examples/gtalign.md
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+
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+```
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+#!/usr/bin/env bash
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+
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+## gtalign 0.16.0-alpha
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+## demo with 1CIF vs 1YCC
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+## Extracted from GTalign_demo.ipynb
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+##
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+## James Vincent help@sbgrid.org
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+## Jan 10, 2025
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+
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+## !! User required vars
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+my_arch=gpu # Set to gpu or mp
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+model_one=1CIF # ID of structure one
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+model_two=1YCC # ID of structure two
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+
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+## Set MP or GPU:
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+my_gtalign=gtalign_${my_arch}
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+
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+if [[ "$my_arch" == *"gpu"* ]]; then
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+ echo "## Using GPU: ${my_gtalign} "
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+ echo "## Verify GPU"
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+ ${my_gtalign} --dev-list
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+else
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+ echo "## Using CPU (mp): ${my_gtalign} "
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+fi
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+
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+## Set models for comparison
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+model_one_file=${model_one}.cif.gz
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+model_one_url=https://files.rcsb.org/download/${model_one_file}
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+
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+model_two_file=${model_two}.cif.gz
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+model_two_url=https://files.rcsb.org/download/${model_two_file}
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+
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+
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+echo "## Start SBGrid environment"
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+export SBGRID_ALLOW=true # SBGrid internal dev only
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+source /programs/sbgrid.shrc
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+export GTALIGN_X=0.16.0-alpha
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+echo "## Using GTALIGN version: ${GTALIGN_X} "
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+
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+echo "## Download structures:"
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+wget ${model_one_url}
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+wget ${model_two_url}
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+
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+echo "## Run gtalign: "
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+${my_gtalign} -v --qrs=${model_one_file} --rfs=${model_two_file} -o out2_${model_one}_${model_two}_speed6 --dev-queries-per-chunk=1 --dev-queries-total-length-per-chunk=40000 --dev-max-length=40000 --speed=6 --pre-score=0 --ter=0 -s 0 --cpu-threads-reading=1
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+
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+echo "## Check output: "
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+cat out2_${model_one}_${model_two}_speed6/${model_one}.cif__0.out
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+ls -la out2_${model_one}_${model_two}_speed6```
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gtalign.md
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@@ -1,51 +0,0 @@
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-
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-```
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-#!/usr/bin/env bash
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-
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-## gtalign 0.16.0-alpha
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-## demo with 1CIF vs 1YCC
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-## Extracted from GTalign_demo.ipynb
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-##
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-## James Vincent help@sbgrid.org
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-## Jan 10, 2025
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-
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-## !! User required vars
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-my_arch=gpu # Set to gpu or mp
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-model_one=1CIF # ID of structure one
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-model_two=1YCC # ID of structure two
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-
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-## Set MP or GPU:
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-my_gtalign=gtalign_${my_arch}
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-
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-if [[ "$my_arch" == *"gpu"* ]]; then
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- echo "## Using GPU: ${my_gtalign} "
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- echo "## Verify GPU"
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- ${my_gtalign} --dev-list
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-else
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- echo "## Using CPU (mp): ${my_gtalign} "
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-fi
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-
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-## Set models for comparison
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-model_one_file=${model_one}.cif.gz
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-model_one_url=https://files.rcsb.org/download/${model_one_file}
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-
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-model_two_file=${model_two}.cif.gz
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-model_two_url=https://files.rcsb.org/download/${model_two_file}
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-
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-
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-echo "## Start SBGrid environment"
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-export SBGRID_ALLOW=true # SBGrid internal dev only
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-source /programs/sbgrid.shrc
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-export GTALIGN_X=0.16.0-alpha
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-echo "## Using GTALIGN version: ${GTALIGN_X} "
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-
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-echo "## Download structures:"
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-wget ${model_one_url}
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-wget ${model_two_url}
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-
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-echo "## Run gtalign: "
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-${my_gtalign} -v --qrs=${model_one_file} --rfs=${model_two_file} -o out2_${model_one}_${model_two}_speed6 --dev-queries-per-chunk=1 --dev-queries-total-length-per-chunk=40000 --dev-max-length=40000 --speed=6 --pre-score=0 --ter=0 -s 0 --cpu-threads-reading=1
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-
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-echo "## Check output: "
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-cat out2_${model_one}_${model_two}_speed6/${model_one}.cif__0.out
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-ls -la out2_${model_one}_${model_two}_speed6```
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