Re: [Rdkit-discuss] FW: rdkit - ctest mulitiple failures
Dear Ryan, I recently got the same ctest failure messages as those you reported. After typing 'make', I did not type 'make install' before typing 'cest'. After typing 'make install', I obtained 100% success for 'ctest'. Even though identical effects may have different origins, I hope my observation will help you. Best regards, Jean-Marc Nuzillard -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] unreadable SD File
Dear Jean-Marc, On Tue, Apr 3, 2012 at 10:41 PM, JEAN-MARC NUZILLARD jm.nuzill...@univ-reims.fr wrote: I have generated 265 isomers of zadirachtin, a natural product. When I tried to use RDKit for the creation of 2D depictions, one of the structures failed to be read. The corresponding SD file with the only problematic structure is attached. I generated a depiction by myself that is also attached (as a postscript file). It seems to be a bug in the ring-finding code. The algorithm expects to be able to find 8 rings, but it can actually only find 7. I will try and track this down over the next few days and let you know when I've found it. Best Regards, -greg -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKit-based implementation of QED (quantitative estimation of drug-likeness)
Hi Gregory (long time since we met)! Why did you use your own 11 smarts for hydrogen bond acceptors instead of rdkit's CalcNumHBA or NumHAcceptors ($([O,S;H1;v2]-[!$(*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),$([N;v3;!$(N-*=!@[O,N,P,S])]),$([nH0,o,s;+0]))? The reason why I used a different implementation for the calculation of hydrogen bond acceptors (HBA) is indeed as you described already: the HBA values in the (limited) examples of the original publication are quite different than those returned by RDKit's NumHAcceptors method. Interesting, the correspondence for the hydrogen bond donors seemed to be OK, but - again - there are not too many examples provided in the supporting materials to really check this. I compared your implementation with PipelinePilot and rdkit, and it correlates better with PP (r^2=0.978) than rdkit (0.916). Maybe Greg you can comment on this? (In PipelinePilot, HBA is described as number of heteroatoms (Oxygen, Nitrogen, Sulfur, or Phosphorus) with one or more lone pairs, excluding atoms with positive formal charges, amide and pyrrole-type Nitrogens, and aromatic Oxygen and Sulfur atoms in heterocyclic rings) On your website, you mention that discrepancies can be noted in the results from the logP calculations; I agree that the end result won't be much different using MolLogP vs. ALogP. Interesting is that both PP and RDKit's MolLogP are using the same method. With RDKit this can be validated (I didn't do this though), but with PP it can't... But to be consistent I collected the structures of the 771 drugs mentioned in the original publication, calculated their MolLogP using rdkit, and fitted the binned distribution using the described approach. 700 compounds out of 771 gave the same ALogP as listed in the original paper (i.e. same structure), however for the 71 remaining drugs some discrepancies were observed, maybe due to different structures (I collected them from PubChem) or a different version of Pipeline Pilot (I used version 8.5). I ended up with a bin size of 0.97 and the following parameters: a 0.486849448 b 186.2293718 c 2.066177165 d 3.902720615 e 1.027025453 f 0.913012565 Dmax 145.43148 Thanks! I'll add these to the implementation. - Hans Feel free to use them! Best, Grégori -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKit-based implementation of QED (quantitative estimation of drug-likeness)
Gregory -the update QED is online.Thx for the contribution.- Hans www.silicos-it.comA division of Imacosi bvbaDe Roskam 35,2970 SchildeBelgium On 04 Apr 2012, at 16:07, Gerebtzoff, Gregori wrote:Hi -A RDKit-based implementation of the QED measure as described by Richard Bickerton (Nature Chemistry, 2012, 4, 90-98) has been implemented and made available for download from our website ( www.silicos-it.com Biscu-it).Regards,- HansHi Hans,Thanks for the implementation!Why did you use your own 11 smarts for hydrogen bond acceptors instead of rdkit's CalcNumHBA or NumHAcceptors ($([O,S;H1;v2]-[!$(*=[O,N,P,S])]),$([O,S;H0;v2]),$([O,S;-]),$([N;v3;!$(N-*=!@[O,N,P,S])]),$([nH0,o,s;+0]))?I compared your implementation with PipelinePilot and rdkit, and it correlates better with PP (r^2=0.978) than rdkit (0.916). Maybe Greg you can comment on this?(In PipelinePilot, HBA is described as "number of heteroatoms (Oxygen, Nitrogen, Sulfur, or Phosphorus) with one or more lone pairs, excluding atoms with positive formal charges, amide and pyrrole-type Nitrogens, and aromatic Oxygen and Sulfur atoms in heterocyclic rings")On your website, you mention that "discrepancies can be noted in the results from the logP calculations"; I agree that the end result won't be much different using MolLogP vs. ALogP.But to be consistent I collected the structures of the 771 drugs mentioned in the original publication, calculated their MolLogP using rdkit, and fitted the binned distribution using the described approach.700 compounds out of 771 gave the same ALogP as listed in the original paper (i.e. same structure), however for the 71 remaining drugs some discrepancies were observed, maybe due to different structures (I collected them from PubChem) or a different version of Pipeline Pilot (I used version 8.5).I ended up with a bin size of 0.97 and the following parameters:a 0.486849448b 186.2293718c 2.066177165d 3.902720615e 1.027025453f 0.913012565Dmax 145.43148Feel free to use them!Best,Grégori--Better than sec? Nothing is better than sec when it comes tomonitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free.http://p.sf.net/sfu/Boundary-dev2dev___Rdkit-discuss mailing listRdkit-discuss@lists.sourceforge.nethttps://lists.sourceforge.net/lists/listinfo/rdkit-discuss-- Better than sec? Nothing is better than sec when it comes to monitoring Big Data applications. Try Boundary one-second resolution app monitoring today. Free. http://p.sf.net/sfu/Boundary-dev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
