I'm using the logp plugin to get the logPtrue value, and it seems very slow. If I run this against 2000 smiles it takes 77 seconds, compared with another vendor's logp which takes 7 seconds. Am I doing anything wrong ? Tests are run on the same hardware.
final Molecule mol = MolImporter.importMol(smiles);
plugin = new logPPlugin ();
The logP calculation speed was improved recently. I calculated the logP value of approx. 50000 molecules using the 5.2 version. Calculation speed was about 180 molecule/sec.
May be you have an old version of logP calculator.
Sorry I misstyped: The improved speed available from 5.1.4. So you can download the new version 5.1.05 as you say. It will be more fast than the older versions.
I'm using the latest jar and I'm not getting any where near 180 Molecules per second more like 22 per sec.
Could you send me the smiles / structure list you use for your test ? (I can't supply you with my list).
With those test smiles I'm getting 180 mol per sec, but our compounds are more complex and I get 29 mol per sec compared to 330 mol per from our other vendor.