import sys

sys.path.append('..')
sys.path.append('/home/slars/software/amber11/src/mmpbsa_py')

import os, time, math         # (1)
import inputparse, utils, alamdcrd # (2)

output_file = "FINAL_RESULTS.out"
inputfile_name = "../gb.in"
strip_mdcrd = "whatever.mdcrd"
solvated_prmtop = "none"
complex_prmtop = "1XCK_hept_MGATP_noWAT.prmtop"
receptor_mdcrd = "none"
solvated_receptor_prmtop = "none"
ligand_mdcrd = "none"
solvated_ligand_prmtop = "none"
receptor_prmtop = "none"
ligand_prmtop = "none"
mdcrd = "26-50ns_noWAT_800frames_wATP_hept_1.nc"
mutant_complex_prmtop = ""
mutant_receptor_prmtop = ""
mutant_ligand_prmtop = ""
maskholder = ['', '']
numres_lig =""
numframes = 500
nmoderun = "" 
numframesnmode = ""
pbrun = 0
sanderpb = ""
entropy = 0
mutant_only = ""
mutstring = ""
warnings = ""
keep_files = ""
ala_entropy = 0
alarun = 0
gbrun = 1
debug = ""
one_trajectory = ""
onetraj = 1
verbose = 1
sander_apbs = ""
decompout = ""
idecomp = ""
dec_verbose = ""
ligstart = ""
decomprun = ""
surften = ""
cavity_surften = ""
temp = ""



keep_files = utils.PrintFinalResults(output_file, gbrun, debug, numframes, onetraj, verbose)


#output_file, inputfile_name, strip_mdcrd, solvated_prmtop, \
#                 complex_prmtop, receptor_mdcrd, solvated_receptor_prmtop, ligand_mdcrd,           \
#                 solvated_ligand_prmtop, receptor_prmtop, ligand_prmtop, mdcrd, mutant_complex_prmtop, \
#                 mutant_receptor_prmtop, mutant_ligand_prmtop, maskholder, numres_lig, numframes,  \
#                 nmoderun, numframesnmode, pbrun, sanderpb, entropy, mutant_only, mutstring, warnings, \
#                 keep_files, ala_entropy, alarun, gbrun, debug, one_trajectory, verbose, sander_apbs,  \
#                 decompout, idecomp, dec_verbose, ligstart, decomprun, surften, cavity_surften, temp)