diff --git a/run_af2/src/run_af2/_shared.py b/run_af2/src/run_af2/_shared.py index 9886788d18eb277a17ebcbf24b84ae0f05b51256..bec393f7038fdc5b26c7226dfb35dfb2d3f7a0ec 100644 --- a/run_af2/src/run_af2/_shared.py +++ b/run_af2/src/run_af2/_shared.py @@ -116,14 +116,6 @@ def parse_af2_arguments(parser): 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", diff --git a/run_af2/src/run_af2/run_singularity.py b/run_af2/src/run_af2/run_singularity.py index 1c90ef631171d65b318e1db2d6701b917dcacd79..1628534636607713e9d36e7376efd3f1c7112739 100644 --- a/run_af2/src/run_af2/run_singularity.py +++ b/run_af2/src/run_af2/run_singularity.py @@ -117,7 +117,6 @@ def _assemble_singularity_call( # pylint: disable=too-many-arguments db_preset, model_preset, use_precomputed_msas, - no_run_relax, use_gpu_relax, num_multimer_predictions_per_model, data_paths, @@ -161,7 +160,6 @@ def _assemble_singularity_call( # pylint: disable=too-many-arguments 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(): @@ -213,7 +211,6 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments db_preset="full_dbs", model_preset="monomer", use_precomputed_msas=False, - no_run_relax=False, use_gpu_relax=False, num_multimer_predictions_per_model=5, af2_image_file=None, @@ -276,11 +273,6 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments :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` @@ -418,7 +410,6 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments db_preset, model_preset, use_precomputed_msas, - no_run_relax, use_gpu_relax, num_multimer_predictions_per_model, data_paths, @@ -490,7 +481,6 @@ def main(): opts.db_preset, opts.model_preset, opts.use_precomputed_msas, - opts.no_run_relax, opts.use_gpu_relax, opts.num_multimer_predictions_per_model, opts.singularity_image,