| --- singularity/run_singularity.py.orig 2023-02-04 01:14:20.425092745 +0900
+++ singularity/run_singularity.py 2023-02-04 01:17:07.223577644 +0900
@@ -1,3 +1,4 @@
+#!/apps/pyenv/versions/anaconda3-2022.10/envs/alphafold_singularity/bin/python
# Copyright 2021 DeepMind Technologies Limited
#
# Licensed under the Apache License, Version 2.0 (the "License");
@@ -44,12 +45,15 @@
flags.DEFINE_bool(
'use_gpu', True, 'Enable NVIDIA runtime to run with GPUs.')
-flags.DEFINE_boolean(
- 'run_relax', True,
- 'Whether to run the final relaxation step on the predicted models. Turning '
- 'relax off might result in predictions with distracting stereochemical '
- 'violations but might help in case you are having issues with the '
- 'relaxation stage.')
+flags.DEFINE_enum('models_to_relax', 'best', ['best', 'all', 'none'],
+ 'The models to run the final relaxation step on. '
+ 'If `all`, all models are relaxed, which may be time '
+ 'consuming. If `best`, only the most confident model is '
+ 'relaxed. If `none`, relaxation is not run. Turning off '
+ 'relaxation might result in predictions with '
+ 'distracting stereochemical violations but might help '
+ 'in case you are having issues with the relaxation '
+ 'stage.')
flags.DEFINE_bool(
'enable_gpu_relax', True, 'Run relax on GPU if GPU is enabled.')
flags.DEFINE_string(
@@ -145,7 +149,7 @@
# Path to the MGnify database for use by JackHMMER.
mgnify_database_path = os.path.join(
- FLAGS.data_dir, 'mgnify', 'mgy_clusters_2018_12.fa')
+ FLAGS.data_dir, 'mgnify', 'mgy_clusters_2022_05.fa')
# Path to the BFD database for use by HHblits.
bfd_database_path = os.path.join(
@@ -156,9 +160,9 @@
small_bfd_database_path = os.path.join(
FLAGS.data_dir, 'small_bfd', 'bfd-first_non_consensus_sequences.fasta')
- # Path to the Uniclust30 database for use by HHblits.
- uniclust30_database_path = os.path.join(
- FLAGS.data_dir, 'uniclust30', 'uniclust30_2018_08', 'uniclust30_2018_08')
+ # Path to the Uniref30 database for use by HHblits.
+ uniref30_database_path = os.path.join(
+ FLAGS.data_dir, 'uniref30', 'UniRef30_2021_03')
# Path to the PDB70 database for use by HHsearch.
pdb70_database_path = os.path.join(FLAGS.data_dir, 'pdb70', 'pdb70')
@@ -211,7 +215,7 @@
database_paths.append(('small_bfd_database_path', small_bfd_database_path))
else:
database_paths.extend([
- ('uniclust30_database_path', uniclust30_database_path),
+ ('uniref30_database_path', uniref30_database_path),
('bfd_database_path', bfd_database_path),
])
for name, path in database_paths:
@@ -221,7 +225,7 @@
command_args.append(f'--{name}={target_path}')
output_target_path = os.path.join(_ROOT_MOUNT_DIRECTORY, 'output')
- binds.append(f'{output_dir}:{output_target_path}')
+ binds.append(f'{FLAGS.output_dir}:{output_target_path}')
use_gpu_relax = FLAGS.enable_gpu_relax and FLAGS.use_gpu
@@ -233,7 +237,7 @@
f'--benchmark={FLAGS.benchmark}',
f'--use_precomputed_msas={FLAGS.use_precomputed_msas}',
f'--num_multimer_predictions_per_model={FLAGS.num_multimer_predictions_per_model}',
- f'--run_relax={FLAGS.run_relax}',
+ f'--models_to_relax={FLAGS.models_to_relax}',
f'--use_gpu_relax={use_gpu_relax}',
'--logtostderr',
])
@@ -242,6 +246,7 @@
'--bind', f'{",".join(binds)}',
'--env', 'TF_FORCE_UNIFIED_MEMORY=1',
'--env', 'XLA_PYTHON_CLIENT_MEM_FRACTION=4.0',
+ '--env', f'NVIDIA_VISIBLE_DEVICES={FLAGS.gpu_devices}',
'--env', 'OPENMM_CPU_THREADS=12'
]
|