Hi John, Thanks for the fix. When will it be merged into the main branch? Andrés
El vie, 26 de nov. de 2021 a la(s) 03:21, John Mayfield ( john.wilkinson...@gmail.com) escribió: > Hi Andres, > > Excellent analysis - thank you. Good to see that the recent Phenol change > should bring things more in agreement. > > John > > On Wed, 24 Nov 2021 at 21:29, Andres Fernando Bernal Escobar < > andresf.bern...@utadeo.edu.co> wrote: > >> Hello John, thanks for your answer. I ran a quick comparison between CDK >> and PubChem, with a few hand-picked molecules. These are the results: >> https://docs.google.com/spreadsheets/d/1yl3b05W319ZQW5K9TZf0iMYHbPoJyP5BV8QMLhf1kLE/edit?usp=sharing >> >> I split the molecules in four subsets. The first comprises seemingly >> non-problematic molecules: carboxylic acids, amines, aliphatic esters, >> aliphatic ethers. In these cases CDK, PubChem and my own intuition are all >> in agreement. >> >> The second subset comprises molecules where I think CDK is wrong and >> PubChem is correct: phenols. This is due to the issue that you corrected in >> the branch you linked. >> >> The third subset comprises molecules where I think CDK is correct and >> PubChem is wrong: aromatic ethers, amides, nitro compounds. In the case of >> aromatic ethers, we know CDK explicitly introduces a correction to exclude >> aromatic ether oxygens from the HB acceptors count. I am not a specialist, >> but I understand there are sound reasons to make this exception. PubChem >> doesn't seem to implement it. In the case of amides and nitro compounds I >> don't quite understand what is going on with PubChem, but CDK's answer >> seems the correct one to me. >> >> The last subset comprises aromatic esters (acyloxy substituents). I >> honestly don't know what is correct in this case. Are oxygen atoms from >> aromatic esters also an exception, just as those from aromatic ethers? That >> would mean CDK is right. Otherwise, another correction is needed to make >> sure CDK excludes no oxygens on aromatic rings other than those of ethers. >> >> El mar, 23 de nov. de 2021 a la(s) 04:27, John Mayfield ( >> john.wilkinson...@gmail.com) escribió: >> >>> Thanks for your email. I've always thought the CDK HBond acceptor/donor >>> code is a little wonky and needs investigating. I don't have time to look >>> deeply at it but yes my reading of this is it doesn't check for the ether >>> oxygen correctly. If someone was inclined checking CDK's (and RDKit's) >>> values with PubChem would be a quick project that may provide some insight >>> onto missed cases and disagreements. >>> >>> I've made a change here to get the correct value for phenol: >>> https://github.com/cdk/cdk/compare/bug/hbondacceptor?expand=1 >>> >>> On Fri, 15 Oct 2021 at 11:27, Guillermo Restrepo < >>> guillermo.restr...@mis.mpg.de> wrote: >>> >>>> We are working with some descriptors taken from Reaxys database, which >>>> according to its owner are computed using your CDK library. We found >>>> something unexpected and would very much appreciate it if you could >>>> help >>>> us to understand. >>>> >>>> We noted that some phenols are reported as having 0 hydrogen bond >>>> acceptors, whereas we expected them to have at least one. We checked >>>> CDK >>>> source code and found this comment on HBondAcceptorCountDescriptor.java: >>>> >>>> The following groups are counted as hydrogen bond acceptors: >>>> - any oxygen where the formal charge of the oxygen is non-positive >>>> (i.e. >>>> formal charge <= 0) except >>>> - an aromatic ether oxygen (i.e. an ether oxygen that is >>>> adjacent >>>> to at least one aromatic carbon) >>>> - an oxygen that is adjacent to a nitrogen >>>> - any nitrogen where the formal charge of the nitrogen is non-positive >>>> (i.e. formal charge <= 0) except >>>> - a nitrogen that is adjacent to an oxygen >>>> >>>> The way we understood it, this means that phenols should have at least >>>> one hydrogen bond acceptor. But further down in the same file, these >>>> lines seem to specify otherwise: >>>> >>>> // looking for suitable oxygen atoms >>>> else if (atom.getAtomicNumber() == IElement.O && >>>> atom.getFormalCharge() <= 0) { >>>> //excluding oxygens that are adjacent to a nitrogen or >>>> to an aromatic carbon >>>> List<IBond> neighbours = >>>> ac.getConnectedBondsList(atom); >>>> for (IBond bond : neighbours) { >>>> IAtom neighbor = bond.getOther(atom); >>>> if (neighbor.getAtomicNumber() == IElement.N || >>>> (neighbor.getAtomicNumber() == IElement.C && >>>> neighbor.isAromatic() && >>>> bond.getOrder() != IBond.Order.DOUBLE)) >>>> continue atomloop;; >>>> } >>>> hBondAcceptors++; >>>> } >>>> >>>> Is this intended, or is it a bug, or are we misunderstanding something? >>>> >>>> >>>> >>>> _______________________________________________ >>>> Cdk-user mailing list >>>> Cdk-user@lists.sourceforge.net >>>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>>> >>> _______________________________________________ >>> Cdk-user mailing list >>> Cdk-user@lists.sourceforge.net >>> https://lists.sourceforge.net/lists/listinfo/cdk-user >>> >> >> >> -- >> >> >> *Andrés Bernal* >> *Área de Ciencias Básicas y Modelado* >> *Profesor Asociado* >> Ext. 1705 >> andresf.bern...@utadeo.edu.co >> Dirección Utadeo: Carrera 4 # 22-61 >> >> >> >> *ADVERTENCIA SOBRE CONFIDENCIALIDAD* >> >> Las opiniones expresadas en el presente mensaje no representan >> necesariamente la opinión oficial de La Universidad de Bogotá Jorge Tadeo >> lozano. 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