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
>
>
>
>
>
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