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MingyuanXu / TreeInvent-Community

Tree-Invent examples for the various drug design strategy
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reproduction case in paper of celecoxib #2

Open aishiba0721 opened 10 months ago

aishiba0721 commented 10 months ago

Hello, I am currently validating some data from the paper using this project. I have encountered some issues during the reproduction of the case depicted in the attached image. Could you please provide a reference JSON configuration file to guide me on how to correctly define the skeleton in the graph? Your assistance would be greatly appreciated. image

MingyuanXu commented 10 months ago

Sorry for the late of response! Regarding a given molecule, assuming its SMILES is CC1=CC=C(C=C1)C2=CC(=NN2C3=CC=C(C=C3)S(=O)(=O)N), which is also the SMILES for Celecoxib. You can create the MolFragTree object defined in TreeInvent. The MolFragTree.get_CL_states() attribute function allows direct access to the topological structures at each step during the generation process. The Gclique_To_Constrain() function can be used to obtain the topological constraints corresponding to the molecule, facilitating scaffold hopping and reinforcement learning based on a reference molecule. The example script (also a reinforcement learning script for topological constraints on Celecoxib) and the configuration file are attached. Celecoxib.zip