fix:add back boltz1 option to run_grid_search.py, correct arguments in run_all_models.sh

Author: marcuscollins

run_all_models.sh

@@ -58,8 +58,8 @@ docker run $DOCKER_OPTS \
     diffuseproject/sampleworks:latest \
     -e boltz run_grid_search.py \
     --proteins "/data/inputs/proteins.csv" \
-    --models boltz2 \
-    --methods "X-RAY DIFFRACTION" \
+    --model boltz2 \
+    --method "X-RAY DIFFRACTION" \
     --scalers pure_guidance \
     --partial-diffusion-step 120 \
     --ensemble-sizes "8" \
@@ -80,8 +80,8 @@ docker run $DOCKER_OPTS \
     diffuseproject/sampleworks:latest \
     -e boltz run_grid_search.py \
     --proteins "/data/inputs/proteins.csv" \
-    --models boltz2 \
-    --methods "MD" \
+    --model boltz2 \
+    --method "MD" \
     --scalers pure_guidance \
     --partial-diffusion-step 120 \
     --ensemble-sizes "8" \
@@ -102,7 +102,7 @@ docker run $DOCKER_OPTS \
     diffuseproject/sampleworks:latest \
     -e rf3 run_grid_search.py \
     --proteins "/data/inputs/proteins.csv" \
-    --models rf3 \
+    --model rf3 \
     --partial-diffusion-step 120 \
     --scalers pure_guidance \
     --ensemble-sizes "8" \
@@ -123,7 +123,7 @@ docker run $DOCKER_OPTS \
     diffuseproject/sampleworks:latest \
     -e protenix run_grid_search.py \
     --proteins "/data/inputs/proteins.csv" \
-    --models protenix \
+    --model protenix \
     --scalers pure_guidance \
     --partial-diffusion-step 120 \
     --ensemble-sizes "8" \

run_grid_search.py

@@ -432,7 +432,7 @@ def parse_args() -> argparse.Namespace:
     parser.add_argument(
         "--model",
         default="boltz2",
-        choices=["boltz2", "protenix", "rf3"],
+        choices=["boltz1", "boltz2", "protenix", "rf3"],
         help="The protein structure predictor model to use"
     )
     parser.add_argument(
@@ -536,11 +536,12 @@ def log_args(args: argparse.Namespace, gpus: list[str]):
     log.info("=" * 50)
     log.info("Starting grid search")
     log.info(f"Model: {args.model}")
+    if args.model == "boltz2":
+        log.info(f"Boltz2 method: {args.method}")
     log.info(f"Scalers: {args.scalers}")
     log.info(f"Ensemble sizes: {args.ensemble_sizes}")
     log.info(f"Gradient weights: {args.gradient_weights}")
     log.info(f"GD steps: {args.num_gd_steps}")
-    log.info(f"Boltz2 method: {args.method}")
     log.info(f"Output directory: {args.output_dir}")
     log.info(f"GPUs: {gpus}")
     log.info(f"Dry run: {args.dry_run}")