#!/home/tanu/anaconda3/envs/ContactMap/bin/python3
# Read a DSSP file into a data frame and pretty-print it

#https://jbloomlab.github.io/dms_tools2/dms_tools2.dssp.html
import sys, os
import pandas as pd
import pprint as pp
import dms_tools2
import dms_tools2.dssp

#%%
# my working dir
homedir = os.path.expanduser('~')  # spyder/python doesn't recognise tilde
os.getcwd()
os.chdir(homedir + '/git/LSHTM_analysis/meta_data_analysis/struct_params')
os.getcwd()
#%%
# sample example
dssp_file = "./3pl1.dssp"
dssp_df = dms_tools2.dssp.processDSSP(dssp_file, chain='A')

# outputs to console
#returns df with ASA and RSA (base on Tien at al 2013 (theor.) values)
#Link: https://en.wikipedia.org/wiki/Relative_accessible_surface_area
pp.pprint(dssp_df)

# write to csv
dssp_df.to_csv('3pl1_dssp_df', header=True, index = False)

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

datadir = homedir + "/git/Data"
basedir =  datadir + "/" + drug + "/input"

# input
inpath = "/processed"
in_filename  = "/3pl1.dssp"
infile = basedir + inpath + in_filename
#print(infile)

# output file 
outpath = "/output"
outdir =   datadir + "/" + drug + outpath
out_filename = "/3pl1_dssp_df"
outfile =  outdir + out_filename
print(outdir); print(outfile)

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
#%% <----- fixme
dssp_file = infile
dssp_df = dms_tools2.dssp.processDSSP(dssp_file, chain='A')

#%%
# write to csv
dssp_df.to_csv(outfile, header=True, index = False)