def test_prepare_structure():
protein_file = os.path.join(test_path, "PPI/1tnf_prep.pdb")
new_protein_file = "1tnf_prep_prep.pdb"
ligand_pdb = os.path.join(test_path, "PPI/1tnf_ligand.pdb")
chain = ["A", "B"]
prepare_structure(protein_file, ligand_pdb, chain, remove_water=True)
with open(new_protein_file, "r") as file:
lines = file.readlines()
chains = []
no_water = True
for line in lines:
if "HOH" in line:
no_water = False
if line.startswith("HETATM") or line.startswith("ATOM"):
chains.append(line[21:22].strip())
assert "C" not in chains
assert no_water
for f in glob.glob("*_prep.pdb"):
os.remove(f)
def run_ppi(parsed_yaml: dict) -> (pv.ParametersBuilder, pv.ParametersBuilder):
# Let user choose working folder
original_dir = os.path.abspath(os.getcwd())
working_folder = os.path.abspath("{}_Pele".format(parsed_yaml.residue))
if not parsed_yaml.folder:
working_folder = is_repeated(
working_folder) if not parsed_yaml.adaptive_restart else is_last(
working_folder)
else:
working_folder = os.path.abspath(parsed_yaml.folder)
# Set main folder
parsed_yaml.folder = os.path.join(working_folder,
"1_interface_exploration")
# Check n_waters before launching the simulation
#water_checker(parsed_yaml)
# get arguments from input.yaml
n_waters = parsed_yaml.n_waters
parsed_yaml.n_waters = None
protein_file = parsed_yaml.system
chain = parsed_yaml.protein
ligand_pdb = parsed_yaml.ligand_pdb
# no waters in the first simulation
parsed_yaml.water_arg = None
# remove chains except for "protein" flag
protein_file = prepare_structure(protein_file, ligand_pdb, chain, True)
parsed_yaml.system = protein_file
# start simulation 1 - induced fit
parsed_yaml.induced_fit_exhaustive = True
simulation1 = si.run_adaptive(parsed_yaml)
simulation1_path = os.path.join(simulation1.pele_dir, simulation1.output)
# cluster best structures
if not parsed_yaml.debug:
with cd(simulation1_path):
cluster_best_structures("5",
n_components=simulation1.n_components,
residue=simulation1.residue,
topology=simulation1.topology,
directory=working_folder,
logger=simulation1.logger)
# adjust original input.yaml
if not parsed_yaml.skip_refinement:
parsed_yaml.system = os.path.join(working_folder,
"refinement_input/*.pdb")
parsed_yaml.folder = os.path.join(working_folder,
"2_refinement_simulation")
parsed_yaml.induced_fit_exhaustive = None
parsed_yaml.ppi = None
parsed_yaml.poses = None
parsed_yaml.rescoring = True
del parsed_yaml.water_arg
# Set waters ony if specified by user
if n_waters != 0:
parsed_yaml.waters = "all_waters"
parsed_yaml.n_waters = n_waters
else:
parsed_yaml.waters = None
parsed_yaml.n_waters = n_waters
parsed_yaml.adaptive_restart = False
if not parsed_yaml.test:
parsed_yaml.iterations = 1
parsed_yaml.steps = 100
parsed_yaml.box_center = simulation1.box_center
parsed_yaml.box_radius = 100 # We should have a look at how to set no box but at the moment super big
# start simulation 2 - minimisation
with cd(original_dir):
if not parsed_yaml.debug:
simulation2 = launch_simulation(parsed_yaml)
else:
simulation2 = None
else:
simulation2 = None
return simulation1, simulation2
def run_ppi(parsed_yaml: dict) -> (pv.ParametersBuilder, pv.ParametersBuilder):
# Let user choose working folder
original_dir = os.path.abspath(os.getcwd())
working_folder = os.path.abspath("{}_Pele".format(parsed_yaml.residue))
if not parsed_yaml.folder:
working_folder = get_next_peledir(working_folder) if not parsed_yaml.adaptive_restart else get_latest_peledir(
working_folder)
else:
working_folder = os.path.abspath(parsed_yaml.folder)
# Set main folder
parsed_yaml.folder = os.path.join(working_folder, "1_interface_exploration")
# get arguments from input.yaml
n_waters = parsed_yaml.n_waters
parsed_yaml.n_waters = None
protein_file = parsed_yaml.system
chain = parsed_yaml.protein
ligand_pdb = parsed_yaml.ligand_pdb
# Parametrize hetero molecules before merging PDBs, if using peleffy. Otherwise they will go through Plop in
# Adaptive.simulation.
if parsed_yaml.use_peleffy:
templates, rotamers, to_skip = parametrize_hetero_ppi(parsed_yaml)
parsed_yaml.template = parsed_yaml.template.extend(templates) if parsed_yaml.template else templates
parsed_yaml.rotamers = parsed_yaml.rotamers.extend(rotamers) if parsed_yaml.rotamers else rotamers
parsed_yaml.skip_ligand_prep = parsed_yaml.skip_ligand_prep.extend(to_skip) if parsed_yaml.skip_ligand_prep else to_skip
# no waters in the first simulation
parsed_yaml.water_arg = None
parsed_yaml.use_peleffy = parsed_yaml.use_peleffy if parsed_yaml.use_peleffy is not None else False
# remove chains except for "protein" flag
protein_file = prepare_structure(protein_file, ligand_pdb, chain, True, peleffy=parsed_yaml.use_peleffy)
parsed_yaml.system = protein_file
# start simulation 1 - induced fit
parsed_yaml.induced_fit_long = True
simulation1 = si.run_adaptive(parsed_yaml)
simulation1_path = os.path.join(simulation1.pele_dir, simulation1.output)
# cluster best structures
if not parsed_yaml.debug:
with cd(simulation1_path):
cluster_best_structures("5", n_components=simulation1.n_components,
residue=simulation1.residue, topology=simulation1.topology,
directory=working_folder, logger=simulation1.logger)
# adjust original input.yaml
if not parsed_yaml.skip_refinement:
parsed_yaml.system = os.path.join(working_folder, "refinement_input/*.pdb")
parsed_yaml.folder = os.path.join(working_folder, "2_refinement_simulation")
parsed_yaml.induced_fit_long = None
parsed_yaml.ppi = None
parsed_yaml.poses = None
parsed_yaml.rescoring = True
del parsed_yaml.water_arg
# Set waters only if specified by user
if n_waters != 0:
parsed_yaml.waters = "all_waters"
parsed_yaml.n_waters = n_waters
else:
parsed_yaml.waters = None
parsed_yaml.n_waters = n_waters
parsed_yaml.adaptive_restart = False
if not parsed_yaml.test:
parsed_yaml.iterations = 1
parsed_yaml.steps = 100
parsed_yaml.box_center = simulation1.box_center
parsed_yaml.box_radius = 100 # We should have a look at how to set no box but at the moment super big
# start simulation 2 - minimisation
with cd(original_dir):
if not parsed_yaml.debug:
simulation2 = launch_simulation(parsed_yaml)
else:
simulation2 = None
else:
simulation2 = None
return simulation1, simulation2