germany Tel: +49 6221 43851 209 Fax: +49 6221 43851 100 Email: [email protected] www.molecularhealth.com ---------------------------------------------------------- Molecular Health GmbH Geschaeftsfuehrer: Dr. Stephan Brock/ Dr. Friedrich von Bohlen und Halbach Sitz der Gesellschaft: Heidelberg Handelsregister: Amtsgericht Mannheim - HRB 338037 ---------------------------------------------------------- |
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