def setUp(self):
trajfile_list = [
"../data/run1/protein_lipids.xtc",
"../data/run2/protein_lipids.xtc"
]
topfile_list = [
"../data/run1/protein_lipids.gro",
"../data/run2/protein_lipids.gro"
]
lipid = "CHOL"
cutoffs = [0.55, 0.8]
file_dir = os.path.dirname(os.path.abspath(__file__))
self.save_dir = os.path.join(file_dir, "binding_site")
self.li = LipidInteraction(trajfile_list,
topfile_list,
cutoffs=cutoffs,
lipid=lipid,
nprot=1,
save_dir=self.save_dir)
self.li.collect_residue_contacts(write_log=False, print_log=True)
node_list = self.li.compute_binding_nodes(print_data=False)
binding_site_map = {
bs_id: nodes
for bs_id, nodes in enumerate(node_list)
}
contact_residue_dict = self.li.contact_residues_low
self.pose_pool = collect_bound_poses(binding_site_map,
contact_residue_dict,
self.li.trajfile_list[0],
self.li.topfile_list[0],
self.li.lipid, self.li.stride,
self.li.nprot)
class TestKinetics(unittest.TestCase):
def setUp(self):
trajfile_list = [
"../data/run1/protein_lipids.xtc",
"../data/run2/protein_lipids.xtc"
]
topfile_list = [
"../data/run1/protein_lipids.gro",
"../data/run2/protein_lipids.gro"
]
lipid = "CHOL"
cutoffs = [0.55, 1.0]
file_dir = os.path.dirname(os.path.abspath(__file__))
self.save_dir = os.path.join(file_dir, "test_kinetics")
self.li = LipidInteraction(trajfile_list,
topfile_list,
cutoffs=cutoffs,
lipid=lipid,
nprot=1,
save_dir=self.save_dir)
self.li.collect_residue_contacts()
self.t_total = np.max(self.li._T_total)
self.timestep = np.min(self.li._timesteps)
def test_cal_survivla_function(self):
delta_t_list = np.arange(0, self.t_total, self.timestep)
survival_func = cal_survival_func(
np.concatenate(self.li.durations[25]), self.t_total, delta_t_list)
self.assertIsInstance(survival_func, dict)
def test_cal_koff(self):
koff, restime, properties = cal_koff(np.concatenate(
self.li.durations[25]),
self.t_total,
self.timestep,
nbootstrap=20,
initial_guess=[1, 1, 1, 1])
print(koff)
print(restime)
print(properties)
self.assertIsInstance(properties, dict)
def tearDown(self):
shutil.rmtree(self.li.save_dir)
def setUp(self):
trajfile_list = [
"../data/run1/protein_lipids.xtc",
"../data/run2/protein_lipids.xtc"
]
topfile_list = [
"../data/run1/protein_lipids.gro",
"../data/run2/protein_lipids.gro"
]
lipid = "CHOL"
cutoffs = [0.55, 0.8]
file_dir = os.path.dirname(os.path.abspath(__file__))
self.save_dir = os.path.join(file_dir, "test_binding_site")
self.li = LipidInteraction(trajfile_list,
topfile_list,
cutoffs=cutoffs,
lipid=lipid,
nprot=1,
save_dir=self.save_dir)
self.li.collect_residue_contacts(write_log=False, print_log=True)
class TestBindingSites(unittest.TestCase):
def setUp(self):
trajfile_list = [
"../data/run1/protein_lipids.xtc",
"../data/run2/protein_lipids.xtc"
]
topfile_list = [
"../data/run1/protein_lipids.gro",
"../data/run2/protein_lipids.gro"
]
lipid = "CHOL"
cutoffs = [0.55, 0.8]
file_dir = os.path.dirname(os.path.abspath(__file__))
self.save_dir = os.path.join(file_dir, "test_binding_site")
self.li = LipidInteraction(trajfile_list,
topfile_list,
cutoffs=cutoffs,
lipid=lipid,
nprot=1,
save_dir=self.save_dir)
self.li.collect_residue_contacts(write_log=False, print_log=True)
def test_get_node_list(self):
corrcoef = self.li.interaction_corrcoef
node_list = get_node_list(corrcoef)
self.assertIsInstance(node_list, list)
def test_collect_binding_poses(self):
binding_site_map = {
bs_id: nodes
for bs_id, nodes in enumerate(self.li._node_list)
}
contact_list = self.li.contact_residues_low
pose_pool = collect_bound_poses(binding_site_map, contact_list,
self.li.trajfile_list[0],
self.li.topfile_list[0], self.li.lipid,
self.li.stride, self.li.nprot)
self.assertIsInstance(pose_pool, dict)
def tearDown(self):
shutil.rmtree(self.save_dir)
def setUp(self):
trajfile_list = [
"../data/run1/protein_lipids.xtc",
"../data/run2/protein_lipids.xtc"
]
topfile_list = [
"../data/run1/protein_lipids.gro",
"../data/run2/protein_lipids.gro"
]
lipid = "CHOL"
cutoffs = [0.55, 1.0]
file_dir = os.path.dirname(os.path.abspath(__file__))
self.save_dir = os.path.join(file_dir, "test_kinetics")
self.li = LipidInteraction(trajfile_list,
topfile_list,
cutoffs=cutoffs,
lipid=lipid,
nprot=1,
save_dir=self.save_dir)
self.li.collect_residue_contacts()
self.t_total = np.max(self.li._T_total)
self.timestep = np.min(self.li._timesteps)
class TestBindingPoses(unittest.TestCase):
def setUp(self):
trajfile_list = [
"../data/run1/protein_lipids.xtc",
"../data/run2/protein_lipids.xtc"
]
topfile_list = [
"../data/run1/protein_lipids.gro",
"../data/run2/protein_lipids.gro"
]
lipid = "CHOL"
cutoffs = [0.55, 0.8]
file_dir = os.path.dirname(os.path.abspath(__file__))
self.save_dir = os.path.join(file_dir, "binding_site")
self.li = LipidInteraction(trajfile_list,
topfile_list,
cutoffs=cutoffs,
lipid=lipid,
nprot=1,
save_dir=self.save_dir)
self.li.collect_residue_contacts(write_log=False, print_log=True)
node_list = self.li.compute_binding_nodes(print_data=False)
binding_site_map = {
bs_id: nodes
for bs_id, nodes in enumerate(node_list)
}
contact_residue_dict = self.li.contact_residues_low
self.pose_pool = collect_bound_poses(binding_site_map,
contact_residue_dict,
self.li.trajfile_list[0],
self.li.topfile_list[0],
self.li.lipid, self.li.stride,
self.li.nprot)
def test_vectorize_poses(self):
for bs_id, nodes in enumerate(self.li._node_list):
dist_matrix, pose_traj = vectorize_poses(self.pose_pool[bs_id],
nodes,
self.li._protein_ref,
self.li._lipid_ref)
self.assertEqual(dist_matrix.shape[0], self.li._lipid_ref.n_atoms)
self.assertEqual(dist_matrix.shape[1], len(self.pose_pool[bs_id]))
self.assertEqual(dist_matrix.shape[2],
len(self.li._node_list[bs_id]))
return
def test_calculate_scores(self):
for bs_id, nodes in enumerate(self.li._node_list):
dist_matrix, pose_traj = vectorize_poses(self.pose_pool[bs_id],
nodes,
self.li._protein_ref,
self.li._lipid_ref)
scores = calculate_scores(dist_matrix)
self.assertEqual(len(scores), pose_traj.n_frames)
scores = calculate_scores(dist_matrix, score_weights={"RHO": 10})
self.assertEqual(len(scores), pose_traj.n_frames)
def test_write_binding_poses(self):
for bs_id, nodes in enumerate(self.li._node_list):
dist_matrix, pose_traj = vectorize_poses(self.pose_pool[bs_id],
nodes,
self.li._protein_ref,
self.li._lipid_ref)
scores = calculate_scores(dist_matrix)
num_of_poses = min(5, pose_traj.n_frames)
pose_indices = np.argsort(scores)[::-1][:num_of_poses]
write_bound_poses(pose_traj,
pose_indices,
self.save_dir,
pose_prefix="BSid{}_top".format(bs_id),
pose_format="gro")
def test_calculate_site_surface_area(self):
binding_site_map = {
bs_id: nodes
for bs_id, nodes in enumerate(self.li._node_list)
}
radii_book = {"BB": 0.36, "SC1": 0.33, "SC2": 0.33, "SC3": 0.33}
surface_area = calculate_site_surface_area(
binding_site_map, radii_book, self.li.trajfile_list,
self.li.topfile_list, self.li.nprot, self.li.timeunit,
self.li.stride, self.li.dt_traj)
def tearDown(self):
shutil.rmtree(self.save_dir)
def setUp(self):
trajfile_list = [
"../data/run1/protein_lipids.xtc",
"../data/run2/protein_lipids.xtc"
]
topfile_list = [
"../data/run1/protein_lipids.gro",
"../data/run2/protein_lipids.gro"
]
lipid = "CHOL"
cutoffs = [0.55, 0.8]
file_dir = os.path.dirname(os.path.abspath(__file__))
self.save_dir = os.path.join(file_dir, "binding_site")
self.li = LipidInteraction(trajfile_list,
topfile_list,
cutoffs=cutoffs,
lipid=lipid,
nprot=1,
save_dir=self.save_dir)
self.li.collect_residue_contacts(write_log=False, print_log=True)
node_list = self.li.compute_binding_nodes(print_data=False)
binding_site_map = {
bs_id: nodes
for bs_id, nodes in enumerate(node_list)
}
contact_residue_dict = self.li.contact_residues_low
self.pose_pool = collect_bound_poses(binding_site_map,
contact_residue_dict,
self.li.trajfile_list[0],
self.li.topfile_list[0],
self.li.lipid, self.li.stride,
self.li.nprot)
def test_cluster_DBSCAN(self):
for bs_id, nodes in enumerate(self.li._node_list):
dist_matrix, pose_traj = vectorize_poses(
self.pose_pool[bs_id], nodes, self.li._protein_ref,
self.li._lipid_ref)
lipid_dist_per_pose = [
dist_matrix[:, pose_id, :].ravel()
for pose_id in np.arange(dist_matrix.shape[1])
]
transformed_data = PCA(
n_components=0.95).fit_transform(lipid_dist_per_pose)
cluster_labels = cluster_DBSCAN(transformed_data,
eps=None,
min_samples=None,
metric="euclidean")
self.assertEqual(len(cluster_labels), len(lipid_dist_per_pose))
cluster_id_set = [
label for label in np.unique(cluster_labels) if label != -1
]
selected_pose_id = [
np.random.choice(
np.where(cluster_labels == cluster_id)[0], 1)[0]
for cluster_id in cluster_id_set
]
write_bound_poses(
pose_traj,
selected_pose_id,
self.save_dir,
pose_prefix="BSid{}_cluster_DBSCAN".format(bs_id),
pose_format="gro")
def test_cluster_KMeans(self):
for bs_id, nodes in enumerate(self.li._node_list):
dist_matrix, pose_traj = vectorize_poses(
self.pose_pool[bs_id], nodes, self.li._protein_ref,
self.li._lipid_ref)
lipid_dist_per_pose = [
dist_matrix[:, pose_id, :].ravel()
for pose_id in np.arange(dist_matrix.shape[1])
]
transformed_data = PCA(
n_components=0.95).fit_transform(lipid_dist_per_pose)
cluster_labels = cluster_KMeans(transformed_data, n_clusters=5)
self.assertEqual(len(cluster_labels), len(lipid_dist_per_pose))
cluster_id_set = [
label for label in np.unique(cluster_labels) if label != -1
]
selected_pose_id = [
np.random.choice(
np.where(cluster_labels == cluster_id)[0], 1)[0]
for cluster_id in cluster_id_set
]
write_bound_poses(
pose_traj,
selected_pose_id,
self.save_dir,
pose_prefix="BSid{}_cluster_KMeans".format(bs_id),
pose_format="gro")
def tearDown(self):
shutil.rmtree(self.save_dir)