2 days ago :-) https://github.com/cdk/cdk/commit/dfbc32822e7d471bfb5a60aaf39a701371541280
On Fri, 26 Nov 2021 at 19:11, Andres Fernando Bernal Escobar < andresf.bern...@utadeo.edu.co> wrote: > 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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If you are not the intended recipient, you are >>> hereby notified that any disclosure, copying, distribution, or any other >>> use of the information is strictly prohibited and has legal repercussions. >>> Therefore, if you have received this document by mistake, please notify the >>> sender immediately and destroy this document and attachments without making >>> any copy of any kind. >>> This message has been tested by antivirus software. Nonetheless, the >>> Universidad de Bogotá Jorge Tadeo Lozano assumes no liability for any >>> damages or loss of any kind that might arise from the use of, misuse of, or >>> the inability to use the materials contained on this electronic message. It >>> is the responsibility of the recipient to verify by his own means the >>> presence of a virus or any other harmful components, defects or errors. >> >> > *ADVERTENCIA SOBRE CONFIDENCIALIDAD* > > Las opiniones expresadas en el presente mensaje no representan > necesariamente la opinión oficial de La Universidad de Bogotá Jorge Tadeo > lozano. La información contenida en este correo electrónico, incluyendo sus > anexos, está dirigida exclusivamente a su destinatario y puede contener > datos de carácter confidencial protegidos por la ley. Si usted no es el > destinatario de este mensaje por favor infórmenos y elimínelo a la mayor > brevedad. Cualquier retención, difusión, distribución, divulgación o copia > de éste mensaje es prohibida y será sancionada por la ley. > > Este mensaje ha sido sometido a programas antivirus. No obstante, La > Universidad de Bogotá Jorge Tadeo lozano no asume ninguna responsabilidad > por eventuales daños generados por el recibo y uso de este material, siendo > responsabilidad del destinatario verificar con sus propios medios de la > existencia de virus u otros defectos. > > *WARNING ABOUT CONFIDENTIAL INFORMATION* > > The opinions expressed herein do not necessarily reflect the positions of > the Universidad de Bogotá Jorge Tadeo Lozano. The information contained in > this electronic mail and attachments is confidential and intended only for > the use of the individual or entity to whom it is addressed and may have > confidential data. If you are not the intended recipient, you are hereby > notified that any disclosure, copying, distribution, or any other use of > the information is strictly prohibited and has legal repercussions. > Therefore, if you have received this document by mistake, please notify the > sender immediately and destroy this document and attachments without making > any copy of any kind. > This message has been tested by antivirus software. Nonetheless, the > Universidad de Bogotá Jorge Tadeo Lozano assumes no liability for any > damages or loss of any kind that might arise from the use of, misuse of, or > the inability to use the materials contained on this electronic message. It > is the responsibility of the recipient to verify by his own means the > presence of a virus or any other harmful components, defects or errors. > _______________________________________________ > Cdk-user mailing list > Cdk-user@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/cdk-user >
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