gen_energygrp.sh

#!/bin/bash

# generate energygrps and energygrp_table variables for .mdp file.
# Append script output to .mdp file.
# do not include SC - SC (they use the generic table.xvg).
# read in 1 letter-code sequence to determine list of interactions.
#
# Optional: 
#  -no_lipid:  don't include lipid parameters
# 
# name of amino acids. 
# Special 1-letter codes: 
#  - Z corresponds to end cap (CAP);
#  - B: Arginine (+); 
#  - J: Aspartic acid (-);
#  - O: Glutamic acid (-);
#  - U: Lysine (+);


die() {
    echo $@
    exit 1
}

flag_lipid=0

[ -z $1 ] && die "Missing sequence file"
for (( c=1; c<=$#; c++ )); do
    eval arg=\$$c
    d=`echo "$c + 1" | bc -l`
    eval argn=\$$d
    if [ $arg == "-no_lipid" ]; then
        flag_lipid=1
    else
        seq_file=$arg
    fi
done

seq_lines=`cat $seq_file | wc -l`

list_lipid=(CH PH GL ES AS AD AE)
list_pep_bb=(N C)
list3aa=(ALA ARG0 ARGP ASN ASP0 ASPM CYS GLN GLU0 GLUM GLY HIS ILE LEU LYS0 LYSP MET PHE PRO SER THR TRP TYR VAL CAP)
list1aa=(A   R    B    N   D    J    C   Q   E    O    G   H   I   L   K    U    M   F   P   S   T   W   Y   V   Z  )
seq_aa=()

for (( l=1; l<=$seq_lines; ++l )); do
    seq_length=`head -n $l $seq_file | tail -1 | wc -c`
    seq=`head -n $l $seq_file | tail -1`
    for (( i=0; i<$seq_length; ++i )); do
        letter=${seq:$i:1}
        if [ "$letter" != "" ] && [ "$letter" != " " ] && [ "$letter" != "\n" ]; then
	          seq_index=-1
	          for (( j=0; j<${#list1aa[@]}; ++j )); do
	              [ "$letter" == "${list1aa[$j]}" ] && seq_index=$j
	          done
	          [ "$seq_index" == "-1" ] && die "Amino acid code $letter is unrecognized."
	          
   	        # if the residue hasn't been added to the list yet, add it now
	          res_in_list=0
	          for (( k=0; k<${#seq_aa[@]}; ++k )); do
	              [ "${seq_aa[$k]}" == "$seq_index" ] && res_in_list=1
	          done
            # Exclude GLY
	          [ "$res_in_list" == "0" ] && [ "$seq_index" != "10" ] \
                && seq_aa=( ${seq_aa[@]-} $seq_index )
        fi
    done
done

n_list_lipid=${#list_lipid[@]}
n_laa=${#list3aa[@]}

echo -ne "energygrps               = "
if [ $flag_lipid == 0 ]; then
    for ((i=0;i<$n_list_lipid;++i)); do
        echo -ne "${list_lipid[$i]} ";
    done;
fi
# backbone
for (( k=0; k<${#list_pep_bb[@]}; ++k)); do
    echo -ne "${list_pep_bb[$k]} ";
done;
# side chains
for (( k=0; k<${#seq_aa[@]}; ++k )); do
    echo -ne "${list3aa[${seq_aa[$k]}]} ";
done;


echo -ne "\nenergygrp_table          = "
if [ $flag_lipid == 0 ]; then
    for ((i=0;i<$n_list_lipid;++i)); do 
        for ((j=$i;j<$n_list_lipid;++j)); do 
	          echo -ne "${list_lipid[$i]} ${list_lipid[$j]}  "; 
        done; 
    done; 
    
    for ((i=0;i<$n_list_lipid;++i)); do 
        for (( k=0; k<${#seq_aa[@]}; ++k )); do
	          echo -ne "${list3aa[${seq_aa[$k]}]} ${list_lipid[$i]}  "; 
        done; 
    done; 

    for ((i=0;i<$n_list_lipid;++i)); do 
        for (( k=0; k<${#list_pep_bb[@]}; ++k )); do
              echo -ne "${list_pep_bb[$k]} ${list_lipid[$i]}  "; 
        done; 
    done;   
fi

# backbone backbone
for ((i=0;i<${#list_pep_bb[@]};++i)); do
    for (( k=$i; k<${#list_pep_bb[@]}; ++k)); do
        echo -ne "${list_pep_bb[$k]} ${list_pep_bb[$i]}  ";
    done;
done;

# backbone sidechain
for ((i=0;i<${#seq_aa[@]};++i)); do
    for (( k=0; k<${#list_pep_bb[@]}; ++k)); do
        echo -ne "${list_pep_bb[$k]} ${list3aa[${seq_aa[$i]}]}  ";
    done;
done;

echo ""