def test_analysis_flags(yaml_file, n_expected_outputs, expected_files):
"""
Runs full simulation with input.yaml with some unusual flags, check the number of created plots and their names to
ensure correct metrics were take into account.
Parameters
----------
yaml_file : str
Path to input.yaml
n_expected_outputs : int
Number of expected plots.
expected_files : List[str]
List of expected plot names.
Returns
-------
Folder with plots
"""
output_folder = "../pele_platform/Examples/analysis/data/results/plots/"
if os.path.exists(output_folder):
shutil.rmtree(output_folder)
main.run_platform(yaml_file)
for file in expected_files:
file_path = os.path.join(output_folder, file)
assert os.path.exists(file_path)
all_files = glob.glob(os.path.join(output_folder, "*png"))
assert len(all_files) == n_expected_outputs
def test_analysis_flag(ext_args=ANALYSIS_FLAGS):
main.run_platform(ext_args)
assert os.path.exists(
"data/results/Plots/numberOfAcceptedPeleSteps_currentEnergy_distance0_plot.png"
)
assert os.path.exists(
"data/results/Plots/distance0_currentEnergy_plot.png")
assert len(glob.glob("data/results/Plots/*.png")) == 2
def test_rotamer_error(yaml=yaml):
try:
job = main.run_platform(yaml)
except ce.RotamersFileNotFound as e:
assert str(e).strip("'") == "File mgadeaz not found"
return
assert False
def test_lig_preparation_error(args=LIG_PREP_ARGS):
try:
job = main.run_platform(args)
except ce.LigandPreparationError:
assert True
return
assert False
def test_mutagenesis_production():
"""
Tests end-to-end saturated mutagenesis run on 5 CPUs to make sure we get the right output and pele.conf looks
as expected (i.e. has induced_fit_exhaustive defaults).
TODO: This is a very primitive implementation, needs a lot more testing!
"""
yaml = os.path.join(test_path, "saturated_mutagenesis.yaml")
all_jobs = main.run_platform(yaml)
# List of mutated PDBs expected in each job
expected_pdbs = [('T454A_processed.pdb', 'T454D_processed.pdb'),
('T454E_processed.pdb', )]
for i, job in enumerate(all_jobs):
# Output files exist
output_files = glob.glob(os.path.join(job.pele_dir, job.output, "*/traj*.pdb"))
assert output_files
# Check if the default induced fit exhaustive lines are present in pele configuration file
induced_fit_lines = test_adaptive_defaults.INDUCE_FIT_PELE
errors = test_adaptive_defaults.check_file(job.pele_dir, "pele.conf", induced_fit_lines, [])
assert not errors
# Make sure all subset directories have correct names
assert "Subset" in os.path.basename(job.pele_dir)
# Analysis should not run
results_folder = os.path.exists(os.path.join(job.pele_dir, "results"))
assert not results_folder
# Check if the jobs were properly split between subsets based on available CPUs
job_dir = os.path.join(job.pele_dir, "input", "*.pdb")
job_input = [os.path.basename(file) for file in glob.glob(job_dir)]
for expected_pdb in expected_pdbs[i]:
assert expected_pdb in job_input
def test_yaml_errors(yaml_file, error):
try:
job = main.run_platform(yaml_file)
except Exception as e:
assert str(e) == error
return
assert False
def test_global_defaults(ext_args=GLOBAL_ARGS):
errors = []
job = main.run_platform(ext_args)
errors = check_file(job.pele_dir, "adaptive.conf", GLOBAL_DEFAULTS_ADAPTIVE, errors)
errors = check_file(job.pele_dir, "pele.conf", GLOBAL_DEFAULTS_PELE, errors)
assert len(glob.glob(os.path.join(job.inputs_dir, "input*.pdb"))) == (job.cpus-1)
assert not errors
def test_gpcr_defaults(ext_args=GPCR_ARGS):
errors = []
job = main.run_platform(ext_args)
errors = check_file(job.pele_dir, "adaptive.conf", GPCR_DEFAULTS_ADAPTIVE,
errors)
errors = check_file(job.pele_dir, "pele.conf", GPCR_DEFAULTS_PELE, errors)
assert not errors
def test_rescoring_defaults(ext_args=RESCORING_ARGS):
errors = []
job = main.run_platform(ext_args)
errors = check_file(job.pele_dir, "adaptive.conf", REF_DEFAULTS_ADAPTIVE,
errors)
errors = check_file(job.pele_dir, "pele.conf", REF_DEFAULTS_PELE, errors)
assert not errors
def test_water(yaml=yaml):
water_lines = [
"HETATM 1699 OW HOH A 202 51.000 92.000 14.000 1.00 0.00 O",
"HETATM 1700 1HW HOH A 202 51.757 92.586 14.000 1.00 0.00 H",
"HETATM 1701 2HW HOH A 202 50.243 92.586 14.000 1.00 0.00 H",
"HETATM 1702 OW HOH A 203 71.000 60.000 20.000 1.00 0.00 O",
"HETATM 1703 1HW HOH A 203 71.757 60.586 20.000 1.00 0.00 H",
"HETATM 1704 2HW HOH A 203 70.243 60.586 20.000 1.00 0.00 H",
"HETATM 1705 OW HOH A 204 82.000 86.000 74.000 1.00 0.00 O",
"HETATM 1706 1HW HOH A 204 82.757 86.586 74.000 1.00 0.00 H",
"HETATM 1707 2HW HOH A 204 81.243 86.586 74.000 1.00 0.00 H"
]
water_output = []
# Function to test
job = main.run_platform(yaml)
# checkpoints
output = glob.glob(os.path.join(job.pele_dir,
"results/top_poses/0.1.0*"))[0]
with open(output, "r") as file:
lines = file.readlines()
for line in lines:
if line[17:21].strip() == "HOH":
water_output.append(line.strip())
# test
assert water_lines == water_output
def test_induced_fast_defaults(ext_args=INDUCED_FAST_ARGS):
errors = []
job = main.run_platform(ext_args)
errors = check_file(job.pele_dir, "adaptive.conf",
INDUCE_FIT_FAST_DEFAULTS_ADAPTIVE, errors)
errors = check_file(job.pele_dir, "pele.conf", INDUCE_FIT_PELE, errors)
assert not errors
def test_softexit_defaults(ext_args=EXITSOFT_ARGS):
errors = []
job = main.run_platform(ext_args)
errors = check_file(job.pele_dir, "adaptive.conf",
EXIT_SOFT_DEFAULTS_ADAPTIVE, errors)
errors = check_file(job.pele_dir, "pele.conf", EXIT_DEFAULTS_PELE, errors)
assert not errors
def test_env_variable(ext_args=ENV_ARGS):
try:
job = main.run_platform(ext_args)
except ce.EnvVariableNotFound as e:
assert True
return
assert False
def test_sdf_joiner(ext_args=FRAG_JOINER_ARGS):
files = glob.glob(ext_args)
for file in files:
try:
job = main.run_platform(file)
except Exception:
assert False
def test_allosteric_skipref(yaml=yaml):
job, job2 = main.run_platform(yaml)
refinement_simulation = os.path.join(os.path.dirname(job.pele_dir), "2_refinement_simulation")
# checkpoints
assert not os.path.exists(refinement_simulation)
assert not job2
def test_all_metal_constraints(ext_args=ALL_METAL_CONSTR_ARGS,
ext_args_permissive=PERMISSIVE_EXCEPTION):
# checks constrain_all_metals -> should add whatever atoms in range
errors = []
job = main.run_platform(ext_args)
errors = tk.check_file(job.pele_dir, "pele.conf", ALL_METAL_CONSTR, errors)
assert not errors
# same system, but permissive -> should fail due to lack of geometry
try:
job = main.run_platform(ext_args_permissive)
except ce.NoGeometryAroundMetal:
assert ce.NoGeometryAroundMetal
return
assert False
def test_input_yaml_error():
yaml = os.path.join(test_path, "gpcr/complex.pdb")
try:
job = main.run_platform(yaml)
except ce.WrongYamlFile:
assert True
return
assert False
def test_atom_error(ext_args=ATOM_GPCR_ERROR_ARGS):
try:
job = main.run_platform(ext_args)
except ce.WrongAtomSpecified as e:
assert str(e).strip(
"'") == "Atom A:114:CM could not be found in structure"
return
assert False
def test_atom_string_underscore(yaml=yaml):
try:
job = main.run_platform(yaml)
except ce.WrongAtomStringFormat as e:
assert (
str(e).strip("'") ==
"The specified atom is wrong 'A_106:OH'. Should be 'chain:resnumber:atomname"
)
def test_permissive_constraints(passed=PASS_PERMISSIVE_METAL_CONSTR_ARGS,
failed=FAIL_PERMISSIVE_METAL_CONSTR_ARGS):
# non-permissive -> supposed to fail due to lack of geometry
try:
job = main.run_platform(failed)
except ce.NoGeometryAroundMetal:
assert ce.NoGeometryAroundMetal
return
assert False
# same system, but permissive -> should add constraints around the metal
errors = []
job = main.run_platform(passed)
errors = tk.check_file(job.pele_dir, "pele.conf", PASS_METAL_CONSTR,
errors)
assert not errors
def test_polarisation(ext_args_true=POLARISATION_ARGS,
ext_args_false=SQUARE_PLANAR_ARGS):
# no polarisation
job1 = main.run_platform(ext_args_false)
mg_template_file_false = glob.glob(
os.path.join(job1.pele_dir,
"DataLocal/Templates/OPLS2005/HeteroAtoms/mgz"))
assert not mg_template_file_false
# polarisation with factor 10
errors = []
job2 = main.run_platform(ext_args_true)
errors = tk.check_file(job2.pele_dir,
"DataLocal/Templates/OPLS2005/HeteroAtoms/mgz",
POLARISATION, errors)
assert not errors
def test_site_finder_skipref():
yaml_file = os.path.join(test_path, "site_finder/input_skipref.yaml")
job, job2 = main.run_platform(yaml_file)
refinement_simulation = os.path.join(os.path.dirname(job.pele_dir),
"2_refinement_simulation")
assert not os.path.exists(refinement_simulation)
assert not job2
def test_out_in_flag(yaml=yaml):
try:
job = main.run_platform(yaml)
except ce.OutInError as e:
assert (str(e).strip("'") ==
"flag final_site must be specified for out_in package")
return
assert False
def test_gpcr(args=GPCR_ARGS):
errors = []
job = main.run_platform(args)
errors = check_file(job.pele_dir, "pele.conf", GPCR_VALUES, errors)
input_file = os.path.join(job.inputs_dir, "complex_processed.pdb")
if not os.path.exists(input_file):
errors.append("skip_ppp")
assert not errors
def test_flag_similarity():
yaml = os.path.join(test_path, "checker/input.yaml")
try:
job = main.run_platform(yaml)
except KeyError as e:
assert str(e).strip("'") == "Incorrect flag posis. Did you mean poses?"
return
assert False
def test_str_pca(ext_args=PCA2_ARGS, output="PCA_result"):
if os.path.exists(output):
shutil.rmtree(output, ignore_errors=True)
errors = []
job = main.run_platform(ext_args)
folder = job.folder
errors = check_file(folder, "pele.conf", PCA_VALUES, errors)
assert not errors
def test_checker():
yaml = os.path.join(test_path, "checker/input.yaml")
try:
job = main.run_platform(yaml)
except KeyError:
assert KeyError
return
assert False
def test_water_with_previous_water(yaml=yaml_previous_water):
# Function to test
errors = []
job = main.run_platform(yaml)
errors = tk.check_file(job.pele_dir, "pele.conf", WATER_PREVIOUS_PELE,
errors)
errors = tk.check_file(job.pele_dir, "adaptive.conf",
WATER_PREVIOUS_ADAPTIVE, errors)
assert not errors
def test_allosteric_skipref(yaml=yaml):
job, _ = main.run_platform(yaml)
# checkpoints
files_refinement = glob.glob(os.path.join(job.pele_dir, "refinement_simulation/results/BestStructs/epoch*"))
# test
assert not files_refinement
def test_allosteric_restart(yaml=yaml):
job, job2 = main.run_platform(yaml)
# checkpoints
output_csv = pd.read_csv(os.path.join(job.pele_dir, "output/clustering_output.csv"))
nfiles = len(glob.glob(os.path.join(os.path.dirname(job.pele_dir), "refinement_input/*.pdb")))
nfiles_refinement = len(glob.glob(os.path.join(job2.pele_dir, "results/BestStructs/epoch*")))
# test
assert nfiles == job.n_components
assert nfiles_refinement
