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11 December 2024

6 December 2024

  • 21:5721:57, 6 December 2024 diff hist +130 Small change analogsNo edit summary
  • 21:5521:55, 6 December 2024 diff hist +655 N Small change analogsCreated 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

26 November 2024

  • 19:4519:45, 26 November 2024 diff hist +1,137 N Combinatorial analogsCreated 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

21 September 2023

20 September 2023

  • 21:4221:42, 20 September 2023 diff hist +2,034 N Olivier's way of computing noveltyCreated 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

20 January 2023