Add option --num-multimer-predictions-per-model

CHANGELOG.md

+Changes in Release 3.1.0
+=================================================================================
+
+* `run_af2` Python package:
+  * Add command line option `--num-multimer-predictions-per-model`
+  * Switch default value of option `--use-gpu-relax` to False
+
+
 Changes in Release 3.0.0
 =================================================================================
 

run_af2/src/run_af2/_shared.py

@@ -128,7 +128,15 @@ def parse_af2_arguments(parser):
         "--use-gpu-relax",
         action="store_true",
         help="Use GPU for relaxation (if GPU is enabled).",
-        default=True,
+        default=False,
+    )
+    af2_group.add_argument(
+        "--num-multimer-predictions-per-model",
+        type=int,
+        help="Number of models per prediction. Only applies with "
+        + "--model-preset=multimer.",
+        metavar="<NUMBER>",
+        default=5,
     )
     af2_group.add_argument(
         "--version",
@@ -244,6 +252,16 @@ def parse_af2_arguments(parser):
                 flush=True,
             )
 
+    # check that --use-gpu-relax is only enabled together with --use-gpu
+    if opts.use_gpu_relax and not opts.use_gpu:
+        print(
+            "WARNING: Enabling --use-gpu-relax on non-gpu compute nodes "
+            + "will fail. You are seeing this warning since you enabled "
+            + "--use-gpu-relax but not --use-gpu.",
+            file=sys.stderr,
+            flush=True,
+        )
+
     if opts.singularity_image is not None:
         if not os.path.exists(opts.singularity_image):
             print(

run_af2/src/run_af2/run_singularity.py

@@ -119,6 +119,7 @@ def _assemble_singularity_call(  # pylint: disable=too-many-arguments
     use_precomputed_msas,
     no_run_relax,
     use_gpu_relax,
+    num_multimer_predictions_per_model,
     data_paths,
     extra_arg_list,
 ):
@@ -152,6 +153,8 @@ def _assemble_singularity_call(  # pylint: disable=too-many-arguments
             f"--max_template_date={max_template_date}",
             f"--db_preset={db_preset}",
             f"--model_preset={model_preset}",
+            "--num_multimer_predictions_per_model="
+            + f"{num_multimer_predictions_per_model}",
             "--logtostderr",
         ]
     )
@@ -207,7 +210,8 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
     model_preset="monomer",
     use_precomputed_msas=False,
     no_run_relax=False,
-    use_gpu_relax=True,
+    use_gpu_relax=False,
+    num_multimer_predictions_per_model=5,
     af2_image_file=None,
     # af2_image_dir="/export/soft/singularity-containers/alphafold",
     af2_image_dir="/scicore/home/schwede/GROUP/alphafold_data/",
@@ -280,6 +284,12 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
     :param use_gpu_relax: Run relaxation on GPU. Corresponds to the
                           use_gpu_relax parameter in AF2.
     :type use_gpu_relax: :class:`bool`
+    :param num_multimer_predictions_per_model: In multimer mode, no. of
+                                               predictions per model.
+                                               Corresponds to the
+                                               num_multimer_predictions_per_model
+                                               parameter in AF2.
+    :type num_multimer_predictions_per_model: :class:`int`
     :param af2_image_file: Declare a Singularity image to run the AF2 pipeline
                            from. If None, an image from af2_image_dir will be
                            used.
@@ -410,6 +420,7 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
         use_precomputed_msas,
         no_run_relax,
         use_gpu_relax,
+        num_multimer_predictions_per_model,
         data_paths,
         extra_arg_list,
     )
@@ -481,6 +492,7 @@ def main():
             opts.use_precomputed_msas,
             opts.no_run_relax,
             opts.use_gpu_relax,
+            opts.num_multimer_predictions_per_model,
             opts.singularity_image,
             extra_arg_list=extra_arg_list,
             **data_paths,