from AlGDock import HREX

import os, shutil, glob

# Run the AlGDock job
while not os.path.exists('dock/f_RL.pkl.gz'):
# if True:
# initialize an instance of class BindingPMF
    self = HREX.BindingPMF(\
    dir_dock='dock', dir_cool='cool',\
    ligand_database='prmtopcrd/ligand.db', \
    forcefield='prmtopcrd/gaff.dat', \
    ligand_prmtop='prmtopcrd/ligand.prmtop', \
    ligand_inpcrd='prmtopcrd/ligand.trans.inpcrd', \
    receptor_prmtop='prmtopcrd/receptor.prmtop', \
    receptor_inpcrd='prmtopcrd/receptor.trans.inpcrd', \
    receptor_fixed_atoms='prmtopcrd/receptor.pdb', \
    complex_prmtop='prmtopcrd/complex.prmtop', \
    complex_inpcrd='prmtopcrd/complex.trans.inpcrd', \
    complex_fixed_atoms='prmtopcrd/complex.pdb', \
    rmsd=True, \
    dir_grid='grids', \
    protocol='Adaptive', cool_therm_speed=1.0, dock_therm_speed=1.5,\
    sampler='NUTS', seeds_per_state=50, steps_per_seed=100, sweeps_per_cycle=50, \
    steps_per_sweep=100, cool_repX_cycles=3, dock_repX_cycles=2, \
    site='Sphere', site_center=[1.80624, 1.80624, 1.80624], \
    site_max_R=0.01, site_density=10., do_calc_random_dock_stats=False, \
    receptor_NAMD_GBSA=[-9053.10071], receptor_NAMD_Gas=[0.00000], \
    MCMC_moves=0, 
    run_type='one_step')
    del self
from AlGDock import HREX

import os, shutil, glob

# Run the AlGDock job
while not os.path.exists('dock/f_RL.pkl.gz'):
# if True:
# initialize an instance of class BindingPMF
    self = HREX.BindingPMF(\
    dir_dock='dock', dir_cool='cool',\
    ligand_database='prmtopcrd/ligand.db', \
    forcefield='prmtopcrd/gaff.dat', \
    ligand_prmtop='prmtopcrd/ligand.prmtop', \
    ligand_inpcrd='prmtopcrd/ligand.trans.inpcrd', \
    receptor_prmtop='prmtopcrd/receptor.prmtop', \
    receptor_inpcrd='prmtopcrd/receptor.trans.inpcrd', \
    receptor_fixed_atoms='prmtopcrd/receptor.pdb', \
    complex_prmtop='prmtopcrd/complex.prmtop', \
    complex_inpcrd='prmtopcrd/complex.trans.inpcrd', \
    complex_fixed_atoms='prmtopcrd/complex.pdb', \
    rmsd=True, \
    dir_grid='grids', \
    protocol='Adaptive', cool_therm_speed=1.0, dock_therm_speed=1.5,\
    sampler='NUTS', seeds_per_state=50, steps_per_seed=100, sweeps_per_cycle=50, \
    steps_per_sweep=100, cool_repX_cycles=3, dock_repX_cycles=2, \
    site='Sphere', site_center=[1.80624, 1.80624, 1.80624], \
    site_max_R=0.01, site_density=10., do_calc_random_dock_stats=False, \
    receptor_NAMD_GBSA=[-9053.10071], receptor_NAMD_Gas=[0.00000], \
    MCMC_moves=0, 
    run_type='one_step')
    del self
# Run the AlGDock job # if True: # initialize an instance of class BindingPMF