#!/bin/csh

############## SETUP ##########################################################
######### MAKE SURE THE TOPOLOGY FILES TO MERGE ARE OK ########################
#
#USAGE: GRO_MERGE_TOP <file1>.top/itp <file2>.top/itp > <outfile>.top/itp
#


set TOP1 = $1 	# .top or .itp
set TOP2 = $2 	# .top or .itp

set FF = "ffoplsaa.itp"
set MOLTYPE = "Protein"
set NREXCL = 3

############# GENERATE SCRIPTS TO MERGE TOP1 AND TOP2 #########################

cat << EOF > extract_atoms.awk
/\[ atoms ]/{
	getline
        while(\$1&&\$1!="["){
                if(\$1!~/\;/){
                        print
                        }
                getline
                }
        }
EOF

cat << EOF > extract_types.awk
BEGIN{
	if (type == "bond" || type == "bonds"){
		match_string = "[ bonds ]"
		}
	else if (type == "pair" || type == "pairs"){
		match_string = "[ pairs ]"
		}
	else if (type == "angle" || type == "angles"){
		match_string = "[ angles ]"
		}
	else if (type == "dihedral" || type == "dihedrals"){
		match_string = "[ dihedrals ]"
		}
	else {
		print "\nYOU MUST PROVIDE A VALID TYPE\n"
		exit 5
		}
	if(flag>0){flag=1}
	}

/\[ atoms ]/{
	getline
	while(\$1&&\$1!="["){
		if(\$1!~/\;/){
			natoms=\$1
			}
		getline
		}
	}
\$0 == match_string {
	if(flag==0){
		getline
		while(\$1&&\$1!="["){
			if(\$1!~/\;/){
				print
				}
			getline
			}
		}
	flag--
	}

END{
	print "NATOMS\t" natoms
	}
EOF

cat << EOF > merge_atoms.awk
BEGIN{
	print "[ atoms ]"
	}
{
	if(\$1==1){
		++mol
		xat = at
		xres = res
		xchgg = chgg
		xtotchg = totchg
		}
	at = \$1 + xat
	res = \$3 + xres
	chgg = \$6 + xchgg
	chgchk = \$11 + xtotchg
	printf("%6d%11s%7d%7s%7s%7d%11.5f%11.5f   ; qtot %9.5f\n",at,\$2,res,\$4,\$5,chgg,\$7,\$8,\$11)
	}
END{printf("\n")}
EOF

cat << EOF > merge_types.awk
BEGIN{
	if (type == "bond" || type == "bonds"){
		def = 3
		print "[ bonds ]"
		}
	else if (type == "pair" || type == "pairs"){
		def = 3
		print "[ pairs ]"
		}
	else if (type == "angle" || type == "angles"){
		def = 4
		print "[ angles ]"
		}
	else if (type == "dihedral" || type == "dihedrals"){
		def = 5
		print "[ dihedrals ]"
		}
	}
{
	if(\$1=="NATOMS"){
		xat = \$2
		}
	else{
		nfields = split(\$0,field)
		printf("%5d",field[1]+xat)
		for(i=2;i<def;i++){
			printf("%6d",field[i]+xat)
			}
		printf("%6d",field[def])
		if (nfields > def){
			printf("  "field[def+1])
			for(i=def+2;i<=nfields;i++){
				printf("%10.5f",field[i])
				}
			}
		printf("\n")
		}
	}
END{
	printf("\n")
	}
EOF

#################### NOW DO THE WORK ###################################


awk -f extract_atoms.awk $TOP1 > at1.tmp
awk -f extract_atoms.awk $TOP2 >> at1.tmp
awk -v type="bond" -f extract_types.awk $TOP1 > bd1.tmp
awk -v type="bond" -f extract_types.awk $TOP2 >> bd1.tmp
awk -v type="pairs" -f extract_types.awk $TOP1 > pa1.tmp
awk -v type="pairs" -f extract_types.awk $TOP2 >> pa1.tmp
awk -v type="angles" -f extract_types.awk $TOP1 > an1.tmp
awk -v type="angles" -f extract_types.awk $TOP2 >> an1.tmp
awk -v type="dihedral" -f extract_types.awk $TOP1 > di1.tmp
awk -v type="dihedral" -f extract_types.awk $TOP2 >> di1.tmp
awk -v type="dihedral" -v flag=1 -f extract_types.awk $TOP1 > di2.tmp
awk -v type="dihedral" -v flag=1 -f extract_types.awk $TOP2 >> di2.tmp

awk -f merge_atoms.awk at1.tmp > at1_merged.tmp
awk -v type="bond" -f merge_types.awk bd1.tmp > bd1_merged.tmp
awk -v type="pair" -f merge_types.awk pa1.tmp > pa1_merged.tmp
awk -v type="angle" -f merge_types.awk an1.tmp > an1_merged.tmp
awk -v type="dihedral" -f merge_types.awk di1.tmp > di1_merged.tmp
awk -v type="dihedral" -f merge_types.awk di2.tmp > di2_merged.tmp

# MOST OF THE WORK IS DONE

echo '#include "'$FF'"'"\n"
echo "[ moleculetype ]"
echo "$MOLTYPE      $NREXCL\n"
cat at1_merged.tmp
cat bd1_merged.tmp
cat pa1_merged.tmp
cat an1_merged.tmp
cat di1_merged.tmp
cat di2_merged.tmp
echo "[ system ]"
echo "UNNAMED\n"
echo "[ molecules ]"
echo "Protein             1"

# CLEANING UP

/bin/rm *.tmp
/bin/rm extract_atoms.awk extract_types.awk
/bin/rm merge_atoms.awk merge_types.awk

# DONE

exit