def test_analyze_modes():
for mask in ['@CA', '@N,CA', '@CA,H']:
command = '''
matrix mwcovar name tz2 {}
diagmatrix tz2 name my_modes vecs 20
modes fluct name my_modes
'''.format(mask)
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
# cpptraj
state = pt.load_cpptraj_state(command, traj)
# pt._verbose()
state.run()
pt._verbose(False)
state.run()
cpp_dict = state.data[1:].to_dict()
c_dslist = state.data[1:]
cpp_modes = c_dslist[1]
# pytraj
mat = pt.matrix.mwcovar(traj, mask)
indices = traj.top.select(mask)
dslist = pt.matrix.diagonalize(mat,
n_vecs=20,
scalar_type='mwcovar',
mass=traj.top.mass[indices],
dtype='dataset')
evecs, evals = dslist[0].eigenvectors, dslist[0].eigenvalues
aa_eq(cpp_dict['tz2'], mat)
aa_eq(evals, cpp_modes.eigenvalues)
aa_eq(evecs, cpp_modes.eigenvectors)
with pytest.raises(AssertionError):
# wrong mass
dslist = pt.matrix.diagonalize(
mat,
n_vecs=20,
scalar_type='mwcovar',
mass=traj.top.mass[indices].tolist() + [1],
dtype='dataset')
with pytest.raises(AssertionError):
# mass is None
dslist = pt.matrix.diagonalize(mat,
n_vecs=20,
scalar_type='mwcovar',
mass=None,
dtype='dataset')
# pt._verbose()
fluct = pt.analyze_modes('fluct',
evecs,
evals,
scalar_type='mwcovar',
dtype='dataset')
# pt._verbose(False)
p_rms = fluct['FLUCT_00001[rms]'].values
c_rms = c_dslist['FLUCT_00003[rms]'].values
aa_eq(p_rms, c_rms)
def test_options(self):
'''specify cpptraj options
'''
# restart, keep extension
try:
os.remove('output/test.rst7')
except OSError:
pass
pt._verbose()
self.traj_tz2_ortho[:1].save('output/test.rst7', options='keepext')
pt._verbose(False)
assert os.path.exists('output/test.1.rst7')
def test_extra_coverage(self):
'''all kind of tests that do not belong to anywhere else
'''
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
# show_versions
pt.show_versions()
pt._verbose()
pt._verbose(False)
# info
pt.info()
pt.info('parallel')
misc.parallel_info('pmap')
misc.parallel_info('openmp')
misc.parallel_info(None)
eq([2, 3], [2, 3])
dslist = pt.multidihedral(traj)
str(dslist[0])
def test_spam():
peaks_xyz = os.path.join(cpptraj_test_dir, 'Test_SPAM', 'peaks.xyz')
command = """
parm {}
trajin {}
autoimage
spam {} name SPAM cut 12.0 info spam.info out spam.dat reorder \
summary summary.dat
trajout test.mdcrd onlyframes 1-2
""".format(tz2_truncoct_top, tz2_truncoct_trajin, peaks_xyz)
state = pt.load_cpptraj_state(command)
with tempfolder():
state.run()
traj = pt.iterload(tz2_truncoct_trajin, tz2_truncoct_top)
# cm = 'SPAM cut 12.0 info spam.info out spam.dat reorder summary summary.dat'
cm = 'SPAM cut 12.0 reorder'
pt._verbose()
with tempfolder():
spam_out = pt.spam(traj, peak_file=peaks_xyz, command=cm)
print(spam_out)
def test_extra_coverage(self):
'''all kind of tests that do not belong to anywhere else
'''
traj = pt.iterload("./data/tz2.nc", "./data/tz2.parm7")
# show_versions
pt.show_versions()
pt._verbose()
pt._verbose(False)
print(version)
# info
pt.info()
pt.info('parallel')
pt.misc.parallel_info('pmap')
pt.misc.parallel_info('openmp')
pt.misc.parallel_info(None)
eq([2, 3], [2, 3])
# raise if comparing NaN
self.assertRaises(ValueError, lambda: aa_eq(np.nan, np.nan))
dslist = pt.multidihedral(traj)
string_ = str(dslist[0])
def test_extra_coverage(self):
'''all kind of tests that do not belong to anywhere else
'''
traj = pt.iterload("./data/tz2.nc", "./data/tz2.parm7")
# show_versions
pt.show_versions()
pt._verbose()
pt._verbose(False)
print(version)
# info
pt.info()
pt.info('parallel')
pt.misc.parallel_info('pmap')
pt.misc.parallel_info('openmp')
pt.misc.parallel_info(None)
eq([2, 3], [2, 3])
# raise if comparing NaN
self.assertRaises(ValueError, lambda: aa_eq(np.nan, np.nan))
dslist = pt.multidihedral(traj)
string_ = str(dslist[0])