Hi Per
Just by looking at your code I would assume you have a sanitization issue. You
create your pentane molecule and then add H’s. This will saturate each single
carbon. When you then add a bond between the two fragments your atom 3 will
have a valence of 5 and this causes issues.
Maybe do the
Hi Nikolaus and Ling,
Thanks for your help (the atom numbe shouldnt be 43 but it still gives the
error I will clarify)- yes Nikolaus you are right it is a sanitization
issue and in this case I am trying to use it as a molecular editor to build
a model molecule (a transition state model to be exact
Hello,
This might be a nit picky question. I am attempting to read in the smiles
string for the 1.7 million non-biological compounds in the latest chembl23
release. As it turns out 382 compounds fail to be read by RDkit.
The errors are either kekulization failure or valence errors.
Has anyone
Hi Brian,
It's not that surprising. The RDKit is stricter about allowing unreasonable
chemistry that the tool the ChEMBL group uses to produce SMILES or mol
blocks.
There are always some molecules that the RDKit just won't process.
If you are concerned and see any in that group of failures that y
From: Bennion, Brian
Sent: Monday, August 07, 2017 11:39
To: 'Konrad Koehler'
Subject: RE: [Rdkit-discuss] using rdkit to read in chembl23 1.7 million
compounds
Hello Konrad,
Thank you for your response.
For the handful of compounds i looked at:
multiple ringed compounds that had %11 up to %14
Hi Brian, Konrad,
Just a sidenote - It's not a crash. Python/Boost is just complaining, that
the first argument is in fact None and it should be RDKit Mol instance.
Instead of filtering all lowercase s from smiles, you should check if mol
is None in your for loop, and skip those which are.
P
I've not tried to read in ChEMBL but I have tried to process other large
datasets e.g. ZINC. My impression was that problems arose with small
heterocyclic systems, particularly if fused or containing multiple different
heteroatoms. I did wonder if the different aromaticity models might be the
i
The carbocations are in small heterocyclic molecules. see CHEMBL3815233
Brian
From: Chris Swain
Sent: Monday, August 7, 2017 11:46:30 AM
To: rdkit-discuss@lists.sourceforge.net
Subject: [Rdkit-discuss] . Re: using rdkit to read in chembl23 1.7 million
compounds
That molecule's SMILES is correctly rendered by RDKit, or at least by the
version of RDKit behind Slack:
[image: Inline image 1]
-P.
On Mon, Aug 7, 2017 at 3:54 PM, Bennion, Brian wrote:
> The carbocations are in small heterocyclic molecules. see CHEMBL3815233
>
> Brian
>
>
>
Hello Peter,
Great, that just made me realize that I was not using my most recent conda
environment version of RDkit.
I reread the 2D sdf file with the latest rdkit version and now only 31
molecules are tossed out by the SDMolsupplier in RDKit. 51 compounds had
errors when reading in the smiles
Hi Per,
I can think of 2 approaches to solve this.
The 1st is to have fragments of molecules that have an explicit connection
point, i.e. OH[*] and C[*], and use RDKit's functionality of combining
fragments.
The 2nd is to use define a reaction for this using SMIRKS or Reaction
SMILES, i.e. [O
I don't think I understand the question. The Conformer object is normally
attached to/associated with a mol object.
-greg
On Sun, Aug 6, 2017 at 11:41 AM, Per Jr. Greisen wrote:
> Thanks - worked perfectly if I was to do this conformers is there an easy
> way to transform between conformer obj
The other answers on this thread have been right on point with the
exception of neglecting to explicitly encourage you to call
Chem.SanitizeMol() on your joined molecule before you do anything else with
it. In your case you'd call:
Chem.SanitizeMol(back)
This will lead to the error that Nik explain
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