run_pretrained_openfold.py

# Copyright 2021 AlQuraishi Laboratory
# Copyright 2021 DeepMind Technologies Limited
# 
# Licensed under the Apache License, Version 2.0 (the "License");
# you may not use this file except in compliance with the License.
# You may obtain a copy of the License at
#
#      http://www.apache.org/licenses/LICENSE-2.0
#
# Unless required by applicable law or agreed to in writing, software
# distributed under the License is distributed on an "AS IS" BASIS,
# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
# See the License for the specific language governing permissions and
# limitations under the License.

import argparse
from datetime import date
import logging
import numpy as np
import os

import pickle
import random
import sys
import time
import torch

from openfold.config import model_config
from openfold.data import (
    data_pipeline,
    feature_pipeline, 
    templates, 
)
from openfold.data.tools import hhsearch, hmmsearch
from openfold.model.model import AlphaFold
from openfold.model.torchscript import script_preset_
from openfold.np import residue_constants, protein
import openfold.np.relax.relax as relax
from openfold.utils.import_weights import (
    import_jax_weights_,
)
from openfold.utils.tensor_utils import (
    tensor_tree_map,
)

from scripts.utils import add_data_args


def main(args):
    config = model_config(args.model_name)
    model = AlphaFold(config)
    model = model.eval()
    import_jax_weights_(model, args.param_path, version=args.model_name)
    #script_preset_(model)
    model = model.to(args.model_device)

    is_multimer = "multimer" in args.model_name

    if(is_multimer):
        if(not args.use_precomputed_alignments):
            template_searcher = hmmsearch.Hmmsearch(
                binary_path=args.hmmsearch_binary_path,
                hmmbuild_binary_path=args.hmmbuild_binary_path,
                database_path=args.pdb_seqres_database_path,
            )
        else:
            template_searcher = None

        template_featurizer = templates.HmmsearchHitFeaturizer(
            mmcif_dir=args.template_mmcif_dir,
            max_template_date=args.max_template_date,
            max_hits=config.data.predict.max_templates,
            kalign_binary_path=args.kalign_binary_path,
            release_dates_path=args.release_dates_path,
            obsolete_pdbs_path=args.obsolete_pdbs_path
        )
    else:
        if(not args.use_precomputed_alignments):
            template_searcher = hhsearch.HHSearch(
                binary_path=args.hhsearch_binary_path,
                databases=[args.pdb70_database_path],
            )
        else:
            template_searcher = None

        template_featurizer = templates.HhsearchHitFeaturizer(
            mmcif_dir=args.template_mmcif_dir,
            max_template_date=args.max_template_date,
            max_hits=config.data.predict.max_templates,
            kalign_binary_path=args.kalign_binary_path,
            release_dates_path=args.release_dates_path,
            obsolete_pdbs_path=args.obsolete_pdbs_path
        )

    if(not args.use_precomputed_alignments):
        alignment_runner = data_pipeline.AlignmentRunner(
            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,
            uniclust30_database_path=args.uniclust30_database_path,
            uniprot_database_path=args.uniprot_database_path,
            template_searcher=template_searcher,
            use_small_bfd=(args.bfd_database_path is None),
            no_cpus=args.cpus,
        )
    else:
        alignment_runner = None

    data_processor = data_pipeline.DataPipeline(
        template_featurizer=template_featurizer,
    )

    if(is_multimer):
        data_processor = data_pipeline.DataPipelineMultimer(
            monomer_data_pipeline=data_processor,
        )

    output_dir_base = args.output_dir
    random_seed = args.data_random_seed
    if random_seed is None:
        random_seed = random.randrange(sys.maxsize)
    
    feature_processor = feature_pipeline.FeaturePipeline(
        config.data
    )
    
    if not os.path.exists(output_dir_base):
        os.makedirs(output_dir_base)
    if(not args.use_precomputed_alignments):
        alignment_dir = os.path.join(output_dir_base, "alignments")
    else:
        alignment_dir = args.use_precomputed_alignments

    for fasta_path in os.listdir(args.fasta_dir):
        if(not ".fasta" == os.path.splitext(fasta_path)[-1]):
            print(f"Skipping {fasta_path}. Not a .fasta file...")
            continue
   
        fasta_path = os.path.join(args.fasta_dir, fasta_path)

        # Gather input sequences
        with open(fasta_path, "r") as fp:
            data = fp.read()

        lines = [
            l.replace('\n', '') 
            for prot in data.split('>') for l in prot.strip().split('\n', 1)
        ][1:]
        tags, seqs = lines[::2], lines[1::2]

        if((not is_multimer) and len(tags) != 1):
            print(
                f"{fasta_path} contains more than one sequence but "
                f"multimer mode is not enabled. Skipping..."
            )
            continue
        
        for tag, seq in zip(tags, seqs):
            tag, seq = tags[0], seqs[0]
            local_alignment_dir = os.path.join(alignment_dir, tag)
            if(args.use_precomputed_alignments is None):
                if not os.path.exists(local_alignment_dir):
                    os.makedirs(local_alignment_dir)
                
                alignment_runner.run(
                    fasta_path, local_alignment_dir
                )
       
        if(is_multimer):
            local_alignment_dir = alignment_dir
        else:
            local_alignment_dir = os.path.join(
                alignment_dir,
                tags[0],
            )

        feature_dict = data_processor.process_fasta(
            fasta_path=fasta_path, alignment_dir=local_alignment_dir
        )

        processed_feature_dict = feature_processor.process_features(
            feature_dict, mode='predict', is_multimer=is_multimer,
        )
        
        logging.info("Executing model...")
        batch = processed_feature_dict
        with torch.no_grad():
            batch = {
                k:torch.as_tensor(v, device=args.model_device) 
                for k,v in batch.items()
            }
        
            t = time.perf_counter()
             
            chunk_size = model.globals.chunk_size
            try:
                model.globals.chunk_size = None
                out = model(batch)
            except RuntimeError as e:
                model.globals.chunk_size = chunk_size
                out = model(batch)
            logging.info(f"Inference time: {time.perf_counter() - t}")

        # Toss out the recycling dimensions --- we don't need them anymore
        batch = tensor_tree_map(lambda x: np.array(x[..., -1].cpu()), batch)
        out = tensor_tree_map(lambda x: np.array(x.cpu()), out)
        
        plddt = out["plddt"]
        mean_plddt = np.mean(plddt)
        
        plddt_b_factors = np.repeat(
            plddt[..., None], residue_constants.atom_type_num, axis=-1
        )
        
        unrelaxed_protein = protein.from_prediction(
            features=batch,
            result=out,
            b_factors=plddt_b_factors
        )

        # Save the unrelaxed PDB.
        unrelaxed_output_path = os.path.join(
            args.output_dir, f'{tag}_{args.model_name}_unrelaxed.pdb'
        )
        with open(unrelaxed_output_path, 'w') as f:
            f.write(protein.to_pdb(unrelaxed_protein))

        amber_relaxer = relax.AmberRelaxation(
            use_gpu=(args.model_device != "cpu"),
            **config.relax,
        )
        
        # Relax the prediction.
        t = time.perf_counter()
        visible_devices = os.getenv("CUDA_VISIBLE_DEVICES", default="")
        if("cuda" in args.model_device):
            device_no = args.model_device.split(":")[-1]
            os.environ["CUDA_VISIBLE_DEVICES"] = device_no
        relaxed_pdb_str, _, _ = amber_relaxer.process(prot=unrelaxed_protein)
        os.environ["CUDA_VISIBLE_DEVICES"] = visible_devices
        logging.info(f"Relaxation time: {time.perf_counter() - t}")
        
        # Save the relaxed PDB.
        relaxed_output_path = os.path.join(
            args.output_dir, f'{tag}_{args.model_name}_relaxed.pdb'
        )
        with open(relaxed_output_path, 'w') as f:
            f.write(relaxed_pdb_str)

        if(args.save_outputs):
            output_dict_path = os.path.join(
                args.output_dir, f'{tag}_{args.model_name}_output_dict.pkl'
            )
            with open(output_dict_path, "wb") as fp:
                pickle.dump(out, fp, protocol=pickle.HIGHEST_PROTOCOL)


if __name__ == "__main__":
    parser = argparse.ArgumentParser()
    parser.add_argument(
        "fasta_dir", type=str,
    )
    parser.add_argument(
        "template_mmcif_dir", type=str,
    )
    parser.add_argument(
        "--use_precomputed_alignments", type=str, default=None,
        help="""Path to alignment directory. If provided, alignment computation 
                is skipped and database path arguments are ignored."""
    )
    parser.add_argument(
        "--output_dir", type=str, default=os.getcwd(),
        help="""Name of the directory in which to output the prediction""",
    )
    parser.add_argument(
        "--model_device", type=str, default="cpu",
        help="""Name of the device on which to run the model. Any valid torch
             device name is accepted (e.g. "cpu", "cuda:0")"""
    )
    parser.add_argument(
        "--model_name", type=str, default="model_1",
        help="""Name of a model config. Choose one of model_{1-5} or 
             model_{1-5}_ptm, as defined on the AlphaFold GitHub."""
    )
    parser.add_argument(
        "--param_path", type=str, default=None,
        help="""Path to model parameters. If None, parameters are selected
             automatically according to the model name from 
             openfold/resources/params"""
    )
    parser.add_argument(
        "--save_outputs", type=bool, default=False,
        help="Whether to save all model outputs, including embeddings, etc."
    )
    parser.add_argument(
        "--cpus", type=int, default=4,
        help="""Number of CPUs with which to run alignment tools"""
    )
    parser.add_argument(
        '--preset', type=str, default='full_dbs',
        choices=('reduced_dbs', 'full_dbs')
    )
    parser.add_argument(
        '--data_random_seed', type=str, default=None
    )
    add_data_args(parser)
    args = parser.parse_args()

    if(args.param_path is None):
        args.param_path = os.path.join(
            "openfold", "resources", "params", 
            "params_" + args.model_name + ".npz"
        )

    if(args.model_device == "cpu" and torch.cuda.is_available()):
        logging.warning(
            """The model is being run on CPU. Consider specifying 
            --model_device for better performance"""
        )

    main(args)