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_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 tst_02():
# Test for remove_clashes
import mmtbx.model
from mmtbx.clashes import remove_clashes
import iotbx.pdb
import sys
pdb_inp = iotbx.pdb.input(lines=pdb_poor.splitlines(), source_info='None')
model = mmtbx.model.manager(model_input=pdb_inp, )
model.set_log(log=null_out())
print "\n", "-" * 79
print " Summary of input model statistics "
print "-" * 79
model.get_restraints_manager()
geometry = model.geometry_statistics()
geometry.show(log=sys.stdout)
rc = remove_clashes(model=model)
print "\n", "-" * 79
print "Starting residues: %d " % (
rc.model.get_hierarchy().overall_counts().n_residues)
print "Side-chains removed: %d Residues removed: %d" % (
rc.side_chains_removed, rc.residues_removed)
print "Final residues: %d " % (
rc.new_model.get_hierarchy().overall_counts().n_residues)
rc.new_model.set_log(log=null_out())
rc.new_model.get_restraints_manager()
new_geometry = rc.new_model.geometry_statistics()
new_geometry.show(log=sys.stdout)
assert rc.side_chains_removed == 1
assert rc.residues_removed == 0
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)
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)
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)
