def test_Runner_openmm_other_settings(tmp_path):
if not os.path.exists(tmp_path):
os.mkdir(tmp_path)
mymodel = make_test_model.make_test_model(tmp_path)
#sim_openmm_factory = sim_openmm.Sim_openmm_factory()
myanchor = mymodel.anchors[1]
mmvt_output_filename = os.path.join(
tmp_path, myanchor.name, "prod", "%s%d.%s" %
(mmvt_base.OPENMMVT_BASENAME, 1, mmvt_base.OPENMMVT_EXTENSION))
loading_state_filename = os.path.join(tmp_path, "start.state")
runner = runner_openmm.Runner_openmm(mymodel, myanchor)
default_output_file, state_file_prefix, restart_index = runner.prepare(
False, True)
my_sim_openmm = mmvt_sim_openmm.create_sim_openmm(mymodel, myanchor,
mmvt_output_filename,
state_file_prefix)
my_sim_openmm.simulation.saveState(loading_state_filename)
runner.run(my_sim_openmm, False, load_state_file=loading_state_filename)
assert my_sim_openmm.integrator.getOutputFileName() == mmvt_output_filename
lines = 0
assert os.path.exists(mmvt_output_filename)
assert os.path.exists(loading_state_filename)
#print("glob.glob(state_file_prefix+'*')", glob.glob(state_file_prefix+'*'))
#assert len(glob.glob(state_file_prefix+'*')) > 0
with open(mmvt_output_filename, "r") as f:
for line in f:
lines += 1
def test_mmvt_sim_openmm_forcefield(tmp_path):
mymodel = make_test_model.make_test_model(tmp_path, mode='forcefield')
myanchor = mymodel.anchors[1]
output_file = os.path.join(tmp_path, "output.txt")
my_sim_openmm = mmvt_sim_openmm.create_sim_openmm(mymodel, myanchor,
output_file)
return
def test_mmvt_sim_namd_amber(tmp_path):
mymodel = make_test_model.make_test_model(tmp_path, engine="namd")
myanchor = mymodel.anchors[1]
output_file = os.path.join(tmp_path, "output.txt")
my_sim_openmm = mmvt_sim_namd.create_sim_namd(mymodel, myanchor,
output_file)
return
def test_Runner_openmm_forcefield(tmp_path):
if not os.path.exists(tmp_path):
os.mkdir(tmp_path)
mymodel = make_test_model.make_test_model(tmp_path, mode="forcefield")
#sim_openmm_factory = sim_openmm.Sim_openmm_factory()
myanchor = mymodel.anchors[1]
mmvt_output_filename = os.path.join(
tmp_path, myanchor.name, "prod", "%s%d.%s" %
(mmvt_base.OPENMMVT_BASENAME, 1, mmvt_base.OPENMMVT_EXTENSION))
runner = runner_openmm.Runner_openmm(mymodel, myanchor)
default_output_file, state_file_prefix, restart_index = runner.prepare()
my_sim_openmm = mmvt_sim_openmm.create_sim_openmm(mymodel, myanchor,
mmvt_output_filename)
runner.run(my_sim_openmm, False)
assert os.path.exists(mmvt_output_filename)
lines = 0
with open(mmvt_output_filename, "r") as f:
for line in f:
lines += 1
def test_Runner_namd_default(tmp_path):
if not os.path.exists(tmp_path):
os.mkdir(tmp_path)
mymodel = make_test_model.make_test_model(tmp_path, engine="namd")
#sim_namd_factory = sim_namd.Sim_namd_factory()
myanchor = mymodel.anchors[1]
mmvt_output_filename = os.path.join(
tmp_path, myanchor.name, "prod",
"%s%d" % (mmvt_base.NAMDMMVT_BASENAME, 1))
namd_command = "namd2"
namd_arguments = ""
runner = runner_namd.Runner_namd(mymodel, myanchor, namd_command,
namd_arguments)
default_output_file, output_basename, state_file_prefix, restart_index = \
runner.prepare()
#sim_namd_factory = sim_namd.Sim_namd_factory()
my_sim_namd = mmvt_sim_namd.create_sim_namd(mymodel, myanchor,
mmvt_output_filename)
my_sim_namd.namd_root.periodic_boundary_conditions.PMEGridSpacing = None
print("PME turned off")
runner.run(my_sim_namd, mmvt_output_filename+".out")
myglob = mmvt_output_filename+".out*"
outfiles = glob.glob(myglob)
outfile = outfiles[0]
assert os.path.exists(outfile)
has_correct_line1 = False
has_correct_line2 = False
with open(outfile,"r") as f:
for line in f:
if re.search("^WallClock", line):
has_correct_line1 = True
if re.search("^WRITING", line):
has_correct_line2 = True
assert has_correct_line1 == True
assert has_correct_line2 == True
"""
namd_arguments = "+wtf"
runner = runner_namd.Runner_namd(mymodel, myanchor, namd_command,
namd_arguments)
default_output_file, output_basename, state_file_prefix, restart_index = \
runner.prepare(force_overwrite=True)
#sim_namd_factory = sim_namd.Sim_namd_factory()
my_sim_namd = mmvt_sim_namd.create_sim_namd(mymodel, myanchor,
mmvt_output_filename)
runner.run(my_sim_namd, mmvt_output_filename+".out")
myglob = mmvt_output_filename+".out*"
outfiles = glob.glob(myglob)
outfile = outfiles[0]
assert os.path.exists(outfile)
has_correct_line1 = False
has_correct_line2 = False
with open(outfile,"r") as f:
for line in f:
print("line:", line)
if re.search("^WallClock", line):
has_correct_line1 = True
if re.search("^WRITING", line):
has_correct_line2 = True
with pytest.raises(Exception):
assert has_correct_line1 == True
with pytest.raises(Exception):
assert has_correct_line2 == True
"""
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