amu_add_to_protocol

#!/bin/bash
protocol=
mdin=
to=

me=amu_add_protocol

function usage 
{
    echo "$me <[-p|--protocol file> [-m|--mdin file] [-t|--to num]"
}

ARGS=$(getopt -o 'm:p:t:' --long 'mdin:,protocol:,to:' -n "${me}" -- "$@")
eval set -- "$ARGS"
unset ARGS
while true; do
    case $1 in
        '-m'|'--mdin')
            mdin=$2
            shift 2
            continue
        ;;
        '-p'|'--protocol')
            protocol=$2
            shift 2
            continue
        ;;
        '-t'|'--to')
            to=$2
            shift 2
            continue
        ;;
        '--')
            shift
            break
        ;;
        '')
            usage
            exit 0
        ;;
        *)
            echo "Internal error" >&2
            exit 1
        ;;
    esac
done

[ $AMU_HOME ] || { echo "AMU_HOME not set. Exiting." ; exit ; }

[ "$protocol" ] || { 
   echo "protocol file not supplied." ; 
   usage ;
   exit 1; 
}

source $AMU_HOME/ambermd_util.bash

last=$(amu_protocol_rm_comment $protocol | tail -n 1 | awk '{print $1}' | egrep -o '[1-9][0-9]*' )
num=$(( last + 1 ))
s="steps $((last + 1)) to $to"
if [ -z $to ] ; then
    s="one step"
    to=$num
fi
( 
    for (( ; num < $((to + 1)) ; num=$((num + 1)) )) { 
        echo -e "$(printf %d $num)\t${mdin}\t# added `date +%Y/%m/%d`" >> $protocol || exit 1
        mdin=""
    }
)
if  [ ! $num -gt $to ] ; then
    if [ $? -eq 0 ] ; then
        echo -n "Added $s on the protocol file $protocol"
        if [ "$mdin" ] ; then echo -n " using mdin file $mdin" ; fi
        echo
    else
        echo "Error on adding step ${num}. Exiting." >&2
    fi
else
    echo "First step to add is $num but --to=${to}. Exiting."
fi