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Update run_relax option to models_to_relax #60

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Update run_relax option to models_to_relax #60

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6e70895
Change run_relax to models_to_relax
dxu16 Mar 22, 2023
b4dba19
Fix space in parameter description
dxu16 Mar 22, 2023
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2 changes: 1 addition & 1 deletion README.md
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Original file line number Diff line number Diff line change
Expand Up @@ -96,7 +96,7 @@ Required Parameters:
-t <max_template_date> Maximum template release date to consider (ISO-8601 format - i.e. YYYY-MM-DD). Important if folding historical test sets
Optional Parameters:
-g <use_gpu> Enable NVIDIA runtime to run with GPUs (default: true)
-r <run_relax> 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 (default: true)
-r <models_to_relax> The models to run the final relaxation step on ('all', 'best', or 'none' ). Turning relax off might result in predictions with distracting stereochemical violations but might help in case you are having issues with the relaxation stage (default: 'all')
-e <enable_gpu_relax> Run relax on GPU if GPU is enabled (default: true)
-n <openmm_threads> OpenMM threads (default: all available cores)
-a <gpu_devices> Comma separated list of devices to pass to 'CUDA_VISIBLE_DEVICES' (default: 0)
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10 changes: 5 additions & 5 deletions run_alphafold.sh
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Expand Up @@ -13,7 +13,7 @@ usage() {
echo "-t <max_template_date> Maximum template release date to consider (ISO-8601 format - i.e. YYYY-MM-DD). Important if folding historical test sets"
echo "Optional Parameters:"
echo "-g <use_gpu> Enable NVIDIA runtime to run with GPUs (default: true)"
echo "-r <run_relax> 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 (default: true)"
echo "-r <models_to_relax> The models to run the final relaxation step on ('all', 'best', or 'none' ). Turning relax off might result in predictions with distracting stereochemical violations but might help in case you are having issues with the relaxation stage (default: 'all')"
echo "-e <enable_gpu_relax> Run relax on GPU if GPU is enabled (default: true)"
echo "-n <openmm_threads> OpenMM threads (default: all available cores)"
echo "-a <gpu_devices> Comma separated list of devices to pass to 'CUDA_VISIBLE_DEVICES' (default: 0)"
Expand Down Expand Up @@ -44,7 +44,7 @@ while getopts ":d:o:f:t:g:r:e:n:a:m:c:p:l:b:" i; do
use_gpu=$OPTARG
;;
r)
run_relax=$OPTARG
models_to_relax=$OPTARG
;;
e)
enable_gpu_relax=$OPTARG
Expand Down Expand Up @@ -90,8 +90,8 @@ if [[ "$gpu_devices" == "" ]] ; then
gpu_devices=0
fi

if [[ "$run_relax" == "" ]] ; then
run_relax="true"
if [[ "$models_to_relax" == "" ]] ; then
models_to_relax="all"
fi

if [[ "$enable_gpu_relax" == "" ]] ; then
Expand Down Expand Up @@ -179,7 +179,7 @@ hhsearch_binary_path=$(which hhsearch)
jackhmmer_binary_path=$(which jackhmmer)
kalign_binary_path=$(which kalign)

command_args="--fasta_paths=$fasta_path --output_dir=$output_dir --max_template_date=$max_template_date --db_preset=$db_preset --model_preset=$model_preset --benchmark=$benchmark --use_precomputed_msas=$use_precomputed_msas --num_multimer_predictions_per_model=$num_multimer_predictions_per_model --run_relax=$run_relax --use_gpu_relax=$use_gpu_relax --logtostderr"
command_args="--fasta_paths=$fasta_path --output_dir=$output_dir --max_template_date=$max_template_date --db_preset=$db_preset --model_preset=$model_preset --benchmark=$benchmark --use_precomputed_msas=$use_precomputed_msas --num_multimer_predictions_per_model=$num_multimer_predictions_per_model --models_to_relax=$models_to_relax --use_gpu_relax=$use_gpu_relax --logtostderr"

database_paths="--uniref90_database_path=$uniref90_database_path --mgnify_database_path=$mgnify_database_path --data_dir=$data_dir --template_mmcif_dir=$template_mmcif_dir --obsolete_pdbs_path=$obsolete_pdbs_path"

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