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#!/usr/local/bin/python3

"""Description of the 'connect' module.

The 'connect' module prepares the BioFET-SIM calculation.
It carries out the following steps:
    - Download of the PDB file
    - Fixing the PDB file with PDB2PQR
    - Realigning the protein structure with VMD
    - From the realignment, the dimensions are obtained
    - Calculation of overall charge with PROPKA 3.
""" 

# NOTE:
# - Calls all functions in order to obtain the
#   charge, charge-carrier number and dimensions
#   of the protein.

# Default modules
import sys
import os
import time
from os.path    import splitext
from subprocess import call 

# Custom modules
import propka 
import getCharge 
import getDimension

# Builtin modules 
#import realign 
#import getPointCharges
#import getCharge 
from signature import signature
from tests     import hasExt
from parse     import parse

# ************************************************************
# ************************************************************
# SETUP
def setup(pdbfile): 
    """Setting up the run.

    The function handles the submitted argument, ie. it checks
    if there is an extension or not. Incase it is missing, it is
    appended, incase it is present, the extension remains.

    setup(<PDB_ID[.pdb]>) --> target

    The return value is an uppercase string including the '.pdb'
    extension.
    """
    signature('SETUP')

    # Handle the case with/without extension in the argument
    if hasExt(pdbfile):
        target = pdbfile.upper() 
    else:
        target = pdbfile.upper() + '.pdb' 
    return target 

def getPDB(target):
    """Obtain the PDB file.
    The 'target' argument is the correct file name, including
    the '.pdb' extension, eg. '1AVD.pdb'.

    The file is written to disc after download."""

    print("Provided PDB file: " + target) 
    print("Requesting PDB file: " + target)
    #call(['wget', 'http://www.pdb.org/pdb/files/'\
    #        + target])
    os.system("wget http://www.pdb.org/pdb/files/"\
            + target)
# ------------------------------------------------------------



# ************************************************************
# ************************************************************
# PDB2PQR Part 
def callPDB2PQR(target): 
    signature('PDB2PQR')
    call(['pdb2pqr.py', '-v', '--ff=CHARMM', target,\
            splitext(target)[0] + '-out.pqr'])
    #os.system('pdb2pqr.py -v --ff=CHARMM ' + target\
    #        + ' ' + splitext(target)[0] + '-out.pqr')
    print('PDB2PQR done.')
    print() 
# ------------------------------------------------------------



# ************************************************************
# ************************************************************
# VMD Part
def callVMD(target):
    signature('VMD') 
    #call(['align.py', target])
    os.system('realign.py ' + target[0:4] + '-out.pqr')
    print('VMD done.')
    print() 
# ------------------------------------------------------------ 



# ************************************************************
# ************************************************************
# PROPKA Part
def callPropka3(target):
    signature('PROPKA') 
    #call(['cp', splitext(target)[0] + '-out.pqr',\
    #            splitext(target)[0] + '-out.pdb'])
    #call(['propka.py', splitext(target)[0] + '-out.pdb'])
    #os.system('cp ' + splitext(target)[0] + '-out.pqr'\
    #        ' ' + splitext(target)[0] + '-out.pdb')
    if os.system('propka.py ' + splitext(target)[0] +\
            '-out-new.pdb') == 0:
        print('Propka 3 done.') 
    print() 
# ------------------------------------------------------------



# ************************************************************
# ************************************************************
# BOX Part
def callBox(target):
    signature('BOX')
    dim = getDimension.BoxPDB(target)
    print(dim.boxIt())
# ------------------------------------------------------------



# ************************************************************
# ************************************************************
# COLLECT Part 
def collectData(pH, target):
    signature("COLLECTING DATA") 
    charge = getCharge.getCharge(pH, target)
    print('Charge at pH {0}: {1}'.format(pH, charge[1])) 
    print()
# ------------------------------------------------------------ 



# ************************************************************
# ************************************************************
# Entry point of Python.  
try:
    # Get the argument
    pdbfile = sys.argv[1] 
    target = setup(pdbfile)

    # Download
    getPDB(target) 
    # OUT: 'PDB.pdb'

    # Correction
    # IN:  'PDB.pdb'
    callPDB2PQR(target) 
    # OUT: 'PDB-out.pqr'

    # Realignment
    # IN:  'PDB-out.pqr'
    callVMD(target)
    # OUT: 'PDB-out-new.pdb'

    # Charging
    # IN:  'PDB-out-new.pdb'
    callPropka3(target) 
    # OUT: 'PDB-out-new.pka'


    if 1:
        # pH=7
        parse(target)
        collectData(7, target)
    else:
        for i in range(1,15):
            collectData(i, target)
    print(callBox(target))



except IndexError:
    if len(sys.argv) == 1:
        print("No argument provided.")
        print("$ connect.py <PDB>") 

# End of the program.
# ************************************************************
# ************************************************************