On 1 June 2012 11:22, <[email protected]> wrote: > Pity! ALogP is one of the most popular and potentially useful descriptors >
Agree. The code is obviously buggy, needs a volunteer to fix it up :) Nina P.S. unfortunately nobody picked up my last year challenge for a good open source LogP model ... http://www.opentox.org/pipermail/development/2011/001575.html > -----Original Message----- > From: Nina Jeliazkova [mailto:[email protected]] > Sent: 01 June 2012 09:01 > To: Lawson Kevin GBJH > Cc: [email protected] > Subject: Re: [Cdk-user] ALOGP Descriptor > > Kevin, > > Better not use ALogP at all. Back at the list you could find reports > it is not performing well. I think it was decided to be removed / > deprecated. > > Best regards, > Nina > > On 1 June 2012 10:58, <[email protected]> wrote: >> Hi >> >> >> >> I am getting some strange results from the ALOGP descriptor algorithm. >> LICSS uses the following code to prep molecules for descriptor calculation: >> >> >> >> atomContainer = sp.parseSmiles(s); >> >> >> >> AtomContainerManipulator.percieveAtomTypesAndConfigureAtoms(atomContainer); >> >> >> CDKHueckelAromaticityDetector.detectAromaticity(atomContainer); >> >> CDKHydrogenAdder ha = >> CDKHydrogenAdder.getInstance(DefaultChemObjectBuilder.getInstance()); >> >> ha.addImplicitHydrogens(atomContainer); >> >> >> AtomContainerManipulator.convertImplicitToExplicitHydrogens(atomContainer); >> >> >> >> With this preparation, the ALOGP descriptor returns 0.0 for both the Smiles >> c1ccccc1 and for c1ncccc1 (benzene and pyridine) >> >> I also ran the first 1000 compounds from the Wellcome AntiMalarial dataset >> through the calculation. As you can see from the attachment (the first 250 >> compounds), >> >> the values are usually much lower than the quoted values in the data set (~4 >> log units on average) and are, indeed usually obviously too low. >> >> >> >> To check that I wasn't making a mistake with the submission code, I ran all >> 1000 compounds through Rajarshi's CDK Descriptor calculator: >> >> http://rguha.net/code/java/cdkdesc.html with identical results (Rajarshi's >> calculator also returns 0.0 for benzene). I have also converted the >> >> compounds to Kekule form using the FixBondOrdersTool. Results are >> different, but no better! (also in the attached file). I have tried >> changing the >> >> order of the preparation steps but it doesn't make any difference to the >> results. >> >> >> >> Any thoughts? >> >> >> >> Best wishes >> >> >> >> Kevin >> >> >> >> >> >> ________________________________ >> This message may contain confidential information. If you are not the >> designated recipient, please notify the sender immediately, and delete the >> original and any copies. Any use of the message by you is prohibited. >> >> ------------------------------------------------------------------------------ >> Live Security Virtual Conference >> Exclusive live event will cover all the ways today's security and >> threat landscape has changed and how IT managers can respond. Discussions >> will include endpoint security, mobile security and the latest in malware >> threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ >> _______________________________________________ >> Cdk-user mailing list >> [email protected] >> https://lists.sourceforge.net/lists/listinfo/cdk-user >> > > > > > This message may contain confidential information. If you are not the > designated recipient, please notify the sender immediately, and delete the > original and any copies. Any use of the message by you is prohibited. > ------------------------------------------------------------------------------ > Live Security Virtual Conference > Exclusive live event will cover all the ways today's security and > threat landscape has changed and how IT managers can respond. Discussions > will include endpoint security, mobile security and the latest in malware > threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ > _______________________________________________ > Cdk-user mailing list > [email protected] > https://lists.sourceforge.net/lists/listinfo/cdk-user ------------------------------------------------------------------------------ Live Security Virtual Conference Exclusive live event will cover all the ways today's security and threat landscape has changed and how IT managers can respond. Discussions will include endpoint security, mobile security and the latest in malware threats. http://www.accelacomm.com/jaw/sfrnl04242012/114/50122263/ _______________________________________________ Cdk-user mailing list [email protected] https://lists.sourceforge.net/lists/listinfo/cdk-user
