User contributions for Omailhot
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11 December 2024
- 22:5522:55, 11 December 2024 diff hist +241 m Small change analogs No edit summary current
6 December 2024
- 21:5721:57, 6 December 2024 diff hist +130 Small change analogs No edit summary
- 21:5521:55, 6 December 2024 diff hist +655 N 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..."
3 December 2024
- 21:0221:02, 3 December 2024 diff hist +427 Combinatorial analogs No edit summary current
26 November 2024
- 19:4519:45, 26 November 2024 diff hist +1,137 N 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..."
22 September 2023
- 20:1020:10, 22 September 2023 diff hist +171 m Olivier's way of computing novelty No edit summary current
21 September 2023
- 01:1201:12, 21 September 2023 diff hist −1 Olivier's way of computing novelty No edit summary
20 September 2023
- 21:4221:42, 20 September 2023 diff hist +2,034 N 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..."
27 January 2023
- 23:5423:54, 27 January 2023 diff hist +198 Interactive ligands visualizer No edit summary current
- 23:1723:17, 27 January 2023 diff hist +1,103 Interactive ligands visualizer No edit summary
- 22:3722:37, 27 January 2023 diff hist +82 Interactive ligands visualizer No edit summary
20 January 2023
- 23:1223:12, 20 January 2023 diff hist +119 Interactive ligands visualizer No edit summary
- 23:0723:07, 20 January 2023 diff hist +153 Interactive ligands visualizer No edit summary
- 23:0423:04, 20 January 2023 diff hist +5 Interactive ligands visualizer No edit summary
- 23:0423:04, 20 January 2023 diff hist +26 Interactive ligands visualizer No edit summary
- 23:0323:03, 20 January 2023 diff hist 0 N File:Mor zoom example.gif No edit summary current
- 22:5222:52, 20 January 2023 diff hist +625 Interactive ligands visualizer No edit summary
- 22:4522:45, 20 January 2023 diff hist +1,189 Interactive ligands visualizer No edit summary
- 22:2122:21, 20 January 2023 diff hist +247 Interactive ligands visualizer No edit summary
- 22:1922:19, 20 January 2023 diff hist 0 N File:Chembl mor3.png No edit summary current
- 22:1922:19, 20 January 2023 diff hist 0 N File:Chembl mor2.png No edit summary current
- 22:1922:19, 20 January 2023 diff hist 0 N File:Chembl mor1.png No edit summary current
- 21:5421:54, 20 January 2023 diff hist −1 Interactive ligands visualizer No edit summary
- 21:5321:53, 20 January 2023 diff hist 0 N File:Chemspace vis example.gif No edit summary current
- 00:4300:43, 20 January 2023 diff hist +37 Interactive ligands visualizer No edit summary
- 00:4000:40, 20 January 2023 diff hist 0 N File:Chemspace vis example1.png No edit summary current
- 00:3800:38, 20 January 2023 diff hist +1,532 N 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..."