LogP calculation takes unusually long

User 036058eabf

07-04-2008 13:09:56


I've found that, while for most molecules the LogP calculation (using the LogP plugin) takes a fraction of a second, for some molecules it takes really long, up to an hour and half in a few cases (on a Intel Core2 Duo system).

The problem seems to be related to the size of the molecule, but not always.

I've collected the molecules which LogP calculation took more than 5 seconds, and attached them in a csv file (the first column is the time in milliseconds).

Those molecules come from a ~150k molecules screening, so it's really a small percentage; it's not really a problem for me, and this is just a report. Anyway, I think that a way to set a time limit, just like other plugins, would be useful.

A small snippet to try this:

   public static void main(String[] args) {

      try {

         System.out.println( "starting..." );

         Molecule mol = MolImporter.importMol("[H]N1C([H])=C(C(=O)N([H])C1=O)[C@]1(OC(=O)N([H])c2c([H])c([H])c(Cl)c([H])c12)[C@]1(OC(=O)N([H])c2c([H])c([H])c(Cl)c([H])c12)c1nc(SC([H])([H])C([H])([H])[H])c(Br)c(n1)N([H])C1=C(C(=O)N([H])C(=O)N1OC1=C([H])C(=O)N([H])c2c([H])c([H])c(Cl)c([H])c12)C([H])([H])C([H])([H])[H]");

         logPPlugin logP = new logPPlugin();






         System.out.println( logP.getlogPTrue() );

      } catch (Exception e1) {





Thank you!


User 851ac690a0

07-04-2008 21:15:06


Thanks for this info.

This step is the most time consuming in your code: "logP.setTakeMajorTatomericForm(true)"

Try to calculate the logP in two different ways.

a.) first run without tautomerization

b. ) second run with tautomerization (at night)

May be you will get significant difference between the a.) and the b.) running.

We are going to build a "time limit" option into the tautomer generator.

The new release (5.0.3) will come on the next week.