ftdmp-dock-symmetric

#!/bin/bash

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

'ftdmp-dock-symmetric' produces many complex structures by performing symmetry docking with a single monomeric structure

Options:
    --monomer                 string  *  mobile monomer input file path
    --symmetry                string  *  symmetry class for SAM
    --output-dir              string  *  output directory path
    --job-name                string     job name to use as prefix for identifiers, default is 'sym'
    --sam-parameters          string     additional SAM parameters, default is '-top=8000 -show=2000 -clusters=2000'
    --sbatch-parameters       string     sbatch parameters to run on cluster, default is ''
    --help | -h                          flag to display help message and exit

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

    ftdmp-dock-symmetric --monomer monomer.pdb --symmetry '-c2' --output-dir output

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}:${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 sam2.0.4.x64 &> /dev/null || { echo >&2 "Error: 'sam2.0.4.x64' executable not in binaries path"; exit 1; }

MONOMERFILE=""
SYMMETRYCLASS=""
OUTDIR=""
JOBNAME="sym"
SAM_PARAMETERS="-top=8000 -show=2000 -clusters=2000"
SBATCH_PARAMETERS=""
HELP_MODE="false"

while [[ $# > 0 ]]
do
	OPTION="$1"
	OPTARG="$2"
	shift
	case $OPTION in
	--monomer)
		MONOMERFILE="$OPTARG"
		shift
		;;
	--symmetry)
		SYMMETRYCLASS="$OPTARG"
		shift
		;;
	--output-dir)
		OUTDIR="$OPTARG"
		shift
		;;
	--job-name)
		JOBNAME="$OPTARG"
		shift
		;;
	--sam-parameters)
		SAM_PARAMETERS="$OPTARG"
		shift
		;;
	--sbatch-parameters)
		SBATCH_PARAMETERS="$OPTARG"
		shift
		;;
	-h|--help)
		HELP_MODE="true"
		;;
	*)
		echo >&2 "Error: invalid command line option '$OPTION'"
		exit 1
		;;
	esac
done

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

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

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

if [ -z "$SYMMETRYCLASS" ]
then
	echo >&2 "Error: no symmetry specified"
	exit 1
fi

if [ -z "$OUTDIR" ]
then
	echo >&2 "Error: no output directory specified"
	exit 1
fi

if [ -z "$JOBNAME" ]
then
	JOBNAME="sym"
fi

SYMMETRYCLASS="$(echo $SYMMETRYCLASS | sed 's/^\(..\)\(.\+\)/\1 \2/')"

readonly TMPLDIR=$(mktemp -d)
trap "rm -r $TMPLDIR" EXIT

if [ -n "$SBATCH_PARAMETERS" ]
then
	mkdir -p "$TMPLDIR/slurm_logs"
	
	sbatch -o "$TMPLDIR/slurm_logs/slurmjob-%j.out" -e "$TMPLDIR/slurm_logs/slurmjob-%j.err" $SBATCH_PARAMETERS "$ZEROARG" "${ALLARGS[@]}" --sbatch-parameters "" \
	| 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 "$TMPLDIR/slurm_logs/" -type f -name '*.err' -not -empty | xargs -L 1 cat >&2
	find "$TMPLDIR/slurm_logs/" -type f -name '*.out' -not -empty | xargs -L 1 cat
	exit 0
fi

ftdmp-prepare-monomer --input "$MONOMERFILE" --output-for-ftdock "${TMPLDIR}/${JOBNAME}.pdb"

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

cd "$TMPLDIR"

sam2.0.4.x64 "./${JOBNAME}.pdb" $SYMMETRYCLASS $SAM_PARAMETERS > stdout.txt

cd - &> /dev/null

find "${TMPLDIR}/" -type f -name '*.pdb' -not -empty \
| egrep -v "${TMPLDIR}/${JOBNAME}\.pdb" \
> "$TMPLDIR/list_of_generated_complexes.txt"

if [ "$(cat $TMPLDIR/list_of_generated_complexes.txt | wc -l)" -lt "2" ]
then
	cat "$TMPLDIR/stdout.txt" >&2
	echo >&2 "Error: failed to generate complexes"
	exit 1
fi

OUTDIR="${OUTDIR}"
mkdir -p "$OUTDIR"

cat "$TMPLDIR/list_of_generated_complexes.txt" \
| while read MFILE_IN
do
	MFILE_NAME="$(basename ${MFILE_IN})"
	MFILE_OUT="${OUTDIR}/${MFILE_NAME}"

{
cat << EOF
var params={}
params.input_pdb_file='$MFILE_IN';
params.output_pdb_file='$MFILE_OUT';
EOF

cat << 'EOF'
try
{
voronota_import("-file", params.input_pdb_file);
voronota_assert_partial_success("Failed to import file");

voronota_set_chain_names_by_guessing();
voronota_assert_full_success("Failed to set chain IDs");

voronota_export_atoms("-file", params.output_pdb_file, "-as-pdb", "-pdb-ter");
voronota_assert_full_success("Failed to export atoms");
}
catch(error)
{
	log("Failed with '"+common_params.input_pdb_file+"': "+error);
}
EOF
} \
| voronota-js --no-setup-defaults

	if [ -s "$MFILE_OUT" ]
	then
		echo "$MFILE_OUT"
	fi
done \
> "$TMPLDIR/refined_list_of_generated_complexes.txt"

{
echo "ID"
cat "$TMPLDIR/refined_list_of_generated_complexes.txt" | xargs basename -s .pdb | sort
}