ftdmp-form-casp15-assembly-answer

#!/bin/bash

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

'ftdmp-form-casp15-assembly-answer' generates an assembly answer for CASP15

Options:
    --target-name             string  *  TARGET line value
    --author-id               string  *  AUTHOR line value
    --method-line             string     METHOD line value, default is 'Various methods'
    --help | -h                          flag to display help message and exit

Standard input:
    model file paths

Standard output:
    CASP15 assembly answer file

Example:

    find ./selected_models/ -type f -name '*.pdb' | sort \
    | ftdmp-form-casp15-assembly-answer --target-name 'T1999' --author-id '1234-5678-9000'

EOF
exit 1
}

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

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

TARGET_NAME=""
AUTHOR_ID=""
METHOD_LINE="Various methods"
HELP_MODE="false"

while [[ $# > 0 ]]
do
	OPTION="$1"
	OPTARG="$2"
	shift
	case $OPTION in
	--target-name)
		TARGET_NAME="$OPTARG"
		shift
		;;
	--author-id)
		AUTHOR_ID="$OPTARG"
		shift
		;;
	--method-line)
		METHOD_LINE="$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 "$TARGET_NAME" ]
then
	echo >&2 "Error: target name not specified"
	exit 1
fi

if [ -z "$AUTHOR_ID" ]
then
	echo >&2 "Error: author ID not specified"
	exit 1
fi

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

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

cat \
| tr ' ' '\n' \
| egrep '.' \
> "$TMPLDIR/models_list"

if [ ! -s "$TMPLDIR/models_list" ]
then
	echo >&2 "Error: no model files specified"
	exit 1
fi

while read -r MFILE
do
	if [ ! -s "$MFILE" ] || [ "$(cat ${MFILE} | egrep '^ATOM ' | wc -l)" -lt "1" ]
	then
		echo >&2 "Error: invalid model file '$MFILE'"
		exit 1
	fi
done < "$TMPLDIR/models_list"

echo "PFRMAT TS"
echo "TARGET ${TARGET_NAME}"
echo "AUTHOR ${AUTHOR_ID}"
echo "METHOD $METHOD_LINE"

cat "$TMPLDIR/models_list" \
| awk '{print NR " " $1}' \
| while read -r MNUM MFILE
do
	echo "MODEL  ${MNUM}"
	echo "PARENT N/A"
	cat "$MFILE" | egrep '^ATOM |^TER'
	echo "END"
done