ftdmp-multiply-chains

#!/bin/bash

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

'ftdmp-multiply-chains' multiplies chains in complex using structural alignment

Options:
    --input                   string  *  input file path
    --output                  string  *  output file path, setting to '_same_as_input' will overwrite input file
    --static-align-sel        string  *  selection of atoms in static copy to align
    --mobile-align-sel        string  *  selection of atoms in mobile copy to align
    --multiply-sel            string  *  selection of atoms in mobile copy to keep after alignment
    --rename-chain            string  *  chain name to set or chain renaming rule to apply
    --help | -h                          flag to display help message and exit

Examples:

	ftdmp-multiply-chains --input input/complex1.pdb --output output/complex2.pdb \
	  --static-align-sel '[-chain A]' --mobile-align-sel '[-chain B]' \
	  --multiply-sel '[-chain C,D]' --rename-chain 'C=E,D=F'

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}:${PATH}"
fi

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

INFILE=""
OUTFILE=""
STATIC_ALIGN_SEL=""
MOBILE_ALIGN_SEL=""
MULTIPLY_SEL=""
RENAME_CHAIN=""
HELP_MODE="false"

while [[ $# > 0 ]]
do
	OPTION="$1"
	OPTARG="$2"
	shift
	case $OPTION in
	--input)
		INFILE="$OPTARG"
		shift
		;;
	--output)
		OUTFILE="$OPTARG"
		shift
		;;
	--static-align-sel)
		STATIC_ALIGN_SEL="$OPTARG"
		shift
		;;
	--mobile-align-sel)
		MOBILE_ALIGN_SEL="$OPTARG"
		shift
		;;
	--multiply-sel)
		MULTIPLY_SEL="$OPTARG"
		shift
		;;
	--rename-chain)
		RENAME_CHAIN="$OPTARG"
		shift
		;;
	-h|--help)
		HELP_MODE="true"
		;;
	*)
		echo >&2 "Error: invalid command line option '$OPTION'"
		exit 1
		;;
	esac
done

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

if [ -z "$INFILE" ]
then
	echo >&2 "Error: input file path not provided"
	exit 1
fi

if [ -z "$OUTFILE" ]
then
	echo >&2 "Error: output file path not provided"
	exit 1
fi

if [ "$OUTFILE" == "_same_as_input" ]
then
	OUTFILE="$INFILE"
fi

if [ -z "$STATIC_ALIGN_SEL" ]
then
	echo >&2 "Error: selection of atoms in static copy to align not provided"
	exit 1
fi

if [ -z "$MOBILE_ALIGN_SEL" ]
then
	echo >&2 "Error: selection of atoms in mobile copy to align not provided"
	exit 1
fi

if [ -z "$MULTIPLY_SEL" ]
then
	echo >&2 "Error: selection of atoms in static copy to keep after alignment not provided"
	exit 1
fi

if [ -z "$RENAME_CHAIN" ]
then
	echo >&2 "Error: chain name to set or chain renaming rule to apply not provided"
	exit 1
fi

if [ ! -s "$INFILE" ]
then
	echo >&2 "Error: input file '$INFILE' does not exist"
	exit 1
fi

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

{
cat << EOF
params={}
params.input_file='$INFILE';
params.output_file='$TMPLDIR/result.pdb';
params.static_align_sel='$STATIC_ALIGN_SEL';
params.mobile_align_sel='$MOBILE_ALIGN_SEL';
params.multiply_sel='$MULTIPLY_SEL';
params.rename_chain='$RENAME_CHAIN';
EOF

cat << 'EOF'
voronota_import("-file", params.input_file, "-include-heteroatoms", "-include-hydrogens", "-title", "static");
voronota_assert_full_success("Failed to import file");

voronota_copy_object("static", "mobile");
voronota_assert_full_success("Failed to copy object");

voronota_tmalign("-target", "static", "-model", "mobile", "-target-sel", params.static_align_sel, "-model-sel", params.mobile_align_sel);
voronota_assert_full_success("Failed to run tmalign using provided selections");

voronota_pick_objects("-names", "mobile");
voronota_assert_full_success("Failed to pick object");

voronota_restrict_atoms("-use", params.multiply_sel);
voronota_assert_full_success("Failed to restrict input atoms by the input query");

voronota_set_chain_name("-chain-name", params.rename_chain);
voronota_assert_full_success("Failed to rename chains");

voronota_merge_objects("-names", ["static", "mobile"], "-title", "merged");
voronota_assert_full_success("Failed to merge objects");

voronota_pick_objects("-names", "merged");
voronota_assert_full_success("Failed to pick object");

voronota_export_atoms("-file", params.output_file, "-as-pdb");
voronota_assert_full_success("Failed to export atoms");
EOF
} | voronota-js --no-setup-defaults

if [ ! -s "$TMPLDIR/result.pdb" ]
then
	echo >&2 "Error: failed to generate result structure"
	exit 1
fi

mkdir -p "$(dirname "$OUTFILE")"
mv "$TMPLDIR/result.pdb" "${OUTFILE}"