Small change analogs
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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.analogs import get_all_analogs_smiles_set all_analogs_smiles = get_all_analogs_smiles_set('YOUR_SMILES')
If you want to do multiple smiles, just call the function for each one :-)
These are the small changes considered: H->CH3, H->OH, H->F, H->Cl, H->Br, aryl carbon to nitrogen, aromatic nitrogen to carbon.
To generate a single .csv file of all small change analogs (that you can send directly to Enamine for a quote) from a .smi file, do this:
from bksltk.analogs import get_csv_analogs get_csv_analogs('your_input.smi', 'your_output.csv')