mirror of
https://github.com/rdk/p2rank.git
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550ab9e1a0
Runs the full per-pocket + per-grid-point descriptor menu with visualizations on the 4 main datasets. Kept out of all() — opt-in.
906 lines
54 KiB
Bash
Executable File
906 lines
54 KiB
Bash
Executable File
#!/usr/bin/env bash
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###################################################################################################################
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ROUTINE=$1
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shift
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TIMESTAMP=$(date +'%Y%m%d_%H%M%S')
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LOGDIR="local-logs/$TIMESTAMP"
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mkdir -pv $LOGDIR
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RUN_LOG="$LOGDIR/run.log"
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DEBUG_LOG="$LOGDIR/debug.log"
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SUMMARY_LOG="$LOGDIR/summary.log"
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ERRORS_LOG="$LOGDIR/errors.log"
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###################################################################################################################
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red=`tput setaf 1`
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green=`tput setaf 2`
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blue=`tput setaf 3`
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cyan=`tput setaf 6`
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reset=`tput sgr0`
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function format_time {
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local T=$1
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local D=$((T/60/60/24))
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local H=$((T/60/60%24))
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local M=$((T/60%60))
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local S=$((T%60))
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(( $D > 0 )) && printf '%d days ' $D
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(( $H > 0 )) && printf '%d hours ' $H
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(( $M > 0 )) && printf '%d min ' $M
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(( $D > 0 || $H > 0 || $M > 0 ))
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printf '%d s\n' $S
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}
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# test command and write exit code and running time
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test() {
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CMD="$@"
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echo "${reset}testing command [${blue}$CMD${reset}]${reset}"
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start=$(date +%s)
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# run command
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# echo error $CMD >> $APPLOG
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$CMD &>> $RUN_LOG
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EXIT_CODE=$?
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end=$(date +%s)
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runtime=$((end-start))
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ftime=$(format_time runtime)
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if [[ $EXIT_CODE == 0 ]]; then
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echo "${green}[OK]${reset}" "time: $ftime"
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else
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echo "${red}[ERROR]${reset} (exit code: $EXIT_CODE)" "time: $ftime"
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fi
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}
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# Like test() but asserts the command must FAIL. Used for fail-fast validation
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# checks (bad params, missing prerequisites) where a non-zero exit code is the
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# success criterion. Green [OK] means the command failed as expected; red
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# [ERROR] means it unexpectedly succeeded.
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test_expect_fail() {
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CMD="$@"
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echo "${reset}testing command (expect fail) [${blue}$CMD${reset}]${reset}"
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start=$(date +%s)
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$CMD &>> $RUN_LOG
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EXIT_CODE=$?
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end=$(date +%s)
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runtime=$((end-start))
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ftime=$(format_time runtime)
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if [[ $EXIT_CODE != 0 ]]; then
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echo "${green}[OK]${reset} (expected fail, exit code: $EXIT_CODE)" "time: $ftime"
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else
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echo "${red}[ERROR]${reset} (expected fail but command succeeded)" "time: $ftime"
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fi
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}
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title() {
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echo
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echo "${cyan}${@}${reset}"
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echo
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}
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###################################################################################################################
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dummy() {
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title DUMMY TEST COMMANDS
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test echo dummy 1
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test echo dummy 2
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test echo dummy 3
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}
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quick() {
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title RUNNING QUICK TESTS
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# files relative to distro/test_data/
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# uses default config
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# therefore the results are stored in distro/test_output/
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test ./prank.sh predict -f distro/test_data/1fbl.pdb -out_subdir TEST/TESTS
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test ./prank.sh predict -f distro/test_data/1fbl.pdb.gz -out_subdir TEST/TESTS
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test ./prank.sh predict -f distro/test_data/1fbl.pdb.zst -c alphafold -out_subdir TEST/TESTS
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test ./prank.sh predict -f distro/test_data/1fbl.cif -c alphafold -out_subdir TEST/TESTS
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test ./prank.sh predict -f distro/test_data/1fbl.cif.gz -c alphafold -out_subdir TEST/TESTS
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test ./prank.sh predict -f distro/test_data/1fbl.cif.zst -out_subdir TEST/TESTS
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test ./prank.sh predict test.ds -out_subdir TEST/TESTS
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test ./prank.sh eval-predict -f distro/test_data/liganated/1aaxa.pdb -out_subdir TEST/TESTS
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test ./prank.sh eval-predict test.ds -out_subdir TEST/TESTS
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test ./prank.sh rescore fpocket.ds -out_subdir TEST/TESTS
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test ./prank.sh rescore fpocket3.ds -out_subdir TEST/TESTS
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test ./prank.sh rescore concavity.ds -out_subdir TEST/TESTS
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test ./prank.sh eval-rescore fpocket.ds -out_subdir TEST/TESTS
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test ./prank.sh eval-rescore concavity.ds -out_subdir TEST/TESTS
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test ./prank.sh traineval -t fpocket.ds -e test.ds -loop 1 -fail_fast 1 -out_subdir TEST/TESTS
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test ./prank.sh crossval fpocket.ds -folds 4 -loop 1 -fail_fast 1 -out_subdir TEST/TESTS
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# test grid optimization
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test ./prank.sh ploop -t fpocket.ds -e test.ds -loop 1 -fail_fast 1 -r_generate_plots 0 -feature_filters '((-chem.*),(-chem.*,chem.atoms),(protrusion.*,bfactor.*))' -out_subdir TEST/TESTS
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# test different tessellation
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test ./prank.sh traineval -t fpocket.ds -e test.ds -loop 1 -fail_fast 1 -tessellation 1 -train_tessellation 3 -out_subdir TEST/TESTS
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# test export_points feature
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test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_points 1 -export_points_format csv.gz -out_subdir TEST/TESTS
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# test export-points command (no model)
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test ./prank.sh export-points -f distro/test_data/1fbl.pdb -export_points_format csv.gz -out_subdir TEST/TESTS
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# test pocket grid + descriptors + PyMOL viz (all three exports in one go)
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test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -export_pocket_descriptors 1 -vis_pocket_grid 1 -out_subdir TEST/TESTS
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# cofactors feature smoke test
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test ./prank.sh predict -f distro/test_data/liganated/1t7qa.pdb -cofactors COA -out_subdir TEST/TESTS
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test ./prank.sh analyze cofactors -f distro/test_data/liganated/1t7qa.pdb -out_subdir TEST/TESTS
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}
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quick_train() {
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test ./prank.sh traineval -loop 1 -t fpocket.ds -e test.ds -fail_fast 1 -out_subdir TEST/TESTS
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}
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basic() {
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title RUNNING BASIC TESTS
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# -fail_fast 0 because of missing ligands
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test ./prank.sh eval-predict chen11.ds -c config/train-default -out_subdir TEST/TESTS
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test ./prank.sh eval-predict 'joined(mlig).ds' -c config/train-default -out_subdir TEST/TESTS
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test ./prank.sh traineval -t chen11-fpocket.ds -e chen11-fpocket.ds -c config/train-default -loop 1 -fail_fast 1 -out_subdir TEST/TESTS
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test ./prank.sh traineval -t chen11-fpocket.ds -e 'joined(mlig).ds' -c config/train-default -loop 1 -fail_fast 0 -out_subdir TEST/TESTS
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test ./prank.sh crossval chen11-fpocket.ds -c config/train-default -loop 1 -fail_fast 1 -out_subdir TEST/TESTS
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#test ./prank.sh eval-predict mlig-joined.ds -c config/train-default -visualizations 1 -tessellation 3 -l VISUALIZATIONS_TES3 -c config/train-default -out_subdir TEST/TESTS
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#test ./prank.sh eval-predict mlig-joined.ds -c config/train-default -visualizations 1 -l VISUALIZATIONS -c config/train-default -out_subdir TEST/TESTS
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}
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# test prediction on all datasets
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predict() {
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title PREDICTIONS ON ALL DATASETS
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test ./prank.sh predict joined.ds -c config/test-default -out_subdir TEST/PREDICT
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test ./prank.sh predict holo4k.ds -c config/test-default -out_subdir TEST/PREDICT
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test ./prank.sh predict coach420.ds -c config/test-default -out_subdir TEST/PREDICT
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test ./prank.sh predict ah4h.holoraw.ds -c config/test-default -out_subdir TEST/PREDICT
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test ./prank.sh predict chen11.ds -c config/test-default -out_subdir TEST/PREDICT
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test ./prank.sh predict fptrain.ds -c config/test-default -out_subdir TEST/PREDICT
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test ./prank.sh predict 'joined(mlig).ds' -c config/test-default -out_subdir TEST/PREDICT
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test ./prank.sh predict 'holo4k(mlig).ds' -c config/test-default -out_subdir TEST/PREDICT
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}
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# test prediction with flattened forest
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# doesn't make sense since default is already flat
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#predict_flattened() {
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#
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# title PREDICTIONS WITH FLATTENED FOREST
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#
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# test ./prank.sh predict joined.ds -c config/test-default -rf_flatten 1 -rf_flatten_target FlatBinaryForest -out_subdir TEST/PREDICT_FLATTENED
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# test ./prank.sh predict holo4k.ds -c config/test-default -rf_flatten 1 -rf_flatten_target LegacyFlatBinaryForest -out_subdir TEST/PREDICT_FLATTENED
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# test ./prank.sh predict coach420.ds -c config/test-default -rf_flatten 1 -rf_flatten_target ShortFlatBinaryForest -out_subdir TEST/PREDICT_FLATTENED
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# test ./prank.sh predict ah4h.holoraw.ds -c config/test-default -rf_flatten 1 -rf_flatten_target SuperShortLegacyFlatBinaryForest -out_subdir TEST/PREDICT_FLATTENED
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#
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# test ./prank.sh predict chen11.ds -c config/test-default -rf_flatten 1 -rf_flatten_target FlatBinaryForest -out_subdir TEST/PREDICT_FLATTENED
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# test ./prank.sh predict fptrain.ds -c config/test-default -rf_flatten 1 -rf_flatten_target FlatBinaryForest -out_subdir TEST/PREDICT_FLATTENED
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# test ./prank.sh predict 'joined(mlig).ds' -c config/test-default -rf_flatten 1 -rf_flatten_target InterleavedBfsForest -out_subdir TEST/PREDICT_FLATTENED
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# test ./prank.sh predict 'holo4k(mlig).ds' -c config/test-default -rf_flatten 1 -rf_flatten_target InterleavedBfsForest -out_subdir TEST/PREDICT_FLATTENED
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#
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#}
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conservation() {
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title PREDICTIONS USING CONSERVATION
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test ./prank.sh predict joined.ds -c config/test-conservation -conservation_dirs 'joined/conservation/hmm/scores' -fail_fast 0 -log_cases 1 -out_subdir TEST/CONSERVATION
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test ./prank.sh predict coach420.ds -c config/test-conservation -conservation_dirs 'coach420/conservation/hmm/scores' -fail_fast 0 -log_cases 1 -out_subdir TEST/CONSERVATION
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test ./prank.sh predict holo4k.ds -c config/test-conservation -conservation_dirs 'holo4k/conservation/hmm/scores' -fail_fast 0 -log_cases 1 -out_subdir TEST/CONSERVATION
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title EVALUATING PREDICTIONS USING CONSERVATION
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test ./prank.sh eval-predict joined.ds -c config/test-conservation -conservation_dirs 'joined/conservation/hmm/scores' -fail_fast 0 -log_cases 1 -out_subdir TEST/CONSERVATION
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test ./prank.sh eval-predict coach420.ds -c config/test-conservation -conservation_dirs 'coach420/conservation/hmm/scores' -fail_fast 0 -log_cases 1 -out_subdir TEST/CONSERVATION
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test ./prank.sh eval-predict holo4k.ds -c config/test-conservation -conservation_dirs 'holo4k/conservation/hmm/scores' -fail_fast 0 -log_cases 1 -out_subdir TEST/CONSERVATION
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title TRAIN/EVAL USING CONSERVATION
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test ./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c config/test-conservation -conservation_dirs 'joined/conservation/hmm/scores' -fail_fast 0 -log_cases 1 -out_subdir TEST/CONSERVATION
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test ./prank.sh traineval -t chen11-fpocket.ds -e coach420.ds -c config/test-conservation -conservation_dirs 'coach420/conservation/hmm/scores' -fail_fast 0 -log_cases 1 -out_subdir TEST/CONSERVATION
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test ./prank.sh traineval -t chen11-fpocket.ds -e holo4k.ds -c config/test-conservation -conservation_dirs 'holo4k/conservation/hmm/scores' -fail_fast 0 -log_cases 1 -out_subdir TEST/CONSERVATION
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}
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# evaluate default model/settings on main datasets
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eval_predict() {
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title EVALUATING PREDICTIONS ON MAIN DATASETS
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test ./prank.sh eval-predict joined.ds -c config/test-default -out_subdir TEST/EVAL
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test ./prank.sh eval-predict coach420.ds -c config/test-default -out_subdir TEST/EVAL
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test ./prank.sh eval-predict holo4k.ds -c config/test-default -out_subdir TEST/EVAL
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# test ./prank.sh predict ah4h.holoraw.ds -c config/test-default -out_subdir TEST/PREDICT
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}
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eval_predict_flattened() {
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title EVALUATING PREDICTIONS WITH FLATTENED FOREST
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test ./prank.sh eval-predict joined.ds -c config/test-default -rf_flatten 1 -rf_flatten_target FlatBinaryForest -out_subdir TEST/EVAL_FLATTENED
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test ./prank.sh eval-predict coach420.ds -c config/test-default -rf_flatten 1 -rf_flatten_target FlatBinaryForest -out_subdir TEST/EVAL_FLATTENED
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test ./prank.sh eval-predict holo4k.ds -c config/test-default -rf_flatten 1 -rf_flatten_target FlatBinaryForest -out_subdir TEST/EVAL_FLATTENED -l FlatBinaryForest
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test ./prank.sh eval-predict holo4k.ds -c config/test-default -rf_flatten 1 -rf_flatten_target NativePanamaForest -out_subdir TEST/EVAL_FLATTENED_NATIVE
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}
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eval_predict_uop() {
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title EVALUATING PREDICTIONS ON MAIN DATASETS
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test ./prank.sh eval-predict joined.ds -c config/test-default -use_only_positive_score 1 -out_subdir TEST/EVAL_UOP
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test ./prank.sh eval-predict holo4k.ds -c config/test-default -use_only_positive_score 1 -out_subdir TEST/EVAL_UOP
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test ./prank.sh eval-predict coach420.ds -c config/test-default -use_only_positive_score 1 -out_subdir TEST/EVAL_UOP
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# test ./prank.sh predict ah4h.holoraw.ds -c config/test-default -out_subdir TEST/PREDICT
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}
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eval_predict_flattened_uop() {
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title EVALUATING PREDICTIONS WITH FLATTENED FOREST
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test ./prank.sh eval-predict joined.ds -c config/test-default -rf_flatten 1 -use_only_positive_score 1 -out_subdir TEST/EVAL_FLATTENED_UOP
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test ./prank.sh eval-predict holo4k.ds -c config/test-default -rf_flatten 1 -use_only_positive_score 1 -out_subdir TEST/EVAL_FLATTENED_UOP
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test ./prank.sh eval-predict coach420.ds -c config/test-default -rf_flatten 1 -use_only_positive_score 1 -out_subdir TEST/EVAL_FLATTENED_UOP
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}
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eval_predict_alphafold() {
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title EVALUATING PREDICTIONS ON MAIN DATASETS
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test ./prank.sh eval-predict joined.ds -c config/test-alphafold -out_subdir TEST/EVAL_ALPHAFOLD
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test ./prank.sh eval-predict holo4k.ds -c config/test-alphafold -out_subdir TEST/EVAL_ALPHAFOLD
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test ./prank.sh eval-predict coach420.ds -c config/test-alphafold -out_subdir TEST/EVAL_ALPHAFOLD
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}
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# evaluate default model/settings on main datasets
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eval_predict_rest() {
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title EVALUATING PREDICTIONS ON OTHER DATASETS
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# train=test for the reference
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test ./prank.sh eval-predict chen11.ds -c config/test-default -out_subdir TEST/EVAL
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test ./prank.sh eval-predict fptrain.ds -c config/test-default -out_subdir TEST/EVAL
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# -fail_fast 0 because of missing ligands
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test ./prank.sh eval-predict 'joined(mlig).ds' -c config/test-default -fail_fast 0 -out_subdir TEST/EVAL
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test ./prank.sh eval-predict 'coach420(mlig).ds' -c config/test-default -fail_fast 0 -out_subdir TEST/EVAL
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test ./prank.sh eval-predict 'holo4k(mlig).ds' -c config/test-default -fail_fast 0 -out_subdir TEST/EVAL
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#test ./prank.sh eval-predict mlig-moad-nr.ds -c config/test-default -log_cases 1 -fail_fast 1 -out_subdir TEST/EVAL
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#test ./prank.sh eval-predict moad-nr.ds -c config/test-default -log_cases 1 -fail_fast 1 -out_subdir TEST/EVAL
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}
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eval_rescore() {
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title EVALUATING RESCORING ON ALL DATASETS
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test ./prank.sh eval-rescore joined-fpocket.ds -c config/test-default -out_subdir TEST/EVAL
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test ./prank.sh eval-rescore coach420-fpocket.ds -c config/test-default -out_subdir TEST/EVAL
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test ./prank.sh eval-rescore holo4k-fpocket.ds -c config/test-default -out_subdir TEST/EVAL
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test ./prank.sh eval-rescore chen11-fpocket.ds -c config/test-default -out_subdir TEST/EVAL
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# -fail_fast 0 because of missing ligands
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test ./prank.sh eval-rescore 'joined(mlig)-fpocket.ds' -c config/test-default -fail_fast 0 -out_subdir TEST/EVAL
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test ./prank.sh eval-rescore 'coach420(mlig)-fpocket.ds' -c config/test-default -fail_fast 0 -out_subdir TEST/EVAL
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test ./prank.sh eval-rescore 'holo4k(mlig)-fpocket.ds' -c config/test-default -fail_fast 0 -out_subdir TEST/EVAL
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}
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fpocket_rescore() {
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title "EVALUATING FPOCKT-RESCORE (RUNNING FPOCKET AD-HOC)"
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test ./prank.sh fpocket-rescore joined.ds -c config/test-default -out_subdir TEST/RESCORE
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test ./prank.sh fpocket-rescore coach420.ds -c config/test-default -out_subdir TEST/RESCORE
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test ./prank.sh fpocket-rescore holo4k.ds -c config/test-default -out_subdir TEST/RESCORE
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test ./prank.sh fpocket-rescore chen11.ds -c config/test-default -out_subdir TEST/RESCORE
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}
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# train and evaluate new model/settings on main datasets
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eval_train() {
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title TRAIN/EVAL ON MAIN DATASETS
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test ./prank.sh crossval chen11-fpocket.ds -c config/train-default -loop 1 -cache_datasets 0 -out_subdir TEST/EVAL_TRAIN
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test ./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c config/train-default -loop 1 -cache_datasets 0 -out_subdir TEST/EVAL_TRAIN
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test ./prank.sh traineval -t chen11-fpocket.ds -e coach420.ds -c config/train-default -loop 1 -cache_datasets 0 -out_subdir TEST/EVAL_TRAIN
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test ./prank.sh traineval -t chen11-fpocket.ds -e holo4k.ds -c config/train-default -loop 1 -cache_datasets 0 -out_subdir TEST/EVAL_TRAIN
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}
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eval_train_rest() {
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title TRAIN/EVAL ON OTHER DATASETS
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# train=test for the reference
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test ./prank.sh traineval -t chen11-fpocket.ds -e chen11-fpocket.ds -c config/train-default -loop 1 -cache_datasets 0 -out_subdir TEST/EVAL_TRAIN
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test ./prank.sh traineval -t chen11-fpocket.ds -e fptrain.ds -c config/train-default -loop 1 -cache_datasets 0 -out_subdir TEST/EVAL_TRAIN
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test ./prank.sh traineval -t chen11-fpocket.ds -e 'joined(mlig).ds' -c config/train-default -loop 1 -cache_datasets 0 -out_subdir TEST/EVAL_TRAIN
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test ./prank.sh traineval -t chen11-fpocket.ds -e 'coach420(mlig).ds' -c config/train-default -loop 1 -cache_datasets 0 -out_subdir TEST/EVAL_TRAIN
|
|
test ./prank.sh traineval -t chen11-fpocket.ds -e 'holo4k(mlig).ds' -c config/train-default -loop 1 -cache_datasets 0 -out_subdir TEST/EVAL_TRAIN
|
|
}
|
|
|
|
eval_ploop() {
|
|
|
|
title GRID OPTIMIZATION
|
|
|
|
test ./prank.sh ploop -t chen11-fpocket.ds -e coach420.ds -c config/train-default -loop 1 -fail_fast 1 -r_generate_plots 0 -rf_trees '(20,40,100)' -rf_features '(6,0)' -out_subdir TEST/PLOOP
|
|
test ./prank.sh ploop -t chen11-fpocket.ds -e speed5.ds -c config/train-default -loop 1 -fail_fast 1 -r_generate_plots 0 -rf_trees '[10:30:10]' -feature_filters '((-chem.*),(-chem.*,chem.atoms),(protrusion.*,bfactor.*))' -out_subdir TEST/PLOOP
|
|
|
|
# test ability to separate normal param features (type: list) and iterative feature_filters (type: list)
|
|
# test feature_filters
|
|
test ./prank.sh ploop -t chen11-fpocket.ds -e speed5.ds -c config/train-default -loop 1 -fail_fast 1 -r_generate_plots 0 -features '(volsite,bfactor)' -feature_filters '((-volsite.*),(volsite.*,-volsite.vsCation),(volsite.*,bfactor.*))' -out_subdir TEST/PLOOP
|
|
}
|
|
|
|
analyze() {
|
|
|
|
title PRINT/ANALYZE COMMANDS
|
|
|
|
test ./prank.sh print features -c config/train-default -out_subdir TEST/ANALYZE
|
|
test ./prank.sh print model-info -c config/train-default -out_subdir TEST/ANALYZE
|
|
|
|
test ./prank.sh analyze fasta-masked -f distro/test_data/liganated/1aaxa.pdb -c config/train-default -out_subdir TEST/ANALYZE
|
|
|
|
test ./prank.sh analyze fasta-masked chen11.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
test ./prank.sh analyze fasta-masked joined.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
test ./prank.sh analyze fasta-masked coach420.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
test ./prank.sh analyze fasta-masked holo4k.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
|
|
test ./prank.sh analyze residues joined.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
test ./prank.sh analyze binding-residues joined.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
test ./prank.sh analyze labeled-residues joined.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
test ./prank.sh analyze chains joined.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
test ./prank.sh analyze chains-residues joined.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
test ./prank.sh analyze aa-propensities joined.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
test ./prank.sh analyze aa-surf-seq-duplets joined.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
test ./prank.sh analyze aa-surf-seq-triplets joined.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
test ./prank.sh analyze fasta-raw joined.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
|
|
test ./prank.sh analyze residues holo4k.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
test ./prank.sh analyze binding-residues holo4k.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
test ./prank.sh analyze labeled-residues holo4k.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
test ./prank.sh analyze chains holo4k.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
test ./prank.sh analyze chains-residues holo4k.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
|
|
test ./prank.sh analyze cofactors joined.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
test ./prank.sh analyze cofactors holo4k.ds -c config/train-default -cache_datasets 0 -out_subdir TEST/ANALYZE
|
|
|
|
}
|
|
|
|
|
|
|
|
cofactors() {
|
|
|
|
title COFACTORS FEATURE
|
|
|
|
# analyze cofactors: survey mode (no -cofactors) on file + dataset
|
|
test ./prank.sh analyze cofactors -f distro/test_data/liganated/1t7qa.pdb -out_subdir TEST/COFACTORS
|
|
test ./prank.sh analyze cofactors test.ds -out_subdir TEST/COFACTORS
|
|
|
|
# analyze cofactors: dry-run mode with each specifier form
|
|
test ./prank.sh analyze cofactors -f distro/test_data/liganated/1t7qa.pdb -cofactors COA -out_subdir TEST/COFACTORS
|
|
test ./prank.sh analyze cofactors -f distro/test_data/liganated/1t7qa.pdb -cofactors 'COA[atom_id:9551]' -out_subdir TEST/COFACTORS
|
|
test ./prank.sh analyze cofactors -f distro/test_data/liganated/1t7qa.pdb -cofactors 'COA[contact_res_ids:A_K258]' -out_subdir TEST/COFACTORS
|
|
test ./prank.sh analyze cofactors -f distro/test_data/liganated/1t7qa.pdb -cofactors ZZZZ -out_subdir TEST/COFACTORS
|
|
|
|
# predict with cofactors
|
|
test ./prank.sh predict -f distro/test_data/liganated/1t7qa.pdb -cofactors COA -out_subdir TEST/COFACTORS
|
|
# R18: never-present specifier must be a no-op (drop-in safety)
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -cofactors ZZZZ -out_subdir TEST/COFACTORS
|
|
# R22: case-mismatched name must still match (parser auto-uppercases the group name)
|
|
test ./prank.sh predict -f distro/test_data/liganated/1t7qa.pdb -cofactors coa -out_subdir TEST/COFACTORS
|
|
# R22: contact_res_ids must survive comma-splitting (bracket-aware parse)
|
|
test ./prank.sh predict -f distro/test_data/liganated/1t7qa.pdb -cofactors 'COA[contact_res_ids:A_K258,A_D246]' -out_subdir TEST/COFACTORS
|
|
|
|
# knobs
|
|
test ./prank.sh predict -f distro/test_data/liganated/1t7qa.pdb -cofactors COA -cofactor_max_protein_dist 0 -out_subdir TEST/COFACTORS
|
|
test ./prank.sh predict -f distro/test_data/liganated/1t7qa.pdb -cofactors COA -vis_highlight_cofactors 0 -out_subdir TEST/COFACTORS
|
|
|
|
# R19: aa_mapping collision warning (MSE is in built-in minimal mapping)
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -cofactors MSE -out_subdir TEST/COFACTORS
|
|
|
|
# drop-in safety benchmark
|
|
test ./benchmark/cofactors_dropin_safety.sh distro/test_data/concavity.ds
|
|
}
|
|
|
|
cofactors_full() {
|
|
|
|
title COFACTOR DATASETS
|
|
|
|
local DS_BASE="../p2rank-datasets2/other/cofactors"
|
|
if [ ! -f "$DS_BASE/cofactors-demo-cif.ds" ]; then
|
|
echo " [SKIP] $DS_BASE/cofactors-demo-cif.ds not found"
|
|
return
|
|
fi
|
|
|
|
# --- A. predict on the demo dataset, both formats ---
|
|
test ./prank.sh predict cofactors-demo-cif.ds -dataset_base_dir $DS_BASE -fail_fast 1 -out_subdir TEST/COF_DS
|
|
test ./prank.sh predict cofactors-demo-pdb.ds -dataset_base_dir $DS_BASE -fail_fast 1 -out_subdir TEST/COF_DS
|
|
|
|
# --- B. baseline runs (no cofactors column) for delta comparison ---
|
|
test ./prank.sh predict cofactors-demo-baseline-cif.ds -dataset_base_dir $DS_BASE -fail_fast 1 -out_subdir TEST/COF_DS
|
|
test ./prank.sh predict cofactors-demo-baseline-pdb.ds -dataset_base_dir $DS_BASE -fail_fast 1 -out_subdir TEST/COF_DS
|
|
|
|
# --- C. analyze cofactors on the demo dataset (matches.csv, summary) ---
|
|
test ./prank.sh analyze cofactors cofactors-demo-cif.ds -dataset_base_dir $DS_BASE -fail_fast 1 -out_subdir TEST/COF_DS
|
|
test ./prank.sh analyze cofactors cofactors-demo-baseline-cif.ds -dataset_base_dir $DS_BASE -fail_fast 1 -out_subdir TEST/COF_DS
|
|
|
|
# --- D. combined with -aa_mapping pdbfixer (R19 collision on TPQ family) ---
|
|
test ./prank.sh predict cofactors-demo-cif.ds -dataset_base_dir $DS_BASE -aa_mapping pdbfixer -out_subdir TEST/COF_DS
|
|
|
|
# --- E. visualization spot-check on two well-known cofactors ---
|
|
test ./prank.sh predict -f $DS_BASE/structures/pdb/4REK.pdb -cofactors FAD -visualizations 1 -out_subdir TEST/COF_DS
|
|
test ./prank.sh predict -f $DS_BASE/structures/pdb/4BEU.pdb -cofactors PLP -visualizations 1 -out_subdir TEST/COF_DS
|
|
|
|
# --- F. export-points (cofactor atoms must propagate into the points output) ---
|
|
test ./prank.sh export-points -f $DS_BASE/structures/pdb/4REK.pdb -cofactors FAD -out_subdir TEST/COF_DS
|
|
|
|
# --- G. full-dataset stress test (523 structures across 43 cofactor codes) ---
|
|
if [ -f "$DS_BASE/cofactors-full.ds" ]; then
|
|
test ./prank.sh predict cofactors-full.ds -dataset_base_dir $DS_BASE -fail_fast 1 -out_subdir TEST/COF_DS_FULL
|
|
test ./prank.sh predict cofactors-full-baseline.ds -dataset_base_dir $DS_BASE -fail_fast 1 -out_subdir TEST/COF_DS_FULL
|
|
test ./prank.sh analyze cofactors cofactors-full.ds -dataset_base_dir $DS_BASE -fail_fast 1 -out_subdir TEST/COF_DS_FULL
|
|
fi
|
|
}
|
|
|
|
aa_mapping() {
|
|
|
|
title AA MAPPING FEATURE
|
|
|
|
# bundled pdbfixer preset (87-entry table)
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -aa_mapping pdbfixer -out_subdir TEST/AA_MAPPING
|
|
|
|
# dataset paths (predict / rescore / eval)
|
|
test ./prank.sh predict test.ds -aa_mapping pdbfixer -out_subdir TEST/AA_MAPPING
|
|
test ./prank.sh rescore fpocket.ds -aa_mapping pdbfixer -out_subdir TEST/AA_MAPPING
|
|
test ./prank.sh eval-predict -f distro/test_data/liganated/1aaxa.pdb -aa_mapping pdbfixer -out_subdir TEST/AA_MAPPING
|
|
}
|
|
|
|
transform() {
|
|
|
|
title TRANSFORM COMMANDS
|
|
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif -chains A # output: <out_dir>/2W83_A.cif
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/2W83.pdb -chains A # output: <out_dir>/2W83_A.pdb
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif.gz -chains A,B # output: <out_dir>/2W83_A,B.cif.gz
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif.gz -chains A,B -out_file distro/test_output/2W83_A,B.cif.gz # output: distro/test_output/2W83_A,B.cif.gz
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif -chains keep # output: <out_dir>/2W83.cif
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif -chains keep -out_format pdb.gz # output: <out_dir>/2W83.pdb.gz
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif -chains all # output: <out_dir>/2W83_all.cif
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif -chains A -out_format keep # output: <out_dir>/2W83_A.cif
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/2W83.cif.gz -chains A -out_format pdb.gz # output: <out_dir>/2W83_A.pdb.gz
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/2W83.pdb.gz -chains A,B -out_format cif # output: <out_dir>/2W83_A,B.cif
|
|
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/1fbl.cif -chains A
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/1fbl.pdb -chains A
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/1fbl.cif.gz -chains A,B
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/1fbl.cif.gz -chains A,B -out_file distro/test_output/1fbl_A,B.cif.gz
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/1fbl.cif -chains keep
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/1fbl.cif -chains keep -out_format pdb.gz
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/1fbl.cif -chains all
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/1fbl.cif -chains A -out_format keep
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/1fbl.cif.gz -chains A -out_format pdb.gz
|
|
test ./prank.sh transform reduce-to-chains -f distro/test_data/1fbl.pdb.gz -chains A,B -out_format cif
|
|
|
|
}
|
|
|
|
export_points() {
|
|
|
|
title EXPORT POINTS FEATURE
|
|
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_points 1 -export_points_format csv -out_subdir TEST/EXPORT_POINTS
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_points 1 -export_points_format csv.gz -out_subdir TEST/EXPORT_POINTS
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_points 1 -export_points_format csv.zst -out_subdir TEST/EXPORT_POINTS
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_points 1 -export_points_format arrow -out_subdir TEST/EXPORT_POINTS
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_points 1 -export_points_format arrow.gz -out_subdir TEST/EXPORT_POINTS
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_points 1 -export_points_format arrow.zst -out_subdir TEST/EXPORT_POINTS
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_points 1 -export_points_format parquet -out_subdir TEST/EXPORT_POINTS
|
|
|
|
# export-points command (no model needed)
|
|
test ./prank.sh export-points -f distro/test_data/2W83.cif -extra_features 'surface_protrusion' -export_points_format arrow -out_subdir TEST/EXPORT_POINTS
|
|
test ./prank.sh export-points -f distro/test_data/1fbl.pdb -out_subdir TEST/EXPORT_POINTS
|
|
test ./prank.sh export-points -f distro/test_data/1fbl.pdb -export_points_format csv.gz -out_subdir TEST/EXPORT_POINTS
|
|
test ./prank.sh export-points -f distro/test_data/1fbl.pdb -export_points_format csv.zst -out_subdir TEST/EXPORT_POINTS
|
|
test ./prank.sh export-points -f distro/test_data/1fbl.pdb -export_points_format arrow -out_subdir TEST/EXPORT_POINTS
|
|
test ./prank.sh export-points -f distro/test_data/1fbl.pdb -export_points_format arrow.gz -out_subdir TEST/EXPORT_POINTS
|
|
test ./prank.sh export-points -f distro/test_data/1fbl.pdb -export_points_format arrow.zst -out_subdir TEST/EXPORT_POINTS
|
|
test ./prank.sh export-points -f distro/test_data/1fbl.pdb -export_points_format parquet -out_subdir TEST/EXPORT_POINTS
|
|
|
|
# predict/rescore on datasets
|
|
test ./prank.sh predict chen11.ds -c config/test-default -export_points 1 -export_points_format arrow.zst -out_subdir TEST/EXPORT_POINTS
|
|
test ./prank.sh rescore coach420-fpocket.ds -c config/test-default -export_points 1 -export_points_format csv.zst -out_subdir TEST/EXPORT_POINTS
|
|
test ./prank.sh rescore chen11-fpocket.ds -c config/test-default -export_points 1 -export_points_format parquet -out_subdir TEST/EXPORT_POINTS
|
|
|
|
# export-points command on datasets
|
|
test ./prank.sh export-points chen11.ds -c config/test-default -export_points_format arrow.zst -out_subdir TEST/EXPORT_POINTS
|
|
test ./prank.sh export-points coach420-fpocket.ds -c config/test-default -export_points_format csv.zst -out_subdir TEST/EXPORT_POINTS
|
|
test ./prank.sh export-points chen11-fpocket.ds -c config/test-default -export_points_format parquet -out_subdir TEST/EXPORT_POINTS
|
|
}
|
|
|
|
pocket_grid() {
|
|
|
|
title POCKET GRID + DESCRIPTORS EXPORT
|
|
|
|
# Basic combinations on a single file
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_descriptors 1 -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -export_pocket_descriptors 1 -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -vis_pocket_grid 1 -out_subdir TEST/POCKET_GRID
|
|
|
|
# All grid file formats
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_format csv -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_format csv.gz -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_format csv.zst -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_format arrow -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_format arrow.gz -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_format arrow.zst -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_format parquet -out_subdir TEST/POCKET_GRID
|
|
|
|
# Full descriptor menu (all seven shipped, including principal_moments)
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_descriptors 1 -pocket_descriptors 'volume,sphericity,radius_of_gyration,num_residues,num_surface_atoms,num_grid_points,principal_moments' -out_subdir TEST/POCKET_GRID
|
|
|
|
# Per-grid-point descriptors (volsite, volsite_smooth), each at least once
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_point_descriptors 'volsite' -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_point_descriptors 'volsite_smooth' -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_point_descriptors 'volsite,volsite_smooth' -out_subdir TEST/POCKET_GRID
|
|
|
|
# Per-grid-point descriptor knobs
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_point_descriptors 'volsite' -pocket_grid_volsite_radius 5.0 -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_point_descriptors 'volsite_smooth' -pocket_grid_volsite_sigma 1.5 -out_subdir TEST/POCKET_GRID
|
|
|
|
# Full combo: per-pocket descriptors + per-grid-point descriptors + viz in one run
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -export_pocket_descriptors 1 -pocket_grid_point_descriptors 'volsite,volsite_smooth' -vis_pocket_grid 1 -out_subdir TEST/POCKET_GRID
|
|
|
|
# Grid-free descriptors only — exercises the grid-build short-circuit (no
|
|
# "PocketGrid built" log line should appear for these invocations).
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_descriptors 1 -pocket_descriptors 'num_residues,num_surface_atoms' -export_pocket_grid 0 -out_subdir TEST/POCKET_GRID
|
|
|
|
# Fill strategies (only morph_closing and none are valid; convex_hull is rejected at startup)
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_fill morph_closing -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_fill none -out_subdir TEST/POCKET_GRID
|
|
|
|
# Knobs: include unassigned, tighter spacing, larger reach, custom atom buffer
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_include_unassigned 1 -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_spacing 0.75 -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_max_dist 8 -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_atom_buffer 1.0 -out_subdir TEST/POCKET_GRID
|
|
|
|
# Validation: fail-fast checks (each must exit non-zero — uses test_expect_fail so the green [OK] is shown only when the command fails as designed)
|
|
test_expect_fail ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_fill cubist -out_subdir TEST/POCKET_GRID
|
|
test_expect_fail ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_descriptors 1 -pocket_descriptors 'not_a_descriptor' -out_subdir TEST/POCKET_GRID
|
|
test_expect_fail ./prank.sh predict -f distro/test_data/1fbl.pdb -export_pocket_grid 1 -pocket_grid_point_descriptors 'not_a_descriptor' -out_subdir TEST/POCKET_GRID
|
|
test_expect_fail ./prank.sh predict -f distro/test_data/1fbl.pdb -vis_pocket_grid 1 -out_subdir TEST/POCKET_GRID
|
|
|
|
# Rescore + dataset paths
|
|
test ./prank.sh rescore fpocket.ds -export_pocket_grid 1 -export_pocket_descriptors 1 -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict test.ds -export_pocket_grid 1 -export_pocket_descriptors 1 -pocket_grid_format parquet -out_subdir TEST/POCKET_GRID
|
|
|
|
# Cofactor interaction — cofactor atoms must show up in the grid's exclusion zone
|
|
test ./prank.sh predict -f distro/test_data/liganated/1t7qa.pdb -cofactors COA -export_pocket_grid 1 -export_pocket_descriptors 1 -out_subdir TEST/POCKET_GRID
|
|
|
|
|
|
# Single timed run per dataset at the env default thread count (PRANK_LOCALENV_PARAMS,
|
|
# typically -threads 16). No -threads override here on purpose — measures real
|
|
# end-to-end wall time on each dataset rather than isolating per-protein cost.
|
|
test ./prank.sh predict joined.ds -c config/test-default -export_pocket_grid 1 -export_pocket_descriptors 1 -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict holo4k.ds -c config/test-default -export_pocket_grid 1 -export_pocket_descriptors 1 -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict coach420.ds -c config/test-default -export_pocket_grid 1 -export_pocket_descriptors 1 -out_subdir TEST/POCKET_GRID
|
|
test ./prank.sh predict chen11.ds -c config/test-default -export_pocket_grid 1 -export_pocket_descriptors 1 -out_subdir TEST/POCKET_GRID
|
|
#test ./prank.sh predict fptrain.ds -c config/test-default -export_pocket_grid 1 -export_pocket_descriptors 1 -out_subdir TEST/POCKET_GRID
|
|
|
|
test ./prank.sh predict fptrain.ds -c config/test-default -export_pocket_grid 1 -export_pocket_descriptors 1 -visualizations 1 -vis_pocket_grid 1 -out_subdir TEST/POCKET_GRID
|
|
|
|
|
|
}
|
|
|
|
pocket_grid_bench() {
|
|
|
|
title POCKET GRID BENCHMARK
|
|
|
|
test ./prank.sh predict joined.ds -c config/test-default -export_pocket_grid 1 -export_pocket_descriptors 1 -out_subdir TEST/POCKET_GRID/BENCH
|
|
test ./prank.sh predict holo4k.ds -c config/test-default -export_pocket_grid 1 -export_pocket_descriptors 1 -out_subdir TEST/POCKET_GRID/BENCH
|
|
test ./prank.sh predict coach420.ds -c config/test-default -export_pocket_grid 1 -export_pocket_descriptors 1 -out_subdir TEST/POCKET_GRID/BENCH
|
|
test ./prank.sh predict chen11.ds -c config/test-default -export_pocket_grid 1 -export_pocket_descriptors 1 -out_subdir TEST/POCKET_GRID/BENCH
|
|
test ./prank.sh predict fptrain.ds -c config/test-default -export_pocket_grid 1 -export_pocket_descriptors 1 -out_subdir TEST/POCKET_GRID/BENCH
|
|
|
|
}
|
|
|
|
# Long-running sweep: full descriptor menu (per-pocket + per-grid-point) on the
|
|
# 4 main datasets with visualizations enabled. Not part of all() — opt-in only.
|
|
pocket_grid_long() {
|
|
|
|
title POCKET GRID LONG - ALL DESCRIPTORS ON MAIN DATASETS
|
|
|
|
PG_DESCRIPTORS='volume,sphericity,radius_of_gyration,num_residues,num_surface_atoms,num_grid_points,principal_moments'
|
|
PG_POINT_DESCRIPTORS='volsite,volsite_smooth'
|
|
|
|
test ./prank.sh predict joined.ds -c config/test-default -export_pocket_grid 1 -export_pocket_descriptors 1 -pocket_descriptors "$PG_DESCRIPTORS" -pocket_grid_point_descriptors "$PG_POINT_DESCRIPTORS" -visualizations 1 -vis_pocket_grid 1 -out_subdir TEST/POCKET_GRID_LONG
|
|
test ./prank.sh predict holo4k.ds -c config/test-default -export_pocket_grid 1 -export_pocket_descriptors 1 -pocket_descriptors "$PG_DESCRIPTORS" -pocket_grid_point_descriptors "$PG_POINT_DESCRIPTORS" -visualizations 1 -vis_pocket_grid 1 -out_subdir TEST/POCKET_GRID_LONG
|
|
test ./prank.sh predict coach420.ds -c config/test-default -export_pocket_grid 1 -export_pocket_descriptors 1 -pocket_descriptors "$PG_DESCRIPTORS" -pocket_grid_point_descriptors "$PG_POINT_DESCRIPTORS" -visualizations 1 -vis_pocket_grid 1 -out_subdir TEST/POCKET_GRID_LONG
|
|
test ./prank.sh predict chen11.ds -c config/test-default -export_pocket_grid 1 -export_pocket_descriptors 1 -pocket_descriptors "$PG_DESCRIPTORS" -pocket_grid_point_descriptors "$PG_POINT_DESCRIPTORS" -visualizations 1 -vis_pocket_grid 1 -out_subdir TEST/POCKET_GRID_LONG
|
|
|
|
}
|
|
|
|
classifiers() {
|
|
|
|
title TRAIN/EVAL USING DIFFERENT CLASSIFIERS
|
|
|
|
test ./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c config/train-default -classifier RandomForest -label RF -loop 1 -cache_datasets 0 -out_subdir TEST/CLASSIFIERS
|
|
test ./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c config/train-default -classifier FastRandomForest -label FRF -loop 1 -cache_datasets 0 -out_subdir TEST/CLASSIFIERS
|
|
test ./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c config/train-default -classifier FasterForest -label FF -loop 1 -cache_datasets 0 -out_subdir TEST/CLASSIFIERS
|
|
test ./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c config/train-default -classifier FasterForest2 -label FF2 -loop 1 -cache_datasets 0 -out_subdir TEST/CLASSIFIERS
|
|
|
|
}
|
|
|
|
feature_importances() {
|
|
|
|
title CALCULATING FEATURE IMPORTANCES
|
|
|
|
test ./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c config/train-default -feature_importances 1 -classifier RandomForest -label RF -loop 1 -cache_datasets 0 -out_subdir TEST/IMPORTANCES
|
|
test ./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c config/train-default -feature_importances 1 -classifier FastRandomForest -label FRF -loop 1 -cache_datasets 0 -out_subdir TEST/IMPORTANCES
|
|
test ./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c config/train-default -feature_importances 1 -classifier FasterForest -label FF -loop 1 -cache_datasets 0 -out_subdir TEST/IMPORTANCES
|
|
test ./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c config/train-default -feature_importances 1 -classifier FasterForest2 -label FF2 -loop 1 -cache_datasets 0 -out_subdir TEST/IMPORTANCES
|
|
}
|
|
|
|
|
|
|
|
###################################################################################################################
|
|
|
|
|
|
quick_train_new() {
|
|
test ./prank.sh traineval -t chen11-fpocket.ds -e 'joined(mlig).ds' -c config/new -loop 3 -out_subdir TEST/EVAL_TRAIN
|
|
test ./prank.sh traineval -t chen11-fpocket.ds -e 'holo4k(mlig).ds' -c config/new -loop 1 -cache_datasets 0 -out_subdir TEST/EVAL_TRAIN
|
|
test ./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c config/new -loop 3 -out_subdir TEST/EVAL_TRAIN
|
|
test ./prank.sh traineval -t chen11-fpocket.ds -e holo4k.ds -c config/new -loop 1 -cache_datasets 0 -out_subdir TEST/EVAL_TRAIN
|
|
test ./prank.sh crossval chen11-fpocket.ds -c config/new -loop 3 -out_subdir TEST/EVAL_TRAIN
|
|
}
|
|
|
|
|
|
# evaluate particular config on main datasets
|
|
# usage: ./testsets.sh traineval_config <config> <label>
|
|
traineval_config() {
|
|
CONFIG=$1
|
|
LABEL=$2
|
|
test ./prank.sh traineval -t chen11.ds -e 'joined(mlig).ds' -c ${CONFIG} -loop 10 -out_subdir EVAL/CONFIG_${LABEL}
|
|
test ./prank.sh traineval -t chen11.ds -e 'holo4k(mlig).ds' -c ${CONFIG} -loop 3 -cache_datasets 0 -out_subdir EVAL/CONFIG_${LABEL}
|
|
test ./prank.sh traineval -t chen11.ds -e joined.ds -c ${CONFIG} -loop 10 -out_subdir EVAL/CONFIG_${LABEL}
|
|
test ./prank.sh traineval -t chen11.ds -e holo4k.ds -c ${CONFIG} -loop 3 -cache_datasets 0 -out_subdir EVAL/CONFIG_${LABEL}
|
|
test ./prank.sh crossval chen11.ds -c ${CONFIG} -loop 10 -out_subdir EVAL/CONFIG_${LABEL}
|
|
}
|
|
|
|
# evaluate particular config on all datasets
|
|
# usage: ./testsets.sh traineval_config_all <config> <label>
|
|
traineval_config_all() {
|
|
traineval_config $@
|
|
|
|
CONFIG=$1
|
|
LABEL=$2
|
|
test ./prank.sh traineval -t chen11.ds -e fptrain.ds -c ${CONFIG} -loop 10 -out_subdir EVAL/CONFIG_${LABEL}
|
|
|
|
}
|
|
|
|
|
|
###################################################################################################################
|
|
|
|
|
|
speed() {
|
|
|
|
title SPEED TESTS
|
|
|
|
misc/test-scripts/benchmark.sh 1 "FPTRAIN" "1 2 4 8 16" "./prank.sh predict fptrain.ds -c config/test-default -out_subdir TEST/SPEED"
|
|
misc/test-scripts/benchmark.sh 5 "1FILE" "1" "./prank.sh predict -f distro/test_data/liganated/1aaxa.pdb -c config/test-default -out_subdir TEST/SPEED"
|
|
}
|
|
|
|
speed_basic() {
|
|
|
|
title SPEED TESTS
|
|
|
|
misc/test-scripts/benchmark.sh 3 "PREDICT" "1 8" "./prank.sh predict fptrain.ds -c config/test-default -out_subdir TEST/SPEED"
|
|
misc/test-scripts/benchmark.sh 3 "TRAINEVAL" "1 8" "./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c config/train-default -loop 1 -out_subdir TEST/SPEED"
|
|
misc/test-scripts/benchmark.sh 3 "TRAINEVAL" "1 8" "./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c config/train-default -loop 3 -out_subdir TEST/SPEED"
|
|
}
|
|
|
|
speed_ff() {
|
|
|
|
title SPEED TESTS - FASTER FOREST
|
|
|
|
misc/test-scripts/benchmark.sh 3 "TRAINEVAL" "1 8" "./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c config/train-default -classifier FasterForest -loop 1 -out_subdir TEST/SPEED"
|
|
misc/test-scripts/benchmark.sh 3 "TRAINEVAL" "1 8" "./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c config/train-default -classifier FasterForest -loop 3 -out_subdir TEST/SPEED"
|
|
}
|
|
|
|
speed_ff_quick() {
|
|
|
|
title SPEED TESTS - FASTER FOREST
|
|
|
|
misc/test-scripts/benchmark.sh 3 "TRAINEVAL" "1 8" "./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c config/train-default -classifier FasterForest -loop 1 -out_subdir TEST/SPEED"
|
|
}
|
|
|
|
speed_quick() {
|
|
|
|
title "SPEED TESTS (QUICK)"
|
|
|
|
misc/test-scripts/benchmark.sh 3 "FPTRAIN" "1 2 4 5 6 8 9 12 13 24" "./prank.sh predict fptrain.ds -c config/test-default -out_subdir TEST/SPEED"
|
|
misc/test-scripts/benchmark.sh 10 "1FILE" "1" "./prank.sh predict -f distro/test_data/liganated/1aaxa.pdb -c config/test-default -out_subdir TEST/SPEED"
|
|
}
|
|
|
|
speed_quick_tes3() {
|
|
|
|
title "SPEED TESTS (QUICK)"
|
|
|
|
misc/test-scripts/benchmark.sh 3 "FPTRAIN" "1 2 4 5 6 8 9 12 13 24" "./prank.sh predict fptrain.ds -c config/test-default -tessellation 3 -out_subdir TEST/SPEED"
|
|
misc/test-scripts/benchmark.sh 10 "1FILE" "1" "./prank.sh predict -f distro/test_data/liganated/1aaxa.pdb -c config/test-default -tessellation 3 -out_subdir TEST/SPEED"
|
|
}
|
|
|
|
speed_joined_flattening() {
|
|
|
|
title SPEED TESTS
|
|
|
|
misc/test-scripts/benchmark.sh 1 "JOINED" "1 2 4 8 12 16 17 18" "./prank.sh predict joined.ds -c config/test-default -rf_flatten 0 -rf_batch_prediction 0 -out_subdir TEST/SPEED"
|
|
misc/test-scripts/benchmark.sh 1 "JOINED" "1 2 4 8 12 16 17 18" "./prank.sh predict joined.ds -c config/test-default -rf_flatten 1 -rf_batch_prediction 0 -out_subdir TEST/SPEED"
|
|
misc/test-scripts/benchmark.sh 1 "JOINED" "1 2 4 8 12 16 17 18" "./prank.sh predict joined.ds -c config/test-default -rf_flatten 0 -rf_batch_prediction 1 -out_subdir TEST/SPEED"
|
|
misc/test-scripts/benchmark.sh 1 "JOINED" "1 2 4 8 12 16 17 18" "./prank.sh predict joined.ds -c config/test-default -rf_flatten 1 -rf_batch_prediction 1 -out_subdir TEST/SPEED"
|
|
}
|
|
|
|
speed_joined_flattening3() {
|
|
|
|
title SPEED TESTS
|
|
|
|
misc/test-scripts/benchmark.sh 3 "JOINED" "1 2 4 8 12 16 17 18" "./prank.sh predict joined.ds -c config/test-default -rf_flatten 0 -rf_batch_prediction 0 -out_subdir TEST/SPEED"
|
|
misc/test-scripts/benchmark.sh 3 "JOINED" "1 2 4 8 12 16 17 18" "./prank.sh predict joined.ds -c config/test-default -rf_flatten 1 -rf_batch_prediction 0 -out_subdir TEST/SPEED"
|
|
misc/test-scripts/benchmark.sh 3 "JOINED" "1 2 4 8 12 16 17 18" "./prank.sh predict joined.ds -c config/test-default -rf_flatten 0 -rf_batch_prediction 1 -out_subdir TEST/SPEED"
|
|
misc/test-scripts/benchmark.sh 3 "JOINED" "1 2 4 8 12 16 17 18" "./prank.sh predict joined.ds -c config/test-default -rf_flatten 1 -rf_batch_prediction 1 -out_subdir TEST/SPEED"
|
|
}
|
|
|
|
speed_joined16() {
|
|
|
|
title SPEED TESTS
|
|
|
|
misc/test-scripts/benchmark.sh 3 "JOINED" "1 2 3 4 5 6 7 8 9 10 12 15 16 17" "./prank.sh predict joined.ds -c config/test-default -out_subdir TEST/SPEED"
|
|
misc/test-scripts/benchmark.sh 10 "1FILE" "1" "./prank.sh predict -f distro/test_data/liganated/1aaxa.pdb -c config/test-default -out_subdir TEST/SPEED"
|
|
}
|
|
|
|
|
|
dummy_speed() {
|
|
misc/test-scripts/benchmark.sh 10 "JOINED" "1 2 4 8 12 16 20 24" "echo dummy"
|
|
misc/test-scripts/benchmark.sh 50 "1FILE" "1" "echo dummy"
|
|
}
|
|
|
|
###################################################################################################################
|
|
|
|
eval_predict_all() {
|
|
eval_predict
|
|
eval_predict_alphafold
|
|
eval_predict_rest
|
|
}
|
|
|
|
eval_train_all() {
|
|
eval_train
|
|
eval_train_rest
|
|
}
|
|
|
|
tests() {
|
|
quick
|
|
basic
|
|
cofactors
|
|
cofactors_full
|
|
aa_mapping
|
|
}
|
|
|
|
all() {
|
|
tests
|
|
predict
|
|
conservation
|
|
eval_predict_all
|
|
eval_rescore
|
|
eval_train_all
|
|
classifiers
|
|
feature_importances
|
|
eval_ploop
|
|
analyze
|
|
transform
|
|
export_points
|
|
pocket_grid
|
|
speed
|
|
}
|
|
|
|
###################################################################################################################
|
|
|
|
printcmd() {
|
|
echo
|
|
echo "[$@]"
|
|
echo
|
|
$@ 2>&1 | sed 's/^/ /'
|
|
}
|
|
|
|
print_env() {
|
|
echo
|
|
echo
|
|
echo ENVIRONMENT: ============================================================================================
|
|
printcmd ./distro/prank -version
|
|
printcmd date
|
|
printcmd hostname
|
|
printcmd uname -a
|
|
printcmd java -version
|
|
printcmd echo $JAVA_HOME
|
|
printcmd lscpu
|
|
printcmd WMIC CPU Get /Format:List
|
|
}
|
|
|
|
###################################################################################################################
|
|
|
|
run() {
|
|
$ROUTINE $@
|
|
}
|
|
|
|
rm -f $RUN_LOG
|
|
rm -f $DEBUG_LOG
|
|
rm -f $SUMMARY_LOG
|
|
rm -f $ERRORS_LOG
|
|
|
|
xstart=`date +%s`
|
|
|
|
print_env >> $SUMMARY_LOG
|
|
|
|
# colors are stripped from stream that goes to the file
|
|
run $@ > >( tee >( sed 's/\x1B\[[0-9;]*[A-Za-z]//g' | sed 's/[\x01-\x1F\x7F]//g' | sed 's/(B//g' >> $SUMMARY_LOG ) )
|
|
|
|
|
|
xend=`date +%s`
|
|
runtime=$((xend-xstart))
|
|
ftime=`format_time runtime`
|
|
|
|
echo
|
|
echo "ERRORS (from stdout -> see $ERRORS_LOG):"
|
|
echo
|
|
cat $RUN_LOG | grep --color=always ERROR | tee $ERRORS_LOG | wc -l
|
|
echo
|
|
echo "ERRORS (from summary):"
|
|
echo
|
|
cat $SUMMARY_LOG | grep --color=always ERROR | wc -l
|
|
echo
|
|
cat $SUMMARY_LOG | grep --color=always ERROR
|
|
|
|
echo "summary saved to [$SUMMARY_LOG]"
|
|
echo "stdout went to [$RUN_LOG]"
|
|
echo "stderr went to [$DEBUG_LOG]"
|
|
|
|
printf "\nDONE in $ftime\n" | tee -a $SUMMARY_LOG
|