Method process_input

src/simplefold/wrapper.py:293–319

(self, aa_seq)

        )

    def process_input(self, aa_seq):
        # process fasta files to input format
        download_fasta_utilities(self.cache)
        # save the input sequence to a fasta file
        with open(self.cache / "input.fasta", "w") as f:
            f.write(f">A|Protein\n{aa_seq}\n")
        data = [self.cache / "input.fasta"]
        process_fastas(
            data=data,
            out_dir=self.cache,
            ccd_path=self.cache / "ccd.pkl",
        )

        # prepare the target protein data for inference
        struct_file = self.cache / "structures" / "input.npz"
        record_file = self.cache / "records" / "input.json"
        batch, structure, record = process_one_inference_structure(
            struct_file,
            record_file,
            self.tokenizer,
            self.featurizer,
            self.processor,
            self.esm_model,
            self.esm_dict,
            self.af2_to_esm,
        )
        return batch, structure, record

    def run_inference(self, batch, model, plddt_model, device):
        # run inference for target protein