def test_buffer_not_c_contiguous(self):
# source code was lightly adapted from jmborr
# https://github.com/Amber-MD/pytraj/issues/991
traj = pt.load('data/issue991/short.dcd',
'data/issue991/pdb.gz',
mask='(!:1-256)&(@H1,@H2,@H3,@H4,@H5)')
# Trajectory of the center of mass of the first two residues
minitraj = np.empty((2, traj.n_frames, 3))
minitraj[0] = pt.center_of_mass(traj, mask=':1')
minitraj[1] = pt.center_of_mass(traj, mask=':2')
minitraj = minitraj.transpose((1, 0, 2))
# "topology" using the first two atoms
minitop = traj.top['@1,2']
# Save trajectory
# make sure there is no ValueError
# something is wrong with pdb, crd extension when loading with
# minitop (poor topology?)
# make issue in cpptraj too?
for ext in ['nc', 'dcd', 'mdcrd', 'crd', 'pdb', 'trr']:
fn = 'output/junk.' + ext
pt.write_traj(filename=fn,
traj=minitraj,
top=minitop,
overwrite=True)
# load coord back to make sure we correctly write it
new_traj = pt.iterload(fn, minitop)
# mdcrd, crd, pdb has only 3 digits after decimal
decimal = 5 if ext in ['nc', 'dcd', 'trr'] else 3
aa_eq(minitraj, new_traj.xyz, decimal=decimal)
def testsuperpose_alias(self):
'''testsuperpose_alias'''
t0 = self.traj[:]
t1 = self.traj[:]
pt.transform(t0, ['superpose'])
pt.transform(t1, ['rms'])
aa_eq(t0.xyz, t1.xyz)
def test_frame_fit(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
f0 = traj[0]
f1 = traj[1]
arr0 = list(f0[0])
arr1 = list(f1[0])
f0.rmsd(f1)
aa_eq(arr0, f0[0])
aa_eq(arr1, f1[0])
f1.rmsfit(ref=f0)
# expect reference `f0` xyz are not changed
aa_eq(arr0, f0[0])
trajsaved = pt.iterload("./data/fit_to_1stframe.Tc5b.x",
"./data/Tc5b.top")
f1saved = trajsaved[1]
# make sure we reproduce cpptraj output
aa_eq(f1.xyz, f1saved.xyz, decimal=3)
farray = traj[:]
farray.rmsfit(ref=traj[0])
aa_eq(farray[1].xyz, f1saved.xyz, decimal=3)
def test_frame_indices(self):
traj = pt.iterload("data/tz2.truncoct.nc", "data/tz2.truncoct.parm7")
traj2 = pt.iterload("data/tz2.truncoct.nc",
"data/tz2.truncoct.parm7",
frame_slice=(2, 8))
txt = '''
reference ./data/tz2.truncoct.nc 2 2
rmsd :2-11 refindex 0 perres perresout center.agr range 1 perrescenter
'''
state = pt.load_batch(traj2, txt)
state.run()
frame_indices = range(2, 8)
rmsd0 = pt.rmsd(traj, ref=1, mask=':2-11', frame_indices=frame_indices)
rmsdperres = pt.rmsd_perres(traj,
ref=1,
mask=':2-11',
perres_mask='*',
resrange='1',
perres_center=True,
frame_indices=frame_indices)
aa_eq(rmsd0, state.data[2])
aa_eq(rmsdperres[1], state.data[3].values)
def test_split_and_write_traj(self):
fn = "data/Tc5b.x"
traj = pt.iterload([fn, fn], "./data/Tc5b.top")
# duplcate
assert traj.n_frames == 20
top = traj.top
# test TrajectoryIterator object
pt.tools.split_and_write_traj(traj,
n_chunks=4,
root_name='./output/trajiterx',
overwrite=True)
flist = sorted(glob("./output/trajiterx*"))
traj4 = pt.iterload(flist, top)
aa_eq(traj4.xyz, traj.xyz)
# dcd ext
pt.tools.split_and_write_traj(traj,
4,
root_name='./output/ts',
ext='dcd',
overwrite=True)
flist = sorted(glob("./output/ts.*.dcd"))
traj4 = pt.iterload(flist, top)
aa_eq(traj4.xyz, traj.xyz)
def test_fit_and_then_nofit(self):
traj = pt.iterload("data/Tc5b.x", "data/Tc5b.top")
t0 = traj[:]
pt.superpose(t0, ref=traj[3], mask='@CA')
rmsd_0 = pt.rmsd_nofit(traj, ref=traj[3], mask='@CB')
rmsd_1 = pt.rmsd(traj, ref=traj[3], mask='@CB', nofit=True)
aa_eq(rmsd_1, rmsd_0)
def main():
# require 'sanderapi' and 'parmed' packages in AmberTools15
# http://ambermd.org/#AmberTools
# more info about `sanderapi` in Amber15 manual
# http://ambermd.org/doc12/Amber15.pdf (page 341)
traj = io.iterload("../tests/data/Tc5b.x",
"../tests/data/Tc5b.top")
print(traj)
edict0 = pyca.energy_decomposition(parm="../tests/data/Tc5b.top",
traj=traj,
igb=8,
input_options=None)
print(edict0)
# edict1: use default igb=8
edict1 = pyca.energy_decomposition(traj=traj)
print(edict1)
aa_eq(edict0['tot'], edict1['tot'])
# update `input` and get minimal output
import sander
inp = sander.gas_input(6)
edict2 = pyca.energy_decomposition(traj, input_options=inp, mode='minimal')
print(edict2)
def testsuperpose_vs_rmsd(self):
# load frames to immutable traj
traj = pt.iterload("data/tz2.nc", "data/tz2.parm7")
t0 = traj[:]
t1 = traj[:]
pt.rmsd(t0, ref=traj[0], mask='@CA')
pt.superpose(t1, ref=traj[0], mask='@CA')
aa_eq(t0.xyz, t1.xyz)
def test_autoimage(self):
traj = pt.iterload("data/tz2.ortho.nc", "data/tz2.ortho.parm7")
t0 = traj[:]
t0.autoimage()
avg_0 = pt.mean_structure(t0, '@CA')
avg_1 = pt.mean_structure(traj(autoimage=True), '@CA')
aa_eq(avg_0.xyz, avg_1.xyz)
def test_vs_cpptraj(self):
data = pt.dssp(self.traj, "*", dtype='cpptraj_dataset')
data_int = np.array(
[d0.values for d0 in data if d0.dtype == 'integer'],
dtype='i4')
# load cpptraj output
cpp_data = np.loadtxt("./data/dssp.Tc5b.dat", skiprows=1)[:, 1:].T
aa_eq(data_int.flatten(), cpp_data.flatten())
def test_1(self):
traj = pt.iterload("./data/tz2.truncoct.nc",
"./data/tz2.truncoct.parm7")
f0 = traj[0]
f0cp = f0.copy()
adict['autoimage']("", f0, traj.top)
fsaved = pt.iterload("./data/tz2.truncoct.autoiamge.save.r",
"./data/tz2.truncoct.parm7")[0]
aa_eq(fsaved.xyz, f0.xyz, decimal=3)
def order_(modes):
data = _ired(state_vecs, modes=modes)
order_s2_v0 = data['IRED_00127[S2]']
# make sure the S2 values is 1st array
# load cpptraj's output and compare to pytraj' values for S2 order paramters
cpp_order_s2 = np.loadtxt(os.path.join(
cpptraj_test_dir, 'Test_IRED', 'orderparam.save')).T[-1]
aa_eq(order_s2_v0.values, cpp_order_s2, decimal=4)
def test_not_update_coordinates(self):
traj = self.traj[:]
data = pt.rmsd(traj, ref=3, update_coordinate=False)
# make sure coordinates are not updated
aa_eq(traj.xyz, self.traj.xyz)
# make sure give the same rmsd values
aa_eq(pt.rmsd(traj, ref=3), data)
def test_0(self):
traj = pt.iterload("./data/tz2.ortho.nc", "./data/tz2.ortho.parm7")
cout = pt.datafiles.load_cpptraj_output("""
parm ./data/tz2.ortho.parm7
trajin ./data/tz2.ortho.nc
rms first nofit
rms first mass
""")
aa_eq(pt.rmsd(traj, nofit=True), cout[1])
aa_eq(pt.rmsd(traj, mass=True), cout[2])
def test_0(self):
trajcpp = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
farray = trajcpp[:]
# bugs: trajcpp[0, 0, 0] != farray[0, 0, 0] (must be equal)
assert farray[0][0, 0] == trajcpp[0][0, 0]
farray[0, 0, 0] = 100.10
assert farray[0, 0, 0] == 100.10
farray[0, 0, :] = [100.10, 101.1, 102.1]
aa_eq(farray[0, 0, :], [100.10, 101.1, 102.1])
def test_load_samples(self):
traj = pt.load_sample_data()[:]
assert isinstance(traj, pt.Trajectory) == True
assert traj.top.n_atoms == 34
assert traj.shape == (1, 34, 3)
traj2 = pt.load_sample_data()
assert isinstance(traj2, pt.TrajectoryIterator) == True
assert traj2.top.n_atoms == 34
assert traj2.shape == (1, 34, 3)
aa_eq(traj.xyz, traj2.xyz)
def test_1(self):
# status: OK
from pytraj.compat import zip
# note: use `load` instead of `iterload`
traj = pt.load("./data/tz2.ortho.nc", "./data/tz2.ortho.parm7")
traj.autoimage()
traj.rmsfit(mask='@CA,C,N')
saved_traj = pt.load('data/tz2.autoimage_with_rmsfit.nc', traj.top)
# PASSED
aa_eq(saved_traj.xyz, traj.xyz)
def test_noreference(self):
from pytraj.datafiles import load_cpptraj_output, tz2_ortho_trajin
traj = pt.iterload("./data/tz2.ortho.nc", "./data/tz2.ortho.parm7")
cout = load_cpptraj_output(tz2_ortho_trajin + """
rmsd first @CA perres range 2-7""")
d = pt.rmsd_perres(traj,
ref=0,
mask='@CA',
resrange='2-7',
dtype='ndarray')
aa_eq(cout[1:].values, d)
def test_watershell(self):
traj = pt.iterload("data/tz2.truncoct.nc", "data/tz2.truncoct.parm7")
state = pt.load_batch(traj, '''
watershell :1-7
''')
d0 = pt.watershell(traj, solute_mask=':1-7')
state.run()
aa_eq(d0.values, state.data[[1, 2]].values)
# need to provide solute_mask
self.assertRaises(ValueError, lambda: pt.watershell(traj))
def test_2(self):
from pytraj.all_actions import do_autoimage
# test do_autoimage
traj = pt.iterload("./data/tz2.truncoct.nc",
"./data/tz2.truncoct.parm7")
f0 = traj[0]
f0cp = f0.copy()
do_autoimage(traj=f0, top=traj.top)
fsaved = pt.iterload("./data/tz2.truncoct.autoiamge.save.r",
"./data/tz2.truncoct.parm7")[0]
aa_eq(fsaved.xyz, f0.xyz, decimal=3)
def test_2(self):
import numpy as np
box = Box()
arr0 = np.arange(6).astype(np.float64)
box.data[:] = arr0
for idx, x in enumerate(arr0):
assert box.data[idx] == x
# set Box for Frame
f1 = Frame()
f1.box = box
aa_eq(f1.box.values, box.values, decimal=7)
def test_0(self):
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")
if has_("numpy"):
import numpy as np
from numpy.testing import assert_almost_equal
arr0 = traj.xyz
aa_eq(arr0, traj[:, :, :].xyz)
# create Trajectory
farray = traj[:]
aa_eq(arr0, farray[:, :, :].xyz)
else:
pass
def test_combine_nofit_mass_nomod(self):
cm = '''
parm data/tz2.parm7
trajin data/tz2.nc
rms @CA nofit mass nomod
'''
state = pt.load_cpptraj_state(cm)
state.run()
unmut_traj = pt.iterload('data/tz2.nc', 'data/tz2.parm7')
mut_traj = unmut_traj[:]
data = pt.rmsd(mut_traj, mask='@CA', mass=True, nofit=True, update_coordinate=False)
aa_eq(data, state.data[-1])
def test_slice(self):
traj1 = TrajectoryIterator(filename="data/Tc5b.x",
top="./data/Tc5b.top")
frame_indices = slice(9, 6, -1)
traj0 = pt.load(filename="./data/Tc5b.x",
top=pt.load_topology("./data/Tc5b.top"),
frame_indices=frame_indices)
aa_eq(traj0[0].xyz, traj1[9].xyz)
aa_eq(traj0[1].xyz, traj1[8].xyz)
aa_eq(traj0[2].xyz, traj1[7].xyz)
assert traj0[0].rmsd(traj1[9]) < 1E-4
rmsdlist = []
ref = traj1[0].copy()
for frame in traj1:
rmsdlist.append(frame.rmsd(ref))
nparr = np.array(rmsdlist)
# make sure we don't suport other frame_indices
traj2 = Trajectory()
traj2 = pt.load(
filename="./data/Tc5b.x",
top=pt.load_topology("./data/Tc5b.top"),
frame_indices=list(range(4)) + list(range(9, 5, -1)) + [4, ])
aa_eq(traj2[-1].xyz, traj1[4].xyz)
def test_frame_indices(self):
# load frames to immutable traj
traj = pt.iterload("data/tz2.nc", "data/tz2.parm7")
# convert to numpy traj
frame_indices = [0, 3, 5]
t00 = traj[:]
t01 = traj[:]
t10 = traj[frame_indices]
t11 = traj[frame_indices]
aa_eq(t00[frame_indices].xyz, t11.xyz)
ref = traj[-1]
t00.superpose(ref=ref, frame_indices=frame_indices)
ref = traj[-1]
pt.superpose(t01, ref=ref, frame_indices=frame_indices)
ref = traj[-1]
t10.superpose(ref=ref)
ref = traj[-1]
pt.superpose(t11, ref=ref, frame_indices=frame_indices)
aa_eq(t00.xyz, t01.xyz)
aa_eq(t10.xyz, t11.xyz)
aa_eq(t00[frame_indices].xyz, t10.xyz)
def test_radgyr(self):
traj = pt.iterload(top="./data/Tc5b.top",
filename='data/Tc5b.x', )
txt = '''
parm ./data/Tc5b.top
trajin ./data/Tc5b.x
radgyr @CA nomax
radgyr nomax
radgyr !@H= nomax
'''
# exclude DatasetTopology
data = pt.datafiles.load_cpptraj_output(txt)[1:]
for mask, out in zip(['@CA', '', '!@H='], data):
aa_eq(pt.radgyr(traj, mask), out)
def test_0(self):
# TrajectoryIterrator
# status: failed
from pytraj.compat import zip
traj = pt.iterload("./data/tz2.ortho.nc", "./data/tz2.ortho.parm7")
pt.write_traj("./output/tz2.autoimage_with_rmsfit.nc",
traj(autoimage=True,
rmsfit=(0, '@CA,C,N')),
overwrite=True)
saved_traj = pt.load('data/tz2.autoimage_with_rmsfit.nc', traj.top)
p_traj = pt.load('./output/tz2.autoimage_with_rmsfit.nc', traj.top)
aa_eq(saved_traj.xyz, p_traj.xyz)
for f1, f2 in zip(p_traj, saved_traj):
pass
def test_frame_indices(self):
traj = pt.iterload('data/tz2.nc', 'data/tz2.parm7')
frame_indices = [0, 6, 7, 4, 5]
data_without_frame_indices = pt.energy_decomposition(traj, igb=8)
data_with_frame_indices = pt.energy_decomposition(
traj,
igb=8,
frame_indices=frame_indices)
data_with_frame_indices_2 = pt.energy_decomposition(
traj[frame_indices],
igb=8)
for key in data_without_frame_indices:
aa_eq(data_without_frame_indices[key][frame_indices],
data_with_frame_indices[key])
aa_eq(data_without_frame_indices[key][frame_indices],
data_with_frame_indices_2[key])
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_buffer1d(self):
FRAME._buffer1d[0] = 199.
assert FRAME[0, 0] == 199.
FRAME[0] = 0.1
assert FRAME[0, 0] == 0.1
assert FRAME._buffer1d[-1] == FRAME[-1, 2]
FRAME._buffer1d[:3] = array('d', [1, 2.3, 3.4])
aa_eq(FRAME.xyz[0], array('d', [1, 2.3, 3.4]))
arr0 = np.asarray(FRAME._buffer1d)
arr1 = arr0.reshape(10, 3)
arr1[1] = [100., 200., 300.]
start = 0
stop = 10
strip = 2
arr = np.asarray(FRAME[start:stop:strip])
def test_principal_axes_and_lign_principal_axis(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
cm = '''
principal * dorotation mass name pout
createcrd myname
'''
state = pt.load_cpptraj_state(cm, traj)
state.run()
mut_traj_0 = traj[:]
mut_traj_1 = traj[:]
data = pt.principal_axes(mut_traj_0,
mask='*',
dorotation=True,
mass=True)
pt.align_principal_axis(mut_traj_1, mask='*', mass=True)
aa_eq(data[0], state.data[1].values)
aa_eq(data[1], state.data[2].values)
aa_eq(state.data[-1].xyz, mut_traj_0.xyz)
aa_eq(state.data[-1].xyz, mut_traj_1.xyz)
def test_projection_for_pca(self):
traj = pt.load(fn('tz2.nc'), fn('tz2.parm7'))
state = pt.load_cpptraj_state(command)
state.run()
cpp_modes = state.data['MyEvecs']
cpp_arr_crd = np.array(cpp_modes._get_avg_crd())
cpp_arr_crd = cpp_arr_crd.reshape(117, 3)
mask = '!@H='
pt.superpose(traj, mask=mask)
avg = pt.mean_structure(traj)
atom_indices = traj.top(mask).indices
avg.xyz[atom_indices]
pt.superpose(traj, mask=mask, ref=avg)
avg2 = pt.mean_structure(traj, mask=mask)
mat = pt.matrix.covar(traj, mask)
modes = pt.matrix.diagonalize(mat, n_vecs=2, dtype='dataset')[0]
aa_eq(cpp_arr_crd, avg2.xyz)
aa_eq(np.abs(modes.eigenvalues),
np.abs(state.data['MyEvecs'].eigenvalues))
aa_eq(np.abs(modes.eigenvectors),
np.abs(state.data['MyEvecs'].eigenvectors))
projection_data = pt.all_actions.projection(
traj,
mask=mask,
average_coords=avg2.xyz,
eigenvalues=modes.eigenvalues,
eigenvectors=modes.eigenvectors,
scalar_type='covar')
aa_eq(np.abs(projection_data),
np.abs(state.data[-2:].values),
decimal=3)
def test_1(self):
# TODO: get absolute path so we can use `tempfolder`
# if not: wrong dir if using TrajectoryIterator
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")[:]
trajout = TrajectoryWriter()
# multiple pdb in multiple files, using `save` method in traj
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = mdio.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in multiple files, using `mdio.write_traj`
with tempfolder():
basename = "test_pdb_files_mdio_write_traj.pdb"
mdio.write_traj(basename, traj, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = pt.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in SINGLE file
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True)
traj2 = mdio.load(basename, traj.top)
aa_eq(traj.xyz, traj2.xyz)
# multiple pdb in SINGLE file with `model` keyword
# write to output so we can manually check
basename = "./output/test_pdb_files_model.pdb"
traj.save(basename, overwrite=True, options='model')
traj3 = mdio.load(basename, traj.top)
aa_eq(traj.xyz, traj3.xyz)
def test_rotation_matrix_in_rmsd_calculation(self):
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
saved_mat = pt.rotation_matrix(traj, ref=traj[3], mask='@CA')
saved_rmsd = pt.rmsd(traj, ref=traj[3], mask='@CA')
for n_cores in [2, 3]:
out = pt.pmap(pt.rotation_matrix, traj, ref=traj[3], mask='@CA')
out_with_rmsd = pt.pmap(pt.rotation_matrix,
traj,
ref=traj[3],
mask='@CA',
with_rmsd=True)
mat = out[list(out.keys())[0]]
mat2, rmsd_ = out_with_rmsd[list(out_with_rmsd.keys())[0]]
aa_eq(saved_mat, mat)
aa_eq(saved_mat, mat2)
aa_eq(saved_rmsd, rmsd_)
def test_atom_distance(self):
traj = pt.iterload(tz2_trajin, tz2_top)
top = traj.top
ref = traj[0]
# test for 1st frame
top.set_reference(ref)
ref.top = top
# all atoms within 5 Angtrom from :3@CA
indices = top.select(":3@CA <@5.0")
saved_indices = np.loadtxt(
fn("mask.tz2.dat"), skiprows=1, usecols=(1, ))
neighbors_smaller = pt.search_neighbors(
traj, mask=':3@CA <@5.0', frame_indices=[
0,
])
# subtract by '1' since cpptraj uses "1" as starting index for output
saved_indices = saved_indices - 1
aa_eq(indices, saved_indices)
aa_eq(neighbors_smaller.values, indices)
# re-calculate the distance
ca_indices = pt.select_atoms(':3@CA', traj.top)
all_pairs = list(product(ca_indices, indices))
distances = pt.tools.flatten(pt.distance(ref, all_pairs))
for dist in distances:
assert dist < 5.0, 'all distances must be smaller than 5.0 Angstrom'
# test larger
# why do we need to set reference frame again?
top.set_reference(ref)
indices_larger = top.select(":3@CA >@5.0")
all_pairs_larger = list(product(ca_indices, indices_larger))
distances = pt.tools.flatten(pt.distance(ref, all_pairs_larger))
for dist in distances:
assert dist > 5.0, 'all distances must be larger than 5.0 Angstrom'
# search_neighbors
neighbors_larger = pt.search_neighbors(
traj, mask=':3@CA >@5.0', frame_indices=[
0,
])
aa_eq(neighbors_larger.values, indices_larger)
def test_0(self):
# create Trajectory from Trajing_Single
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")[:]
aa_eq(traj[3, 3], traj[3][3, :])
frame1 = traj[1]
aa_eq(frame1[0], traj[1][:, :][0])
assert traj[0, 0, 0] == -16.492
assert traj[:, :, 0][0, 0] == traj[0, 0, 0]
f0 = traj[0]
farr0 = traj[:2]
fa = traj[2:4]
# we don't support traj[:, idx] or traj[:, idx, idy] since this give wrong answer
# got ~0.0 value
aa_eq(traj[:, 0, 0], np.asarray(traj[0][0]))
for i in range(traj[0]._buffer2d.shape[0]):
aa_eq(traj[:, :, 0][i], traj[0]._buffer2d[i])
# slicing with mask
atm = traj.top("@CA")
traj[atm]
traj[:, atm]
def testsuper_dispatch(self):
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
funclist = [pt.radgyr, pt.molsurf]
for func in funclist:
mask = '@CA'
atom_indices = pt.select_atoms(mask, traj.top)
# mask
aa_eq(func(traj, mask=mask), func(traj, mask=atom_indices))
# specify traj=traj
aa_eq(func(traj=traj, mask=mask), func(traj, mask=atom_indices))
# frame_indices with mask
frame_indices = [0, 5, 8]
aa_eq(
func(traj[frame_indices], mask=mask),
func(traj, mask=atom_indices, frame_indices=frame_indices))
def test_len_on_disk(self):
N = ts.n_frames
old_xyz_5_10 = ts[5].xyz[:10].copy()
assert ts[:3].n_frames == 3
assert ts[1:3].n_frames == 2
assert ts[3:1].n_frames == 0
assert ts[3:1:-1].n_frames == 2
assert ts[-1:-3].n_frames == 0
assert ts[-1:-3:-1].n_frames == 2
# need to store xyz
xyz = ts[-1].xyz.copy()
aa_eq(xyz, ts[N - 1].xyz)
# need to create a temp farray
subfarray = ts[5:1:-1]
aa_eq(subfarray[0].xyz, ts[5].xyz)
aa_eq(old_xyz_5_10, ts[5].xyz[:10])
def test_3(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
count = 0
for frame in traj.iterframe():
count += 1
aa_eq(frame.xyz, traj[-1].xyz)
count = 0
for frame in traj.iterframe(2, 8, 2):
count += 1
assert count == 3
aa_eq(frame.xyz, traj[6].xyz)
count = 0
for frame in traj[:].iterframe():
count += 1
aa_eq(frame.xyz, traj[-1].xyz)
def test_calc_atomicfluct_with_unitcell(self):
# use iterload for load_batch
traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
state = pt.load_cpptraj_state(
'''
distance :3 :7
atomicfluct @CA
distance :3 :7''', traj)
state.run()
# use `load` method
t0 = pt.load(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
data = pt.atomicfluct(traj, '@CA')
aa_eq(data, state.data[-2].values)
# make sure that traj's coordinates were not altered
# https://github.com/Amber-MD/pytraj/issues/1166
aa_eq(pt.distance(t0, ':3 :7'), state.data[-1])
aa_eq(traj.xyz, t0.xyz)
def test_0(self):
import numpy as np
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
traj2 = traj[:]
d1 = pt.calc_center_of_mass(traj, dtype='dataset')
d2 = pt.calc_center_of_mass(traj2, dtype='dataset')
for frame in traj:
pass
saved_d0 = np.loadtxt(fn('vec.out'), skiprows=1, usecols=(1, 2, 3))
aa_eq(d1.to_ndarray().flatten(), saved_d0.flatten())
aa_eq(d2.to_ndarray().flatten(), saved_d0.flatten())
aa_eq(pt.center_of_geometry(traj, dtype='ndarray'),
pt.center_of_geometry(traj2, dtype='ndarray'))
def test_len_in_memory(self):
N = 10
farray = FARRAY[:N].copy()
assert farray.n_frames == N
old_xyz_5_10 = farray[5].xyz[:10]
assert farray[:3].n_frames == 3
assert farray[1:3].n_frames == 2
assert farray[3:1].n_frames == 0
assert farray[3:1:-1].n_frames == 2
assert farray[-1:-3].n_frames == 0
assert farray[-1:-3:-1].n_frames == 2
aa_eq(farray[-1].xyz, farray[N - 1].xyz)
# need to create a temp farray
subfarray = farray[5:1:-1]
aa_eq(subfarray[0].xyz, farray[5].xyz)
aa_eq(old_xyz_5_10, farray[5].xyz[:10])
f_last = farray[-3:-1][-1]
def test_iterframe_indices(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
t0 = traj[:]
indices = range(3)
d1 = pt.radgyr(traj[indices])
d2 = pt.radgyr(traj, frame_indices=indices)
aa_eq(d2, d1)
n_frames = traj.n_frames
aa_eq(
np.array([frame.xyz.copy() for frame in
traj._iterframe_indices([-2, -1])]),
traj[[n_frames-2, n_frames-1]].xyz) # yapf: disable
aa_eq(
traj[[-2, -1]].xyz,
traj[[n_frames-2, n_frames-1]].xyz) # yapf: disable
def test_len_TrajectoryIterator(self):
# create alias of `ts` (TrajectoryIterator instance created above)
farray = ts
N = ts.n_frames
assert farray.n_frames == N
old_xyz_5_10 = farray[5].xyz[:10].copy()
assert farray[:3].n_frames == 3
assert farray[1:3].n_frames == 2
assert farray[3:1].n_frames == 0
assert farray[3:1:-1].n_frames == 2
assert farray[-1:-3].n_frames == 0
assert farray[-1:-3:-1].n_frames == 2
# need to store xyz
xyz = farray[-1].xyz.copy()
aa_eq(xyz, farray[N - 1].xyz)
# need to create a temp farray
subfarray = farray[5:1:-1]
aa_eq(subfarray[0].xyz, farray[5].xyz)
aa_eq(old_xyz_5_10, farray[5].xyz[:10])
def test_molsurf(self):
traj = self.traj
text = '''
parm {0}
trajin {1}
molsurf @CA
molsurf @CA probe 1.2
molsurf @CA probe 1.2 offset 0.3
'''.format(traj.top.filename, traj.filename)
state = pt.load_cpptraj_state(text)
state.run()
cpp_data = state.data[1:].values
atom_indices = traj.top.select("@CA")
for mask in [atom_indices, '@CA']:
aa_eq(pt.molsurf(traj, mask), cpp_data[0])
aa_eq(pt.molsurf(traj, mask, probe=1.2), cpp_data[1])
aa_eq(pt.molsurf(traj, mask, probe=1.2, offset=0.3), cpp_data[2])
def test_distances(self):
traj = pt.iterload(tc5b_trajin, tc5b_top)[:]
trajin = """
parm {}
trajin {}
distance @CB @CA
distance @CA @H
""".format(fn('Tc5b.parm7'), fn('Tc5b.x'))
cout = pt.datafiles.load_cpptraj_output(trajin)[1:]
mask_list = ('@CB @CA', '@CA @H')
dslist = pt.calc_distance(traj, mask_list)
dslist3_0 = pt.calc_distance(traj, mask_list[0])
dslist3_1 = pt.calc_distance(traj, mask_list[1])
# compare to cpptraj output
aa_eq(dslist.flatten(), cout.values.flatten())
aa_eq(dslist3_0, dslist[0])
aa_eq(dslist3_1, dslist[1])
def test_simple_for_coverage(self):
'''
'''
traj = pt.iterload(traj_dir, parm_dir)
h_indices = pt.select_atoms('@H', traj.top)
n_indices = pt.select_atoms('@H', traj.top) - 1
nh_indices = list(zip(n_indices, h_indices))
vecs_and_mat = pt.ired_vector_and_matrix(traj, nh_indices, dtype='tuple')
vecs_and_mat = pt.ired_vector_and_matrix(traj, nh_indices, dtype='tuple')
state_vecs = vecs_and_mat[0]
mat_ired = vecs_and_mat[1]
# get eigenvalues and eigenvectors
modes = pt.matrix.diagonalize(mat_ired, n_vecs=len(state_vecs))
evals, evecs = modes
data_0 = _ired(state_vecs,
modes=(evals, evecs),
NHbond=True,
tcorr=10000,
tstep=1.)
data_1 = _ired(state_vecs,
modes=modes,
NHbond=True,
tcorr=10000,
tstep=1)
for d0, d1 in zip(data_0, data_1):
if d0.dtype not in ['modes', ]:
aa_eq(d0.values, d1.values)
else:
# modes
# values: tuple
aa_eq(d0.values[0], d1.values[0])
aa_eq(d0.values[1], d1.values[1])
# try different dtype
out_try_new_dtype = pt.ired_vector_and_matrix(traj, nh_indices, dtype='cpptraj_dataset')
def test_multivector(self):
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
state = pt.load_batch(
traj, '''
multivector resrange 3-7 name1 C name2 N
''')
state.run()
cpp_data = state.data[1:].values
aa_eq(
pt.multivector(traj,
resrange='3-7',
names=('C', 'N'),
dtype='ndarray'), cpp_data)
aa_eq(
pt.multivector(traj, resrange='3-7', names='C N', dtype='ndarray'),
cpp_data)
aa_eq(
pt.multivector(traj,
resrange='3-7',
names='name1 C name2 N',
dtype='ndarray'), cpp_data)
def testTwoTrajTypes(self):
'''test different metrics with different traj objects
'''
funclist = [pt.iterload, pt.load]
txt = '''
parm ./data/Tc5b.top
trajin ./data/Tc5b.x
rms2d @CA metric_holder rmsout tmp.out
'''
for func in funclist:
traj = func("./data/Tc5b.x", "./data/Tc5b.top")
for metric in ['rms', 'nofit', 'dme']:
d0 = pt.pairwise_rmsd(traj(mask='@CA'), metric=metric)
d1 = pt.pairwise_rmsd(traj, mask='@CA', metric=metric)
d2 = pt.pairwise_rmsd(traj(), mask='@CA', metric=metric)
txt0 = txt.replace('metric_holder', metric)
state = pt.datafiles.load_cpptraj_output(txt0, dtype='state')
d3 = state.datasetlist[-1].values
aa_eq(d0, d1)
aa_eq(d0, d2)
aa_eq(d0, d3)
def test_superpose_trajectory_iterator_pytraj_method(self):
traj_on_disk = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
traj_on_disk2 = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
traj_on_mem = pt.load(fn('Tc5b.x'), fn('Tc5b.top'))
ref = pt.iterload(fn("Tc5b.crd"), fn('Tc5b.top'))[0]
pt.superpose(traj_on_mem, ref=ref, mask='@CA')
pt.superpose(traj_on_disk, ref=ref, mask='@CA')
assert traj_on_disk._being_transformed == True, '_being_transformed must be True'
aa_eq(traj_on_mem.xyz, traj_on_disk.xyz)
# test saving
with tempfolder():
traj_on_mem.save('t0.nc', overwrite=True)
traj_on_disk.save('t1.nc', overwrite=True)
aa_eq(
pt.load('t0.nc', traj_on_mem.top).xyz,
pt.load('t1.nc', traj_on_disk.top).xyz)
# turn off superpose
traj_on_disk._being_transformed = False
aa_eq(traj_on_disk.xyz, traj_on_disk2.xyz)
def test_assert(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
fa = Trajectory.from_iterable(iterframe_master(traj), top=traj.top)
for f0, f1 in zip(fa, traj):
aa_eq(f0.xyz, f1.xyz)
def test_ired_vector(self):
'''test mask as a list of strings or as a 2D array of integers
'''
parm_dir = os.path.join(cpptraj_test_dir, 'Test_IRED',
'1IEE_A_prot.prmtop')
trajin_dir = os.path.join(cpptraj_test_dir, 'Test_IRED',
'1IEE_A_test.mdcrd')
traj = pt.iterload(trajin_dir, parm_dir)
# get a list of mask from cpptraj input
maskes = []
lines = None
n_indices_cpp = []
with open('data/ired.in', 'r') as fh:
lines = fh.readlines()
for line in lines:
if 'vector' in line and 'ired' in line:
# example: vector v100 @1541 ired @1542
sline = line.split()
mask = ' '.join((sline[2], sline[4]))
n_indices_cpp.append(int(sline[2][1:]) - 1)
maskes.append(mask)
h_indices_cpp = [i + 1 for i in n_indices_cpp]
# calcuate vector from a list of strings
data_vec = va.vector_mask(traj, maskes)
# calcuate vector from a 2d array of integers
nh_indices = np.array(list(zip(n_indices_cpp, h_indices_cpp)))
data_vec_2 = va.vector_mask(traj, nh_indices)
# re-create cpptraj input to run cpptraj
txt = ''.join(lines)
# add parm and trajin lines
txt = 'parm ' + parm_dir + '\n' + \
'trajin ' + trajin_dir + '\n' + \
txt
state = pt.datafiles.load_cpptraj_output(txt, dtype='state')
state.run()
cpp_data = state.datasetlist
cpp_vectors = cpp_data.grep('vector', mode='dtype').values
cpp_matired = cpp_data.grep('matrix', mode='dtype')['matired']
# assert between pytraj's data_vec and cpptraj's cpp_vectors
aa_eq(data_vec, cpp_vectors)
# from a 2D array of integers
aa_eq(data_vec_2, cpp_vectors)
# test ired vector with ired matrix
# open file
with open('data/ired_reduced.in', 'r') as fh:
text = ''.join(fh.readlines())
state2 = pt.load_batch(traj, text)
state2.run()
data = pt.ired_vector_and_matrix(traj, nh_indices, order=2)
data_vec_3 = data[0]
assert len(data_vec_3) == 126, 'must have 126 vectors'
matired = data[1]
# TODO: know why??
matired /= matired[0, 0]
aa_eq(data_vec_3, cpp_vectors)
assert pt.tools.rmsd(matired.flatten(),
cpp_matired.values) < 1E-6, 'matired'
def test_iterframe_from_array(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
# no mass
fi = pt.iterframe_from_array(traj.xyz, traj.n_atoms,
range(traj.n_frames))
for f_traj, f_fi in zip(traj, fi):
aa_eq(f_traj.xyz, f_fi.xyz)
# f_fi mass must be [1.0, ...]
aa_eq(f_fi.mass, [1.0 for _ in range(traj.n_atoms)])
# mass from Topology
fi = pt.iterframe_from_array(traj.xyz, traj.n_atoms,
range(traj.n_frames), traj.top)
for f_traj, f_fi in zip(traj, fi):
aa_eq(f_traj.xyz, f_fi.xyz)
aa_eq(f_fi.mass, f_traj.mass)
aa_eq(f_fi.mass, traj.top.mass)
# mass from array
fi = pt.iterframe_from_array(traj.xyz,
traj.n_atoms,
range(traj.n_frames),
mass=traj.top.mass)
for f_traj, f_fi in zip(traj, fi):
aa_eq(f_traj.xyz, f_fi.xyz)
aa_eq(f_fi.mass, f_traj.mass)
aa_eq(f_fi.mass, traj.top.mass)
def test_pickle_datasetlist(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
dslist = pt.multidihedral(traj)
pt.to_pickle(dslist, 'ds.pk')
dslist2 = pt.read_pickle('ds.pk')
aa_eq(dslist.values, dslist2.values)
def test_frame_indices_for_function(self):
traj = self.traj
pdict = pt.__dict__
funclist = list(
set(pdict[key] for key in dir(pt)
if hasattr(pdict[key], '_issuper_dispatched')))
frame_indices = [0, 2]
# remove 'calc_jcoupling' since does not have kfile on travis
# remove energy_decomposition since does not have sander
# remove center, why?
# remove search_neighbors, why? (got messup with Frame memory owner)
excluded_fn = [
jcoupling,
volmap,
center,
search_neighbors,
atomiccorr,
autoimage,
closest,
volume,
superpose,
randomize_ions,
check_structure,
align_principal_axis,
]
func_nu = [
calc_epsilon,
calc_alpha,
calc_zeta,
calc_beta,
calc_nu1,
calc_nu2,
calc_delta,
calc_chin,
calc_gamma,
]
# default mask, default ref
for func in funclist:
if func not in excluded_fn:
if func is pt.calc_multivector:
data_0 = func(
traj,
resrange='1-6',
names='C N',
frame_indices=frame_indices)
data_1 = func(
traj[frame_indices], resrange='1-6', names='C N')
elif func is pt.volmap:
# use water
data_0 = func(
self.traj_ortho,
mask=':WAT@O',
grid_spacing=(0.2, 0.2, 0.2),
centermask='!:1-13',
frame_indices=frame_indices)
data_1 = func(
self.traj_ortho[frame_indices],
mask=':WAT@O',
centermask='!:1-13',
grid_spacing=(0.2, 0.2, 0.2))
elif func in func_nu:
data_0 = func(self.traj_nu, frame_indices=frame_indices)
data_1 = func(self.traj_nu[frame_indices])
else:
data_0 = func(traj, frame_indices=frame_indices)
data_1 = func(traj[frame_indices])
if isinstance(data_0, np.ndarray):
aa_eq(data_0, data_1)
elif isinstance(data_0, pt.DatasetList):
for arr0, arr1 in zip(data_0, data_1):
# do each element in case we can not convert DatasetList to
# ndarray
if not isinstance(arr0[0], string_types):
aa_eq(arr0.values, arr1.values)
elif isinstance(data_0, DatasetHBond):
aa_eq(data_0.data.values, data_1.data.values)
elif isinstance(data_0, (list, tuple)):
# dssp
aa_eq(data_0[-1].values, data_1[-1].values)
else:
raise RuntimeError(
'must return ndarray or DatasetList or DatasetHBond')
# test excluded fns
aa_eq(
pt.atomiccorr(traj[frame_indices], '@CA'),
pt.atomiccorr(traj, '@CA', frame_indices=frame_indices))
# align_principal_axis
indices = [0, 3, 7]
t0 = self.traj[:]
t1 = self.traj[indices]
pt.align_principal_axis(t0, frame_indices=indices)
pt.align_principal_axis(t1)
aa_eq(t0[indices].xyz, t1.xyz)
# make sure that other frames are not affected
other_indices = list(set(range(10)) - set(indices))
aa_eq(self.traj[other_indices].xyz, t0[other_indices].xyz)
def test_load_comprehensive():
traj = traj_tz2_ortho
trajin, tn = fn("tz2.ortho.nc"), fn("tz2.ortho.parm7")
# load from filelist
t0 = pt.load([trajin, trajin], tn)
n_frames_half = int(t0.n_frames / 2)
aa_eq(traj.xyz, t0[:n_frames_half].xyz)
aa_eq(traj.xyz, t0[n_frames_half:].xyz)
# frame_slice
t0 = pt.io.load_traj(trajin, tn, frame_slice=(0, 3))
aa_eq(traj_tz2_ortho[:3].xyz, t0.xyz)
# mask
t1 = pt.load(trajin, tn, mask='@CA')
aa_eq(t1.xyz, traj['@CA'].xyz)
# frame_indices, list
t1 = pt.load(trajin, tn, frame_indices=[0, 3])
aa_eq(t1.xyz, traj[[0, 3]].xyz)
# frame_indices, tuple
t1 = pt.load(trajin, tn, frame_indices=(0, 3))
aa_eq(t1.xyz, traj[[0, 3]].xyz)
# frame_indices with negative index
t12 = pt.load(trajin, tn, frame_indices=(-2, -1))
aa_eq(t12.xyz, traj[[traj.n_frames - 2, traj.n_frames - 1]].xyz)
# mask and frame_indices
t2 = pt.load(trajin, tn, mask='@CA', frame_indices=[3, 8])
aa_eq(t2.xyz, traj[[3, 8], '@CA'].xyz)
# stride
t2 = pt.load(trajin, tn, stride=2)
aa_eq(t2.xyz, traj[::2].xyz)
# stride with mask
t2 = pt.load(trajin, tn, stride=2, mask='@CA')
aa_eq(t2.xyz, traj[::2, '@CA'].xyz)
# stride, ignore frame_indices if stride is given
t2 = pt.load(trajin, tn, stride=2, frame_indices=[2, 5, 8])
aa_eq(t2.xyz, traj[::2].xyz)
def test_load_url():
url = 'https://raw.githubusercontent.com/Amber-MD/pytraj/master/tests/data/1L2Y.pdb'
local_traj = pt.load(fn('1L2Y.pdb'))
github_traj = pt.io.load_url(url)
aa_eq(local_traj.xyz, github_traj.xyz)
def test_iterload_comprehensive():
trajin, tn = fn("tz2.ortho.nc"), fn("tz2.ortho.parm7")
# frame_slice
t0 = pt.iterload(trajin, tn, frame_slice=(0, -1, 0))
aa_eq(traj_tz2_ortho.xyz, t0.xyz)
t0 = pt.iterload(trajin, tn, frame_slice=(0, -1, 2))
aa_eq(traj_tz2_ortho.xyz[::2], t0.xyz)
# stride
t0 = pt.iterload(trajin, tn, stride=2)
aa_eq(traj_tz2_ortho.xyz[::2], t0.xyz)
# stride, ignore frame_slice
t0 = pt.iterload(trajin, tn, stride=2, frame_slice=(0, -1, 3))
aa_eq(traj_tz2_ortho.xyz[::2], t0.xyz)
# stride, load two files
t0 = pt.iterload([trajin, trajin], tn, stride=2)
xyz_2 = np.vstack((traj_tz2_ortho.xyz[::2], traj_tz2_ortho.xyz[::2]))
aa_eq(xyz_2, t0.xyz)
# stride, load two files, ignore frame_slice
t0 = pt.iterload([trajin, trajin],
tn,
stride=2,
frame_slice=[(0, -1, 5), (0, -1, 2)])
xyz_2 = np.vstack((traj_tz2_ortho.xyz[::2], traj_tz2_ortho.xyz[::2]))
aa_eq(xyz_2, t0.xyz)
# stride, 4 trajs
filenames, tn = get_remd_fn('remd_ala2')
t0 = pt.iterload(filenames, tn, stride=3)
# add frame_slice
t1 = pt.iterload(filenames, tn, frame_slice=[
(0, -1, 3),
] * 4)
xyz_expected = np.vstack(
[pt.iterload(fname, tn)[::3].xyz for fname in filenames])
aa_eq(xyz_expected, t0.xyz)
aa_eq(xyz_expected, t1.xyz)
# stride, 4 trajs, ignore frame_slice
filenames, tn = get_remd_fn('remd_ala2')
t0 = pt.iterload(filenames, tn, stride=3, frame_slice=(0 - 1, 4))
xyz_expected = np.vstack(
[pt.iterload(fname, tn)[::3].xyz for fname in filenames])
aa_eq(xyz_expected, t0.xyz)
def test_get_coordinates_trajecotoryiterator():
'''immutable pytraj.TrajectoryIterator
'''
traj = traj_tz2_ortho.copy()
# all coordinates
xyz = pt.get_coordinates(traj)
aa_eq(traj.xyz, xyz)
# given frames
xyz = pt.get_coordinates(traj, frame_indices=[0, 5])
aa_eq(traj[[0, 5]].xyz, xyz)
# given frames, autoimage=True
xyz = pt.get_coordinates(traj, frame_indices=[0, 5], autoimage=True)
aa_eq(traj[[0, 5]].autoimage().xyz, xyz)
# given frames, autoimage=True, rmsfit=ref
ref = traj[-3]
pt.autoimage(ref, top=traj.top)
xyz = pt.get_coordinates(traj,
frame_indices=[0, 5],
autoimage=True,
rmsfit=ref)
aa_eq(traj[[0, 5]].autoimage().superpose(ref=ref).xyz, xyz)
xyz = pt.get_coordinates(traj,
frame_indices=range(3),
autoimage=True,
rmsfit=ref)
# with mask
xyz = pt.get_coordinates(traj, mask='@CA')
aa_eq(xyz, traj['@CA'].xyz)
# slow
fi = pt.pipe(traj, ['autoimage'])
aa_eq(pt.get_coordinates(fi), traj[:].autoimage().xyz)
# raise
with pytest.raises(ValueError):
pt.get_coordinates(traj(), frame_indices=[0, 2])
def test_nupars_vs_x3dna(self):
traj = pt.iterload(fn('Test_NAstruct/x3dna/rna.pdb'))
ref = pt.iterload(fn('Test_NAstruct/x3dna/rna_nab.pdb'))
nu = pt.nastruct(traj, ref=ref, groove_3dna=True)
root = fn('Test_NAstruct/x3dna/')
# helical pars
saved_helical_pars = np.loadtxt(root + 'bp_helical.par',
skiprows=3,
usecols=range(1, 13)).T
aa_eq(nu.shear[1][0], saved_helical_pars[0], decimal=3)
aa_eq(nu.stretch[1][0], saved_helical_pars[1], decimal=3)
aa_eq(nu.stagger[1][0], saved_helical_pars[2], decimal=3)
aa_eq(nu.buckle[1][0], saved_helical_pars[3], decimal=3)
aa_eq(nu.prop[1][0], saved_helical_pars[4], decimal=3)
aa_eq(nu.open[1][0], saved_helical_pars[5], decimal=3)
aa_eq(nu.xdisp[1][0], saved_helical_pars[6][1:], decimal=3)
aa_eq(nu.ydisp[1][0], saved_helical_pars[7][1:], decimal=3)
aa_eq(nu.hrise[1][0], saved_helical_pars[8][1:], decimal=3)
aa_eq(nu.incl[1][0], saved_helical_pars[9][1:], decimal=3)
aa_eq(nu.tip[1][0], saved_helical_pars[10][1:], decimal=3)
aa_eq(nu.htwist[1][0], saved_helical_pars[11][1:], decimal=3)
# bp_step
saved_helical_pars = np.loadtxt(root + 'bp_step.par',
skiprows=3,
usecols=range(1, 13)).T
aa_eq(nu.shift[1][0], saved_helical_pars[6][1:], decimal=3)
aa_eq(nu.slide[1][0], saved_helical_pars[7][1:], decimal=3)
aa_eq(nu.tilt[1][0], saved_helical_pars[9][1:], decimal=3)
aa_eq(nu.roll[1][0], saved_helical_pars[10][1:], decimal=3)
aa_eq(nu.twist[1][0], saved_helical_pars[11][1:], decimal=3)
# grove
aa_eq(nu.minor[1][0], [15.8, 15.8, 15.5], decimal=1)
aa_eq(nu.major[1][0], [19.9, 20.8, 20.0], decimal=1)