Integrated the feature processing pipeline in the 'main' runner script.

run_pretrained_alphafold.py

@@ -19,6 +19,11 @@ import pickle
 import os
 
 # A hack to get OpenMM and PyTorch to peacefully coexist
+import random
+import sys
+
+from openfold.features import data_pipeline, templates, feature_pipeline
+
 os.environ["OPENMM_DEFAULT_PLATFORM"] = "OpenCL"
 
 import time
@@ -41,6 +46,8 @@ from openfold.utils.tensor_utils import (
 
 FEAT_PATH = "tests/test_data/sample_feats.pickle"
 
+MAX_TEMPLATE_HITS = 20
+
 def main(args):
     config = model_config(args.model_name)
     model = AlphaFold(config.model)
@@ -48,9 +55,60 @@ def main(args):
     import_jax_weights_(model, args.param_path)
     model = model.to(args.device)
     
-    with open(FEAT_PATH, "rb") as f:
-        batch = pickle.load(f)
-    
+    # FEATURE COLLECTION AND PROCESSING
+    use_small_bfd = args.preset == "reduced_dbs"
+    num_ensemble = 1
+
+    template_featurizer = templates.TemplateHitFeaturizer(
+        mmcif_dir=args.template_mmcif_dir,
+        max_template_date=args.max_template_date,
+        max_hits=MAX_TEMPLATE_HITS,
+        kalign_binary_path=args.kalign_binary_path,
+        release_dates_path=None,
+        obsolete_pdbs_path=args.obsolete_pdbs_path)
+
+    data_processor = data_pipeline.DataPipeline(
+        jackhammer_binary_path=args.jackhmmer_binary_path,
+        hhblits_binary_path=args.hhblits_binary_path,
+        hhsearch_binary_path=args.hhsearch_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,
+        small_bfd_database_path=args.small_bfd_database_path,
+        pdb70_database_path=args.pdb70_database_path,
+        template_featurizer=template_featurizer,
+        use_small_bfd=use_small_bfd
+    )
+
+    output_dir_base = args.output_dir
+    random_seed = args.random_seed
+    if random_seed is None:
+        random_seed = random.randrange(sys.maxsize)
+    config.data.eval.num_ensemble = num_ensemble
+    feature_processor = feature_pipeline.FeaturePipeline(config)
+    if not os.path.exists(output_dir_base):
+        os.makedirs(output_dir_base)
+    msa_output_dir = os.path.join(output_dir_base, "msas")
+    if not os.path.exists(msa_output_dir):
+        os.makedirs(msa_output_dir)
+
+    print("Collecting data...")
+    feature_dict = data_processor.process(
+        input_fasta_path=args.fasta_path, msa_output_dir=msa_output_dir)
+    # Output the features
+    features_output_path = os.path.join(output_dir_base, 'features.pkl')
+    with open(features_output_path, 'wb') as f:
+        pickle.dump(feature_dict, f, protocol=4)
+
+    print("Generating features...")
+    processed_feature_dict = feature_processor.process_features(feature_dict, random_seed)
+
+    with open(os.path.join(output_dir_base, 'processed_feats.pkl'), 'wb') as f:
+        pickle.dump(processed_feature_dict, f, protocol=4)
+
+    print("Executing model...")
+    batch = processed_feature_dict
     with torch.no_grad():
         batch = {
             k:torch.as_tensor(v, device=args.device) 
@@ -117,6 +175,14 @@ def main(args):
 
 if __name__ == "__main__":
     parser = argparse.ArgumentParser()
+    parser.add_argument(
+        "--fasta_path", type=str, default=None, required=True
+    )
+    parser.add_argument(
+        "--output_dir", type=str, default=os.getcwd(),
+        help="""Name of the directory in which to output the prediction""",
+        required=True
+    )
     parser.add_argument(
         "--device", type=str, default="cpu",
         help="""Name of the device on which to run the model. Any valid torch
@@ -127,16 +193,57 @@ if __name__ == "__main__":
         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(
-        "--output_dir", type=str, default=os.getcwd(),
-        help="""Name of the directory in which to output the prediction"""
-    )
     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(
+        '--jackhmmer_binary_path', type=str, default='/usr/bin/jackhmmer'
+    )
+    parser.add_argument(
+        '--hhblits_binary_path', type=str, default='/usr/bin/hhblits'
+    )
+    parser.add_argument(
+        '--hhsearch_binary_path', type=str, default='/usr/bin/hhsearch'
+    )
+    parser.add_argument(
+        '--kalign_binary_path', type=str, default='/usr/bin/kalign'
+    )
+    parser.add_argument('--uniref90_database_path', type=str, default=None, required=True
+    )
+    parser.add_argument(
+        '--mgnify_database_path', type=str, default=None, required=True
+    )
+    parser.add_argument(
+        '--bfd_database_path', type=str, default=None, required=True
+    )
+    parser.add_argument(
+        '--small_bfd_database_path', type=str, default=None
+    )
+    parser.add_argument(
+        '--uniclust30_database_path', type=str, default=None
+    )
+    parser.add_argument(
+        '--pdb70_database_path', type=str, default=None, required=True
+    )
+    parser.add_argument(
+        '--template_mmcif_dir', type=str, default=None, required=True
+    )
+    parser.add_argument(
+        '--max_template_date', type=str, default=None, required=True
+    )
+    parser.add_argument(
+        '--obsolete_pdbs_path', type=str, default=None
+    )
+    parser.add_argument(
+        '--preset', type=str, default='full_dbs', required=True,
+        choices=('reduced_dbs', 'full_dbs')
+    )
+    parser.add_argument(
+        '--random_seed', type=str, default=None
+    )
 
     args = parser.parse_args()