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Monomerizer

Monomerizer (or SMILES2Seq, #SMILES2FASTA) is a pipeline that converts peptides and peptidomimetics, represented as SMILES (chemical formulae), into sequences of amino acids and terminal modifications.

For more information, visit our paper: Coming soon?🙏.

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To use the output data to finetune our foundation language model for peptidomimetics, visit: GPepT

Usage

To run a Monomerizer demo, use the following command:

python3 run_pipeline.py --input_file demo/example_smiles.txt
  • By default, results will be saved to the output/<datetime> directory. The raw directory contains the raw result, and the standard directory contains the sequences after standardizing them to the standard dictionary accepted by GPepT.
  • Replace demo/example_smiles.txt with the path to your input file containing SMILES strings. (The input file must follow the format of the example files in the demo directory.)

Optional arguments

  • --output_dir <path>
  • --min_amino_acids <int>: Minimum number of amino acids required for processing. Default is 3.
  • --batch_size <int>: Number of SMILES to process in each batch. Default is 100.
  • --max_workers <int>: Maximum number of parallel workers. Default is the number of available CPU cores.
  • -draw: Draws output file like this.

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