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from copy import copy 

import os 

 

tit_mole = None 

sites = {} 

pid = None 

debug = None 

 

input_conversion = {'grid_fill': 'perfil', 

'pbc_dimensions': 'pbc_dim', 

'convergence': 'maxc'} 

stdout = None 

stderr = None 

 

stdout_file = None 

stderr_file = None 

 

njobs = None # to be redeclared in concurrency 

pb_time = None # to be redeclared in concurrency 

total_jobs = None # to be redeclared in concurrency 

 

# DelPhi related 

params = {'perfil': 0.9, 

'gsize': 81, 

'scaleP': 1, 

'scaleM': 4, 

'precision': 'single', 

'ionicstr': 0.1, 

'bndcon': 4, 

'maxc': 0.01, 

'nlit': 500, 

'nonit': 0, 

'relfac': 0.75, 

'relpar': 0.75, 

'pbx': False, 

'pby': False, 

'ffID': 'G54A7', 

'pHmin': 0, 

'pHmax': 10, 

'pHstep': 0.25, 

'epssol': 80.0, 

'temp': 310.0, 

'seed': 1234567, 

'cutoff': 2.5, 

'pbc_dim': 0, 

'ionicstr': 0.1, 

'epsin': 20.0, 

'slice': 0.05, 

'ncpus': 1, 

'clean_pdb': True, 

'couple_min': 2.0, 

'mcsteps': 200000, 

'eqsteps': 1000 

} 

 

# Paths 

# TODO: include in dependencies 

# in dependencies there is a pdb2pqr that has a important dat folder 

fileDir = os.path.dirname(os.path.abspath(__file__)) 

script_dir = fileDir 

pdb2pqr = "{0}/pdb2pqr/pdb2pqr.py".format(fileDir) 

userff = "{0}/pdb2pqr/dat/GROMOS.DAT".format(fileDir) 

usernames = "{0}/pdb2pqr/dat/GROMOS.names".format(fileDir) 

 

 

# Input Files 

f_in = None 

f_in_extension = None 

f_out = None 

f_prot_out = None 

f_log = "LOG" 

f_dat = None 

 

# Force Field Files 

f_crg = None 

f_siz = None 

 

lipids = {'cholesterol': 'CHO', # to edit 

'POPC': 'POP'} 

lipid_residues = ['POX', 'PJ2', 'CHL'] # allowed residue names 

 

# Constants 

kBoltz = 5.98435e-6 # e^2/(Angstrom*K) 

log10 = 2.302585092994046 

 

 

# Tautomer Variables 

terminal_offset = 2000 

 

TITRABLETAUTOMERS = {'LYS': 3, 

'HIS': 2, 

'ASP': 4, 

'GLU': 4, 

'SER': 3, 

'THR': 3, 

'CYS': 3, 

'CTR': 4, 

'NTR': 3, 

'TYR': 2} 

 

TITRABLERESIDUES = TITRABLETAUTOMERS.keys() 

REGULARTITRATINGRES = copy(TITRABLETAUTOMERS.keys()) 

 

for res in REGULARTITRATINGRES: 

ntautomers = TITRABLETAUTOMERS[res] 

for i in range(ntautomers): 

TITRABLERESIDUES.append(res[0:2] + str(i + 1))