#!/usr/bin/env python3
# -*- coding: utf-8 -*-
"""
Created on Sun Feb 16 11:21:44 2020

@author: tanu
"""
#!/usr/bin/bash
# Run dssp exe

#%%
# specify variables for input and output paths and filenames
drug="pyrazinamide"
#gene = "pnca"

datadir="~git/Data"
basedir=${datadir}"/"${drug}
echo${basedir}

# input
inpath="/original"

# uncomment as necessary
in_filename="/3pl1.pdb"

infile=${basedir}${inpath}${in_filename}
echo${infile}

# output file 
outpath="/processed"
outdir=${datadir}"/"${drug}${outpath}
out_filename="/3pl1.dssp"
outfile=${outdir}${out_filename}
echo${outdir}

if not os.path.exists(datadir):
    print('Error!', datadir, 'does not exist. Please ensure it exists. Dir struc specified in README.md')
    os.makedirs(datadir)
    exit()

if not os.path.exists(outdir):
    print('Error!', outdir, 'does not exist.Please ensure it exists. Dir struc specified in README.md')
    exit()
    
else:
    print('Dir exists: Carrying on')
# end of variable assignment for input and output files
#%%
# ommand line args
dssp -i 3pl1.pdb -o 3pl1.dssp
dssp -i