driver.sh

#!/bin/bash
#
#    MAHOMES II app
#    Copyright (C) 2021 University of Kansas
#
#    This program is free software: you can redistribute it and/or modify
#    it under the terms of the GNU Affero General Public License as published
#    by the Free Software Foundation, either version 3 of the License, or
#    (at your option) any later version.
#
#    This program is distributed in the hope that it will be useful,
#    but WITHOUT ANY WARRANTY; without even the implied warranty of
#    MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
#    GNU Affero General Public License for more details.
#
#    You should have received a copy of the GNU Affero General Public License
#    along with this program.  If not, see <https://www.gnu.org/licenses/>.
#
# @file   driver.sh
# @brief  Calculates features and produces predictions using MAHOMES II for structure files in input directory
# @author Ryan Feehan <RFeehan93@gmail.com>
#
# usage: bash driver.sh /path/to/input/dir
# 
# .cif/.pdb files in input directory will get third party calculation outputs.
# Metal ion sites in structure files will be identifed. Feature values will 
# be calculated for these sites, which will be used to make enzyme or non-enzyme
# predictions (input/dir/predictions.csv) with MAHOMES II


JOB_DIR=$1

ROSETTA3="/var/www/apps/mahomes/rosetta/rosetta_src_2021.16.61629_bundle/main/source"
BLUUES_DIR="/var/www/apps/mahomes/bluues"
GHECOM_DIR="/var/www/apps/mahomes/ghecom/"
MAHOMES_II_DIR="/var/www/apps/mahomes/MAHOMES-II-server"

echo "Prepping structure files"
source ${MAHOMES_II_DIR}/venv/bin/activate
cd ${MAHOMES_II_DIR}
python prep_batch_job.py ${JOB_DIR}


## going over all input .pdbs and outputing the needed Rosetta, findgeo, bluues, and ghecom
echo "Starting third party calculations"
THIRD_PARTY_TOOLS=${MAHOMES_II_DIR}/FeatureCalculations/ThirdPartyCalculations
while read pdb; do
        start=`date +%s`
	input_file=${JOB_DIR}/${pdb}.pdb
	output_dir=${JOB_DIR}/${pdb}
	. ${THIRD_PARTY_TOOLS}/runParty3Calc.sh $pdb $input_file $output_dir $ROSETTA3 $BLUUES_DIR $GHECOM_DIR $MAHOMES_II_DIR
        end=`date +%s`
        echo "$pdb time: $((end-start))"
done < ${JOB_DIR}/batch_input.txt

start=`date +%s`
## use the previous outputs to calculate the features for MAHOMES II input
echo "Working on calculating features"
cd ${MAHOMES_II_DIR}/FeatureCalculations
source ${MAHOMES_II_DIR}/venv/bin/activate
python batch_save_features.py ${JOB_DIR}
end=`date +%s`
echo "Calculating features time: $((end-start))" 


start=`date +%s`
## make prediction(s)
cd ${MAHOMES_II_DIR}/MachineLearning/
source ${MAHOMES_II_DIR}/venv/bin/activate
python MakePredictions.py $JOB_DIR
cat $JOB_DIR/predictions.csv
end=`date +%s`
echo "predictions time: $((end-start))"