generate_alphafold_feature_dict.py

import argparse
import os
import pickle

from alphafold.data import pipeline, pipeline_multimer, templates
from alphafold.data.tools import hmmsearch, hhsearch

from scripts.utils import add_data_args


def main(args):
    if (args.multimer):
        template_searcher = hmmsearch.Hmmsearch(
            binary_path=args.hmmsearch_binary_path,
            hmmbuild_binary_path=args.hmmbuild_binary_path,
            database_path=args.pdb_seqres_database_path,
        )

        template_featurizer = templates.HmmsearchHitFeaturizer(
            mmcif_dir=args.template_mmcif_dir,
            max_template_date=args.max_template_date,
            max_hits=20,
            kalign_binary_path=args.kalign_binary_path,
            release_dates_path=args.release_dates_path,
            obsolete_pdbs_path=args.obsolete_pdbs_path
        )
    else:
        template_searcher = hhsearch.HHSearch(
            binary_path=args.hhsearch_binary_path,
            databases=[args.pdb70_database_path],
        )

        template_featurizer = templates.HhsearchHitFeaturizer(
            mmcif_dir=args.template_mmcif_dir,
            max_template_date=args.max_template_date,
            max_hits=20,
            kalign_binary_path=args.kalign_binary_path,
            release_dates_path=None,
            obsolete_pdbs_path=args.obsolete_pdbs_path
        )

    data_pipeline = pipeline.DataPipeline(
        jackhmmer_binary_path=args.jackhmmer_binary_path,
        hhblits_binary_path=args.hhblits_binary_path,
        uniref90_database_path=args.uniref90_database_path,
        mgnify_database_path=args.mgnify_database_path,
        bfd_database_path=args.bfd_database_path,
        uniref30_database_path=args.uniref30_database_path,
        small_bfd_database_path=None,
        template_featurizer=template_featurizer,
        template_searcher=template_searcher,
        use_small_bfd=False,
    )

    if (args.multimer):
        data_pipeline = pipeline_multimer.DataPipeline(
            monomer_data_pipeline=data_pipeline,
            jackhmmer_binary_path=args.jackhmmer_binary_path,
            uniprot_database_path=args.uniprot_database_path)

    feature_dict = data_pipeline.process(
        input_fasta_path=args.fasta_path,
        msa_output_dir=args.output_dir,
    )

    with open(os.path.join(args.output_dir, "feature_dict.pickle"), "wb") as fp:
        pickle.dump(feature_dict, fp, protocol=pickle.HIGHEST_PROTOCOL)

if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument("fasta_path", type=str)
    parser.add_argument("mmcif_dir", type=str)
    parser.add_argument("output_dir", type=str)
    parser.add_argument("--multimer", action='store_true')
    add_data_args(parser)

    args = parser.parse_args()

    main(args)