How to implement SA_score calculation?

[chengthefang]

Hi Connor,

I checked your paper, and the SI table, where you compared the SCScore and SA_score for a library of SMILES-format molecules. I would like to compare those two as well for my library of molecules. However, I have no idea how to implement SA_score calculation using your provided script i.e. "sascorer.py". Would you mind provide a simple example (e.g a SMILES formated molecule) about how to use that for SA_score calculation? Thank you much!

Cheng

[connorcoley]

Cheng,

The sascorer.py is reproduced directly from the RDKit implementation. As an example, see the following:

import utils.SA_Score.sascorer as sascorer # depending on your path
import rdkit.Chem as Chem
m = Chem.MolFromSmiles('CCCN')
sco = sascorer.calculateScore(m)
print(sco)

The first time you call sascorer.calculateScore(), it will probably take a few seconds, since it needs to load some fragment contribution data. Subsequent calls are much faster.

[chengthefang]

@connorcoley Hi Connor, appreciated much for your pretty helpful response. It works well on my end now! Thanks! Cheng

[ghost]

Hi @connorcoley I am having some issues testing SAScore on a subset of compounds I am testing.
I am not a python coder and hence would need some basic guidance from the team.
I have reached this far with the installation.
step 1 conda create --name sccsore python=3.8
conda activate sccsore
conda install numpy
conda install -c rdkit rdkit
git clone https://github.com/connorcoley/scscore.git
now I do cd scscore
Then I have created a test directory here with a txt file containing compound SMILES
HOW DO I know use the scscore script to test it on those compounds?
Do I copy the snippet you shared in the thread and just do python sascorer.py ??
Thanks

[ghost]

I went inside cd scripts
Then did this:

[connorcoley]

The SA Score is a contribution in RDKit, which is a simpler and more direct way to use it: https://github.com/rdkit/rdkit/blob/master/Contrib/SA_Score/sascorer.py

[ghost]

Hello Connor, Thanks for your email. So I copied that snippet you shared and saved it as a score.py inside the score folder and activated the environment as well, I have numpy and RDKit installed inside this environment. I just ran python score.py CC(=O)OC(CC(=O)[O-])C[N+](C)(C)C Getting this error: (sccsore) ***@***.*** scscore]$ python test2.py CC(=O)OC(CC(=O)[O-])C[N+](C)(C)C -bash: syntax error near unexpected token `(' (sccsore) ***@***.*** scscore]$

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On Wed, Jun 21, 2023 at 10:07 AM Connor Coley ***@***.***> wrote: The SA Score is a contribution in RDKit, which is a simpler and more direct way to use it: https://github.com/rdkit/rdkit/blob/master/Contrib/SA_Score/sascorer.py <https://github.com/rdkit/rdkit/blob/master/Contrib/SA_Score/sascorer.py> — Reply to this email directly, view it on GitHub <#4 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AZOA6WZ4LQWIEDPTSDJPGD3XMMS5VANCNFSM4EYMANTA> . You are receiving this because you commented.Message ID: ***@***.***>