name="2Q80"

awk '$0~/^ATOM/ || $0~/^HETATM/' $name.pdb > pdb.tmp

tot_chain=$(awk '$0~/^ATOM/ || $0~/^HETATM/' $name.pdb | cut -c22 | sort -u | wc -l)
chain_id=$(awk '$0~/^ATOM/ || $0~/^HETATM/' $name.pdb | cut -c22 | sort -u)
tot=$((($tot_chain * 2) - 1))

#echo ${chain}_id
#echo $tot

for (( i=0; i <= $tot; i=i+2 )) 
do 
chain=${chain_id:$i:1} 

## File with separated chain ids

awk -v var="$chain" 'BEGIN{
FIELDWIDTHS="6 5 1 4 1 3 1 1 4 1 3 8 8 8 6 6 6"}
$8~var' pdb.tmp > ${name}_${chain}.tmp


## Convert PDB to fasta sequence

echo '>'${name}_${chain} >> sequence.fasta
awk '$0~/^ATOM/ && $3=="CA" {print $4}' ${name}_${chain}.tmp |  tr '\n' ' ' |sed 's/ALA/A/g;s/CYS/C/g;s/ASP/D/g;s/GLU/E/g;s/PHE/F/g;s/GLY/G/g;s/HIS/H/g;s/ILE/I/g;s/LYS/K/g;s/LEU/L/g;s/MET/M/g;s/ASN/N/g;s/PRO/P/g;s/GLN/Q/g;s/ARG/R/g;s/SER/S/g;s/THR/T/g;s/VAL/V/g;s/TRP/W/g;s/TYR/Y/g;s/MSE/M/g' | sed 's/ //g' | fold -w 60 >> sequence.fasta
echo '' >> sequence.fasta


## BEGIN Calculate the ligand Mol wt
awk 'BEGIN{
FIELDWIDTHS="6 5 1 4 1 3 1 1 4 1 3 8 8 8 6 6 6"}
$0~/^HETATM/ {print $6}' ${name}_${chain}.tmp | sort -u | grep -v 'HOH' | grep -v 'MSE' > lig.tmp

#grep -v 'HETATM' ${name}_${chain}.tmp > ${name}_${chain}_1.tmp

tot_lig=$(wc -l lig.tmp | awk '{print $1}')
mol_wt=0

for ((j=1; j<=tot_lig; j++))
do
ligand=$(awk 'NR==xx {print $0}' xx="$j" lig.tmp)
#echo $ligand

grep $ligand ${name}_${chain}.tmp | cut -c77-78 > lig_atm.tmp

lig_len=$(wc -l lig_atm.tmp | awk '{print $1}')
#echo $lig_len

grep -v $ligand ${name}_${chain}.tmp > ${name}_${chain}_1.tmp

for ((k=1; k<=$lig_len; k++))
do
atom=$(awk -v xx="$k" 'NR==xx {print $1}' lig_atm.tmp)
atom_wt=0
if [[ $atom == 'C' ]]
then
atom_wt=12
elif [[ $atom == 'N' ]]
then
atom_wt=14
elif [[ $atom == 'O' ]]
then
atom_wt=16
elif [[ $atom == 'S' ]]
then
atom_wt=32
elif [[ $atom == 'P' ]]
then
atom_wt=32
elif [[ $atom == 'F' ]]
then
atom_wt=19
elif [[ $atom == 'CL' ]]
then
atom_wt=35
elif [[ $atom == 'BR' ]]
then
atom_wt=80
elif [[ $atom == 'I' ]]
then
atom_wt=127
fi
mol_wt=$(($mol_wt + $atom_wt))
done

if [[ $mol_wt > 180 && $mol_wt < 500 ]]
then
#cp ${name}_${chain}.tmp ${name}_${chain}_${ligand}_${mol_wt}.pdb 
grep $ligand ${name}_${chain}.tmp > ligand_$mol_wt.tmp
cat ${name}_${chain}_1.tmp ligand_$mol_wt.tmp > ${name}_${chain}_${ligand}_${mol_wt}.pdb 
fi

mol_wt=0
done
### Mol wt cal END #####

done
rm *.tmp