Initial commit: RoseTTAFold-All-Atom configured for Wes with Harbor images and s3:// paths

rf2aa/data/preprocessing.py

@@ -0,0 +1,35 @@
+import os
+from hydra import initialize, compose
+from pathlib import Path
+import subprocess
+
+#from rf2aa.run_inference import ModelRunner
+
+
+def make_msa(
+    fasta_file,
+    chain,
+    model_runner
+): 
+    out_dir_base = Path(model_runner.config.output_path)
+    hash = model_runner.config.job_name
+    out_dir = out_dir_base / hash / chain
+    out_dir.mkdir(parents=True, exist_ok=True)
+
+    command = model_runner.config.database_params.command
+    search_base = model_runner.config.database_params.sequencedb
+    num_cpus = model_runner.config.database_params.num_cpus
+    ram_gb = model_runner.config.database_params.mem
+    template_database = model_runner.config.database_params.hhdb
+
+    out_a3m = out_dir / "t000_.msa0.a3m"
+    out_atab = out_dir / "t000_.atab"
+    out_hhr = out_dir / "t000_.hhr"
+    if out_a3m.exists() and out_atab.exists() and out_hhr.exists():
+        return out_a3m, out_hhr, out_atab
+
+    search_command = f"./{command} {fasta_file} {out_dir} {num_cpus} {ram_gb} {search_base} {template_database}"
+    print(search_command)
+    _ = subprocess.run(search_command, shell=True)
+    return out_a3m, out_hhr, out_atab
+