def run_browndye2(model, bd_milestone_index, restart, n_trajectories,
force_overwrite=False):
"""Run a Browndye2 simulation."""
import seekr2.modules.runner_browndye2 as runner_browndye2
if bd_milestone_index == "b_surface":
bd_milestone_directory = os.path.join(
model.anchor_rootdir, model.k_on_info.b_surface_directory)
bd_directory_list = [bd_milestone_directory]
for bd_directory in bd_directory_list:
runner_browndye2.run_bd_top(
model.browndye_settings.browndye_bin_dir, bd_directory, restart,
force_overwrite)
n_trajectories_per_output = runner_browndye2.DEFAULT_N_TRAJ_PER_OUT
if n_trajectories is not None:
if n_trajectories_per_output > n_trajectories:
n_trajectories_per_output = n_trajectories
runner_browndye2.modify_variables(
bd_directory, model.k_on_info.bd_output_glob, n_trajectories,
restart=restart, n_trajectories_per_output\
=n_trajectories_per_output)
runner_browndye2.run_nam_simulation(
model.browndye_settings.browndye_bin_dir, bd_directory,
model.k_on_info.bd_output_glob)
return
def test_converge_default_bd_only_mmvt(host_guest_mmvt_model):
model = host_guest_mmvt_model
bd_directory = os.path.join(host_guest_mmvt_model.anchor_rootdir,
"b_surface")
runner_browndye2.run_bd_top(model.browndye_settings.browndye_bin_dir,
bd_directory,
force_overwrite=True)
runner_browndye2.run_nam_simulation(
model.browndye_settings.browndye_bin_dir, bd_directory,
model.k_on_info.bd_output_glob)
cutoff = 0.1
minimum_anchor_transitions = 100
image_directory = common_analyze.make_image_directory(
host_guest_mmvt_model, None)
k_on_state = 0
data_sample_list = converge.converge(host_guest_mmvt_model,
k_on_state,
image_directory=image_directory,
verbose=True)
rmsd_convergence_results = common_converge.calc_RMSD_conv_amount(
host_guest_mmvt_model, data_sample_list)
transition_minima, transition_prob_results, transition_time_results \
= common_converge.calc_transition_steps(
host_guest_mmvt_model, data_sample_list[-1])
bd_transition_counts = data_sample_list[-1].bd_transition_counts
converge.print_convergence_results(host_guest_mmvt_model,
rmsd_convergence_results, cutoff,
transition_prob_results,
transition_time_results,
minimum_anchor_transitions,
bd_transition_counts)
return
def run_browndye2(model,
bd_milestone_index,
restart,
n_trajectories,
force_overwrite=False,
max_b_surface_trajs_to_extract=1000):
"""Run a Browndye2 simulation."""
import seekr2.modules.runner_browndye2 as runner_browndye2
if bd_milestone_index == "b_surface":
bd_milestone_directory = os.path.join(
model.anchor_rootdir, model.k_on_info.b_surface_directory)
bd_directory_list = [bd_milestone_directory]
else:
assert bd_milestone_index >= 0, "only positive indices allowed."
try:
bd_milestone = model.k_on_info.bd_milestones[bd_milestone_index]
except IndexError:
print("Invalid bd_milestone index provided.")
exit()
bd_milestone_directory = os.path.join(model.anchor_rootdir,
bd_milestone.directory)
#assert not b_surface, "Extraction may not be performed on the "\
# "b-surface."
lig_pqr_filenames, rec_pqr_filenames \
= runner_browndye2.extract_bd_surface(
model, bd_milestone, max_b_surface_trajs_to_extract,
force_overwrite, restart)
bd_directory_list = runner_browndye2.make_fhpd_directories(
model, bd_milestone, lig_pqr_filenames, rec_pqr_filenames,
force_overwrite)
for bd_directory in bd_directory_list:
runner_browndye2.run_bd_top(model.browndye_settings.browndye_bin_dir,
bd_directory, restart, force_overwrite)
n_trajectories_per_output = runner_browndye2.DEFAULT_N_TRAJ_PER_OUT
if n_trajectories is not None:
if n_trajectories_per_output > n_trajectories:
n_trajectories_per_output = n_trajectories
runner_browndye2.modify_variables(
bd_directory, model.k_on_info.bd_output_glob, n_trajectories,
restart=restart, n_trajectories_per_output\
=n_trajectories_per_output)
runner_browndye2.run_nam_simulation(
model.browndye_settings.browndye_bin_dir, bd_directory,
model.k_on_info.bd_output_glob)
if bd_milestone_index != "b_surface":
runner_browndye2.combine_fhpd_results(model, bd_milestone,
bd_directory_list)
return
def test_modify_variables(host_guest_mmvt_model):
"""
Test the function that modifies variables within the BD input xml.
"""
bd_directory = os.path.join(
host_guest_mmvt_model.anchor_rootdir,
host_guest_mmvt_model.k_on_info.b_surface_directory)
print("host_guest_mmvt_model.anchor_rootdir:",
host_guest_mmvt_model.anchor_rootdir)
assert os.path.exists(host_guest_mmvt_model.anchor_rootdir)
print("bd_directory:", bd_directory)
assert os.path.exists(bd_directory)
runner_browndye2.run_bd_top(
host_guest_mmvt_model.browndye_settings.browndye_bin_dir,
bd_directory,
force_overwrite=True)
runner_browndye2.modify_variables(
bd_directory,
host_guest_mmvt_model.k_on_info.bd_output_glob,
100,
4,
3456,
"my_out.xml",
restart=False,
n_trajectories_per_output=25)
simulation_filename_base = sim_browndye2.BROWNDYE_RECEPTOR + "_" \
+ sim_browndye2.BROWNDYE_LIGAND + "_simulation.xml"
simulation_filename = os.path.join(bd_directory, simulation_filename_base)
result = extract_xml_line(simulation_filename, "n_trajectories")
assert result == "100"
result = extract_xml_line(simulation_filename, "n_threads")
assert result == "4"
result = extract_xml_line(simulation_filename, "seed")
assert result == "3456"
result = extract_xml_line(simulation_filename, "output")
assert result == "my_out.xml"
result = extract_xml_line(simulation_filename, "n_trajectories_per_output")
assert result == "25"
return
def test_runner_browndye2_b_surface_elber(host_guest_elber_model):
model = host_guest_elber_model
bd_directory = os.path.join(host_guest_elber_model.anchor_rootdir,
"b_surface")
runner_browndye2.run_bd_top(model.browndye_settings.browndye_bin_dir,
bd_directory,
force_overwrite=True)
runner_browndye2.run_nam_simulation(
model.browndye_settings.browndye_bin_dir, bd_directory,
model.k_on_info.bd_output_glob)
assert len(glob.glob(os.path.join(bd_directory, "results*.xml"))) == 1
# Test restart
n_trajectories = model.k_on_info.b_surface_num_trajectories * 2
runner_browndye2.run_bd_top(model.browndye_settings.browndye_bin_dir,
bd_directory,
restart=True)
runner_browndye2.modify_variables(bd_directory,
model.k_on_info.bd_output_glob,
n_trajectories,
restart=True)
runner_browndye2.run_nam_simulation(
model.browndye_settings.browndye_bin_dir, bd_directory,
model.k_on_info.bd_output_glob)
assert len(glob.glob(os.path.join(bd_directory, "results*.xml"))) == 2
# Test force overwrite
n_trajectories = model.k_on_info.b_surface_num_trajectories
runner_browndye2.run_bd_top(model.browndye_settings.browndye_bin_dir,
bd_directory,
force_overwrite=True)
runner_browndye2.modify_variables(bd_directory,
model.k_on_info.bd_output_glob,
n_trajectories,
restart=False)
runner_browndye2.run_nam_simulation(
model.browndye_settings.browndye_bin_dir, bd_directory,
model.k_on_info.bd_output_glob)
assert len(glob.glob(os.path.join(bd_directory, "results*.xml"))) == 1
return
def test_runner_browndye2_b_surface_default(tmp_path):
model = make_test_model.make_test_model(tmp_path)
b_surface_abs_path = os.path.join(tmp_path, "b_surface")
receptor_pqr_filename = os.path.join(
b_surface_abs_path, model.browndye_settings.receptor_pqr_filename)
ligand_pqr_filename = os.path.join(
b_surface_abs_path, model.browndye_settings.ligand_pqr_filename)
bd_milestone = model.k_on_info.bd_milestones[0]
ghost_index_rec = \
sim_browndye2.add_ghost_atom_to_pqr_from_atoms_center_of_mass(
receptor_pqr_filename, bd_milestone.receptor_indices)
ghost_index_lig = \
sim_browndye2.add_ghost_atom_to_pqr_from_atoms_center_of_mass(
ligand_pqr_filename, bd_milestone.ligand_indices)
assert ghost_index_rec == 148
assert ghost_index_lig == 16
receptor_xml_filename = sim_browndye2.make_pqrxml(receptor_pqr_filename)
ligand_xml_filename = sim_browndye2.make_pqrxml(ligand_pqr_filename)
debye_length, reaction_filename = \
runner_browndye2.make_browndye_input_xml(
model, tmp_path, receptor_xml_filename, ligand_xml_filename,
model.k_on_info.b_surface_num_steps)
model.browndye_settings.debye_length = debye_length
assert os.path.exists(os.path.join(b_surface_abs_path, "apbs_input.xml"))
assert os.path.exists(os.path.join(b_surface_abs_path, "input.xml"))
abs_reaction_path = os.path.join(b_surface_abs_path, reaction_filename)
runner_browndye2.make_browndye_reaction_xml(model, abs_reaction_path)
assert os.path.exists(abs_reaction_path)
bd_directory = b_surface_abs_path
runner_browndye2.run_bd_top(model.browndye_settings.browndye_bin_dir,
bd_directory)
#runner_browndye2.modify_variables(bd_directory, 10000)
runner_browndye2.run_nam_simulation(
model.browndye_settings.browndye_bin_dir, bd_directory,
model.k_on_info.bd_output_glob)
#assert os.path.exists(os.path.join(b_surface_abs_path, "results.xml"))
assert len(glob.glob(os.path.join(b_surface_abs_path, "results*.xml"))) > 0
"""
bd_milestone_abs_path = os.path.join(tmp_path, bd_milestone.directory)
assert os.path.exists(bd_milestone_abs_path)
runner_browndye2.extract_bd_surface(model, bd_milestone, 10)
bd_directory_list = runner_browndye2.make_fhpd_directories(
model, bd_milestone)
for bd_directory in bd_directory_list:
runner_browndye2.run_bd_top(model.browndye_settings.browndye_bin_dir,
bd_directory)
runner_browndye2.modify_variables(bd_directory, n_trajectories=1000)
runner_browndye2.run_nam_simulation(
model.browndye_settings.browndye_bin_dir, bd_directory,
model.k_on_info.bd_output_glob)
runner_browndye2.combine_fhpd_results(
model, bd_milestone, bd_directory_list)
assert os.path.exists(os.path.join(bd_milestone_abs_path, "results.xml"))
"""
return
# TODO: bd_milestone test runs