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working config reorganization

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rdk
2017-08-15 17:24:11 +02:00
parent 0341503e4d
commit 44b1cda5a4
12 changed files with 355 additions and 78 deletions
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118
config/aug1.groovy Normal file
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@@ -0,0 +1,118 @@
import cz.siret.prank.program.params.Params
/**
* achieved DCA_4_0 = 0.7939 on joined.ds
*/
(params as Params).with {
/**
* define this if you want dataset program parameters to be evaluated relative to this directory
* (set absolute path or path relative to install dir, null defaults to working dir)
*/
dataset_base_dir = "../../p2rank-datasets"
/**
* all output of the prorgam will be stored in subdirectores of this directory
* (set absolute path or path relative to install dir, null defaults to working dir)
*/
output_base_dir = "../../p2rank-results/${version}"
visualizations = false
delete_models = true
delete_vectors = true
max_train_instances = 0
/**
* stop processing a datsaset on the first unrecoverable error with a dataset item
*/
fail_fast = true
classifier="FasterForest"
seed = 42
loop = 10
predictions = true
crossval_threads = 5
/**
* calculate feature importance
* available only for some classifiers
*/
feature_importances = false
stats_collect_predictions = false
// technical
cache_datasets = true
clear_sec_caches = false
clear_prim_caches = false
log_cases = true
output_only_stats = true
log_to_console = true
log_level = "WARN"
log_to_file = true
ploop_delete_runs = true
zip_log_file = true
out_prefix_date = true
//===========================================================================================================//
/**
* collect negatives just from decoy pockets found by other method
* (alternatively take negative points from all of the protein's surface)
*/
sample_negatives_from_decoys = false
atom_table_feat_keep_sgn = true
atom_table_features = ["ap5sasaValids","ap5sasaInvalids","apRawValids","apRawInvalids","atomicHydrophobicity"]
extra_features = ["chem","volsite","protrusion","bfactor"]
residue_table_features = ["RAx"]
average_feat_vectors = true
//===========================================================================================================//
rf_trees = 200
rf_depth = 9
rf_bagsize = 55
balance_class_weights = true
target_class_weight_ratio = 0.4402
pred_point_threshold = 0.7729
pred_min_cluster_size = 2
pred_clustering_dist = 2
extended_pocket_cutoff = 4
point_score_pow = 10
protrusion_radius = 10
neighbourhood_radius = 6.5963
positive_point_ligand_distance = 4.3529
neutral_points_margin = 0
solvent_radius = 1.8354
avg_pow = 1
avg_weighted = true
weight_function = "INVPOW"
weight_power = 0.1
}

119
config/aug2.groovy Normal file
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import cz.siret.prank.program.params.Params
/**
* achieved DCA_4_0 = 0.7909 on joined.ds
*/
(params as Params).with {
/**
* define this if you want dataset program parameters to be evaluated relative to this directory
* (set absolute path or path relative to install dir, null defaults to working dir)
*/
dataset_base_dir = "../../p2rank-datasets"
/**
* all output of the prorgam will be stored in subdirectores of this directory
* (set absolute path or path relative to install dir, null defaults to working dir)
*/
output_base_dir = "../../p2rank-results/${version}"
visualizations = false
delete_models = true
delete_vectors = true
max_train_instances = 0
/**
* stop processing a datsaset on the first unrecoverable error with a dataset item
*/
fail_fast = true
classifier="FasterForest"
seed = 42
loop = 10
predictions = true
crossval_threads = 5
/**
* calculate feature importance
* available only for some classifiers
*/
feature_importances = false
stats_collect_predictions = false
// technical
cache_datasets = true
clear_sec_caches = false
clear_prim_caches = false
log_cases = true
output_only_stats = true
log_to_console = true
log_level = "WARN"
log_to_file = true
ploop_delete_runs = true
zip_log_file = true
out_prefix_date = true
//===========================================================================================================//
/**
* collect negatives just from decoy pockets found by other method
* (alternatively take negative points from all of the protein's surface)
*/
sample_negatives_from_decoys = false
atom_table_feat_keep_sgn = true
atom_table_features = ["ap5sasaValids","ap5sasaInvalids","apRawValids","apRawInvalids","atomicHydrophobicity"]
extra_features = ["chem","volsite","protrusion","bfactor"]
residue_table_features = ["RAx"]
average_feat_vectors = true
//===========================================================================================================//
rf_trees = 200
rf_depth = 9
rf_bagsize = 55
balance_class_weights = true
target_class_weight_ratio = 0.4634
pred_point_threshold = 0.6919
pred_min_cluster_size = 2
pred_clustering_dist = 2
extended_pocket_cutoff = 5.1516
point_score_pow = 5.8511
protrusion_radius = 10.3444
neighbourhood_radius = 5.8294
positive_point_ligand_distance = 7
neutral_points_margin = 0
solvent_radius = 1.8354
avg_pow = 1
avg_weighted = true
weight_function = "INVPOW2"
weight_power = 0.01
weight_dist_param = 5
}

0
new.groovy → config/new.groovy
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3
config/readme.md Normal file
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@@ -0,0 +1,3 @@
Directory with development/experimantal config files.

0
workdef.groovy → config/workdef.groovy
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0
working.groovy → config/working.groovy
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0
misc/local-env-params.sh → misc/local-env.sh Executable file → Normal file
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189
misc/test-scripts/testsets.sh
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@@ -1,8 +1,9 @@
#!/usr/bin/env bash
\
###################################################################################################################
SET=$1
ROUTINE=$1
shift
RUN_LOG=local-run.log
DEBUG_LOG=local-debug.log
SUMMARY_LOG=local-summary.log
@@ -91,14 +92,14 @@ basic() {
title RUNNING BASIC TESTS
test ./prank.sh eval-predict chen11.ds -c working -out_subdir TEST/TESTS
test ./prank.sh eval-predict mlig-joined.ds -c working -out_subdir TEST/TESTS
test ./prank.sh traineval -t chen11-fpocket.ds -e chen11-fpocket.ds -c working -loop 1 -fail_fast 1 -out_subdir TEST/TESTS
test ./prank.sh traineval -t chen11-fpocket.ds -e mlig-joined.ds -c working -loop 1 -fail_fast 1 -out_subdir TEST/TESTS
test ./prank.sh crossval chen11-fpocket.ds -c working -loop 1 -fail_fast 1 -out_subdir TEST/TESTS
test ./prank.sh eval-predict chen11.ds -c config/working -out_subdir TEST/TESTS
test ./prank.sh eval-predict mlig-joined.ds -c config/working -out_subdir TEST/TESTS
test ./prank.sh traineval -t chen11-fpocket.ds -e chen11-fpocket.ds -c config/working -loop 1 -fail_fast 1 -out_subdir TEST/TESTS
test ./prank.sh traineval -t chen11-fpocket.ds -e mlig-joined.ds -c config/working -loop 1 -fail_fast 1 -out_subdir TEST/TESTS
test ./prank.sh crossval chen11-fpocket.ds -c config/working -loop 1 -fail_fast 1 -out_subdir TEST/TESTS
#test ./prank.sh eval-predict mlig-joined.ds -c working -visualizations 1 -tessellation 3 -l VISUALIZATIONS_TES3 -c working -out_subdir TEST/TESTS
#test ./prank.sh eval-predict mlig-joined.ds -c working -visualizations 1 -l VISUALIZATIONS -c working -out_subdir TEST/TESTS
#test ./prank.sh eval-predict mlig-joined.ds -c config/working -visualizations 1 -tessellation 3 -l VISUALIZATIONS_TES3 -c config/working -out_subdir TEST/TESTS
#test ./prank.sh eval-predict mlig-joined.ds -c config/working -visualizations 1 -l VISUALIZATIONS -c config/working -out_subdir TEST/TESTS
}
# test predieciton on all datasets
@@ -106,18 +107,18 @@ predict() {
title PREDICTIONS ON ALL DATASETS
test ./prank.sh predict joined.ds -c workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict holo4k.ds -c workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict joined.ds -c config/workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict holo4k.ds -c config/workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict chen11.ds -c workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict b48.ds -c workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict u48.ds -c workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict astex.ds -c workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict dt198.ds -c workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict b210.ds -c workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict fptrain.ds -c workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict mlig-joined.ds -c workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict mlig-holo4k.ds -c workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict chen11.ds -c config/workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict b48.ds -c config/workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict u48.ds -c config/workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict astex.ds -c config/workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict dt198.ds -c config/workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict b210.ds -c config/workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict fptrain.ds -c config/workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict mlig-joined.ds -c config/workdef -log_cases 1 -out_subdir TEST/PREDICT
test ./prank.sh predict mlig-holo4k.ds -c config/workdef -log_cases 1 -out_subdir TEST/PREDICT
}
@@ -127,8 +128,8 @@ eval_predict() {
title EVALUATING PREDICTIONS ON MAIN DATASETS
test ./prank.sh eval-predict joined.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict holo4k.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict joined.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict holo4k.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
}
# evaluate default model/settings on main datasets
@@ -137,39 +138,39 @@ eval_predict_rest() {
title EVALUATING PREDICTIONS ON OTHER DATASETS
# train=test for the reference
test ./prank.sh eval-predict chen11.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict chen11.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict b48.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict u48.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict astex.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict dt198.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict b210.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict fptrain.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict b48.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict u48.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict astex.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict dt198.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict b210.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict fptrain.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict mlig-joined.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict mlig-holo4k.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict mlig-joined.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-predict mlig-holo4k.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
#test ./prank.sh eval-predict mlig-moad-nr.ds -c workdef -log_cases 1 -fail_fast 1 -out_subdir TEST/EVAL
#test ./prank.sh eval-predict moad-nr.ds -c workdef -log_cases 1 -fail_fast 1 -out_subdir TEST/EVAL
#test ./prank.sh eval-predict mlig-moad-nr.ds -c config/workdef -log_cases 1 -fail_fast 1 -out_subdir TEST/EVAL
#test ./prank.sh eval-predict moad-nr.ds -c config/workdef -log_cases 1 -fail_fast 1 -out_subdir TEST/EVAL
}
eval_rescore() {
title EVALUATING RESCORING ON ALL DATASETS
test ./prank.sh eval-rescore joined-fpocket.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore holo4k-fpocket.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore joined-fpocket.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore holo4k-fpocket.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore chen11-fpocket.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore b48-fpocket.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore u48-fpocket.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore astex-fpocket.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore dt198-fpocket.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore b210-fpocket.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore fptrain-fpocket.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore chen11-fpocket.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore b48-fpocket.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore u48-fpocket.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore astex-fpocket.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore dt198-fpocket.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore b210-fpocket.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore fptrain-fpocket.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore mlig-joined-fpocket.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore mlig-holo4k-fpocket.ds -c workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore mlig-joined-fpocket.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
test ./prank.sh eval-rescore mlig-holo4k-fpocket.ds -c config/workdef -log_cases 1 -out_subdir TEST/EVAL
}
# train and evaluate new model/settings on main datasets
@@ -177,9 +178,9 @@ eval_train() {
title TRAIN/EVAL ON MAIN DATASETS
test ./prank.sh crossval chen11-fpocket.ds -c working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e holo4k.ds -c working -loop 3 -cache_datasets 0 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh crossval chen11-fpocket.ds -c config/working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c config/working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e holo4k.ds -c config/working -loop 3 -cache_datasets 0 -out_subdir TEST/EVAL_TRAIN
}
eval_train_rest() {
@@ -187,81 +188,117 @@ eval_train_rest() {
title TRAIN/EVAL ON OTHER DATASETS
# train=test for the reference
test ./prank.sh traineval -t chen11-fpocket.ds -e chen11-fpocket.ds -c working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e chen11-fpocket.ds -c config/working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e b48.ds -c working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e u48.ds -c working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e astex.ds -c working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e dt198.ds -c working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e b210.ds -c working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e fptrain.ds -c working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e b48.ds -c config/working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e u48.ds -c config/working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e astex.ds -c config/working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e dt198.ds -c config/working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e b210.ds -c config/working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e fptrain.ds -c config/working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e mlig-joined.ds -c working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e mlig-holo4k.ds -c working -loop 3 -cache_datasets 0 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e mlig-joined.ds -c config/working -loop 10 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e mlig-holo4k.ds -c config/working -loop 3 -cache_datasets 0 -out_subdir TEST/EVAL_TRAIN
}
###################################################################################################################
quick_train_new() {
test ./prank.sh traineval -t chen11-fpocket.ds -e mlig-joined.ds -c new -loop 3 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c new -loop 3 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e mlig-holo4k.ds -c new -loop 1 -cache_datasets 0 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e holo4k.ds -c new -loop 1 -cache_datasets 0 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh crossval chen11-fpocket.ds -c new -loop 3 -out_subdir TEST/EVAL_TRAIN
test ./prank.sh traineval -t chen11-fpocket.ds -e mlig-joined.ds -c config/new -loop 3 -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 mlig-holo4k.ds -c config/new -loop 1 -cache_datasets 0 -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=$2
test ./prank.sh traineval -t chen11.ds -e mlig-joined.ds -c config/${CONFIG} -loop 10 -out_subdir EVAL/CONFIG_${LABEL}
test ./prank.sh traineval -t chen11.ds -e joined.ds -c config/${CONFIG} -loop 10 -out_subdir EVAL/CONFIG_${LABEL}
test ./prank.sh traineval -t chen11.ds -e mlig-holo4k.ds -c config/${CONFIG} -loop 3 -cache_datasets 0 -out_subdir EVAL/CONFIG_${LABEL}
test ./prank.sh traineval -t chen11.ds -e holo4k.ds -c config/${CONFIG} -loop 3 -cache_datasets 0 -out_subdir EVAL/CONFIG_${LABEL}
test ./prank.sh crossval chen11.ds -c config/${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=$2
test ./prank.sh traineval -t chen11.ds -e b48.ds -c config/${CONFIG} -loop 10 -out_subdir EVAL/CONFIG_${LABEL}
test ./prank.sh traineval -t chen11.ds -e u48.ds -c config/${CONFIG} -loop 10 -out_subdir EVAL/CONFIG_${LABEL}
test ./prank.sh traineval -t chen11.ds -e astex.ds -c config/${CONFIG} -loop 10 -out_subdir EVAL/CONFIG_${LABEL}
test ./prank.sh traineval -t chen11.ds -e dt198.ds -c config/${CONFIG} -loop 10 -out_subdir EVAL/CONFIG_${LABEL}
test ./prank.sh traineval -t chen11.ds -e b210.ds -c config/${CONFIG} -loop 10 -out_subdir EVAL/CONFIG_${LABEL}
test ./prank.sh traineval -t chen11.ds -e fptrain.ds -c config/${CONFIG} -loop 10 -out_subdir EVAL/CONFIG_${LABEL}
}
###################################################################################################################
speed() {
title SPEED TESTS
misc/test-scripts/benchmark.sh 5 "U48" "1 2 4 8 12 16 20 24" "./prank.sh predict u48.ds -c workdef -out_subdir TEST/SPEED"
misc/test-scripts/benchmark.sh 25 "1FILE" "1" "./prank.sh predict -f distro/test_data/liganated/1aaxa.pdb -c workdef -out_subdir TEST/SPEED"
misc/test-scripts/benchmark.sh 5 "U48" "1 2 4 8 12 16 20 24" "./prank.sh predict u48.ds -c config/workdef -out_subdir TEST/SPEED"
misc/test-scripts/benchmark.sh 25 "1FILE" "1" "./prank.sh predict -f distro/test_data/liganated/1aaxa.pdb -c config/workdef -out_subdir TEST/SPEED"
}
speed_basic() {
title SPEED TESTS
misc/test-scripts/benchmark.sh 3 "PREDICT" "1 8" "./prank.sh predict u48.ds -c workdef -out_subdir TEST/SPEED"
misc/test-scripts/benchmark.sh 3 "TRAINEVAL" "1 8" "./prank.sh traineval -t chen11-fpocket.ds -e joined.ds -c working -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 working -loop 3 -out_subdir TEST/SPEED"
misc/test-scripts/benchmark.sh 3 "PREDICT" "1 8" "./prank.sh predict u48.ds -c config/workdef -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/working -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/working -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 working -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 working -classifier FasterForest -loop 3 -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/working -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/working -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 working -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/working -classifier FasterForest -loop 1 -out_subdir TEST/SPEED"
}
speed_quick() {
title "SPEED TESTS (QUICK)"
misc/test-scripts/benchmark.sh 3 "U48" "1 2 4 5 8 9 12 13 24" "./prank.sh predict u48.ds -c workdef -out_subdir TEST/SPEED"
misc/test-scripts/benchmark.sh 10 "1FILE" "1" "./prank.sh predict -f distro/test_data/liganated/1aaxa.pdb -c workdef -out_subdir TEST/SPEED"
misc/test-scripts/benchmark.sh 3 "U48" "1 2 4 5 8 9 12 13 24" "./prank.sh predict u48.ds -c config/workdef -out_subdir TEST/SPEED"
misc/test-scripts/benchmark.sh 10 "1FILE" "1" "./prank.sh predict -f distro/test_data/liganated/1aaxa.pdb -c config/workdef -out_subdir TEST/SPEED"
}
speed_joined() {
title SPEED TESTS
misc/test-scripts/benchmark.sh 3 "U48" "1 2 3 4 5 6 7 8 9 10 11 12 13" "./prank.sh predict joined.ds -c workdef -out_subdir TEST/SPEED"
misc/test-scripts/benchmark.sh 10 "1FILE" "1" "./prank.sh predict -f distro/test_data/liganated/1aaxa.pdb -c workdef -out_subdir TEST/SPEED"
misc/test-scripts/benchmark.sh 3 "U48" "1 2 3 4 5 6 7 8 9 10 11 12 13" "./prank.sh predict joined.ds -c config/workdef -out_subdir TEST/SPEED"
misc/test-scripts/benchmark.sh 10 "1FILE" "1" "./prank.sh predict -f distro/test_data/liganated/1aaxa.pdb -c config/workdef -out_subdir TEST/SPEED"
}
speed_joined16() {
title SPEED TESTS
misc/test-scripts/benchmark.sh 3 "U48" "1 2 3 4 5 6 7 8 9 10 12 15 16 17" "./prank.sh predict joined.ds -c workdef -out_subdir TEST/SPEED"
misc/test-scripts/benchmark.sh 10 "1FILE" "1" "./prank.sh predict -f distro/test_data/liganated/1aaxa.pdb -c workdef -out_subdir TEST/SPEED"
misc/test-scripts/benchmark.sh 3 "U48" "1 2 3 4 5 6 7 8 9 10 12 15 16 17" "./prank.sh predict joined.ds -c config/workdef -out_subdir TEST/SPEED"
misc/test-scripts/benchmark.sh 10 "1FILE" "1" "./prank.sh predict -f distro/test_data/liganated/1aaxa.pdb -c config/workdef -out_subdir TEST/SPEED"
}
@@ -321,7 +358,7 @@ print_env() {
###################################################################################################################
run() {
$SET
$SET $@
}
rm $RUN_LOG

0
misc/hidden-commands.md → misc/tutorials/hidden-commands.md
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0
misc/hyperparameter-optimization-tutorial.md → misc/tutorials/hyperparameter-optimization-tutorial.md
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0
misc/training-tutorial.md → misc/tutorials/training-tutorial.md
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4
prank.sh
View File

@@ -3,10 +3,10 @@
#
# script for running development builds in-place from this directory
#
# copy misc/local-env-params.sh to this directory
# copy misc/local-env.sh to this directory
#
. local-env-params.sh
. local-env.sh
echo JAVA_LOCALENV_PARAMS = $JAVA_LOCALENV_PARAMS