ftdmp-all-diversify

#!/bin/bash

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

'ftdmp-all-diversify' selects a diverse set of models based on reference-based CAD-scores

Options:
    --input-scoring-table     string  *  input scoring table file path
    --names-prefix            string     names prefix, default is ''
    --cadscore-step           number     step size for CAD-score values, default is 0.1
    --site-cadscore-step      number     step size for site-based CAD-score values, default is 0.1
    --zero-count              number     number of zero-scored results to include, default is 1
    --build-complexes         number     number of top complexes to build, default is 0
    --help | -h                          flag to display help message and exit

Examples:

    ftdmp-all-diversify --input-scoring-table ./scoring_results.txt --names-prefix 'raw_' \
      --cadscore-step 0.05 --site-cadscore-step 0.05

EOF
exit 1
}

################################################################################

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

FROM_TABLE=""
NAMES_PREFIX=""
CADSCORE_STEP="0.1"
SITE_CADSCORE_STEP="0.1"
ZERO_COUNT="1"
NUMBER_OF_COMPLEXES_TO_BUILD="0"
HELP_MODE="false"

while [[ $# > 0 ]]
do
	OPTION="$1"
	OPTARG="$2"
	shift
	case $OPTION in
	--input-scoring-table)
		FROM_TABLE="$OPTARG"
		shift
		;;
	--names-prefix)
		NAMES_PREFIX="$OPTARG"
		shift
		;;
	--cadscore-step)
		CADSCORE_STEP="$OPTARG"
		shift
		;;
	--site-cadscore-step)
		SITE_CADSCORE_STEP="$OPTARG"
		shift
		;;
	--zero-count)
		ZERO_COUNT="$OPTARG"
		shift
		;;
	--build-complexes)
		NUMBER_OF_COMPLEXES_TO_BUILD="$OPTARG"
		shift
		;;
	-h|--help)
		HELP_MODE="true"
		;;
	*)
		echo >&2 "Error: invalid command line option '$OPTION'"
		exit 1
		;;
	esac
done

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

if [ -z "$FROM_TABLE" ]
then
	echo >&2 "Error: input scoring table file not specified"
	exit 1
fi

if [ ! -s "$FROM_TABLE" ]
then
	echo >&2 "Error: input scoring table file '$FROM_TABLE' does not exist or is empty"
	exit 1
fi

################################################################################

OUTPUT_PATH="$(dirname "$FROM_TABLE")"

PREV_SCORING_RESULTS_FILE="$FROM_TABLE"

################################################################################

NEXT_SCORING_RESULTS_FILE="${OUTPUT_PATH}/${NAMES_PREFIX}diverse_scoring_results.txt"

{
cat "$PREV_SCORING_RESULTS_FILE"
echo "$CADSCORE_STEP"
echo "$SITE_CADSCORE_STEP"
} | ftdmp-check-hash --hash-file "${OUTPUT_PATH}/input_hashes/$(basename "$NEXT_SCORING_RESULTS_FILE")" --dependent-file "$NEXT_SCORING_RESULTS_FILE"

if [ ! -s "$NEXT_SCORING_RESULTS_FILE" ]
then
	cat "$PREV_SCORING_RESULTS_FILE" \
	| ftdmp-diversify-table-by-cadscore \
	  --cadscore-column "${NAMES_PREFIX}FICS_iface_cadscore" \
	  --site-cadscore-column "${NAMES_PREFIX}FICS_iface_site_based_cadscore" \
	  --zero-sort "-${NAMES_PREFIX}FIV_iface_energy" \
	  --cadscore-step "$CADSCORE_STEP" \
	  --site-cadscore-step "$SITE_CADSCORE_STEP" \
	  --zero-count "$ZERO_COUNT" \
	> "$NEXT_SCORING_RESULTS_FILE"
fi

PREV_SCORING_RESULTS_FILE="$NEXT_SCORING_RESULTS_FILE"

if [ ! -s "$PREV_SCORING_RESULTS_FILE" ]
then
	echo >&2 "Error: failed to diversify scoring results"
	exit 1
fi

################################################################################

if [ "$NUMBER_OF_COMPLEXES_TO_BUILD" -gt "0" ]
then
	PREPARED_STATIC_STRUCTURE_FILE="${OUTPUT_PATH}/monomer_static.pdb"
	
	PREPARED_MOBILE_STRUCTURE_FILE="${OUTPUT_PATH}/monomer_mobile.pdb"
	
	if [ ! -s "$PREPARED_STATIC_STRUCTURE_FILE" ] || [ ! -s "$PREPARED_MOBILE_STRUCTURE_FILE" ]
	then
		echo >&2 "Error: required monomers not present in '$OUTPUT_PATH'"
		exit 1
	fi

	NEXT_SCORING_RESULTS_FILE="${OUTPUT_PATH}/${NAMES_PREFIX}diverse_built_results.txt"
	
	TOP_COMPLEXES_DIR="${OUTPUT_PATH}/${NAMES_PREFIX}diverse_complexes"
	
	{
	cat "$PREV_SCORING_RESULTS_FILE"
	cat "$PREPARED_STATIC_STRUCTURE_FILE"
	cat "$PREPARED_MOBILE_STRUCTURE_FILE"
	echo "$NUMBER_OF_COMPLEXES_TO_BUILD"
	} | ftdmp-check-hash --hash-file "${OUTPUT_PATH}/input_hashes/$(basename "$NEXT_SCORING_RESULTS_FILE")" --dependent-file "$NEXT_SCORING_RESULTS_FILE"
	
	if [ ! -s "$NEXT_SCORING_RESULTS_FILE" ]
	then
		rm -rf "$TOP_COMPLEXES_DIR"
		
		cat "$PREV_SCORING_RESULTS_FILE" \
		| head -n "$((NUMBER_OF_COMPLEXES_TO_BUILD+1))" \
		| ftdmp-build-complex --monomer1 "$PREPARED_STATIC_STRUCTURE_FILE" --monomer2 "$PREPARED_MOBILE_STRUCTURE_FILE" \
		  --output-prefix "${TOP_COMPLEXES_DIR}/" \
		  --output-suffix ".pdb" \
		> "$NEXT_SCORING_RESULTS_FILE"
	fi
	
	PREV_SCORING_RESULTS_FILE="$NEXT_SCORING_RESULTS_FILE"
fi

################################################################################