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• 21:55, 6 December 2024 Omailhot talk contribs created page Small change analogs (Created page with "'''Step 0: source my environment''' All I'm developing is part of a single Python package called bksltk (BKS-lab Toolkit). So just source my Python environment on gimel2 (or other gimelX which has Python3) and you'll have access to everything: source /nfs/home/omailhot/pyenv_source.sh Then, you can use the get_all_analogs_smiles_set() method from the toolkit, which will return all smiles of small change analogs, starting from a single smiles string: from bksltk.an...")
• 19:45, 26 November 2024 Omailhot talk contribs created page Combinatorial analogs (Created page with "Here's an example of how to generate combinatorial analogs from the same parent. Make sure to source my environment first: source /nfs/home/omailhot/pyenv_source.sh Then, you will want to create a .png file of your parent with standard numbering on it. We'll use etomidate in this example: from bksltk.analogs import write_numbered_parent_png, make_analogs_combinations eto_smiles = 'CCOC(=O)C1=CN=CN1[C@H](C)C2=CC=CC=C2' write_numbered_parent_png(eto_smiles, 'test_p...")
• 21:42, 20 September 2023 Omailhot talk contribs created page Olivier's way of computing novelty (Created page with "This is my lazy way of doing novelty calculations. '''Step 0: source my environment''' All I'm developing is part of a single Python package called bksltk (BKS-lab Toolkit). So just source my Python environment on gimel2 (or other gimelX which has Python3) and you'll have access to everything: source /nfs/home/omailhot/pyenv_source.sh Eventually the package will be better documented (and probably integrated into pydock). '''Step 1: get all knowns from ChEMBL''' H...")
• 23:03, 20 January 2023 Omailhot talk contribs uploaded File:Mor zoom example.gif
• 23:03, 20 January 2023 Omailhot talk contribs created page File:Mor zoom example.gif
• 22:19, 20 January 2023 Omailhot talk contribs uploaded File:Chembl mor3.png
• 22:19, 20 January 2023 Omailhot talk contribs created page File:Chembl mor3.png
• 22:19, 20 January 2023 Omailhot talk contribs uploaded File:Chembl mor2.png
• 22:19, 20 January 2023 Omailhot talk contribs created page File:Chembl mor2.png
• 22:19, 20 January 2023 Omailhot talk contribs uploaded File:Chembl mor1.png
• 22:19, 20 January 2023 Omailhot talk contribs created page File:Chembl mor1.png
• 21:53, 20 January 2023 Omailhot talk contribs created page File:Chemspace vis example.gif
• 21:53, 20 January 2023 Omailhot talk contribs uploaded File:Chemspace vis example.gif
• 00:40, 20 January 2023 Omailhot talk contribs uploaded File:Chemspace vis example1.png
• 00:40, 20 January 2023 Omailhot talk contribs created page File:Chemspace vis example1.png
• 00:38, 20 January 2023 Omailhot talk contribs created page Interactive ligands visualizer (Created page with "I (Olivier) put together this interactive visualizer to make sure that I don't miss out some chemotypes when coming up with actives at the start of a retrospective campaign. Starting from a downloaded ChEMBL CSV file for a list of ligands, images of each molecule are generated with RDKit and a text file with filtered Smiles is generated. You then need to compute the ECFP fingerprints on Gimel from that file (see below), and then a generated script will show an interactiv...")