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I am getting a ValueError when using the ReactionFilter component with reinvent 4.4.22 under Linux.
```python
Traceback (most recent call last):
File "...bin/reinvent", line 8, in
sys.exi…
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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…
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So far we have PA-VAE up until 11340 drugs (see #1 ). The models are qsar-tested on 500 test samples.
- Aug 16 10:34 averaged_metrics_for_zinc_paired_encoder2_252_to_11340_test_size_500.npy
For S…
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Add RDKit descriptors calculated from SMILES generated from peptide sequence.
- [x] Calculate SMILES for sequence column.
- [ ] Use RDKit on calculated SMILES to get descriptors.
- [ ] Add "Pepti…
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I have a system that is a protein with a cofactor (FAD).
I am trying to generate the topology for this system.
In particular I am trying to do this:
Importing the topology for the ligand from a gro…
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once i have downloaded the data n the folder named "binding_moad" and preprocessed it after that total files iside the binding moad i got as follows :-
![image](https://github.com/user-attachmen…
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Hey again,
I think I've encountered a bug with the Convert module (or I might be overlooking a crucial bit of code). Converting from a BioSimSpace / Sire mol to an rdmol via BSS.Convert.toRDKit() a…
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Hi Guys,
I was wondering if you guys looked into the effect of using random vs canonical SMILES.
I would assume that it might be difficult to identify equal molecules with different SMILES using …
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Hey there!
When reading SMILES strings using PIKAChU, @Mar-Gol ran into the following problem:
### Minimal example for reproduction:
```
>>> smiles = 'CCOC1=CC2=C(C=C1)S(=O)C(=C2C3=CC=CC=C3)C(…
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**Description:**
The following code to generate conformers using `datamol` works fine with RDKit version `2022.09.5`, but fails with RDKit version `2024.03.1`. This inconsistency might be due to chan…