run deepmind/alphafold_casp13 - work to predict 3 d protein structure in gitpod

[geet2019]

this is the link to the file: https://github.com/geet2019/deepmind-research/tree/master/alphafold_casp13 how can I download the dataset and where I can save it.

https://github.com/geet2019/deepmind-research/blob/master/alphafold_casp13/run_eval.sh

Run contact prediction over 4 replicas.

for replica in 0 1 2 3; do
echo "Launching all models for replica ${replica}"
I tried to run these commands from the shell is it possible to do so.

Run the distogram model.

python3 -m alphafold_casp13.contacts
--logtostderr
--cpu=true
--config_path="${DISTOGRAM_MODEL}/${replica}/config.json"
--checkpoint_path="${DISTOGRAM_MODEL}/${replica}/tf_graph_data/tf_graph_data.ckpt"
--output_path="${OUTPUT_DIR}/distogram/${replica}"
--eval_sstable="${TARGET_PATH}/${TARGET}.tfrec"
--stats_file="${DISTOGRAM_MODEL}/stats_train_s35.json" &

WHERE I CAN SEE THE OUTPUT:-
WHERE I NEED TO EXECUTE IT:-
WHEN I AM TRYING TO EXECUTE EACH.PY EXTENSION SEPARATELY. IT IS ASKING FOR SEPARATE INSTALLATION FOR PACKAGES EVEN THOUGH IT INSTALL THOSE PACKAGES IT IS NOT WORKING WHY? HOW CAN I RESOLVE IT

[Kreyren]

From a quick look i would start by opening https://gitpod.io/#https://github.com/geet2019/deepmind-research/tree/master/alphafold_casp13 and then executing your expected payload there?

also FWIW this https://github.com/geet2019/deepmind-research/blob/master/alphafold_casp13/run_eval.sh seems as shell malware assuming lack of quality assurance as shown on https://shellcheck.net/?id=cb87671 and manipulation with eval, see https://mywiki.wooledge.org/BashFAQ/048

[stale]

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