diff --git a/run_af2/src/run_af2/_shared.py b/run_af2/src/run_af2/_shared.py index 0995ccbe8ecdbaac3c5c68846fe8e7e9ac54fa44..eee1d955964b6df6dfe5d3a846720e27a0b38ae4 100644 --- a/run_af2/src/run_af2/_shared.py +++ b/run_af2/src/run_af2/_shared.py @@ -85,14 +85,6 @@ def parse_af2_arguments(parser): metavar="<YYYY-MM-DD>", default=None, ) - af2_group.add_argument( - "-m", - "--model-names", - nargs="+", - help="List of DL models to use for modelling", - metavar="<DL MODEL>", - default=["model_1", "model_2", "model_3", "model_4", "model_5"], - ) af2_group.add_argument( "-g", "--use-gpu", diff --git a/run_af2/src/run_af2/run_singularity.py b/run_af2/src/run_af2/run_singularity.py index 6beef8689c42b509aae9ecedc65cd63377ac1c2d..165f788753dcfb798ec5b2528d10102bcbcb5574 100644 --- a/run_af2/src/run_af2/run_singularity.py +++ b/run_af2/src/run_af2/run_singularity.py @@ -109,7 +109,6 @@ def _assemble_singularity_call( # pylint: disable=too-many-arguments snglrty_fasta, snglrty_out, max_template_date, - model_names, af2_image, snglrty_bin, tmpdir, @@ -145,7 +144,6 @@ def _assemble_singularity_call( # pylint: disable=too-many-arguments f"{af2_image}", f"--fasta_paths={','.join(snglrty_fasta)}", f"--output_dir={snglrty_out}", - f"--model_names={','.join(model_names)}", f"--max_template_date={max_template_date}", f"--db_preset={db_preset}", "--logtostderr", @@ -186,7 +184,6 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments fasta_files, output_dir, max_template_date=None, - model_names=None, use_gpu=False, db_preset="full_dbs", af2_image_file=None, @@ -231,9 +228,6 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments considered.If None, set to tomorrow so all templates are included. :type max_template_date: :class:`str` - :param model_names: model_names parameter of AF2. DL models to use for - modelling. - :type model_names: :class:`list` of :class:`str` :param use_gpu: Run the AF2 pipeline using GPUs or not. :type use_gpu: :class:`bool` :param db_preset: Model configuration - no ensembling and smaller genetic @@ -294,8 +288,6 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments # Since the number of arguments to this function is already high, we allow # more local variables than defined by PEP8. # pylint: disable=too-many-locals - if model_names is None: - model_names = ["model_1", "model_2", "model_3", "model_4", "model_5"] tmpdir = os.getenv(tmpdir_var) if tmpdir is None: raise ValueError(f"tmpdir_var {tmpdir_var} must not be empty.") @@ -339,7 +331,6 @@ def run_af2_singularity_image( # pylint: disable=too-many-arguments snglrty_fasta, bind_out, max_template_date, - model_names, af2_image_file, snglrty_bin, tmpdir, @@ -406,7 +397,6 @@ def main(): opts.fasta_files, opts.output_dir, opts.max_template_date, - opts.model_names, opts.use_gpu, opts.db_preset, af2_image_file=opts.singularity_image,