Thanks for sharing the Colab. I didn't know about !pip install rdkit-pypi
On Tue, Mar 22, 2022 at 9:37 AM Jan Halborg Jensen <jhjen...@chem.ku.dk> wrote: > The SMILES I sent you works fine for me with the same version: > https://colab.research.google.com/drive/19OZtX8IqICZQ4B2jLpr02owkSLc0FeZ6?usp=sharing > > However, the alkali and alkaline earth metals do not behave as I would > expect (as shown in the Colab notebook). This looks like a bug to me and I > suggest filing a GitHub issue > > Best regards, Jan > > On 22 Mar 2022, at 15.26, Marco Stenta <marco.ste...@gmail.com> wrote: > > Thanks, Jan, > the dative bond works in a number of cases with other metals. (rdkit > 2021.9.5) > This one works fine: > > rdmol = Chem.MolFromSmiles('[O-]->[Fe+2]<-[O-]', sanitize=True) # case 1 > coordinate bonds > assert rdmol is not None > > this one with Mg divalent does not > > rdmol = Chem.MolFromSmiles('[O-]->[Mg+2]<-[O-]', sanitize=True) # case 1 > coordinate bonds > assert rdmol is not None > > > > can you read in the smiles you sent me? I can't > I am doing anything wrong here? > cheers, > m > > rdmol = Chem.MolFromSmiles('C1CO->[Fe+2](O)(<-OC1)(<-O)(<-O)(<-O))=O', > sanitize=True) # case 1 coordinate bonds > assert rdmol is not None > print(rdmol) > > > Il giorno mar 22 mar 2022 alle ore 15:13 Jan Halborg Jensen < > jhjen...@chem.ku.dk> ha scritto: > >> Hi Marco >> >> You can define dative bonds like >> this: C1CO->[Fe+2](O)(<-OC1)(<-O)(<-O)(<-O) >> >> Best regards, Jan >> >> On 22 Mar 2022, at 15.07, Marco Stenta <marco.ste...@gmail.com> wrote: >> >> You don't often get email from marco.ste...@gmail.com. Learn why this is >> important <http://aka.ms/LearnAboutSenderIdentification> >> Dear RDKitters, >> I am struggling with working organometals and coordination complexes. >> with a small team, we are creating a series of recommendations to draw >> correctly organometals (catalyst, complexes, etc), so that we can use them >> in our chemoinformatics pipeline. >> >> I know it is a horrible mess out there, but we are trying to achieve some >> consistency, rather than full correctness. >> >> I guess there is something with the accepted valence for Mg. >> >> Now the purpose of this is to have a smiles representation of these metal >> complexes that are not fragmented (with the dot) so that I keep the notion >> of bond where there is (or I believe) one >> >> for instance, for the edta complex this smiles works fine: >> [Na+].[Na+].[Mg++].[O-]C(=O)CN(CCN(CC([O-])=O)CC([O-])=O)CC([O-])=O >> >> but I would really distinguish the fact that there is a bond between the >> [O-]/N and the [Mg++ ] while there is none with the two [Na+] >> >> <image.png> >> I can read it in without sanitization, but it fails for everything I >> nato to do after with the molecules. >> >> >> in theory, dative bonds should not affect the valence of receiving atoms, >> right? >> >> any suggestion for reading in the enclosed v3000 molfile and keeping the >> bonding info? >> or sharing what you are doing with metals >> >> Thanks a lot in advance, >> >> kind regards >> >> Marco >> >> f1 = 'edta_case.mol' >> >> rdmol = Chem.MolFromMolFile(f1, sanitize=True) >> print(rdmol) >> Chem.MolToSmiles(rdmol) >> >> the rdmol is None in my case >> >> >> >> >> >> <edta_case.mol>_______________________________________________ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> >> https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Frdkit-discuss&data=04%7C01%7Cjhjensen%40chem.ku.dk%7C9b36a1f64d3f4a5a243808da0c0dae6b%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637835550154504697%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=E2VK%2BP1lGqICkgnNtQPHpmEDUuD0qV6VbD0FZNt7w5I%3D&reserved=0 >> <https://eur02.safelinks.protection.outlook.com/?url=https%3A%2F%2Flists.sourceforge.net%2Flists%2Flistinfo%2Frdkit-discuss&data=04%7C01%7Cjhjensen%40chem.ku.dk%7Cd425f328d6fb4b92eb5e08da0c10033a%7Ca3927f91cda14696af898c9f1ceffa91%7C0%7C0%7C637835560155987046%7CUnknown%7CTWFpbGZsb3d8eyJWIjoiMC4wLjAwMDAiLCJQIjoiV2luMzIiLCJBTiI6Ik1haWwiLCJXVCI6Mn0%3D%7C3000&sdata=2aw1SMBTere6vDXsJv2Ae3hfrQvgmUI6ZX29LlkuJpI%3D&reserved=0> >> >> >> > _______________________________________________ > Rdkit-discuss mailing list > Rdkit-discuss@lists.sourceforge.net > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss >
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