Cher Jean, Well, the key point is what is the correct value. If you are able to work this out from the original papers and identify which projects are in error, I am sure the individual projects (or cinfony, if it's my fault) will sort them out.
- Noel On 21 May 2010 09:45, JEAN MARC NUZILLARD <[email protected]> wrote: > Dear Noel, > > I recently started to look at descrptor values from various toolkits, > without initially being aware of a two years old blog post of yours: > http://baoilleach.blogspot.com/2008/04/cheminformatics-toolkit-face-off-logp.html > > I used paracetamol and another test compound (mol1) in order to make > comparisons. > > The result is: > > Paracetamol > =========== > > * Pybel > TPSA: 49.330000 > LogP: 1.423600 > > * RDKit > TPSA: 49.330000 > MolLogP: 1.350600 > > * CDK > TPSA: 49.33 > ALOGP: -1.0852000000000002 > ALOGP2: 1.1776590400000004 > XLOGP: 1.079 > > > Mol1 > ==== > > * Pybel > TPSA: 117.560000 > LogP: 4.719300 > > * RDKit > TPSA: 83.880000 > MolLogP: 4.629500 > > * CDK > TPSA: 117.56 > ALOGP: 1.4521000000000013 > ALOGP2: 2.108594410000004 > XLOGP: 0.7899999999999999 > > Mol1 is described by this smiles chain: > CC(=O)c1ccc(/N=C2\SCCCN2C(=O)c2ccc(CS(C)(=O)=O)cc2)cc1 > > > Even TPSA is not consistent across toolkits. > The diversity of LogP implementations makes difficult > to use published works that rely on LogP values > for the molecule property prediction, > especially when descriptors are calculated > by some not freely available software. > More precisely, I refer to a recently published work > Journal of Molecular Graphics and Modelling 28 (2010) 899?903 > that involves LogP(o/w) as calculated by MOE, which is said to be > different from SLogP when calculated by MOE and by RDKit. > What a jungle for a newcomer in the field! > > As the author of Cinfony, I would like to have your > opinion about the origin of different values > I obtained for TPSA on compound "mol1". > > > Best regards, > > Jean-Marc Nuzillard > > > > ------------------------------------------------------------------------------ > > _______________________________________________ > OpenBabel-discuss mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/openbabel-discuss > ------------------------------------------------------------------------------ _______________________________________________ OpenBabel-discuss mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
