Hi Thorsten, Thorsten Meinl <[EMAIL PROTECTED]> schrieb am 27.08.2008 12:13:58:
> > just some comments from my side: First: Yes, it would be very useful to > > automatically add the hydrogens or to be able to configure the SDF_to_CDK > > node to do so. At least, there should be some kind of an error hint if the > > hydrogens are missing. > Already in the SDF->CDK node? I thought about adding them in the XLogP > node if necessary. Are there any situations, where explicit hydrogens > can hurt? If not, then we can really do this upon conversion to CDK. I have just compared "Molecular Properties" results with and without use of the "Hydrogen Adder". There are differences regarding TPSA, Molweight, HB_Donors and even the number of rotatable bonds. That means that these module also use the structures as they are - without adding hydrogens. Therefore the SDF_CDK node should be used to add the hydrogens, or even the SDF_Reader. I think that should be discussed with the CDK people who know what is calculated inside the nodes. I cannot imagine a situation were it is useful to use structures without hydrogens. Of course there are also ions, but than there should be a charged heavy atom and certainly the "Hydrogen Adder" will than add extra or less Hs, respectively. > > TPSA: > > There is a good correlation for nearly all compounds but not for that one > > with sulfur. I suggest to make it possible to configure the node regarding > > the inclusion/exclusion of sulfur (and phosphorus). > What exactly do you mean with that? Should molecules with S or P > excluded from the calculation (what is TPSA BTW :-*))? The PSA is the "polar surface area" of a molecule in Angstrom^2. It is the sum of the accessible surfaces of oxygen and nitrogen atoms and directly connected hydrogen atoms. Depending on the definition, sometimes also sulfurs and phosphoruses are included. Obviously the 3D structure of a molecule is needed to calculate the accessible surface but Peter Ertl et al. developed a fragment based method for its calculation - called Topological PSA (TPSA). Of course, molecules with S or P shall not be excluded from the calculation. The question is only if these S and P are included in the calculation of the TPSA or not. Since some people will like to include them and others not I suggest to make this configurable or to offer two different TPSA types in the Mol Prop node. > > Preferably, one should be able to configure the Molecular Property node > > regarding the used definition. > Hm, I have to check, if the CDK descriptors offer such a possibility. Or, as stated above, offer different types of descriptors, for instance TPSA+S and TPSA or different rotatable bond number counts etc. With best regards Christian ------------------------------------------------------------------------- This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK & win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100&url=/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
