def test_with_no_ligands(self):
self.assertEqual(
mmcif_header.get_ligand_resnum(structure="test",
ligand_resnames=[]), None)
self.assertEqual(
mmcif_header.get_ligand_resnum(structure="test",
ligand_resnames=None), None)
def test_with_chain_model_selection(self):
input_ligand_resnames = ["LIGAND"]
residue_1 = mock.Mock()
residue_2 = mock.Mock()
residue_1.resname = "LIGAND"
residue_2.resname = "NOT_LIGAND"
residue_1.id = ("", 1, "")
residue_2.id = ("", 2, "")
residues = [residue_1, residue_2]
structure = mock.Mock()
structure.return_value = structure
structure.return_value.get_residues.return_value = residues
input_structure = {0: {'A': structure}}
output = mmcif_header.get_ligand_resnum(
structure=input_structure,
ligand_resnames=input_ligand_resnames,
protein_chain='A',
protein_model=0)
self.assertEqual(output, [["LIGAND", 1]])
def update_ligands(Protein, chain_model_selection = False):
"""
If you have a HPC_Drug.structures.protein.Protein instance with some self._ligands
but the files they referr to are obsolete, and maybe the resnums are obsolete too,
if the Protein.pdb_file is a file containing (the protein and) the new ligand coordinates and resnums
this is the function you want to use
returns a HPC_Drug.structures.protein.Protein instance with updated self._ligands
Protein :: HPC_Drug.structures.protein.Protein instance
chain_model_selection :: bool, default False, if True checks only Protein.chain and Protein.model from the PDB file
"""
ligand_resnames = []
old_Protein = copy.deepcopy(Protein)
for lig in Protein.get_ligand_list():
ligand_resnames.append(lig.resname)
Protein.update_structure(struct_type = "biopython")
if chain_model_selection:
protein_chain = Protein.chain
protein_model = Protein.model
else:
protein_chain = protein_model = None
Protein = get_ligands.get_ligands(Protein = Protein,
ligand_resnames_resnums = mmcif_header.get_ligand_resnum(structure = Protein.structure,
ligand_resnames = ligand_resnames,
protein_chain = protein_chain,
protein_model = protein_model))
#in order not to loose the info about itp, gro, etc... files
for i in range(len(old_Protein.get_ligand_list())):
old_Protein.get_ligand_list()[i].resnum = Protein.get_ligand_list()[i].resnum
old_Protein.get_ligand_list()[i].pdb_file = Protein.get_ligand_list()[i].pdb_file
if old_Protein.get_ligand_list()[i].resname.upper() != Protein.get_ligand_list()[i].resname.upper():
raise ValueError("Something went wrong during the ligand update")
return old_Protein
def test_with_wrong_structure_type(self):
with self.assertRaises(TypeError):
mmcif_header.get_ligand_resnum(structure="test_wrong",
ligand_resnames=["aa", "bb"])