LogP calculation takes unusually long

Hi,





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:

Code:

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();          logP.setCloridIonConcentration(0);          logP.setNaKIonConcentration(0);          logP.setTakeMajorTatomericForm(true);          logP.setMolecule(mol);          logP.run();          System.out.println( logP.getlogPTrue() );       } catch (Exception e1) {          e1.printStackTrace();          System.err.println("Error");       }    }

Thank you!


Simone

Hi,








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.





Jozsi