Hi Jeremy,
iirc you have to write mol = Chem.AddHs(mol).
In your code you are not keeping the object with the added Hs so there are
no explicit Hs to find when you iterate.
Cheers,
Fio
On Sat, Oct 7, 2023 at 9:36 PM Jeremy Monat wrote:
> In Python, I'd like to iterate through all the atoms in
Hi everyone,
We are currently looking for a chemoinformatician/computational chemist at
insitro in my group, Computational Drug Design within the Drug discovery
department. We are considering candidates at various levels and also entry
level after a PhD or Masters. See more details here:
raw.
>
> [image: Screen Shot 2021-06-27 at 5.20.55 PM.png]
>
> Hopefully that's all that it was, but please let me know if there was some
> other error you noticed.
>
> Best,
> Matt
>
>
>
> On Sun, Jun 27, 2021 at 3:34 PM Fiorella Ruggiu
> wrote:
>
>> Errat
Errata: My previously given solution actually doesn't work.
On Sun, Jun 27, 2021 at 12:10 PM Fiorella Ruggiu
wrote:
> Hi all,
>
> I initially wrote an fmoc smarts reaction to deprotect molecules as the
> following:
> reaction_smarts='[#7:1]C(=O)OCC1c2c2-c3c13>&
Hi all,
I initially wrote an fmoc smarts reaction to deprotect molecules as the
following:
reaction_smarts='[#7:1]C(=O)OCC1c2c2-c3c13>>[#7:1]'
Here's an example where this fails:
from rdkit import Chem
from rdkit.Chem import AllChem
Hi Ling,
The initial smiles you wrote represents radical carbons with 3 unpaired
valence electrons each as they don't have hydrogens and hence even after
removing the isotope information, the smiles reflect this. I believe you
wanted to write ethane with isotope 13 carbons: '[13CH3][13CH3]'. Your
Hi Francois,
not sure if you have solved this yet. I believe it won't be possible to use
AllChem.ReplaceSubstructs without breaking the rings or enumerating them.
You can however use reactions for this problem. Here's an example based on
yours:
mol = Chem.MolFromSmiles('O=c1[nH]1')
rxn =
er issues with the
> TautomerEnumerator:
> https://github.com/rdkit/rdkit/pull/3327
>
> As soon as it will be merged in the main trunk this functionality will be
> available.
>
> Hope that helps, cheers
> p.
>
> On Thu, Aug 27, 2020 at 9:08 PM Fiorella Ruggiu
> wrote:
>
>
Hi Mark,
it's best to add the hydrogens first and then set your coordinates:
m=Chem.MolFromSmiles('Nc1nnc2n1CCS2')
m2=rdmolops.AddHs(m, False, True);
Chem.rdCoordGen.AddCoords(m2)
Best,
Fio
On Thu, Aug 27, 2020 at 11:25 AM Mark Mackey wrote:
> Hi all,
>
>
>
> I’m trying to generate a 2D
Hi everyone,
I am cleaning up molecules to import into our database and canonicalizing
the tautomer using rdkit in python. Some cases result in a time-out and do
not go into my except to be caught. I would like to try setting the
maxTautomer to lower than 1000. I found there was no direct option
Hello Mike,
you could create a function with your if else structure and use apply on
the pandas dataframe. For example, if you have a SMILES column in your df:
def addMol(smiles):
if Chem.MolFromSmiles(smiles) is None:
Etc
return None # or whatever you
Hi everyone,
I tried to virtually deprotect molecules using
the AllChem.ReplaceSubstructs() function. Stereochemistry of adjacent atoms
gets inverted in ChiralTag but not in _CIPCode. This gives me the wrong
output SMILES:
from rdkit import Chem
from rdkit.Chem import AllChem
from
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