From b91266612153cb48c2e2d2f68008b143815cedf8 Mon Sep 17 00:00:00 2001
From: Ninjani <janani.durairaj@gmail.com>
Date: Wed, 12 Jul 2023 11:26:53 +0200
Subject: [PATCH] remove --no-run-relax
---
run_af2/src/run_af2/_shared.py | 8 --------
run_af2/src/run_af2/run_singularity.py | 10 ----------
2 files changed, 18 deletions(-)
diff --git a/run_af2/src/run_af2/_shared.py b/run_af2/src/run_af2/_shared.py
index 9886788..bec393f 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 efd3efa..b7c9d61 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,
@@ -280,11 +277,6 @@ 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`
@@ -422,7 +414,6 @@ 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,
@@ -494,7 +485,6 @@ 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,
--
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