def test__repair(self):
with mock.patch("HPC_Drug.PDB.repair_pdb.repair.repair", return_value = "repaired", autospec = True):
output = struct_rep.InfoRepair(Protein = "test", repairing_method = "pdbfixer")
output._repair()
self.assertEqual(output.Protein, "repaired")
def test_get_info_and_repair_typeerror(self):
Protein = mock.Mock()
Protein.file_type = "WRONG_TYPE"
output = struct_rep.InfoRepair(Protein = Protein, repairing_method = "pdbfixer")
with self.assertRaises(TypeError):
output.get_info_and_repair()
def test__parse_structure(self):
with mock.patch("HPC_Drug.PDB.structural_information.scan_structure.get_metalbinding_disulf_ligands", return_value = ("protein", "list")):
output = struct_rep.InfoRepair(Protein = "test", repairing_method = "pdbfixer")
output._parse_structure()
self.assertEqual(output.Protein, "protein")
self.assertEqual(output.organic_ligand_list, "list")
def test_cif_header(self):
with mock.patch.object(struct_rep.InfoRepair, "_repair", autospec = True) as mocked_repair:
with mock.patch.object(struct_rep.InfoRepair, "_parse_header", autospec = True) as mocked_parse:
output = struct_rep.InfoRepair(Protein = "test", repairing_method = "pdbfixer")
output._cif()
mocked_repair.assert_called_once()
mocked_parse.assert_called_once()
def test_get_info_and_repair_pdb(self):
with mock.patch.object(struct_rep.InfoRepair, "_pdb", return_value = ("output", "list"), autospec = True) as mocked_pdb:
Protein = mock.Mock()
Protein.file_type = "pdb"
output = struct_rep.InfoRepair(Protein = Protein, repairing_method = "pdbfixer")
out_out = output.get_info_and_repair()
mocked_pdb.assert_called_once()
self.assertEqual(out_out, (output.Protein, output.organic_ligand_list))
def test_cif_structure(self):
with mock.patch.object(struct_rep.InfoRepair, "_repair", autospec = True) as mocked_repair:
with mock.patch.object(struct_rep.InfoRepair, "_parse_header", side_effect = Exception, autospec = True) as mocked_parse:
with mock.patch.object(struct_rep.InfoRepair, "_pdb", autospec = True) as mocked_pdb:
output = struct_rep.InfoRepair(Protein = "test", repairing_method = "pdbfixer")
output._cif()
mocked_repair.assert_not_called()
mocked_parse.assert_called_once()
mocked_pdb.assert_called_once()
def test__init__(self):
output = struct_rep.InfoRepair(Protein = "protein", repairing_method = "pdbfixer")
self.assertEqual(output.Protein, "protein")
self.assertEqual(output.repairing_method, "pdbfixer")
def execute(self):
"""
A pipeline that returns a clean and repaired "protein and ions" PDB and
a PDB file for any not trash organic lingand
starting from both a PDB, an mmCIF file or a protein id
returns a Protein instance
"""
#If requested in input will download pdb file
#If the given local file doesn't exist raises FileNotFounfError
#otherwise updates self.protein_filename with the given path
#all the paths are converted to absolute paths
self.get_protein_file()
# creating protein instance
Protein = protein.Protein(protein_id = self.protein_id,
pdb_file = self.protein_filename,
model = self.model,
chain = self.chain,
file_type = self.protein_filetype,
tpg_file = self.protein_tpg_file,
prm_file = self.protein_prm_file)
#Get Protein.substitutions_dict Protein.sulf_bonds
#repairs the Protein.pdb_file
#returns a list containing the resnames and resnumbers of organic ligands
# [[resname, resnum], [...], ...]
#if there are none will be None item
Info_rep = structural_information_and_repair.InfoRepair(Protein = Protein, repairing_method = self.repairing_method)
Protein, ligand_resnames_resnums = Info_rep.get_info_and_repair()
#remove still present disordered atoms (if any)
Protein = remove_disordered_atoms.remove_disordered_atoms(Protein = Protein)
#selects only a selected model and chain (Protein.model Protein.chain)
Protein = select_model_chain.select_model_chain(Protein = Protein)
#if the protein was a mmCIF I convert it to PDB
Protein = mmcif2pdb.mmcif2pdb(Protein = Protein)
#create the Ligand instances and add them to Protein._ligands
Protein = get_ligands.get_ligands(Protein = Protein, ligand_resnames_resnums = ligand_resnames_resnums)
Protein.update_structure(struct_type = "prody")
prody_select = prody.ProdySelect(structure = Protein.structure)
#gets the protein's structure from the pdb
#The only HETATM remaining are the metal ions
Protein.structure = prody_select.protein_and_ions()
#Write Protein only pdb
Protein.write(file_name = f"{Protein.protein_id}_protein.pdb", struct_type = 'prody')
#removes the remaining trash ions
Protein = remove_trash_metal_ions.remove_trash_metal_ions(Protein = Protein)
#quick patch, will do it better
#The structure is put in the reference system of the
#inertia tensor
orient_obj = orient.Orient(Protein = Protein)
_, _, Rot_matrix = orient_obj.calculate_moment_of_intertia_tensor()
Protein.structure = orient_obj.base_change_structure()
Protein.write()
Ligand = Protein.get_ligand_list()
for i in range(len(Ligand)):
Ligand[i].update_structure(struct_type = "biopython")
Ligand[i].structure = orient_obj.base_change_structure(structure = Ligand[i].structure, rot_matrix = Rot_matrix)
Ligand[i].write()
return Protein