-
Hi,
Thank you for providing the source codes on MOLBERT, which is a great work!
I have two questions on the elements.txt.
1. Why only 'se' is denoted as AromaticSe? How about aromatic C/N/S, e…
-
My training has been on the ZINC database, but when I decode generated vectors into SMILES strings, I pass them into rdkit's canonicalizer. It looks to me like ZINC used a different canonicalization …
-
SMILES strings can store "disconnected molecules" like a ligand with a counter-ion. In OpenFF world, these should be treated as separate molecules - they should be parameterized separately, so they s…
-
What is the measurement of Y in Davis?
Thanks:)
-
**Describe the bug**
A `rdkit` molecule is created from a SMILES whose atom order is specified by the order of coordinate lines in a structure file (using `reordered_smiles_100` from [(this website)…
-
## Environment Information
Open Babel version: Open Babel 3.1.1 (built from GitHub commit [f495cc6](https://github.com/openbabel/openbabel/commit/f495cc6bae6ddd8133a6e78c1655e69611ac8ca6))
Oper…
-
This step follows on from Issue #2 where you will have prepared your ligands from SMILES strings using Gypsum-DL. For this virtual screen I have used the [SARS-CoV2 helicase - holo complex, nsp13](htt…
-
https://drive.google.com/file/d/1XdcIxnAAZN604CCjfbA2CCtpc-hpaCA5/view?usp=drive_link
https://drive.google.com/file/d/1k3TWhGPj-2n4HykelRnC-kPuUUhkety5/view?usp=drive_link
-
The CB7 and GDCC guest input files do not have coordinates which correspond to a bound state in the host.
Per Niel:
> They are close [to bound], but clearly not a plausible bound state. Jane made…
-
We found there are two different smiles for Aspirin that are interpreted as the same structure through Chemdraw however this is not the case for CAR. It abbreviated the molecule to a methylamide. Does…