ftdmp-dock-two-monomers-with-ftdock

#!/bin/bash

function print_help_and_exit
{
cat >&2 << 'EOF'

'ftdmp-dock-two-monomers-with-ftdock' produces many dimeric structures by docking two monomeric structures

Options:
    --monomer1                string  *  static monomer input file path
    --monomer2                string  *  mobile monomer input file path
    --job-name                string     job name to use as prefix for identifiers
    --logs-output             string     logs output directory path
    --parallel                number     total number of parallel parts, default is 1
    --sbatch-parameters       string     sbatch parameters to run in parallel, default is ''
    --ftdock-keep             number     ftdock keep parameter, default is 5
    --ftdock-angle-step       number     ftdock angle step parameter, default is 9
    --ftdock-min-grid-sep     number     ftdock minimum grid separation between same-rotation translations, default is 20
    --help | -h                          flag to display help message and exit

Standard output:
    space-separated table of docking results
    
Examples:

    ftdmp-dock-two-monomers-with-ftdock --monomer1 monomer1.pdb --monomer2 monomer2.pdb --logs-output docking_results --parallel 8

EOF
exit 1
}

readonly ZEROARG=$0
ALLARGS=("$@")

if [ -z "$1" ]
then
	print_help_and_exit
fi

if [ -z "$FTDMPDIR" ]
then
	export FTDMPDIR="$( cd -- "$( dirname -- "${BASH_SOURCE[0]}" )" &> /dev/null && pwd )"
	export PATH="${FTDMPDIR}/core/voronota/expansion_js:${FTDMPDIR}/core/3D_Dock/progs:${FTDMPDIR}:${PATH}"
fi

command -v voronota-js &> /dev/null || { echo >&2 "Error: 'voronota-js' executable not in binaries path"; exit 1; }
command -v ftdmp-prepare-monomer &> /dev/null || { echo >&2 "Error: 'ftdmp-prepare-monomer' executable not in binaries path"; exit 1; }
command -v ftdock &> /dev/null || { echo >&2 "Error: 'ftdock' executable not in binaries path"; exit 1; }

MONOMERFILE1=""
MONOMERFILE2=""
JOBNAME=""
OUTDIR=""
PARALLEL_PARTS="1"
PARALLEL_ID=""
SBATCH_PARAMETERS=""
FTDOCK_KEEP="5"
FTDOCK_ANGLE_STEP="9"
MIN_GRID_SEP="20"
HELP_MODE="false"

while [[ $# > 0 ]]
do
	OPTION="$1"
	OPTARG="$2"
	shift
	case $OPTION in
	--monomer1)
		MONOMERFILE1="$OPTARG"
		shift
		;;
	--monomer2)
		MONOMERFILE2="$OPTARG"
		shift
		;;
	--job-name)
		JOBNAME="$OPTARG"
		shift
		;;
	--logs-output)
		OUTDIR="$OPTARG"
		shift
		;;
	--parallel)
		PARALLEL_PARTS="$OPTARG"
		shift
		;;
	--parallel-id)
		PARALLEL_ID="$OPTARG"
		shift
		;;
	--sbatch-parameters)
		SBATCH_PARAMETERS="$OPTARG"
		shift
		;;
	--ftdock-keep)
		FTDOCK_KEEP="$OPTARG"
		shift
		;;
	--ftdock-angle-step)
		FTDOCK_ANGLE_STEP="$OPTARG"
		shift
		;;
	--ftdock-min-grid-sep)
		MIN_GRID_SEP="$OPTARG"
		shift
		;;
	-h|--help)
		HELP_MODE="true"
		;;
	*)
		echo >&2 "Error: invalid command line option '$OPTION'"
		exit 1
		;;
	esac
done

if [ "$HELP_MODE" == "true" ]
then
	print_help_and_exit
fi

if [ -z "$MONOMERFILE1" ]
then
	echo >&2 "Error: no static monomer input file specified"
	exit 1
fi

if [ ! -s "$MONOMERFILE1" ]
then
	echo >&2 "Error: no static monomer input file '$MONOMERFILE1'"
	exit 1
fi

if [ -z "$MONOMERFILE2" ]
then
	echo >&2 "Error: no mobile monomer input file specified"
	exit 1
fi

if [ ! -s "$MONOMERFILE2" ]
then
	echo >&2 "Error: no mobile monomer input file '$MONOMERFILE2'"
	exit 1
fi

if [ -z "$PARALLEL_PARTS" ] || [ "$PARALLEL_PARTS" -ne "$PARALLEL_PARTS" ] || [ "$PARALLEL_PARTS" -lt "1" ]
then
	echo >&2 "Error: invalid number of parallel parts '$PARALLEL_PARTS', must be a positive number"
	exit 1
fi

if [ -n "$PARALLEL_ID" ]
then
	if [ "$PARALLEL_ID" -ne "$PARALLEL_ID" ] || [ "$PARALLEL_ID" -lt "1" ] || [ "$PARALLEL_ID" -gt "$PARALLEL_PARTS" ]
	then
		echo >&2 "Error: invalid parallel part ID '$PARALLEL_ID', must be a positive number less than the total number of parts ($PARALLEL_PARTS)"
		exit 1
	fi
fi

if [ -n "$SBATCH_PARAMETERS" ]
then
	command -v sbatch &> /dev/null || { echo >&2 "Error: 'sbatch' executable not in binaries path"; exit 1; }
	command -v squeue &> /dev/null || { echo >&2 "Error: 'squeue' executable not in binaries path"; exit 1; }
fi

if [ -z "$FTDOCK_KEEP" ] || [ "$FTDOCK_KEEP" -ne "$FTDOCK_KEEP" ] || [ "$FTDOCK_KEEP" -lt "1" ]
then
	echo >&2 "Error: invalid ftdock keep parameter '$FTDOCK_KEEP', must be a positive integer"
	exit 1
fi

if [ -z "$FTDOCK_ANGLE_STEP" ] || [ "$FTDOCK_ANGLE_STEP" -ne "$FTDOCK_ANGLE_STEP" ] || [ "$FTDOCK_ANGLE_STEP" -lt "3" ]
then
	echo >&2 "Error: invalid ftdock angle step parameter '$FTDOCK_ANGLE_STEP', must be an integer >=3 and a factor of 180"
	exit 1
fi

if [ -z "$MIN_GRID_SEP" ] || [ "$MIN_GRID_SEP" -ne "$MIN_GRID_SEP" ] || [ "$MIN_GRID_SEP" -lt "0" ]
then
	echo >&2 "Error: invalid minimum grid separation '$MIN_GRID_SEP', must be a non-negative integer"
	exit 1
fi

MIN_SQUARED_SEP="$((${MIN_GRID_SEP}*${MIN_GRID_SEP}))"

if [ -z "$OUTDIR" ]
then
	readonly TMPLDIR=$(mktemp -d)
	trap "rm -r $TMPLDIR" EXIT
	
	OUTDIR="${TMPLDIR}/docking"
fi

if [ -z "$PARALLEL_ID" ]
then
	if [ -n "$SBATCH_PARAMETERS" ]
	then
		mkdir -p "$TMPLDIR/slurm_logs"
		
		seq 1 "$PARALLEL_PARTS" \
		| xargs -L 1 sbatch -o "$TMPLDIR/slurm_logs/slurmjob-%j.out" -e "$TMPLDIR/slurm_logs/slurmjob-%j.err" $SBATCH_PARAMETERS "$ZEROARG" "${ALLARGS[@]}" --logs-output "$OUTDIR" --parallel-id \
		| egrep '^Submitted batch job ' \
		| awk '{print $4}' \
		> "$TMPLDIR/slurm_job_ids"
		
		sleep 1
		REMAINING_SLURM_JOBS="$(squeue | grep -f "$TMPLDIR/slurm_job_ids" | wc -l)"
		while [ "$REMAINING_SLURM_JOBS" -gt "0" ]
		do
			sleep 5
			REMAINING_SLURM_JOBS="$(squeue | grep -f "$TMPLDIR/slurm_job_ids" | wc -l)"
		done
		
		find "$TMPLDIR/slurm_logs/" -type f -not -empty | xargs -L 1 cat >&2
	else
		seq 1 "$PARALLEL_PARTS" | xargs -L 1 -P "$PARALLEL_PARTS" "$ZEROARG" "${ALLARGS[@]}" --logs-output "$OUTDIR" --parallel-id
	fi
	
	{
	find "$OUTDIR" -type f -name 'part_results_table.txt' | xargs -L 1 -P 1 head -n 1 | sort | uniq | awk '{print "ID " $0}'
	find "$OUTDIR" -type f -name 'part_results_table.txt' | xargs -L 1 -P 1 tail -n +2 | sort -n -k 1 | tac | awk -v jobname="$JOBNAME" '{print jobname "ftd" $1 "scalevalue" $2 "p" $3 "p" $4 "p" $5 "p" $6 "p" $7 "p" $8 " " $0}' | sed 's|scalevalue\([0-9]\+\)\.|s\1d|' | sed 's|p-|n|g'
	} \
	> "${OUTDIR}/all_parts_results_table.txt"
	
	cat "${OUTDIR}/all_parts_results_table.txt"
	
	exit 0
fi

OUTDIR="${OUTDIR}/part${PARALLEL_ID}"
mkdir -p "$OUTDIR"

ftdmp-prepare-monomer --input "$MONOMERFILE1" --output-for-ftdock "$OUTDIR/monomer1.pdb"

if [ ! -s "$OUTDIR/monomer1.pdb" ]
then
	echo >&2 "Error: failed to prepare monomer 1"
	exit 1
fi

ftdmp-prepare-monomer --input "$MONOMERFILE2" --output-for-ftdock "$OUTDIR/monomer2.pdb"

if [ ! -s "$OUTDIR/monomer2.pdb" ]
then
	echo >&2 "Error: failed to prepare monomer 2"
	exit 1
fi

cd "$OUTDIR"

ftdock -static monomer1.pdb -mobile monomer2.pdb -noelec -keep "$FTDOCK_KEEP" -angle_step "$FTDOCK_ANGLE_STEP" -reduce_translations "$MIN_SQUARED_SEP" -parallel_parts "$PARALLEL_PARTS" -parallel_id "$PARALLEL_ID" > log_ftdock.txt

if [ ! -s "ftdock_global.dat" ]
then
	echo >&2 "Error: failed to run ftdock"
	exit 1
fi

FTDOCK_GRID_SIZE="$(cat ftdock_global.dat | egrep '^Global grid size ' | awk '{print $5}')"

FTDOCK_TOTAL_SPAN="$(cat ftdock_global.dat | egrep '^Global total span ' | awk '{print $6}')"

if [ -z "$FTDOCK_GRID_SIZE" ] || [ -z "$FTDOCK_TOTAL_SPAN" ] || [ "$FTDOCK_GRID_SIZE" -ne "$FTDOCK_GRID_SIZE" ]
then
	echo >&2 "Error: failed to read ftdock grid parameters"
	exit 1
fi

{
echo "scscore scale x y z a1 a2 a3 a4 a5 a6 a7 a8 a9"

cat ftdock_global.dat | egrep '^G_DATA' \
| awk -v gridsize="$FTDOCK_GRID_SIZE" -v totalspan="$FTDOCK_TOTAL_SPAN" '{print $4 " " (totalspan/gridsize) " " $6 " " $7 " " $8 " " $9 " " $10 " " $11 " 0 0 0 0 0 0"}'
} \
> "part_results_table.txt"

rm "monomer1.pdb" "monomer2.pdb"