#!/bin/bash
#=======================================================================
# Task: read a pdb file and generate a dssp output file
# Input:
# pdb file

# Output:
# pdb_code.dssp
# needs dssp exe on linux
# more efficient to run dssp exe locally

# note: double quotes for variable interpolation
#=======================================================================
# #%%specify variables for input and output paths and filenames
drug='pyrazinamide'
gene='pncA'
#convert to lowercase for consistency in filenames
gene_l=$(printf $gene | awk '{print tolower($0)}') 
gene_match="${gene}_p."
#printf "${gene_match}\n"

#==========
# data dir
#==========
#indir = 'git/Data/pyrazinamide/input/original'
#datadir="~git/Data"
datadir="${HOME}/git/Data"

#=======
# input
#=======
indir=${datadir}'/'${drug}'/input'
printf "Input dir: ${indir}\n"
in_filename='3pl1.pdb'
#infile=${basedir}${inpath}${in_filename}
infile=${indir}'/'${in_filename}
printf "Input file: ${infile}\n"

#=======
# output 
#=======
outdir=${datadir}'/'${drug}$'/output'
printf "Output dir: ${outdir}"
#out_filename='3pl1.dssp'
out_filename="${gene_l}.dssp"
outfile=${outdir}'/'${out_filename}
printf "Output file: ${outfile}\n"

#%%end of variable assignment for input and output files
#================================================================
# command line arg to run dssp and create output file
dssp -i ${infile} -o ${outfile}
printf "Finished writing: ${outfile}\n"
#printf "Filename: ${out_filename}\nlocated in: ${outdir}\n"