def test_nitrogen_charges(self):
"""
TestPDB: Verify that nitrogen groups are charged correctly.
"""
# Test ammonium sulfate: (NH4)+(NH4)+(SO4)(2-)
# The labeling should pick up 2 charged nitrogen groups for two
# ammoniums.
ammonium_sulfate_pdb = PDB()
ammonium_sulfate_pdb_path = os.path.join(data_dir(),
"ammonium_sulfate_hyd.pdb")
ammonium_sulfate_pdbqt_path = os.path.join(
data_dir(), "ammonium_sulfate_hyd.pdbqt")
ammonium_sulfate_pdb.load_from_files(ammonium_sulfate_pdb_path,
ammonium_sulfate_pdbqt_path)
nitrogen_charges = ammonium_sulfate_pdb.identify_nitrogen_charges()
assert len(nitrogen_charges) == 2
assert nitrogen_charges[0].positive # Should be positive
assert nitrogen_charges[1].positive # Should be positive
# Test pyrrolidine (CH2)4NH. The nitrogen here should be sp3
# hybridized, so is likely to pick up an extra proton to its nitrogen
# at physiological pH.
pyrrolidine_pdb = PDB()
pyrrolidine_pdb_path = os.path.join(data_dir(), "pyrrolidine_hyd.pdb")
pyrrolidine_pdbqt_path = os.path.join(data_dir(),
"pyrrolidine_hyd.pdbqt")
pyrrolidine_pdb.load_from_files(pyrrolidine_pdb_path,
pyrrolidine_pdbqt_path)
nitrogen_charges = pyrrolidine_pdb.identify_nitrogen_charges()
assert len(nitrogen_charges) == 1
assert nitrogen_charges[0].positive # Should be positive
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 featurize_dude(dude_dir, target, pickle_dir, num_jobs):
"""Featurize DUD-E docked poses and write features to pickle_out.
Parameters
----------
dude_dir: string
Path to DUD-E directory
target: string
Name of DUD-E target.
pickle_dir: string
Path to directory to output pickles
"""
target_dir = os.path.join(dude_dir, target)
actives_dir = os.path.join(target_dir, "actives")
decoys_dir = os.path.join(target_dir, "decoys")
actives = [a for a in os.listdir(actives_dir)]
decoys = [a for a in os.listdir(decoys_dir)]
receptor = os.path.join(target_dir, "receptor.pdb")
pickle_out = os.path.join(target_dir, "out.pkl.gz")
# Just for debugging purposes
actives = actives[:1]
num_per_job = int(math.ceil(len(actives) / float(num_jobs)))
print "Number per job: %d" % num_per_job
protein_pdb_path = "/home/rbharath/DUD-E/aa2ar/receptor_hyd.pdb"
protein_pdbqt_path = "/home/rbharath/DUD-E/aa2ar/receptor_hyd.pdbqt"
print "About to load protein from input files"
protein_pdb_obj = PDB()
protein_pdb_obj.load_from_files(protein_pdb_path, protein_pdbqt_path)
binana = Binana()
feature_len = binana.num_features()
feature_vectors = {}
for compound in actives:
compound_name = compound.split(".")[0]
compound_pdbqt = compound_name + "_hyd_out.pdbqt"
compound_pdbqt = os.path.join(actives_dir, compound_pdbqt)
# Convert the pdbqt to pdb
pdbqt_to_pdb(compound_pdbqt, actives_dir)
compound_pdb = compound_name + "_hyd_out.pdb"
compound_pdb = os.path.join(actives_dir, compound_pdb)
structures = MultiStructure()
structures.load_from_files(compound_pdb, compound_pdbqt)
vectors = []
for key in sorted(structures.molecules.keys()):
structure = structures.molecules[key]
print "type(structure)"
print type(structure)
vectors.append(
binana.compute_input_vector(structure, protein_pdb_obj))
feature_vectors[compound_name] = vectors
with gzip.open(pickle_out, "wb") as f:
pickle.dump(feature_vectors, f)
decoys = decoys[:1]
def test_load_bonds_from_pdb(self):
"""
TestPDB: Verifies that bonds can be loaded from PDB.
"""
pdb = PDB()
# Test that we can load CO2
carbon_atom = Atom(element="C")
oxygen_atom_1 = Atom(element="O")
oxygen_atom_2 = Atom(element="O")
pdb.add_new_atom(carbon_atom)
pdb.add_new_atom(oxygen_atom_1)
pdb.add_new_atom(oxygen_atom_2)
lines = [
"CONECT 1 2 3 "
"CONECT 2 "
"CONECT 3 "
]
with tempfile.NamedTemporaryFile() as temp:
temp.write("\n".join(lines))
temp.flush()
pdb.load_bonds_from_pdb(temp.name)
assert len(carbon_atom.indices_of_atoms_connecting) == 2
assert len(oxygen_atom_1.indices_of_atoms_connecting) == 0
assert len(oxygen_atom_2.indices_of_atoms_connecting) == 0
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 test_metallic_charges(self):
"""
TestPDB: Verify that non-protein charges are assigned properly.
"""
# Test metallic ion charge.
magnesium_pdb = PDB()
magnesium_atom = Atom(element="MG",
coordinates=Point(coords=np.array([0, 0, 0])))
magnesium_pdb.add_new_non_protein_atom(magnesium_atom)
metallic_charges = magnesium_pdb.identify_metallic_charges()
assert len(metallic_charges) == 1
def test_phosphorus_charges(self):
"""
TestPDB: Verify that Phosphorus groups are charged correctly.
"""
# CID82671 contains a phosphate between two aromatic groups.
phosphate_pdb = PDB()
phosphate_pdb_path = os.path.join(data_dir(), "82671_hyd.pdb")
phosphate_pdbqt_path = os.path.join(data_dir(), "82671_hyd.pdb")
phosphate_pdb.load_from_files(phosphate_pdb_path, phosphate_pdbqt_path)
phosphorus_charges = phosphate_pdb.identify_phosphorus_charges()
assert len(phosphorus_charges) == 1
assert not phosphorus_charges[
0].positive # Should be negatively charged.
def test_assign_ligand_aromatics(self):
"""
TestPDB: Test that non-protein aromatic rings are assigned correctly.
"""
### 3ao4 comes from PDBBind-CN and contains some cruft in the PDB file:
### atoms without residues labelled. This triggered some problems with
### non-protein aromatics complaining.
# TODO(rbharath): Add a stub here.
_3ao4_protein = PDB()
_3ao4_protein_pdb = os.path.join(data_dir(), "3ao4_protein_hyd.pdb")
_3ao4_protein_pdbqt = os.path.join(data_dir(),
"3ao4_protein_hyd.pdbqt")
_3ao4_protein.load_from_files(_3ao4_protein_pdb, _3ao4_protein_pdbqt)
def test_sulfur_charges(self):
"""
TestPDB: Verify that sulfur groups are charged correctly.
"""
triflic_acid_pdb = PDB()
triflic_acid_pdb_path = os.path.join(data_dir(),
"triflic_acid_hyd.pdb")
triflic_acid_pdbqt_path = os.path.join(data_dir(),
"triflic_acid_hyd.pdbqt")
triflic_acid_pdb.load_from_files(triflic_acid_pdb_path,
triflic_acid_pdbqt_path)
sulfur_charges = (triflic_acid_pdb.identify_sulfur_charges())
assert len(sulfur_charges) == 1
assert not sulfur_charges[0].positive # Should be negatively charged.
def setUp(self):
"""
Instantiate a dummy PDB file.
"""
self.temp_dir = tempfile.mkdtemp()
self.pdb = PDB()
_, self.pdb_filename = tempfile.mkstemp(suffix=".pdb",
dir=self.temp_dir)
self.prgr_pdb = PDB()
prgr_pdb_path = os.path.join(data_dir(), "prgr_hyd.pdb")
prgr_pdbqt_path = os.path.join(data_dir(), "prgr_hyd.pdbqt")
self.prgr_pdb.load_from_files(prgr_pdb_path, prgr_pdbqt_path)
self._1r5y_protein = PDB()
_1r5y_protein_pdb = os.path.join(data_dir(), "1r5y_protein_hyd.pdb")
_1r5y_protein_pdbqt = os.path.join(data_dir(),
"1r5y_protein_hyd.pdbqt")
self._1r5y_protein.load_from_files(_1r5y_protein_pdb,
_1r5y_protein_pdbqt)
self.proteins = [("prgr", self.prgr_pdb), ("1r5y", self._1r5y_protein)]
def _featurize_complex(self, mol_pdb, protein_pdb):
"""
Compute Binana fingerprint for complex.
"""
### OPEN TEMPDIR
tempdir = tempfile.mkdtemp()
mol_pdb_file = os.path.join(tempdir, "mol.pdb")
with open(mol_pdb_file, "w") as mol_f:
mol_f.writelines(mol_pdb)
protein_pdb_file = os.path.join(tempdir, "protein.pdb")
with open(protein_pdb_file, "w") as protein_f:
protein_f.writelines(protein_pdb)
mol_hyd_file = os.path.join(tempdir, "mol_hyd.pdb")
mol_pdbqt_file = os.path.join(tempdir, "mol_hyd.pdbqt")
hydrogenate_and_compute_partial_charges(
mol_pdb_file, "pdb", tempdir, mol_hyd_file, mol_pdbqt_file)
protein_hyd_file = os.path.join(tempdir, "protein_hyd.pdb")
protein_pdbqt_file = os.path.join(tempdir, "protein_hyd.pdbqt")
hydrogenate_and_compute_partial_charges(
protein_pdb_file, "pdb", tempdir, protein_hyd_file, protein_pdbqt_file)
mol_pdb_obj = PDB()
mol_pdb_obj.load_from_files(mol_pdb_file, mol_pdbqt_file)
protein_pdb_obj = PDB()
protein_pdb_obj.load_from_files(protein_pdb_file, protein_pdbqt_file)
features = self.binana.compute_input_vector(mol_pdb_obj, protein_pdb_obj)
### CLOSE TEMPDIR
shutil.rmtree(tempdir)
return features
def test_ligand_assign_aromatics(self):
"""
TestPDB: Verify that aromatic rings in ligands are identified.
"""
benzene_pdb = PDB()
benzene_pdb_path = os.path.join(data_dir(), "benzene_hyd.pdb")
benzene_pdbqt_path = os.path.join(data_dir(), "benzene_hyd.pdbqt")
benzene_pdb.load_from_files(benzene_pdb_path, benzene_pdbqt_path)
# A benzene should have exactly one aromatic ring.
print benzene_pdb.aromatic_rings
assert len(benzene_pdb.aromatic_rings) == 1
# The first 6 atoms in the benzene pdb form the aromatic ring.
assert (set(benzene_pdb.aromatic_rings[0].indices) == set(
[1, 2, 3, 4, 5, 6]))
def test_carbon_charges(self):
"""
TestPDB: Verify that carbon groups are charged correctly.
"""
# Guanidine is positively charged at physiological pH
guanidine_pdb = PDB()
guanidine_pdb_path = os.path.join(data_dir(), "guanidine_hyd.pdb")
guanidine_pdbqt_path = os.path.join(data_dir(), "guanidine_hyd.pdbqt")
guanidine_pdb.load_from_files(guanidine_pdb_path, guanidine_pdbqt_path)
carbon_charges = guanidine_pdb.identify_carbon_charges()
assert len(carbon_charges) == 1
assert carbon_charges[0].positive # Should be positive
# sulfaguanidine contains a guanidine group that is likely to be
# positively protonated at physiological pH
sulfaguanidine_pdb = PDB()
sulfaguanidine_pdb_path = os.path.join(data_dir(),
"sulfaguanidine_hyd.pdb")
sulfaguanidine_pdbqt_path = os.path.join(data_dir(),
"sulfaguanidine_hyd.pdbqt")
sulfaguanidine_pdb.load_from_files(sulfaguanidine_pdb_path,
sulfaguanidine_pdbqt_path)
carbon_charges = sulfaguanidine_pdb.identify_carbon_charges()
assert len(carbon_charges) == 1
assert carbon_charges[0].positive # Should be positive
# Formic acid is a carboxylic acid, which should be negatively charged.
formic_acid_pdb = PDB()
formic_acid_pdb_path = os.path.join(data_dir(), "formic_acid_hyd.pdb")
formic_acid_pdbqt_path = os.path.join(data_dir(),
"formic_acid_hyd.pdbqt")
formic_acid_pdb.load_from_files(formic_acid_pdb_path,
formic_acid_pdbqt_path)
carbon_charges = formic_acid_pdb.identify_carbon_charges()
assert len(carbon_charges) == 1
assert not carbon_charges[0].positive # Should be negatively charged.
def test_assign_non_protein_charges(self):
"""
TestPDB: Verify that charges are properly added to ligands.
"""
# Test ammonium sulfate: (NH4)+(NH4)+(SO4)(2-)
# There should be 3 charged groups, two positive, one negative
ammonium_sulfate_pdb = PDB()
ammonium_sulfate_pdb_path = os.path.join(data_dir(),
"ammonium_sulfate_hyd.pdb")
ammonium_sulfate_pdbqt_path = os.path.join(
data_dir(), "ammonium_sulfate_hyd.pdbqt")
# Notice that load automatically identifies non-protein charges.
ammonium_sulfate_pdb.load_from_files(ammonium_sulfate_pdb_path,
ammonium_sulfate_pdbqt_path)
assert len(ammonium_sulfate_pdb.charges) == 3
num_pos, num_neg = 0, 0
for charge in ammonium_sulfate_pdb.charges:
if charge.positive:
num_pos += 1
else:
num_neg += 1
assert num_pos == 2
assert num_neg == 1
def featurize_pdbbind(pdbbind_dir, pickle_out):
"""Featurize all entries in pdbbind_dir and write features to pickle_out
pdbbind_dir should be a dir, with K subdirs, one for each protein-ligand
complex to be featurized. The ligand and receptor should each have a pdb
and pdbqt file. The ligand files should end in '_ligand_hyd.${FILETYPE}'
while the receptor files should end in '_protein_hyd.${FILETYPE}'
pdbbind_dir: string
Path to pdbbind directory.
pickle_out: string
Path to write pickle output.
"""
assert os.path.isdir(pdbbind_dir)
# Instantiate copy of binana vector
binana = Binana()
feature_vectors = {}
# Extract the subdirectories in pdbbind_dir
subdirs = [
d for d in os.listdir(pdbbind_dir)
if os.path.isdir(os.path.join(pdbbind_dir, d))
]
# TODO(rbharath): ONLY FOR DEBUGGING!
subdirs = subdirs[900:]
num_atoms = len(Binana.atom_types)
# See features/tests/nnscore_test.py:TestBinana.testComputeInputVector
# for derivation.
feature_len = (3 * num_atoms * (num_atoms + 1) / 2 + num_atoms + 12 + 6 +
3 + 6 + 3 + 6 + 3 + 1)
for count, d in enumerate(subdirs):
print "\nprocessing %d-th pdb %s" % (count, d)
subdir = os.path.join(pdbbind_dir, d)
print "About to extract ligand and protein input files"
ligand_pdb, ligand_pdbqt = None, None
protein_pdb, protein_pdbqt = None, None
for f in os.listdir(subdir):
if re.search("_ligand_hyd.pdb$", f):
ligand_pdb = f
elif re.search("_ligand_hyd.pdbqt$", f):
ligand_pdbqt = f
elif re.search("_protein_hyd.pdb$", f):
protein_pdb = f
elif re.search("_protein_hyd.pdbqt$", f):
protein_pdbqt = f
print "Extracted Input Files:"
print(ligand_pdb, ligand_pdbqt, protein_pdb, protein_pdbqt)
if (not ligand_pdb or not ligand_pdbqt or not protein_pdb
or not protein_pdbqt):
raise ValueError("Required files not present for %s" % d)
ligand_pdb_path = os.path.join(subdir, ligand_pdb)
ligand_pdbqt_path = os.path.join(subdir, ligand_pdbqt)
protein_pdb_path = os.path.join(subdir, protein_pdb)
protein_pdbqt_path = os.path.join(subdir, protein_pdbqt)
print "About to load ligand from input files"
ligand_pdb_obj = PDB()
ligand_pdb_obj.load_from_files(ligand_pdb_path, ligand_pdbqt_path)
print "About to load protein from input files"
protein_pdb_obj = PDB()
protein_pdb_obj.load_from_files(protein_pdb_path, protein_pdbqt_path)
print "About to generate feature vector."
vector = binana.compute_input_vector(ligand_pdb_obj, protein_pdb_obj)
feature_vectors[d] = vector
if len(vector) != feature_len:
raise ValueError("Feature length incorrect on %s" % d)
print "Feature vector generated correctly."
with open(pickle_out, "wb") as f:
pickle.dump(feature_vectors, f)
def setUp(self):
"""
Instantiate local copy of Binana object.
"""
self.binana = Binana()
# TODO(rbharath): This load sequence is getting unwieldy. Refactor.
### PRGR is from the DUD-E collection
prgr_receptor = PDB()
prgr_pdb = os.path.join(data_dir(), "prgr_hyd.pdb")
prgr_pdbqt = os.path.join(data_dir(), "prgr_hyd.pdbqt")
prgr_receptor.load_from_files(prgr_pdb, prgr_pdbqt)
# This compound is CHEMBL1164248
prgr_active = PDB()
prgr_active_pdb = os.path.join(data_dir(), "prgr_active0_hyd.pdb")
prgr_active_pdbqt = os.path.join(data_dir(), "prgr_active0_hyd.pdbqt")
prgr_active.load_from_files(prgr_active_pdb, prgr_active_pdbqt)
### c-Abl is taken from the Autodock Vina examples
cabl_receptor = PDB()
cabl_receptor_pdb = os.path.join(data_dir(), "c-Abl_hyd.pdb")
cabl_receptor_pdbqt = os.path.join(data_dir(), "c-Abl_hyd.pdbqt")
cabl_receptor.load_from_files(cabl_receptor_pdb, cabl_receptor_pdbqt)
# This compound is imatinib
cabl_active = PDB()
cabl_active_pdb = os.path.join(data_dir(), "imatinib_hyd.pdb")
cabl_active_pdbqt = os.path.join(data_dir(), "imatinib_hyd.pdbqt")
cabl_active.load_from_files(cabl_active_pdb, cabl_active_pdbqt)
### 1zea comes from PDBBind-CN
# Python complains about variables starting with numbers, so put an
# underscore in front of everything.
_1zea_protein = PDB()
_1zea_protein_pdb = os.path.join(data_dir(), "1zea_protein_hyd.pdb")
_1zea_protein_pdbqt = os.path.join(data_dir(),
"1zea_protein_hyd.pdbqt")
_1zea_protein.load_from_files(_1zea_protein_pdb, _1zea_protein_pdbqt)
# The ligand is also specified by pdbbind
_1zea_ligand = PDB()
_1zea_ligand_pdb = os.path.join(data_dir(), "1zea_ligand_hyd.pdb")
_1zea_ligand_pdbqt = os.path.join(data_dir(), "1zea_ligand_hyd.pdbqt")
_1zea_ligand.load_from_files(_1zea_ligand_pdb, _1zea_ligand_pdbqt)
### 1r5y comes from PDBBind-CN
_1r5y_protein = PDB()
_1r5y_protein_pdb = os.path.join(data_dir(), "1r5y_protein_hyd.pdb")
_1r5y_protein_pdbqt = os.path.join(data_dir(),
"1r5y_protein_hyd.pdbqt")
_1r5y_protein.load_from_files(_1r5y_protein_pdb, _1r5y_protein_pdbqt)
# The ligand is also specified by pdbbind
_1r5y_ligand = PDB()
_1r5y_ligand_pdb = os.path.join(data_dir(), "1r5y_ligand_hyd.pdb")
_1r5y_ligand_pdbqt = os.path.join(data_dir(), "1r5y_ligand_hyd.pdbqt")
_1r5y_ligand.load_from_files(_1r5y_ligand_pdb, _1r5y_ligand_pdbqt)
### 3ao4 comes from PDBBind-CN
_3ao4_protein = PDB()
_3ao4_protein_pdb = os.path.join(data_dir(), "3ao4_protein_hyd.pdb")
_3ao4_protein_pdbqt = os.path.join(data_dir(),
"3ao4_protein_hyd.pdbqt")
_3ao4_protein.load_from_files(_3ao4_protein_pdb, _3ao4_protein_pdbqt)
# The ligand is also specified by pdbbind
_3ao4_ligand = PDB()
_3ao4_ligand_pdb = os.path.join(data_dir(), "3ao4_ligand_hyd.pdb")
_3ao4_ligand_pdbqt = os.path.join(data_dir(), "3ao4_ligand_hyd.pdbqt")
_3ao4_ligand.load_from_files(_3ao4_ligand_pdb, _3ao4_ligand_pdbqt)
### 2jdm comes from PDBBind-CN
_2jdm_protein = PDB()
_2jdm_protein_pdb = os.path.join(data_dir(), "2jdm_protein_hyd.pdb")
_2jdm_protein_pdbqt = os.path.join(data_dir(),
"2jdm_protein_hyd.pdbqt")
_2jdm_protein.load_from_files(_2jdm_protein_pdb, _2jdm_protein_pdbqt)
# The ligand is also specified by pdbbind
_2jdm_ligand = PDB()
_2jdm_ligand_pdb = os.path.join(data_dir(), "2jdm_ligand_hyd.pdb")
_2jdm_ligand_pdbqt = os.path.join(data_dir(), "2jdm_ligand_hyd.pdbqt")
_2jdm_ligand.load_from_files(_2jdm_ligand_pdb, _2jdm_ligand_pdbqt)
### 3g5k comes from PDBBind-CN
_3g5k_protein = PDB()
_3g5k_protein_pdb = os.path.join(data_dir(), "3g5k_protein_hyd.pdb")
_3g5k_protein_pdbqt = os.path.join(data_dir(),
"3g5k_protein_hyd.pdbqt")
_3g5k_protein.load_from_files(_3g5k_protein_pdb, _3g5k_protein_pdbqt)
# The ligand is also specified by pdbbind
_3g5k_ligand = PDB()
_3g5k_ligand_pdb = os.path.join(data_dir(), "3g5k_ligand_hyd.pdb")
_3g5k_ligand_pdbqt = os.path.join(data_dir(), "3g5k_ligand_hyd.pdbqt")
_3g5k_ligand.load_from_files(_3g5k_ligand_pdb, _3g5k_ligand_pdbqt)
### 3str comes from PDBBind-CN
_3str_protein = PDB()
_3str_protein_pdb = os.path.join(data_dir(), "3str_protein_hyd.pdb")
_3str_protein_pdbqt = os.path.join(data_dir(),
"3str_protein_hyd.pdbqt")
_3str_protein.load_from_files(_3str_protein_pdb, _3str_protein_pdbqt)
# The ligand is also specified by pdbbind
_3str_ligand = PDB()
_3str_ligand_pdb = os.path.join(data_dir(), "3str_ligand_hyd.pdb")
_3str_ligand_pdbqt = os.path.join(data_dir(), "3str_ligand_hyd.pdbqt")
_3str_ligand.load_from_files(_3str_ligand_pdb, _3str_ligand_pdbqt)
### 1nu3 comes from PDBBind-CN
_1nu3_protein = PDB()
_1nu3_protein_pdb = os.path.join(data_dir(), "1nu3_protein_hyd.pdb")
_1nu3_protein_pdbqt = os.path.join(data_dir(),
"1nu3_protein_hyd.pdbqt")
_1nu3_protein.load_from_files(_1nu3_protein_pdb, _1nu3_protein_pdbqt)
# The ligand is also specified by pdbbind
_1nu3_ligand = PDB()
_1nu3_ligand_pdb = os.path.join(data_dir(), "1nu3_ligand_hyd.pdb")
_1nu3_ligand_pdbqt = os.path.join(data_dir(), "1nu3_ligand_hyd.pdbqt")
_1nu3_ligand.load_from_files(_1nu3_ligand_pdb, _1nu3_ligand_pdbqt)
### 2rio comes from PDBBind-CN
_2rio_protein = PDB()
_2rio_protein_pdb = os.path.join(data_dir(), "2rio_protein_hyd.pdb")
_2rio_protein_pdbqt = os.path.join(data_dir(),
"2rio_protein_hyd.pdbqt")
_2rio_protein.load_from_files(_2rio_protein_pdb, _2rio_protein_pdbqt)
# The ligand is also specified by pdbbind
_2rio_ligand = PDB()
_2rio_ligand_pdb = os.path.join(data_dir(), "2rio_ligand_hyd.pdb")
_2rio_ligand_pdbqt = os.path.join(data_dir(), "2rio_ligand_hyd.pdbqt")
_2rio_ligand.load_from_files(_2rio_ligand_pdb, _2rio_ligand_pdbqt)
self.test_cases = [("prgr", prgr_receptor, prgr_active),
("cabl", cabl_receptor, cabl_active),
("1zea", _1zea_protein, _1zea_ligand),
("1r5y", _1r5y_protein, _1r5y_ligand),
("3ao4", _3ao4_protein, _3ao4_ligand),
("2jdm", _2jdm_protein, _2jdm_ligand),
("3g5k", _3g5k_protein, _3g5k_ligand),
("3str", _3str_protein, _3str_ligand),
("2rio", _2rio_protein, _2rio_ligand)]
