Yes, this is a well known problem: first of all, if there is more than one
chemist present, you can always have a long discussions about what the most
stable tautomeric form of a given compound (under certain conditions) might be,
however, in case of InChI, if you ask the algorithm for the
Dear Jennifer,
Many thanks for your response. Very useful tutorial on Inchi. I did not
know about the FixedH option:
inchi = Chem.MolToInchi(mol, options='/FixedH')
Best,
Alexis
On Tue, 18 Jun 2019 at 13:20, Jennifer Hemmerich
wrote:
> Dear Alexis,
>
> if you calculate the Standard Inchi it
Dear Jörg,
I have tried to put together a simple example of constrained alignment
using a constraintMap.
The gist is here:
https://gist.github.com/ptosco/d948935d41c9f2ab6cae958da56b50a4
while its HTML counterpart (easier for visualizing 3Dmol.js objects) is
here:
Dear Alexis,
if you calculate the Standard Inchi it is invariant to tautomers (see
here: https://www.inchi-trust.org/technical-faq-2/#6.1). Therefore the
information which tautomer was converted is lost due to the Inchi
conversion. If you want to keep the tautomer information you need to use
Dear RdKiters,
Why is it that the stable tautomer of the following structure is lost
during inchi/smiles conversion?
[image: image.png]
mol = Chem.MolFromSmiles(*"Cc1ccc([nH]nc2)c2c1"*)
inchi = Chem.MolToInchi(mol)
mol = Chem.MolFromInchi(inchi)
smiles = Chem.MolToSmiles(mol)
print(smiles)
On 18/06/2019 05:41, Mario Lovrić wrote:
Dear all,
Is there any paper discussing some sort of pre-selection/feature
selection with fingerprints?
I know of this one at least:
---
Bender, A., Mussa, H. Y., Glen, R. C., & Reiling, S. (2004). Molecular
similarity searching using atom
Hi Paolo, works like a charm. I did not know you can pass the CID directly,
so had a workaround via molblocks, which did not work. Thanks again.
Now I stumble over another challenge. If I interpret it correctly then I
should be able to SMARTS match atoms, even if they are different elements,
as
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