#!/usr/bin/python
# Read a PDB and output DSSP to console
import sys, os
from Bio.PDB import PDBParser
from Bio.PDB.DSSP import DSSP
import pandas as pd
import pprint as pp

#%%
# TASK: read a pdb file and generate a dssp output file
# FIXME: Pending output dssp hasn't been generated
# needs dssp exe on linux
# may be easier to run the dssp exe locally
#%%
# my working dir
os.getcwd()
homedir = os.path.expanduser('~') # spyder/python doesn't recognise tilde
os.chdir(homedir + '/git/LSHTM_analysis/meta_data_analysis')
os.getcwd()
#%%
# specify variables for input and output paths and filenames
drug = "pyrazinamide"
#gene = "pnca"

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

# input
inpath = "/original"

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

infile = basedir + inpath + in_filename
#print(infile)

# output file 
outpath = "/processed"
outdir =   datadir + "/" + drug + outpath
out_filename = "/3pl1.dssp"
outfile =  outdir + out_filename
#print(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
#%%
p = PDBParser()
structure = p.get_structure("3pl1", infile)

model = structure[0]
dssp = DSSP(model, infile)
#dssp = DSSP(model, infile, dssp='mkdssp') #incase you used DSSP2 exe
pp.pprint(dssp)

#DSSP data is accessed by a tuple - (chain id, residue id): RSA
a_key = list(dssp.keys())[3]
dssp[a_key]

pp.pprint(dssp.keys())
pp.pprint(dssp.property_dict)
pp.pprint(dssp.property_keys)
pp.pprint(dssp.property_list)