def test_Exporter_Gromacs_export_disresDat(self):
exporter = Exporter.export_Gromos_Distance_Restraints(self.disres1)
exporter.get_args(lambda x: (self.out_gromos_disres_path1))
out = exporter.export_restraints()
with open(self.in_solution_disres_path1, "r") as solution:
expected_filelines = solution.readlines()
expected_str = "".join(expected_filelines)
exporter = Exporter.export_Gromos_Distance_Restraints(self.disres2)
exporter.get_args(lambda x: (self.out_gromos_disres_path2))
out = exporter.export_restraints()
with open(self.in_solution_disres_path2, "r") as solution:
expected_filelines = solution.readlines()
expected_str = "".join(expected_filelines)
def test_Exporter_Gromos_export_disresDat(self):
exporter = Exporter.GromosPairRestraintExporter(distance_restraints)
exporter.get_args(lambda x: (out_gromos_disres_path))
out = exporter.export_restraints()
expected_filelines = open(in_solution_disres_path, "r").readlines()
expected_str = "".join(expected_filelines)
self.assertEqual(str(out),
expected_str,
msg="file text is not expected.")
def test_Exporter_Gromacs_getargs(self):
exporter = Exporter.export_Gromacs_Distance_Restraints(self.disres1)
exporter.get_args(lambda x: self.out_gromos_disres_path1)
def test_Exporter_Gromacs_construct(self):
gromos_Exporter = Exporter.export_Gromacs_Distance_Restraints(self.disres1)
cmd.load(out_pdb)
## GET ATOMS
atom_list = up.pymol_selection_to_atom_list("all")
## Filtering for rings
try:
RingFilter = Filter.RingFilter(atom_list)
#pdb_blocks = u.convert_atoms_to_pdb_molecules(atom_list)
pdb_blocks = [cmd.get_pdbstr(pdb_id) for pdb_id in cmd.get_object_list()]
RingFilter.get_args(lambda x: (pdb_blocks))
filtered_atoms = RingFilter.filter()
except Exception as err:
print("failed ", err.args)
## Optimizers
try:
opt = Optimizer.GreedyGraphOptimizer(filtered_atoms)
opt.get_args(lambda x: (nrestraints, distance_treshold, 'shortest', None))
res = opt.make_restraints()
## Export
exporter = Exporter.export_Gromos_Distance_Restraints(restraints=res)
exporter.get_args(lambda x: out_dir_path + "/" + set_name + ".disres")
exporter.export_restraints()
except:
print("manual mode:")
import restraintmaker
restraintmaker.run_plugin_gui()
break
exit()
def test_Exporter_Gromos_getargs(self):
exporter = Exporter.GromosPairRestraintExporter(distance_restraints)
exporter.get_args(lambda x: (out_gromos_disres_path))
def test_Exporter_Gromos_construct(self):
gromos_Exporter = Exporter.GromosPairRestraintExporter(
distance_restraints)