def run_test2():
'''
Test
- occupancy determination for ligands
- adp determination for ligands and neighbors
Tests are combined to decrease computing time (restraints manager is slow).
'''
pdb_fname = libtbx.env.find_in_repositories(
relative_path="mmtbx/regression/pdbs/two_chains_ligand_water.pdb",
test=os.path.isfile)
pdb_inp = iotbx.pdb.input(pdb_fname)
model = mmtbx.model.manager(model_input = pdb_inp)
model.set_log(null_out())
params = iotbx.phil.parse(
input_string=master_params_str, process_includes=True).extract()
vl_manager = validate_ligands.manager(
model = model,
fmodel = None,
params = params.validate_ligands,
log = null_out)
vl_manager.run()
tst_get_occupancies(vl_manager = vl_manager)
tst_get_adps(vl_manager = vl_manager)
def run_test1():
'''
Test if iselection for ligand PG5 (chain A resseq 201) is correct.
'''
pdb_fname = libtbx.env.find_in_repositories(
relative_path="mmtbx/regression/pdbs/one_chain_ligand_water.pdb",
test=os.path.isfile)
pdb_inp = iotbx.pdb.input(pdb_fname)
model = mmtbx.model.manager(model_input = pdb_inp)
model.set_log(null_out())
params = iotbx.phil.parse(
input_string=master_params_str, process_includes=True).extract()
# do not place H atoms for this test
#params.validate_ligands.place_hydrogens = False
vl_manager = validate_ligands.manager(
model = model,
fmodel = None,
params = params.validate_ligands,
log = null_out())
vl_manager.run()
tst_get_ligands(vl_manager = vl_manager)
tst_get_overlaps(vl_manager = vl_manager)
def run(self):
print('Using model file:', self.data_manager.get_default_model_name())
print('Using reflection file:', self.data_manager.get_default_miller_array_name())
cs = self.get_crystal_symmetry()
model = self.data_manager.get_model()
ph = model.get_hierarchy()
xrs = model.get_xray_structure()
if self.data_manager.get_default_miller_array_name():
f_obs, r_free_flags = self.get_fobs_rfree(crystal_symmetry = cs)
print('\nInput data...', file=self.logger)
print(' Reflection data:', f_obs.info().labels, file=self.logger)
if (r_free_flags is not None):
print(' Free-R flags:', r_free_flags.info().labels, file=self.logger)
else:
print(' Free-R flags: not present or not found', file=self.logger)
fmodel = mmtbx.f_model.manager(
f_obs = f_obs,
r_free_flags = r_free_flags,
xray_structure = xrs)
# TODO: delete this keyword for production
if self.params.update_scales:
fmodel.update_all_scales()
print('\nWorking crystal symmetry after inspecting all inputs:', file=self.logger)
cs.show_summary(f=self.logger)
# This is the new class, currently a stub but will be developed
# winter 2018/spring 2019 by DL and NWM
#t0 = time.time()
ligand_manager = validate_ligands.manager(
model = model,
nproc = self.params.nproc,
log = self.logger)
ligand_manager.run()
ligand_manager.print_ligand_counts()
ligand_manager.print_ligand_occupancies()
ligand_manager.print_adps()
#print('time running manager: ', time.time()-t0)
# TODO
# DL: Eventually, delete "old" call below, but leave it for now to keep the
# funcitonality alive, just in case
if self.params.ligand_code and self.data_manager.get_default_miller_array_name() is not None:
if (not(self.params.ligand_code is None or self.params.ligand_code[0] is None)):
make_sub_header("Validating ligands", out=self.logger)
for ligand_code in self.params.ligand_code :
validations = mmtbx.validation.ligands.validate_ligands(
pdb_hierarchy = ph,
fmodel = fmodel,
ligand_code = ligand_code,
reference_structure = self.params.reference_structure,
only_segid = self.params.only_segid)
if (validations is None):
raise Sorry("No ligands named '%s' found." % ligand_code)
mmtbx.validation.ligands.show_validation_results(validations=validations,
out = self.logger,
verbose = self.params.verbose)
def tst_get_occupancies():
pdb_inp = iotbx.pdb.input(lines=pdb_str_2.split("\n"), source_info=None)
model = mmtbx.model.manager(model_input=pdb_inp)
vl_manager = validate_ligands.manager(model=model, log=null_out)
vl_manager.run()
assert (len(vl_manager) == 4)
id_tuple_answer = [('', 'A', ' 2'), ('', 'A', ' 3'), ('', 'A', ' 4'),
('', 'A', ' 5')]
ligand_dict_length_answer = [2, 1, 1, 1]
occupancy_answer = []
for id_tuple, id_tuple_answer, length_answer in zip(
vl_manager.keys(), id_tuple_answer, ligand_dict_length_answer):
ligand_dict = vl_manager[id_tuple]
assert (id_tuple == id_tuple_answer)
assert (len(ligand_dict) == length_answer)
for altloc, lr in ligand_dict.items():
occs = lr.get_occupancies()
id_str = lr.id_str
if (id_str.strip() == 'A 2' and altloc == 'A'):
assert (occs.occ_mean == 0.56)
if (id_str.strip() == 'A 2' and altloc == 'B'):
assert (occs.occ_mean == 0.44)
if (id_str.strip() == 'A 3'):
assert (occs.occ_mean == 0.65)
if (id_str.strip() == 'A 4'):
assert (occs.occ_mean == 0.48)
if (id_str.strip() == 'A 5'):
assert (occs.occ_mean == 0.67)
def tst_get_ligands():
pdb_inp = iotbx.pdb.input(lines=pdb_str_1.split("\n"), source_info=None)
model = mmtbx.model.manager(model_input=pdb_inp)
vl_manager = validate_ligands.manager(model=model, log=null_out)
vl_manager.run()
assert (len(vl_manager) == 1)
for id_tuple, ligand_dict in vl_manager.items():
assert (id_tuple == ('', 'A', ' 201'))
lr = ligand_dict['']
assert (list(
lr.isel) == [84, 85, 86, 87, 88, 89, 90, 91, 92, 93, 94, 95])
def run_test1():
"""Test if iselection for ligand PG5 (chain A resseq 201) is correct."""
pdb_inp = iotbx.pdb.input(lines=pdb_str_1.split("\n"), source_info=None)
model = mmtbx.model.manager(model_input=pdb_inp)
params = iotbx.phil.parse(input_string=master_params_str,
process_includes=True).extract()
# do not place H atoms for this test
#params.validate_ligands.place_hydrogens = False
fn = filenames[0]
vl_manager = validate_ligands.manager(model=model,
model_fn=fn,
params=params.validate_ligands,
log=null_out)
vl_manager.run()
tst_get_ligands(vl_manager=vl_manager)
tst_get_nbos(vl_manager=vl_manager)
def run_test2():
'''
Test
- occupancy determination for ligands
- adp determination for ligands and neighbors
Tests are combined to decrease computing time (restraints manager is slow).
'''
pdb_inp = iotbx.pdb.input(lines=pdb_str_2.split("\n"), source_info=None)
model = mmtbx.model.manager(model_input=pdb_inp)
model.set_log(null_out())
params = iotbx.phil.parse(input_string=master_params_str,
process_includes=True).extract()
vl_manager = validate_ligands.manager(model=model,
fmodel=None,
params=params.validate_ligands,
log=null_out)
vl_manager.run()
tst_get_occupancies(vl_manager=vl_manager)
tst_get_adps(vl_manager=vl_manager)