def test_constructor(self):
pname = fn("tz2.ortho.parm7")
tname = fn("tz2.ortho.nc")
traj = pt.Trajectory(tname, top=pname)
assert traj.n_frames == 10
traj = pt.Trajectory([tname, tname], top=pname)
on_dis_traj = pt.iterload([tname, tname], pname)
assert traj.n_frames == on_dis_traj.n_frames == 20
aa_eq(traj.unitcells, on_dis_traj.unitcells)
def test_raise_construtor(self):
self.assertRaises(ValueError, lambda: pt.Trajectory(pt.trajectory))
# raise if filename is not string or list of string
empty_traj = pt.Trajectory()
empty_traj.top = pt.datafiles.load_tz2()[:].top
self.assertRaises(ValueError, lambda: empty_traj.load(pt.Trajectory))
# raise if empty Topology
xyz = np.arange(90).astype('f8').reshape(3, 10, 3)
self.assertRaises(ValueError, lambda: pt.Trajectory(xyz=xyz, top=pt.Topology()))
def test_closest_compared_to_cpptraj(self):
trajin = fn('tz2.ortho.nc')
parm = fn('tz2.ortho.parm7')
traj = pt.iterload(trajin, parm, frame_slice=[
(0, 2),
])
state = pt.load_cpptraj_state('''
parm {}
trajin {} 1 2
autoimage
closest 100 :1-13
createcrd mycrd'''.format(parm, trajin))
state.run()
fi, top = pt.closest(traj(autoimage=True),
mask=':1-13',
n_solvents=100)
xyz = pt.get_coordinates(fi)
t0 = pt.Trajectory(xyz=xyz, top=top)
aa_eq(state.data['mycrd'].xyz, t0.xyz)
# dtype = 'trajectory'
t1 = pt.closest(traj(autoimage=True),
mask=':1-13',
n_solvents=100,
dtype='trajectory')
aa_eq(state.data['mycrd'].xyz, t1.xyz)
def test_get_coordinates_trajectory():
'''mutable pytraj.Trajectory
'''
traj = pt.Trajectory(xyz=traj_tz2_ortho.xyz, top=traj_tz2_ortho.top)
# make a different copy since ``traj`` is mutable
traj2 = traj.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(traj2[[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(traj2[[0, 5]].autoimage().superpose(ref=ref).xyz, xyz)
def shrink(xtc,gro,simname):
if os.path.exists(simname + '.xtc'):
print simname + '_ai.xtc', "exists"
else:
print "writing", simname + '.xtc'
traj = md.load_xtc(xtc,top=gro)
traj = pt.Trajectory(xyz=m_traj.xyz.astype('f8'), top=topology_name)
traj.autoimage()
traj.save(simname + '_ai.xtc')
traj_pt = []
traj = md.load_xtc(simname + '_ai.xtc',top=gro)
exit()
with md.formats.XTCTrajectoryFile(simname + '.xtc', 'w') as f:
for fr in range(50000)[::100]:
print "frame", fr
structure = traj[fr]
peptide = structure.atom_slice(structure.topology.select('protein'))[0]
peptide.center_coordinates()
f.write(peptide.xyz*10)
peptide.save(simname + '.pdb')
return None
def test_indexing(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
traj2 = pt.TrajectoryIterator()
traj2.top = pt.load_topology(fn('Tc5b.top'))
traj2._load(fn('Tc5b.x'))
farray = traj2[[0, 9, 1]]
assert farray.n_frames == 3
assert traj2[0].atom(0) == farray[0].atom(0)
assert traj2[9].atom(0) == farray[1].atom(0)
assert traj2[1].atom(0) == farray[2].atom(0)
arr = np.asarray(traj2[0]._buffer1d[:])
frame0 = traj2[0]
arr0 = np.asarray(frame0._buffer1d[:])
mat0 = np.asmatrix(arr0).reshape(304, 3)
mat0[:, 0] = np.asmatrix(list(range(304))).reshape(304, 1)
assert frame0[0, 0] == 0.
assert frame0[1, 0] == 1.
assert frame0[2, 0] == 2.
# raise if size = 0
traj3 = pt.Trajectory()
assert traj3.n_frames == 0, 'empty Trajectory, n_frames must be 0'
self.assertRaises(IndexError, lambda: traj3[0])
self.assertRaises(IndexError, lambda: traj3.__setitem__(0, traj[3]))
def test_slice_and_iterate_trajectory_with_force_and_velocity(self):
traj_on_disk = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
n_atoms = traj_on_disk.n_atoms
n_frames = traj_on_disk.n_frames
xyz = traj_on_disk.xyz
force = np.random.rand(n_frames * n_atoms * 3).reshape(
(n_frames, n_atoms, 3))
velocity = np.random.rand(n_frames * n_atoms * 3).reshape(
(n_frames, n_atoms, 3))
top = traj_on_disk.top
traj = pt.Trajectory(xyz=xyz, top=top, force=force, velocity=velocity)
aa_eq(traj.forces, force)
aa_eq(traj.velocities, velocity)
# iterating
for index, frame in enumerate(traj):
aa_eq(frame.force, traj.forces[index])
aa_eq(frame.velocity, traj.velocities[index])
# slicing
aa_eq(traj[0].force, traj.forces[0])
aa_eq(traj[0].velocity, traj.velocities[0])
aa_eq(traj[::2].forces, traj.forces[::2])
aa_eq(traj[::2].velocities, traj.velocities[::2])
ca_indices = traj_on_disk.top.select('@CA')
aa_eq(traj['@CA'].velocities, traj.velocities[:, ca_indices])
aa_eq(traj['@CA'].forces, traj.forces[:, ca_indices])
def test_slice_basic(self):
traj2 = pt.Trajectory()
traj2.top = pt.load_topology(fn('Tc5b.top'))
traj2.load(fn('Tc5b.x'))
traj2.load(fn('Tc5b.x'))
traj2.load(fn('Tc5b.x'))
traj2.load(fn('Tc5b.x'))
fsub = traj2[2:10]
fsub[0][0] = 100.
def test_allocate_frames(self):
traj = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
traj2 = pt.Trajectory()
traj2._allocate(traj.n_frames, traj.n_atoms)
assert (traj2.shape == traj.shape)
traj2.top = traj.top.copy()
traj2.xyz = traj.xyz[:]
aa_eq(traj2.xyz, traj.xyz)
def test_slice_basic(self):
traj2 = pt.Trajectory()
traj2.top = pt.load_topology("./data/Tc5b.top")
traj2.load("./data/Tc5b.x")
traj2.load("./data/Tc5b.x")
traj2.load("./data/Tc5b.x")
traj2.load("./data/Tc5b.x")
fsub = traj2[2:10]
fsub[0][0] = 100.
def test_closest(self):
# raise if not has solvent
traj0 = pt.iterload(fn('tz2.nc'),
fn('tz2.parm7'),
frame_slice=[(0, 2)])
with pytest.raises(RuntimeError):
pt.closest(traj0)
traj = pt.iterload(fn('tz2.ortho.nc'),
fn('tz2.ortho.parm7'),
frame_slice=[(0, 2)])
fi, top = pt.closest(traj)
coords = []
for frame in fi:
coords.append(frame.xyz.copy())
assert isinstance(frame, pt.Frame), 'must be Frame'
# make a Trajectory
fi, top = pt.closest(traj)
xyz = pt.get_coordinates(fi)
t0 = pt.Trajectory(xyz=xyz, top=top)
aa_eq(np.array(coords), t0.xyz)
# test write to disk
fi, top = pt.closest(traj)
new_traj = pt.Trajectory(top=top)
for frame in fi:
new_traj.append(frame)
pt.write_traj(outputname('fi.nc'), new_traj, overwrite=True)
# load back
t1 = pt.load(outputname('fi.nc'), top=top)
aa_eq(t0.xyz, t1.xyz)
# make sure n_sovent=10 (default)
n_solvents = 0
for mol in top.mols:
if mol.is_solvent():
n_solvents += 1
assert n_solvents == 10, 'must be 10 solvents'
def pack(traj, mol, n_copies, unitcells=None, ig=8888, grid_spacing=0.2):
'''
Parameters
----------
traj : pytraj.Trajectory
mol : pytraj.Trajectory
unitcells : None or np.ndarray, dim=2
if None, use box info from traj else use it
n_copies : number of `mol`
ig : int
randome seed
grid_spacing : float
'''
add_to_box_exe = amberbin('AddToBox') or 'AddToBox'
input_pdb = 'input.pdb'
mol_pdb = 'mol.pdb'
out_pdb = 'out.pdb'
assert mol.n_frames == 1
total_n_atoms = traj.n_atoms + mol.n_atoms * n_copies
new_traj_xyz = np.empty((traj.n_frames, total_n_atoms, 3), dtype='f8')
with tempfolder():
mol.save(mol_pdb, overwrite=True)
for index, frame in enumerate(traj):
pytraj.write_traj(input_pdb, traj=frame, top=traj.top, overwrite=True)
parm = parmed.load_file(input_pdb)
if unitcells is not None:
parm.box = unitcells[index]
else:
assert frame.has_box(), 'must have box info'
parm.box = frame.box
# add remark 290
parm.save(input_pdb, overwrite=True)
command = [
add_to_box_exe,
'-c', input_pdb,
'-a', mol_pdb,
'-na', str(n_copies),
'-IG', str(ig),
'-G', str(grid_spacing),
'-o', out_pdb
]
try:
subprocess.check_output(command, stderr=subprocess.STDOUT)
new_traj_xyz[index] = pytraj.load(out_pdb).xyz
except subprocess.CalledProcessError as e:
return e.output.decode()
top = pytraj.load_topology(out_pdb)
return pytraj.Trajectory(xyz=new_traj_xyz, top=top)
def test_ired_need_lapack_cpptraj(self):
state = pt.load_cpptraj_state(txt)
state.run()
xyz = state.data['CRD1'].xyz
top = state.data['CRD1'].top
traj = pt.Trajectory(xyz=xyz, top=top)
state_vecs = state.data[1:-3].values
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))
mat_ired = pt.ired_vector_and_matrix(traj,
mask=nh_indices,
order=2)[-1]
mat_ired /= mat_ired[0, 0]
# matired: make sure to reproduce cpptraj output
aa_eq(mat_ired, state.data['matired'].values)
# get modes
modes = state.data[-2]
cpp_eigenvalues = modes.eigenvalues
cpp_eigenvectors = modes.eigenvectors
evals, evecs = np.linalg.eigh(mat_ired)
# need to sort a bit
evals = evals[::-1]
# cpptraj's eigvenvalues
aa_eq(evals, cpp_eigenvalues)
# cpptraj's eigvenvectors
# use absolute values to avoid flipped sign
# from Dan Roe
# In practice, the "sign" of an eigenvector depends on the math library used to calculate it.
# This is in fact why the modes command displacement test is disabled for cpptraj.
# I bet if you use a different math library (e.g. use your system BLAS/LAPACK instead of the one bundled with Amber
# or vice versa) you will get different signs.
# Bottom line is that eigenvector sign doesn't matter.
aa_eq(np.abs(evecs[:, ::-1].T), np.abs(cpp_eigenvectors), decimal=4)
data = _ired(state_vecs, modes=(cpp_eigenvalues, cpp_eigenvectors))
order_s2 = data['IRED_00127[S2]']
# 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, cpp_order_s2, decimal=5)
def test_append_trajectory(self):
# test append
traj = pt.Trajectory()
t = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
traj.top = t.top
# append single Frame
traj.append(t[0])
assert traj.n_frames == 1
# append xyz
traj.append(t.xyz[:])
assert traj.n_frames == t.n_frames + 1
# append TrajectoryIterator
traj.append(t)
assert traj.n_frames == t.n_frames * 2 + 1
# append frame_iter
traj.append(t.iterframe())
assert traj.n_frames == t.n_frames * 3 + 1
# append pt.iterframe_master
traj.append(pt.iterframe_master(t))
assert traj.n_frames == t.n_frames * 4 + 1
# append itself
NFrames = traj.n_frames
traj.append(traj)
assert traj.n_frames == NFrames * 2
# append itself frame_iter
traj.append(traj.iterframe(stop=2))
assert traj.n_frames == NFrames * 2 + 2
# append pt.iterframe_master for itself
NFrames = traj.n_frames
traj.append(pt.iterframe_master(traj))
assert traj.n_frames == NFrames * 2
# append pt.iterframe_master for itself + other
n0 = traj.n_frames
n1 = t.n_frames
traj.append(pt.iterframe_master([traj, t]))
assert traj.n_frames == 2 * n0 + n1
def test_autoimage_rotatedihedral(self):
traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
farray = traj[:]
t0trajectory = pt.Trajectory(traj)
aa_eq(farray.unitcells, t0trajectory.unitcells)
# autoimage
farray.autoimage()
t0trajectory.autoimage()
aa_eq(farray.xyz, t0trajectory.xyz)
# rotate_dihedral
pt.rotate_dihedral(t0trajectory, '3:phi:120')
pt.rotate_dihedral(farray, '3:phi:120')
aa_eq(farray.xyz, t0trajectory.xyz)
aa_eq(
pt.calc_phi(t0trajectory, '3').values,
[120 for _ in range(t0trajectory.n_frames)])
def test_closest_compared_to_cpptraj(self):
traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
state = pt.load_cpptraj_state(
'''
autoimage
closest 100 :1-13
createcrd mycrd''', traj)
state.run()
fi, top = pt.closest(traj(autoimage=True),
mask=':1-13',
n_solvents=100)
xyz = pt.get_coordinates(fi)
t0 = pt.Trajectory(xyz=xyz, top=top)
aa_eq(state.data['mycrd'].xyz, t0.xyz)
# dtype = 'trajectory'
t1 = pt.closest(traj(autoimage=True),
mask=':1-13',
n_solvents=100,
dtype='trajectory')
aa_eq(state.data['mycrd'].xyz, t1.xyz)
def cal_dih(top, trajectory, dih_mask, dihnum):
'''
top is an amber topology file
trajectory is an amber trajectorty, it can be both netcdf or ascii
dih_mask is the dihedral atom number mask e.g @2 @3 @5 @8
dihnum is the number of dihedral being fitted
cal_dih() returns dihedral values for a given mask
'''
# first load trajectory
traj = pt.Trajectory(trajectory, top)
# if only one dihedral then
if dihnum == 1:
dih_data = pt.dihedral(traj, '%s' % (dih_mask))
return dih_data
# we have multiple dihedrals
else:
dih_data = []
# calculate all dihedrals
for mask in dih_mask:
data = pt.dihedral(traj, '%s' % (mask))
dih_data.append(data)
return dih_data
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(fn('issue991/short.dcd'),
fn('issue991/pdb.gz'),
mask='(!:1-256)&(@H1,@H2,@H3,@H4,@H5)')
# Trajectory of the center of mass of the first two residues
xyz = np.empty((2, traj.n_frames, 3))
xyz[0] = pt.center_of_mass(traj, mask=':1')
xyz[1] = pt.center_of_mass(traj, mask=':2')
# "topology" using the first two atoms
minitop = traj.top['@1,2']
minitraj = pt.Trajectory(xyz=np.ascontiguousarray(
xyz.transpose((1, 0, 2))),
top=minitop)
# 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?
exts = ['nc', 'dcd', 'mdcrd', 'crd', 'pdb', 'trr']
exts.remove('mdcrd')
exts.remove('crd')
for ext in exts:
junk_fn = 'junk.' + ext
pt.write_traj(filename=junk_fn, traj=minitraj, overwrite=True)
# load coord back to make sure we correctly write it
new_traj = pt.iterload(junk_fn, minitop)
# mdcrd, crd, pdb has only 3 digits after decimal
decimal = 5 if ext in ['nc', 'dcd', 'trr'] else 3
aa_eq(minitraj.xyz, new_traj.xyz, decimal=decimal)
def test_closest(self):
# raise if not has solvent
traj0 = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
self.assertRaises(RuntimeError, lambda: pt.closest(traj0))
traj = pt.iterload(fn('tz2.ortho.nc'), fn('tz2.ortho.parm7'))
fi, top = pt.closest(traj)
coords = []
for frame in fi:
coords.append(frame.xyz.copy())
assert isinstance(frame, pt.Frame), 'must be Frame'
# make a Trajectory
fi, top = pt.closest(traj)
xyz = pt.get_coordinates(fi)
t0 = pt.Trajectory(xyz=xyz, top=top)
aa_eq(np.array(coords), t0.xyz)
# test write to disk
fi, top = pt.closest(traj)
pt.write_traj('output/fi.nc', fi, top=top, overwrite=True)
# load back
t1 = pt.load('output/fi.nc', top=top)
aa_eq(t0.xyz, t1.xyz)
# make sure n_sovent=10 (default)
n_solvents = 0
for mol in top.mols:
if mol.is_solvent():
n_solvents += 1
assert n_solvents == 10, 'must be 10 solvents'
fi, top = pt.closest(traj)
pt.write_traj('output/test.pdb', next(fi), top=top, overwrite=True)
from __future__ import print_function
from parmed.utils.netcdf import netcdf_file
import pytraj as pt
import numpy as np
fh = netcdf_file('data/mdfrc',
mmap=False) # change mdfrc to your force filename
forces = fh.variables['forces']
# do similar thing for velocities
top = pt.load_topology(
'data/mdfrc.prmtop') # change prmtop to your parm7 filename
traj = pt.Trajectory(xyz=np.ascontiguousarray(forces[:], dtype='f8'), top=top)
print('original trajectory', traj)
# strip atom atoms
# change ':1-100' to your mask (e.g ':WAT')
new_traj = pt.strip(':1-100', traj)
print('stripped trajectory', new_traj)
# write trajectory
new_traj.save('test.nc', overwrite=True)
# load pytraj
import pytraj as pt
import numpy as np
# load mdtraj
import mdtraj as md
from mdtraj.testing import get_fn
# load h5 file
#filename, topology_name = get_fn('tfit_10.xtc'), get_fn('prot0.pdb')
m_traj = md.load('tfit_10.xtc', top='prot0.pdb')
m_traj
traj = pt.Trajectory(xyz=m_traj.xyz.astype('f8'), top='prot0.pdb')
traj
# creat N-H vector pairs
# select H (backbone) indices with given residue number (from previous step)
#H_mask = ':' + ','.join(str(i) for i in resnums) + '@H'
#print('H_mask: ', H_mask)
h_indices = pt.select_atoms(traj.top, '@H')
# select N (backbone) indices
n_indices = h_indices - 1
# create pairs
nh_pairs = list(zip(n_indices, h_indices))
nh_pairs[:3]
# do calculation
s2 = pt.nh_order_parameters(traj, nh_pairs, tcorr=52801.0, tstep=1.0)
st20 = pt.nh_order_parameters(traj, nh_pairs, tcorr=20000.0, tstep=1.0)
frame = traj[1]
print(frame)
# now you want to rotate omega dihedral angle for residue 3?
# make a list to store new frames
traj_xyz = []
for deg in range(-180, 180, 5):
# since Frame does not hold Topology information, you need to
# pass it
pt.rotate_dihedral(frame, '3:omega:' + str(deg), top=traj.top)
# always make a copy since
# the `rotate_dihedral` inplace-change coords of frame
traj_xyz.append(frame.xyz.copy())
# write multiple pdbs to a single file
# just like multiple pdbs when you load from rcsb
# you can use this pdb file to view in VMD without loading
# prmtop/gro/psf/...
new_traj = pt.Trajectory(xyz=np.asarray(traj_xyz), top=traj.top)
pt.write_traj(
"./output/test0.pdb",
new_traj,
options='model',
overwrite=True)
# you can use VMD to open the new file
# vmd ./output/test0.pdb
import pytraj as pt
try:
import mdtraj as md
# load mdtraj object
m_traj = md.load_netcdf('../tests/data/tz2.ortho.nc',
'../tests/data/tz2.ortho.parm7')
print(m_traj)
# convert to pytraj object
# you can use a pdb file, a mol2 file, ... as Topology too
# as long as pytraj/cpptraj supports
traj = pt.Trajectory(xyz=m_traj.xyz.astype('f8'),
top='../tests/data/tz2.ortho.parm7')
print(traj)
# perform 'action' on traj
traj.autoimage()
# copy data back to mdtraj object
m_traj.xyz = traj.xyz[:]
# mdtraj has very fast rmsd calculation, you can pass pytraj'traj object
# to mdtraj to 'borrow' its action too.
# note that pytraj/cpptraj use Angstrom for unit while mdtraj use nm
print(md.rmsd(traj, traj, 0))
except ImportError:
print("does not have mdtraj")
def __init__(self,
top,
trajs,
rotfit=False,
mask='@CA',
stride=1,
n_blocks=1,
bframes=50000,
skip=25000):
#read sequence
if trajs[0][-3:] == 'dcd':
traj = pt.iterload(trajs[0], top)
else:
#filename, top_name = get_fn(trajs[0]), get_fn(top)
m_traj = md.load(trajs[0], top=top)
traj = pt.Trajectory(xyz=m_traj.xyz.astype('f8'), top=top)
self.sequence = {res.index + 1: res.name for res in traj.top.residues}
self.top = top
self.trajs = trajs
n_frames = len(traj)
self.n_indices = pt.select_atoms('@N & !(:1) & !(:PRO)', traj.top)
self.h_indices = self.n_indices + 1
self.nh_pairs = np.array(list(zip(self.n_indices, self.h_indices)))
res_list = sorted(
[k for k, val in self.sequence.items() if val != 'PRO' and k != 1])
self.acf = dict()
self.S2 = dict()
if n_blocks == 1:
for tt, t in enumerate(self.trajs):
if t[-3:] == 'dcd':
traj = pt.load(t, top, stride=stride)
else:
#filename, top_name = get_fn(t), get_fn(top)
m_traj = md.load(t, top=top)
traj = pt.Trajectory(xyz=m_traj.xyz.astype('f8'), top=top)
if rotfit == True:
#print('RMSD fitting on '+mask)
_ = traj.superpose(ref=-1, mask='@CA')
data_vec = va.vector_mask(traj, self.nh_pairs, dtype='ndarray')
self.acf[tt] = {
res_list[n]: pt.timecorr(vals,
vals,
order=2,
tstep=1,
tcorr=len(vals),
norm=False,
dtype='ndarray')
for n, vals in enumerate(data_vec)
}
self.S2[tt] = {
res_list[n]: S2(vals)
for n, vals in enumerate(data_vec)
}
else:
index = 0
bcount = 0
for tt, t in enumerate(self.trajs):
print(tt + 1, '/', len(self.trajs))
while bcount < n_blocks:
first_frame = bcount * skip
last_frame = first_frame + bframes
if t[-3:] == 'dcd':
traj = pt.load(t,
top,
frame_indices=slice(
first_frame, last_frame, stride))
else:
#filename, top_name = get_fn(t), get_fn(top)
m_traj = md.load(t, top=top)
m_traj = m_traj[first_frame:last_frame:stride]
traj = pt.Trajectory(xyz=m_traj.xyz.astype('f8'),
top=top)
if rotfit == True:
_ = traj.superpose(ref=-1, mask='@CA')
data_vec = va.vector_mask(traj,
self.nh_pairs,
dtype='ndarray')
self.acf[index] = {
res_list[n]: pt.timecorr(vals,
vals,
order=2,
tstep=1,
tcorr=len(vals),
norm=False,
dtype='ndarray')
for n, vals in enumerate(data_vec)
}
self.S2[index] = {
res_list[n]: S2(vals)
for n, vals in enumerate(data_vec)
}
bcount += 1
index += 1
bcount = 0
def load_mutable_traj(filename=filename):
with Dataset(filename, 'r') as fh:
c = fh['coordinates']
traj = pt.Trajectory(xyz=c[:N], top=top.copy())
traj.xyz[:] = traj.xyz.astype('f8')