Adde new command line arguments

CHANGELOG.md

+Changes in Release 2.2.0
+=================================================================================
+
+* `run_af2` Python package:
+  * add command line options `--use-precomputed-msas`, `--no-run-relax` and
+    `--use-gpu-relax`
+
+
 Changes in Release 2.1.0
 =================================================================================
 
@@ -10,7 +18,7 @@ Changes in Release 2.0.0
 
 * `run_af2` Python package:
   * Prepare to run AF2 pipeline 2.1
-  * rename command line options `--pdb70_database_path` and
+  * Rename command line options `--pdb70_database_path` and
     `--obsolete_pdbs_path` to `--pdb70-database-path` and `--obsolete-pdbs-path`
 
 

run_af2/src/run_af2/_shared.py

@@ -120,6 +120,26 @@ def parse_af2_arguments(parser):
         metavar="<true|false>,<true|false>,...",
         default=None,
     )
+    af2_group.add_argument(
+        "--use-precomputed-msas",
+        action="store_true",
+        help="Use existing MSAs from current working directory.",
+        default=False,
+    )
+    af2_group.add_argument(
+        "--no-run-relax",
+        action="store_true",
+        help="Don't Run relaxation on models after prediction. That is "
+        + "inverted of alphafold's own --run_relax, and meant to replace "
+        + "'--run_relax=False'",
+        default=False,
+    )
+    af2_group.add_argument(
+        "--use-gpu-relax",
+        action="store_true",
+        help="Use GPU for relaxation (if GPU is enabled).",
+        default=True,
+    )
     af2_group.add_argument(
         "--version",
         action="version",

run_af2/src/run_af2/run_singularity.py

@@ -117,6 +117,9 @@ def _assemble_singularity_call(  # pylint: disable=too-many-arguments
     db_preset,
     model_preset,
     is_prokaryote_list,
+    use_precomputed_msas,
+    no_run_relax,
+    use_gpu_relax,
     data_paths,
     extra_arg_list,
 ):
@@ -156,6 +159,14 @@ def _assemble_singularity_call(  # pylint: disable=too-many-arguments
     if is_prokaryote_list is not None:
         snglrty_cmd.append(f"--is_prokaryote_list={is_prokaryote_list}")
 
+    bool_args = {
+        "use_precomputed_msas": use_precomputed_msas,
+        "run_relax": not no_run_relax,
+        "use_gpu_relax": use_gpu_relax,
+    }
+    for arg, val in bool_args.items():
+        snglrty_cmd.append(f"--{arg}={str(val)}")
+
     for flag, path in data_paths.items():
         snglrty_cmd.append(f"--{flag}={path}")
 
@@ -198,6 +209,9 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
     db_preset="full_dbs",
     model_preset="monomer",
     is_prokaryote_list=None,
+    use_precomputed_msas=False,
+    no_run_relax=False,
+    use_gpu_relax=True,
     af2_image_file=None,
     # af2_image_dir="/export/soft/singularity-containers/alphafold",
     af2_image_dir="/scicore/home/schwede/GROUP/alphafold_data/",
@@ -264,6 +278,17 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
                                is_prokaryote_list parameter in AF2.
     :type is_prokaryote_list: :class:`str` like needed by AF2, e.g.
                               "true,false,true"
+    :param use_precomputed_msas: Use existing MSAs from cwd. Corresponds to the
+                                 use_precomputed_msas parameter in AF2.
+    :type use_precomputed_msas: :class:`bool`
+    :param no_run_relax: Disable relaxation at the end of modelling.
+                         Corresponds to AF2's no_run_relax parameter but works
+                         oppositely, True means no relaxation, False means
+                         relaxation.
+    :type no_run_relax: :class:`bool`
+    :param use_gpu_relax: Run relaxation on GPU. Corresponds to the
+                          use_gpu_relax parameter in AF2.
+    :type use_gpu_relax: :class:`bool`
     :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.
@@ -392,6 +417,9 @@ def run_af2_singularity_image(  # pylint: disable=too-many-arguments
         db_preset,
         model_preset,
         is_prokaryote_list,
+        use_precomputed_msas,
+        no_run_relax,
+        use_gpu_relax,
         data_paths,
         extra_arg_list,
     )
@@ -461,6 +489,9 @@ def main():
             opts.db_preset,
             opts.model_preset,
             opts.is_prokaryote_list,
+            opts.use_precomputed_msas,
+            opts.no_run_relax,
+            opts.use_gpu_relax,
             opts.singularity_image,
             extra_arg_list=extra_arg_list,
             **data_paths,
@@ -474,4 +505,4 @@ def main():
 #  LocalWords:  str dir snglrty tmpdir tmp argparse os ArgumentParser metavar
 #  LocalWords:  RawDescriptionHelpFormatter nargs getenv startswith ValueError
 #  LocalWords:  RuntimeError bfd BFD dbs mgnify HHblits uniclust Uniclust pdb
-#  LocalWords:  multimer seqres uniprot
+#  LocalWords:  multimer seqres uniprot msas MSAs precomputed