def test_hbonds_from_pdb(self):
traj = pt.load(fn('1L2Y.pdb'))
hb = pt.search_hbonds(traj)
state = pt.load_cpptraj_state('''
parm {pdb}
trajin {pdb}
hbond series
'''.format(pdb=fn('1L2Y.pdb')))
state.run()
for data_p, data_cpp in zip(hb.data, state.data[1:]):
assert len(
data_p) == traj.n_frames == 38, 'size of dataset must be 38'
aa_eq(data_p, data_cpp.values)
# make sure distances are smaller than cutoff
distance_cutoff = 2.5
angle_cutoff = 135.
hb = pt.search_hbonds(traj)
distances = pt.distance(traj, hb.get_amber_mask()[0])
angles = pt.angles(traj, hb.get_amber_mask()[1])
dist_indices = np.where(distances > distance_cutoff)
angle_indices = np.where(angles < angle_cutoff)
saved_donor_acceptors = [
'ASP9_OD2-ARG16_NH1-HH12', 'ASP9_OD2-ARG16_NH2-HH22',
'ASP9_OD2-ARG16_NE-HE', 'ASP9_OD2-ARG16_NH2-HH21',
'ASP9_OD2-ARG16_NH1-HH11'
]
donor_acceptors = pt.search_hbonds(traj, ':9,16').donor_acceptor
assert saved_donor_acceptors == donor_acceptors, 'saved_donor_acceptors'
aa_eq(hb.total_solute_hbonds(), hb.data['total_solute_hbonds'])
def test_indexing_nonrefernce_DSL(self):
# segmentation fault
# new DSL
d0_dummy = pt.search_hbonds(traj)[:][:][:][:][0]
pt.search_hbonds(traj)[0]
# filter
dslist = da.calc_phi(traj)
dslist[0]
def test_indexing_nonrefernce_DSL(self):
from pytraj import dihedral_ as da
# segmentation fault
# new DSL
d0_dummy = pt.search_hbonds(traj)[:][:][:][:][0]
d0 = pt.search_hbonds(traj)[0]
# filter
dslist = da.calc_phi(traj)
x = dslist[0]
def test_1(self):
dslist0 = pt.calc_phi(traj)
dslist1 = pt.calc_psi(traj)
dslist2 = pt.search_hbonds(traj)
self.assertRaises(KeyError, lambda: stack((dslist0, dslist1)))
self.assertRaises(TypeError, lambda: stack((dslist0, dslist2)))
stack((dslist0 for _ in range(3)))
def test_1(self):
dslist0 = pt.calc_phi(traj)
dslist1 = pt.calc_psi(traj)
dslist2 = pt.search_hbonds(traj)
self.assertRaises(KeyError, lambda: stack((dslist0, dslist1)))
self.assertRaises(TypeError, lambda: stack((dslist0, dslist2)))
stack((dslist0 for _ in range(3)))
def test_1(self):
dslist0 = pt.calc_phi(traj)
dslist1 = pt.calc_psi(traj)
dslist2 = pt.search_hbonds(traj)
with pytest.raises(KeyError):
stack((dslist0, dslist1))
with pytest.raises(TypeError):
stack((dslist0, dslist2))
stack((dslist0 for _ in range(3)))
def test_mpi_hbond():
rank = MPI.COMM_WORLD.rank
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
hbond_data_serial = pt.search_hbonds(traj, dtype='dict')
hbond_data_pmap_mpi = pt.pmap_mpi(pt.search_hbonds, traj)
if rank == 0:
assert sorted(hbond_data_serial.keys()) == sorted(
hbond_data_pmap_mpi.keys())
for key in hbond_data_serial.keys():
aa_eq(hbond_data_serial[key], hbond_data_pmap_mpi[key])
def test_pmap_hbond(self):
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
hbond_data_serial = pt.search_hbonds(traj, dtype='dict')
hbond_data_pmap = pt.pmap(pt.search_hbonds, traj, n_cores=3)
assert sorted(hbond_data_serial.keys()) == sorted(
hbond_data_pmap.keys())
for key, value in hbond_data_serial.items():
aa_eq(hbond_data_serial[key], hbond_data_pmap[key])
assert value.dtype == np.int32
with pytest.raises(ValueError):
# cpptraj style
# not support yet.
pt.pmap(['radgyr', 'hbond'], traj, n_cores=3)
def test_hbonds_from_pdb(self):
traj = pt.load('data/1L2Y.pdb')
hb = pt.search_hbonds(traj)
state = pt.load_cpptraj_state('''
parm data/1L2Y.pdb
trajin data/1L2Y.pdb
hbond series
''')
state.run()
for data_p, data_cpp in zip(hb.data, state.data[1:]):
assert len(
data_p) == traj.n_frames == 38, 'size of dataset must be 38'
aa_eq(data_p, data_cpp)
# make sure distances are smaller than cutoff
distance_cutoff = 2.5
angle_cutoff = 135.
hb = pt.search_hbonds(traj)
distances = pt.distance(traj, hb.get_amber_mask()[0])
angles = pt.angles(traj, hb.get_amber_mask()[1])
dist_indices = np.where(distances > distance_cutoff)
angle_indices = np.where(angles < angle_cutoff)
print('FILL ME', dist_indices, angle_indices)
saved_donor_acceptors = ['ASP9_OD2-ARG16_NH1-HH12',
'ASP9_OD2-ARG16_NH2-HH22',
'ASP9_OD2-ARG16_NE-HE',
'ASP9_OD2-ARG16_NH2-HH21',
'ASP9_OD2-ARG16_NH1-HH11']
donor_acceptors = pt.search_hbonds(traj, ':9,16').donor_acceptor
assert saved_donor_acceptors == donor_acceptors, 'saved_donor_acceptors'
aa_eq(hb.total_solute_hbonds(), hb.data['total_solute_hbonds'])
def test_hbond_general(self):
traj = pt.iterload("./data/DPDP.nc", "./data/DPDP.parm7")
dslist = pt.search_hbonds(traj, dtype='dataset')
for key in dslist.keys():
if 'UU' not in key:
assert len(dslist[key].values) == traj.n_frames
mydict = dslist.to_dict()
mydict_np = dslist.to_dict()
assert len(mydict.keys()) == dslist.size
assert len(mydict_np.keys()) == dslist.size
for key in mydict.keys():
mydict[key] = np.asarray(mydict[key])
aa_eq(mydict[key], mydict_np[key])
# raise if dtype='hbond' and series=False
self.assertRaises(ValueError,
lambda: pt.hbond(traj, series=False, dtype='hbond'))
def test_hbonds_with_image(self):
traj = pt.iterload("data/tz2.ortho.nc", "data/tz2.ortho.parm7")
hbonds_0 = pt.search_hbonds(traj(autoimage=True))
hbonds_1 = pt.search_hbonds(traj, image=True)
aa_eq(hbonds_0.values, hbonds_1.values)
import pytraj as pt
pdb = pt.load_pdb_rcsb("1l2y")
print(pdb)
h = pt.search_hbonds(pdb)
print(h)
print(h.donor_acceptor)
print('total solute hbonds: ', h.data['total_solute_hbonds'])
def test_1(self):
pt.search_hbonds(traj)
pt.search_hbonds(traj, 'series')
pt.search_hbonds(traj, 'series, nointramol')
