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14 10 2024 chemoinformatics Tweet

Running REINVENT4 on the M3 chip

As it could not be installed with the original requirements, I modified it and uploaded it to the Mishima-syk repository.

$ git clone https://github.com/Mishima-syk/REINVENT4.git
$ cd REINVENT4
$ conda create --name reinvent4 python=3.11
$ conda activate reinvent4
$ pip install -r requirements-macOS.lock
$ pip install --no-deps .

Now, you can set mps (Metal Performance Shaders) in the device parameter

# mps_sampling.toml
# REINVENT4 TOML input example for sampling
run_type = "sampling"
device = "mps"  # M3 GPU
json_out_config = "_sampling.json"  # write this TOML to JSON

[parameters]

## Reinvent: de novo sampling
model_file = "priors/reinvent.prior"
output_file = 'sampling.csv'  # sampled SMILES and NLL in CSV format
num_smiles = 157  # number of SMILES to be sampled, 1 per input SMILES
unique_molecules = true  # if true remove all duplicatesd canonicalize smiles
randomize_smiles = true # if true shuffle atoms in SMILES randomly

Running the reinvent4 program

$ reinvent -l sampling.log mps_sampling.toml

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