biocheming / TS_Enhanced

Enhanced Thompson Sampling

Enhanced Thompson Sampling for Virtual Screening

This repo accompanies the preprint "Enhanced Thompson Sampling by Roulette Wheel Selection for Screening Ultra-Large Combinatorial Libraries".

Setting up the environment for running Enhanced Thompson Sampling

Create a new conda environment and install rdkit: conda create -c conda-forge -n <your-env-name> rdkit

Activate your environment and install the rest of the requirements: conda activate <your-env-name> pip install -r requirements.txt

How to run Thompson Sampling

python ./src/ts_main.py test.json

Or try the example used in the preprint:

python ./src/ts_paper.py quinazoline_fp_sim.json

Parameters

Required params:

• evaluator_arg: The argument to be passed to the instantiation of the evaluator (e.g. smiles string of the query molecule, filepath to the mol file, etc.) See the relevant Evaluator for more info.
• evaluator_class_name: Required. The scoring function to use. Must be "FPEvaluator" for 2D similarity. To use your own scoring function, implement a subclass of the Evaluator baseclass in evaluators.py.
• reaction_smarts: Required. The SMARTS string for the reaction.
• num_ts_iterations: Required. Number of iterations of Thompson Sampling to run (usually 100 - 2000).
• reagent_file_list: Required. List of filepaths - one for each component of the reaction. Each file should contain the smiles strings of valid reagents for that component.

Optional params:

• num_warmup_trials: Optional. Number of times to randomly sample each reagent in the reaction. 3 is usually sufficient
• results_filename: Optional. Name of the file to output results to. If None, results will not be saved to a file.
• log_filename: Optional. Log filename to save logs to. If not set, logging will be printed to stdout.
• scaling: Optional. Positive if higher score is preferred; negative otherwise. +/- 1 is usually good
• decay: Optional. Temperature control
• num_per_cycle: Optional. e.g., 3, 10, 100