def compute_input_vector_from_files(self, ligand_pdb_filename,
receptor_pdb_filename, line_header):
"""Computes feature vector for ligand-receptor pair.
Parameters
----------
ligand_pdb_filename: string
path to ligand's pdb file.
receptor_pdb_filename: string
path to receptor pdb file.
line_header: string
line separator in PDB files
"""
# Load receptor and ligand from file.
receptor = PDB()
receptor.load_from_files(receptor_pdb_filename, line_header)
receptor.assign_secondary_structure()
ligand = PDB()
ligand.load_from_files(ligand_pdb_filename, line_header)
self.compute_input_vector(ligand, receptor)
def compute_input_vector_from_files(self, ligand_pdb_filename, receptor_pdb_filename, line_header):
"""Computes feature vector for ligand-receptor pair.
Parameters
----------
ligand_pdb_filename: string
path to ligand's pdb file.
receptor_pdb_filename: string
path to receptor pdb file.
line_header: string
line separator in PDB files
"""
# Load receptor and ligand from file.
receptor = PDB()
receptor.load_from_files(receptor_pdb_filename, line_header)
receptor.assign_secondary_structure()
ligand = PDB()
ligand.load_from_files(ligand_pdb_filename, line_header)
self.compute_input_vector(ligand, receptor)
def _featurize_complex(self, mol_pdb, protein_pdb):
"""
Compute Binana fingerprint for complex.
"""
print("In _featurize_complex")
mol_pdb_file = tempfile.NamedTemporaryFile(suffix="pdb")
with open(mol_pdb_file.name, "w") as mol_f:
mol_f.writelines(mol_pdb)
protein_pdb_file = tempfile.NamedTemporaryFile(suffix="pdb")
with open(protein_pdb_file.name, "w") as protein_f:
protein_f.writelines(protein_pdb)
print("Written temp pdb files")
mol_hyd_file = tempfile.NamedTemporaryFile(suffix="pdb")
mol_pdbqt_file = tempfile.NamedTemporaryFile(suffix="pdbqt")
hydrogenate_and_compute_partial_charges(mol_pdb_file.name, "pdb",
mol_hyd_file.name,
mol_pdbqt_file.name)
print("Hydrogenated mol file")
protein_hyd_file = tempfile.NamedTemporaryFile(suffix="pdb")
protein_pdbqt_file = tempfile.NamedTemporaryFile(suffix="pdbqt")
hydrogenate_and_compute_partial_charges(protein_pdb_file.name, "pdb",
protein_hyd_file.name,
protein_pdbqt_file.name)
print("Hydrogenated protein file")
mol_pdb_obj = PDB()
mol_pdb_obj.load_from_files(mol_pdb_file.name, mol_pdbqt_file.name)
print("Loaded mol pdb object")
protein_pdb_obj = PDB()
protein_pdb_obj.load_from_files(protein_pdb_file.name,
protein_pdbqt_file.name)
print("Loaded protein pdb object")
features = self.binana.compute_input_vector(mol_pdb_obj,
protein_pdb_obj)
print("Computed binana features.")
return features
def _featurize_complex(self, mol_pdb, protein_pdb):
"""
Compute Binana fingerprint for complex.
"""
print("In _featurize_complex")
mol_pdb_file = tempfile.NamedTemporaryFile(suffix="pdb")
with open(mol_pdb_file.name, "w") as mol_f:
mol_f.writelines(mol_pdb)
protein_pdb_file = tempfile.NamedTemporaryFile(suffix="pdb")
with open(protein_pdb_file.name, "w") as protein_f:
protein_f.writelines(protein_pdb)
print("Written temp pdb files")
mol_hyd_file = tempfile.NamedTemporaryFile(suffix="pdb")
mol_pdbqt_file = tempfile.NamedTemporaryFile(suffix="pdbqt")
hydrogenate_and_compute_partial_charges(mol_pdb_file.name, "pdb", mol_hyd_file.name, mol_pdbqt_file.name)
print("Hydrogenated mol file")
protein_hyd_file = tempfile.NamedTemporaryFile(suffix="pdb")
protein_pdbqt_file = tempfile.NamedTemporaryFile(suffix="pdbqt")
hydrogenate_and_compute_partial_charges(
protein_pdb_file.name, "pdb", protein_hyd_file.name, protein_pdbqt_file.name
)
print("Hydrogenated protein file")
mol_pdb_obj = PDB()
mol_pdb_obj.load_from_files(mol_pdb_file.name, mol_pdbqt_file.name)
print("Loaded mol pdb object")
protein_pdb_obj = PDB()
protein_pdb_obj.load_from_files(protein_pdb_file.name, protein_pdbqt_file.name)
print("Loaded protein pdb object")
features = self.binana.compute_input_vector(mol_pdb_obj, protein_pdb_obj)
print("Computed binana features.")
return features
def setUp(self):
"""
Instantiate local copy of Binana object.
"""
self.binana = Binana()
### 3zp9 comes from PDBBind-CN
_3zp9_protein = PDB()
_3zp9_protein_pdb = os.path.join(data_dir(), "3zp9_protein_hyd.pdb")
_3zp9_protein_pdbqt = os.path.join(data_dir(), "3zp9_protein_hyd.pdbqt")
_3zp9_protein.load_from_files(_3zp9_protein_pdb, _3zp9_protein_pdbqt)
# The ligand is also specified by pdbbind
_3zp9_ligand = PDB()
_3zp9_ligand_pdb = os.path.join(data_dir(), "3zp9_ligand_hyd.pdb")
_3zp9_ligand_pdbqt = os.path.join(data_dir(), "3zp9_ligand_hyd.pdbqt")
_3zp9_ligand.load_from_files(_3zp9_ligand_pdb, _3zp9_ligand_pdbqt)
### 3bwf comes from PDBBind-CN
_3bwf_protein = PDB()
_3bwf_protein_pdb = os.path.join(data_dir(), "3bwf_protein_hyd.pdb")
_3bwf_protein_pdbqt = os.path.join(data_dir(), "3bwf_protein_hyd.pdbqt")
_3bwf_protein.load_from_files(_3bwf_protein_pdb, _3bwf_protein_pdbqt)
# The ligand is also specified by pdbbind
_3bwf_ligand = PDB()
_3bwf_ligand_pdb = os.path.join(data_dir(), "3bwf_ligand_hyd.pdb")
_3bwf_ligand_pdbqt = os.path.join(data_dir(), "3bwf_ligand_hyd.pdbqt")
_3bwf_ligand.load_from_files(_3bwf_ligand_pdb, _3bwf_ligand_pdbqt)
self.test_cases = [("3bwf", _3bwf_protein, _3bwf_ligand),
("3zp9", _3zp9_protein, _3zp9_ligand)]
def setUp(self):
"""
Instantiate local copy of Binana object.
"""
self.binana = Binana()
### 3zp9 comes from PDBBind-CN
_3zp9_protein = PDB()
_3zp9_protein_pdb = os.path.join(data_dir(), "3zp9_protein_hyd.pdb")
_3zp9_protein_pdbqt = os.path.join(data_dir(),
"3zp9_protein_hyd.pdbqt")
_3zp9_protein.load_from_files(_3zp9_protein_pdb, _3zp9_protein_pdbqt)
# The ligand is also specified by pdbbind
_3zp9_ligand = PDB()
_3zp9_ligand_pdb = os.path.join(data_dir(), "3zp9_ligand_hyd.pdb")
_3zp9_ligand_pdbqt = os.path.join(data_dir(), "3zp9_ligand_hyd.pdbqt")
_3zp9_ligand.load_from_files(_3zp9_ligand_pdb, _3zp9_ligand_pdbqt)
### 3bwf comes from PDBBind-CN
_3bwf_protein = PDB()
_3bwf_protein_pdb = os.path.join(data_dir(), "3bwf_protein_hyd.pdb")
_3bwf_protein_pdbqt = os.path.join(data_dir(),
"3bwf_protein_hyd.pdbqt")
_3bwf_protein.load_from_files(_3bwf_protein_pdb, _3bwf_protein_pdbqt)
# The ligand is also specified by pdbbind
_3bwf_ligand = PDB()
_3bwf_ligand_pdb = os.path.join(data_dir(), "3bwf_ligand_hyd.pdb")
_3bwf_ligand_pdbqt = os.path.join(data_dir(), "3bwf_ligand_hyd.pdbqt")
_3bwf_ligand.load_from_files(_3bwf_ligand_pdb, _3bwf_ligand_pdbqt)
self.test_cases = [("3bwf", _3bwf_protein, _3bwf_ligand),
("3zp9", _3zp9_protein, _3zp9_ligand)]