def calc_density(traj=None,
command="",
top=None,
dtype='ndarray',
frame_indices=None):
# NOTE: trick cpptraj to write to file first and the reload
'''
Examples
--------
>>> import pytraj as pt
>>> traj = pt.datafiles.load_tz2_ortho()
>>> pt.density(traj, 'charge')
'''
with tempfolder():
def _calc_density(traj, command):
# TODO: update this method if cpptraj save data to
# CpptrajDatasetList
dflist = DataFileList()
tmp_filename = "tmp_pytraj_out.txt"
command = "out " + tmp_filename + " " + command
act = c_action.Action_Density()
act(command, traj, top=top, dflist=dflist)
act.post_process()
dflist.write_all_datafiles()
absolute_path_tmp = os.path.abspath(tmp_filename)
return absolute_path_tmp
dslist = CpptrajDatasetList()
fname = _calc_density(traj, command)
dslist.read_data(fname)
return get_data_from_dtype(dslist, dtype)
def calc_density(traj=None,
command="",
top=None,
dtype='ndarray',
frame_indices=None):
# NOTE: trick cpptraj to write to file first and the reload
'''
Examples
--------
>>> import pytraj as pt
>>> traj = pt.datafiles.load_tz2_ortho()
>>> pt.density(traj, 'charge')
'''
with tempfolder():
def _calc_density(traj, command):
# TODO: update this method if cpptraj save data to
# CpptrajDatasetList
dflist = DataFileList()
tmp_filename = "tmp_pytraj_out.txt"
command = "out " + tmp_filename + " " + command
act = c_action.Action_Density()
act(command, traj, top=top, dflist=dflist)
act.post_process()
dflist.write_all_datafiles()
absolute_path_tmp = os.path.abspath(tmp_filename)
return absolute_path_tmp
dslist = CpptrajDatasetList()
fname = _calc_density(traj, command)
dslist.read_data(fname)
return get_data_from_dtype(dslist, dtype)
def get_iterator_from_dslist(traj,
mask,
frame_indices,
top,
crdname='dataset_coords'):
from pytraj import Trajectory, TrajectoryIterator
from pytraj.datasets import CpptrajDatasetList
dslist = CpptrajDatasetList()
dslist.add("coords", crdname)
# need to set "rmsout" to trick cpptraj not giving error
# need " " (space) before crdset too
if isinstance(traj, (Trajectory, TrajectoryIterator)):
# we do atom stripping here before copying to DatasetCoordsCRD to save memory if
# loading from TrajectoryIterator
fi = traj.iterframe(mask=mask, frame_indices=frame_indices)
command = ''
# use Topology from fi (could be stripped to save memory)
dslist[0].top = fi.top
top_ = fi.top
else:
# ignore frame_indices
fi = iterframe_master(traj)
command = mask
top_ = get_topology(traj, top)
dslist[0].top = top_
for frame in fi:
dslist[0].append(frame)
return dslist, top_, command
def test_DatasetDouble(self):
dslist = CpptrajDatasetList()
d = dslist.add_new(dtype='double')
a = range(8)
# append
for i in a:
d.append(i)
aa_eq(a, d)
assert int(d[2]) == a[2] == 2, 'must be equal'
def test_DatasetDouble(self):
dslist = CpptrajDatasetList()
d = dslist.add_new(dtype='double')
a = range(8)
# append
for i in a:
d.append(i)
aa_eq(a, d)
assert int(d[2]) == a[2] == 2, 'must be equal'
def worker_by_actlist(rank,
n_cores=2,
traj=None,
lines=None,
dtype='dict',
ref=None,
kwd=None):
'''worker for cpptraj commands (string)
'''
# need to make a copy if lines since python's list is dangerous
# it's easy to mess up with mutable list
# do not use lines.copy() since this is not available in py2.7
# Note: dtype is a dummy argument, it is always 'dict'
if lines is None:
lines = []
frame_indices = kwd.pop('frame_indices', None)
new_lines, need_ref = check_valid_command(lines)
if frame_indices is None:
my_iter = traj._split_iterators(n_cores, rank=rank)
else:
my_iter = traj.iterframe(
frame_indices=np.array_split(frame_indices, n_cores)[rank])
if ref is not None:
if isinstance(ref, Frame):
reflist = [
ref,
]
else:
# list/tuplex
reflist = ref
else:
reflist = [
traj[0],
] if need_ref else []
dslist = CpptrajDatasetList()
if reflist:
for ref_ in reflist:
ref_dset = dslist.add('reference')
ref_dset.top = traj.top
ref_dset.add_frame(ref_)
# create Frame generator
fi = pipe(my_iter, commands=new_lines, dslist=dslist)
# just iterate Frame to trigger calculation.
for _ in fi:
pass
# remove ref
return (rank, dslist[len(reflist):].to_dict())
def read_data(filename, options=''):
"""same as readdata in cpptraj
Returns
-------
out : CpptrajDatasetList
"""
from pytraj.datasets import CpptrajDatasetList
cdslist = CpptrajDatasetList()
cdslist.read_data(filename, options)
return cdslist
def worker_by_actlist(rank,
n_cores=2,
traj=None,
lines=None,
dtype='dict',
ref=None,
kwd=None):
'''worker for cpptraj commands (string)
'''
# need to make a copy if lines since python's list is dangerous
# it's easy to mess up with mutable list
# do not use lines.copy() since this is not available in py2.7
# Note: dtype is a dummy argument, it is always 'dict'
if lines is None:
lines = []
frame_indices = kwd.pop('frame_indices', None)
new_lines, need_ref = check_valid_command(lines)
if frame_indices is None:
my_iter = traj._split_iterators(n_cores, rank=rank)
else:
my_iter = traj.iterframe(
frame_indices=np.array_split(frame_indices, n_cores)[rank])
if ref is not None:
if isinstance(ref, Frame):
reflist = [ref, ]
else:
# list/tuplex
reflist = ref
else:
reflist = [traj[0],] if need_ref else []
dslist = CpptrajDatasetList()
if reflist:
for ref_ in reflist:
ref_dset = dslist.add('reference')
ref_dset.top = traj.top
ref_dset.add_frame(ref_)
# create Frame generator
fi = pipe(my_iter, commands=new_lines, dslist=dslist)
# just iterate Frame to trigger calculation.
for _ in fi:
pass
# remove ref
return (rank, dslist[len(reflist):].to_dict())
def _rotdif(arr,
nvecs=1000,
rvecin=None,
rseed=80531,
order=2,
ncorr=-1,
tol=1E-6,
d0=0.03,
nmesh=2,
dt=0.002,
ti=0.0,
tf=-1,
itmax=-1.,
dtype='ndarray'):
'''
Parameters
----------
arr : array-like, shape (n_frames, 3, 3) or (n_frames, 9)
'''
_nvecs = 'nvecs ' + str(nvecs)
_rvecin = 'rvecin ' + rvecin if rvecin is not None else ''
_rseed = 'rseed ' + str(rseed)
_order = 'order ' + str(order)
_ncorr = 'ncorr ' + str(ncorr) if ncorr > 0 else ''
_tol = 'tol ' + str(tol)
_d0 = 'd0 ' + str(d0)
_nmesh = 'nmesh ' + str(nmesh)
_dt = 'dt ' + str(dt)
_ti = 'ti ' + str(ti)
_tf = 'tf ' + str(tf)
_itmax = 'itmax ' + str(itmax)
_rmatrix = 'rmatrix mymat'
act = CpptrajAnalyses.Analysis_Rotdif()
dslist = CpptrajDatasetList()
dslist.add_set('mat3x3', 'mymat')
arr = np.asarray(arr, dtype='f8')
msg = 'array must have shape=(n_frames, 9) or (n_frames, 3, 3)'
shape = arr.shape
if arr.ndim == 2:
assert shape[1] == 9, msg
elif arr.ndim == 3:
assert shape[1:3] == (3, 3), msg
# need to reshape to (n_frames, 9)
arr = arr.reshape(shape[0], shape[1] * shape[2])
else:
raise ValueError(msg)
def _rotdif(arr,
nvecs=1000,
rvecin=None,
rseed=80531,
order=2,
ncorr=-1,
tol=1E-6,
d0=0.03,
nmesh=2,
dt=0.002,
ti=0.0,
tf=-1,
itmax=-1.,
dtype='ndarray'):
'''
Parameters
----------
arr : array-like, shape (n_frames, 3, 3) or (n_frames, 9)
'''
_nvecs = 'nvecs ' + str(nvecs)
_rvecin = 'rvecin ' + rvecin if rvecin is not None else ''
_rseed = 'rseed ' + str(rseed)
_order = 'order ' + str(order)
_ncorr = 'ncorr ' + str(ncorr) if ncorr > 0 else ''
_tol = 'tol ' + str(tol)
_d0 = 'd0 ' + str(d0)
_nmesh = 'nmesh ' + str(nmesh)
_dt = 'dt ' + str(dt)
_ti = 'ti ' + str(ti)
_tf = 'tf ' + str(tf)
_itmax = 'itmax ' + str(itmax)
_rmatrix = 'rmatrix mymat'
act = CpptrajAnalyses.Analysis_Rotdif()
dslist = CpptrajDatasetList()
dslist.add_set('mat3x3', 'mymat')
arr = np.asarray(arr, dtype='f8')
msg = 'array must have shape=(n_frames, 9) or (n_frames, 3, 3)'
shape = arr.shape
if arr.ndim == 2:
assert shape[1] == 9, msg
elif arr.ndim == 3:
assert shape[1:3] == (3, 3), msg
# need to reshape to (n_frames, 9)
arr = arr.reshape(shape[0], shape[1] * shape[2])
else:
raise ValueError(msg)
def test_constructor_from_command_list_Trajectory(self):
'''mutable Trajectory'''
# use `load` method rather `iterload`
traj = pt.load(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7"))
# make sure no space-sensitivity
# make the code (commands) ugly is my intention.
commands = [
'autoimage ',
'autoimage',
'rmsd @CA',
'distance :3 :7',
'distance :3 :7',
'vector :2 :3',
' distance :3 :7',
'rms @C,N,O',
]
dslist = CpptrajDatasetList()
actlist = ActionList(commands, traj.top, dslist=dslist)
for frame in traj:
actlist.compute(frame)
aa_eq(pt.rmsd(traj, mask='@CA'), dslist[0])
aa_eq(pt.distance(traj, ':3 :7'), dslist[1])
aa_eq(pt.distance(traj, ':3 :7'), dslist[2])
# do not need to perform rmsfit again.
aa_eq(pt.vector.vector_mask(traj, ':2 :3'), dslist[3].values)
aa_eq(pt.distance(traj, ':3 :7'), dslist[4])
aa_eq(pt.rmsd(traj, mask='@C,N,O'), dslist[5])
def test_combine_with_frame_iterator(self):
traj = pt.iterload(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7"))
dslist = CpptrajDatasetList()
commands = [
'autoimage',
'rms',
]
actlist = ActionList(commands, top=traj.top, dslist=dslist)
def get_frameiter(actlist, traj):
for frame in traj:
actlist.compute(frame)
yield frame
def do_extra(fi):
a = []
for frame in fi:
frame.xyz = frame.xyz + 2.
a.append(frame.copy())
return a
new_list = do_extra(get_frameiter(actlist, traj))
t0 = traj[:].autoimage().superpose()
t0.xyz += 2.
aa_eq(np.array([frame.xyz for frame in new_list]), t0.xyz)
def test_combine_cpptraj_iterating_with_pytraj(self):
traj = pt.iterload(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7"))
commands = [
'autoimage',
'rms',
]
dslist = CpptrajDatasetList()
actlist = ActionList(commands, top=traj.top, dslist=dslist)
def get_fi(actlist, traj):
'''create a frame iterator with pre-processed by cpptraj
'''
for frame in traj:
actlist.compute(frame)
yield frame
ref = traj[3]
pt.autoimage(ref, top=traj.top)
fi = get_fi(actlist, traj)
rmsd_nofit_after_fitting = pt.rmsd_nofit(fi, ref=ref, top=traj.top)
t0 = traj[:].autoimage().superpose()
saved_rmsd_ = pt.rmsd_nofit(t0, ref=ref)
aa_eq(rmsd_nofit_after_fitting, saved_rmsd_)
def test_reference_with_different_topology_basic(self):
traj1 = pt.iterload(filename=tc5b_trajin, top=tc5b_top)
traj2 = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
# re-establish ActionList
dslist = CpptrajDatasetList()
dslist.add('reference', name='myref')
dslist[0].top = traj2.top
dslist[0].add_frame(traj2[0])
actlist = pt.ActionList(['rmsd @1-11 @CB ref myref'],
top=traj1.top,
dslist=dslist)
for frame in traj1:
actlist.compute(frame)
# raise if ref_mask is given but not mask
self.assertRaises(ValueError,
lambda: pt.rmsd(traj1, ref=3, ref_mask='@CB'))
self.assertRaises(
ValueError, lambda: pt.rmsd(traj1, ref=traj2[:1], ref_mask='@CB'))
# assert to cpptraj
tc5b_traj = traj1[:]
tz2_traj = traj2[:1]
cm = '''
parm {} [tc5b]
trajin {}
parm {} [tz2]
reference {} parm [tz2] 1 [myref]
rms myrmsd ref [myref] @1-10 @11-20
'''.format(tc5b_top, tc5b_trajin, tz2_top, tz2_trajin)
print(cm)
state = pt.load_cpptraj_state(cm)
with tempfolder():
state.run()
expected_rmsd = state.data[-1].values
rmsd_data = pt.rmsd(tc5b_traj,
mask='@1-10',
ref=tz2_traj,
ref_mask='@11-20')
aa_eq(expected_rmsd, rmsd_data)
def test_run_0(self):
# load traj
farray = pt.load(filename="./data/tz2.truncoct.nc",
top="./data/tz2.truncoct.parm7")[:2]
fold = farray.copy()
act = allactions.Action_Image()
ptrajin = """
center :2-11
image center familiar com :6
"""
# create 'strip' action
stripact = allactions.Action_Strip()
# creat datasetlist to hold distance data
dsetlist = CpptrajDatasetList()
dflist = DataFileList()
# creat ActionList to hold actions
alist = ActionList()
top = farray.top
# add two actions: Action_Strip and Action_Distance
alist.add(allactions.Action_Center(), ArgList(":2-11"), top=top)
alist.add(allactions.Action_Image(),
ArgList("center familiar com :6"),
top=top)
# do checking
alist.check_topology(top)
farray2 = Trajectory()
frame0 = Frame()
# testing how fast to do the actions
# loop all frames
# use iterator to make faster loop
# don't use "for i in range(farray.n_frames)"
for frame in farray:
# perform actions for each frame
# we make a copy since we want to keep orginal Frame
frame0 = frame.copy()
alist.compute(frame0)
# we need to keep the modified frame in farray2
farray2.append(frame0)
# make sure that Action_Strip does its job in stripping
assert farray2.n_frames == farray.n_frames
fsaved = pt.iterload(cpptraj_test_dir + "/Test_Image/image4.crd.save",
"data/tz2.truncoct.parm7")
assert fsaved.n_frames == 2
def test_reference_with_different_topology_basic(self):
traj1 = pt.iterload(filename="./data/Tc5b.x",
top="./data/Tc5b.top")
traj2 = pt.iterload('data/tz2.nc', 'data/tz2.parm7')
# re-establish ActionList
dslist = CpptrajDatasetList()
dslist.add('reference', name='myref')
dslist[0].top = traj2.top
dslist[0].add_frame(traj2[0])
actlist = pt.ActionList(['rmsd @1-11 @CB ref myref'], top=traj1.top,
dslist=dslist)
for frame in traj1:
actlist.compute(frame)
# raise if ref_mask is given but not mask
self.assertRaises(ValueError, lambda:
pt.rmsd(traj1, ref=3, ref_mask='@CB'))
self.assertRaises(ValueError, lambda:
pt.rmsd(traj1, ref=traj2[:1], ref_mask='@CB'))
# assert to cpptraj
tc5b_traj = traj1[:]
tz2_traj = traj2[:1]
cm = '''
parm data/Tc5b.top [tc5b]
trajin data/Tc5b.x [tc5b]
parm data/tz2.parm7 [tz2]
reference data/tz2.nc parm [tz2] 1 [myref]
rms myrmsd ref [myref] @1-10 @11-20
'''
state = pt.load_cpptraj_state(cm)
state.run()
expected_rmsd = state.data[-1].values
rmsd_data = pt.rmsd(tc5b_traj, mask='@1-10',
ref=tz2_traj,
ref_mask='@11-20')
aa_eq(expected_rmsd, rmsd_data)
def test_run_5(self):
traj = pt.iterload(tc5b_trajin, tc5b_top)
mask_list = ('@CB @CA', '@CA @H')
dslist = CpptrajDatasetList()
actlist = ActionList()
for mask in mask_list:
actlist.add(CA.Action_Distance(), mask, traj.top, dslist=dslist)
actlist.compute(traj)
dslist2 = pt.calc_distance(traj, mask_list)
aa_eq(dslist.values, dslist2)
def calc_linear_interaction_energy(traj=None,
mask="",
top=None,
dtype='dataset',
frame_indices=None,
*args,
**kwd):
command = mask
act = c_action.Action_LIE()
dslist = CpptrajDatasetList()
act(command, traj, top=top, dslist=dslist, *args, **kwd)
return get_data_from_dtype(dslist, dtype)
def test_unstrip(self):
from pytraj.datasets import CpptrajDatasetList
traj = pt.iterload(fn('tz2.nc'), fn('tz2.parm7'))
dslist = CpptrajDatasetList()
actlist = pt.ActionList(['strip !@CA', 'unstrip', 'radgyr nomax'],
top=traj.top,
dslist=dslist)
actlist.compute(traj)
# make sure that after stripping and unstrip the Frame coords are restored
aa_eq(pt.radgyr(traj), dslist.values)
dslist2 = CpptrajDatasetList()
actlist2 = pt.ActionList(['strip !@CA', 'radgyr nomax'],
top=traj.top,
dslist=dslist2)
actlist2.compute(traj)
# make sure get correct radgyr after stripping all but CA atoms
aa_eq(dslist2.values, pt.radgyr(traj, '@CA'))
def test_run_2(self):
# load traj
traj = pt.iterload(tc5b_trajin, tc5b_top)
dslist = CpptrajDatasetList()
dflist = DataFileList()
# creat ActionList to hold actions
alist = ActionList()
alist.add(adict['distance'], ":2@CA :10@CA out _dist.out", traj.top,
dslist, dflist)
with tempfolder():
alist.compute([traj.iterchunk()])
assert len(dslist) == 1
assert dslist[0].size == traj.n_frames
def test_run_2(self):
# load traj
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
dslist = CpptrajDatasetList()
dflist = DataFileList()
# creat ActionList to hold actions
alist = ActionList()
alist.add(adict['distance'], ":2@CA :10@CA out ./output/_dist.out",
traj.top, dslist, dflist)
alist.compute([traj.iterchunk()])
print('dslist', dslist[0].size)
assert len(dslist) == 1
assert dslist[0].size == traj.n_frames
def read_data(cls, filename, arg=""):
'''
>>> from pytraj.datasetlist import DatasetList
>>> DatasetList.read_data('data/tc5b.native_contacts.dat')
<pytraj.DatasetList with 2 datasets>
Contacts_00001[native]
[ 7095. 5904. 5638. 5600. 5695. 5745. 5611. 5556. 5739. 5748.]
<BLANKLINE>
Contacts_00001[nonnative]
[ 0. 2696. 3065. 3552. 3700. 2624. 4000. 3797. 3482. 4265.]
'''
df = DataFile()
dslist = CpptrajDatasetList()
df.read_data(filename, ArgList(arg), dslist)
return DatasetList(dslist)
def test_reference(self):
traj = pt.iterload(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7"))
# store reference
dslist = CpptrajDatasetList()
ref = dslist.add('reference')
ref.top = traj.top
ref.append(traj[3])
fi = pt.pipe(traj, ['autoimage', 'rms refindex 0 @CA'], dslist=dslist)
xyz = np.array([frame.xyz.copy() for frame in fi])
t0 = (traj[:].autoimage().superpose(ref=traj[3], mask='@CA'))
aa_eq(xyz, t0.xyz)
t1 = traj[:].autoimage()
aa_eq(pt.rmsd(t1, ref=traj[3], mask='@CA'), dslist[-1].values)
def lifetime(data, cut=0.5, rawcurve=False, more_options='', dtype='ndarray'):
"""lifetime (adapted lightly from cpptraj doc)
Parameters
----------
data : 1D-array or 2D array-like
cut : cutoff to use when determining if data is 'present', default 0.5
more_options : str, more cpptraj's options. Check cpptraj's manual.
"""
data = np.asarray(data)
if data.ndim == 1:
data_ = [
data,
]
else:
data_ = data
_outname = 'name lifetime_'
_cut = 'cut ' + str(cut)
_rawcurve = 'rawcurve' if rawcurve else ''
# do not sorting dataset's names. We can accessing by indexing them.
_nosort = 'nosort'
namelist = []
cdslist = CpptrajDatasetList()
for idx, arr in enumerate(data_):
# create datasetname so we can reference them
name = 'data_' + str(idx)
if 'int' in arr.dtype.name:
cdslist.add_set("integer", name)
else:
cdslist.add_set("double", name)
cdslist[-1].data = np.asarray(arr)
namelist.append(name)
act = CpptrajAnalyses.Analysis_Lifetime()
_cm = ' '.join(namelist)
command = " ".join((_cm, _outname, _cut, _rawcurve, _nosort, more_options))
act(command, dslist=cdslist)
for name in namelist:
cdslist.remove_set(cdslist[name])
return get_data_from_dtype(cdslist, dtype=dtype)
def test_run_3(self):
dslist = CpptrajDatasetList()
actlist = ActionList()
traj = pt.iterload(tc5b_trajin, tc5b_top)
mask_list = ['@CB @CA @N', '@CA @H @N']
for mask in mask_list:
actlist.add(CA.Action_Angle(), mask, traj.top, dslist=dslist)
actlist.compute(traj)
pt.calc_angle(traj, mask_list)
dslist3_0 = pt.calc_angle(traj, mask_list[0])
dslist3_1 = pt.calc_angle(traj, mask_list[1])
aa_eq(dslist3_0, dslist[0].to_ndarray())
aa_eq(dslist3_1, dslist[1].to_ndarray())
aa_eq(dslist3_0, dslist[0].to_ndarray())
aa_eq(dslist3_1, dslist[1].to_ndarray())
def test_run_4(self):
dslist = CpptrajDatasetList()
actlist = ActionList()
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
mask_list = ['@CB @CA @N @H', '@CA @H @N @H=']
for mask in mask_list:
actlist.add(CA.Action_Dihedral(), mask, traj.top, dslist=dslist)
actlist.compute(traj)
dslist2 = pt.calc_dihedral(traj, mask_list)
dslist3_0 = pt.calc_dihedral(traj, mask_list[0])
dslist3_1 = pt.calc_dihedral(traj, mask_list[1])
aa_eq(dslist3_0, dslist2[0])
aa_eq(dslist3_1, dslist2[1])
aa_eq(dslist3_0, dslist[0].to_ndarray())
aa_eq(dslist3_1, dslist[1].to_ndarray())
def test_run_1(self):
# load traj
traj = pt.iterload(tc5b_trajin, tc5b_top)
dslist = CpptrajDatasetList()
dflist = DataFileList()
# creat ActionList to hold actions
alist = ActionList()
# add two actions: Action_Dihedral and Action_Distance
alist.add(adict['distance'], ":2@CA :10@CA out ./output/_dist.out",
traj.top, dslist, dflist)
alist.add(adict['dihedral'],
":2@CA :3@CA :4@CA :5@CA out ./output/_dih.out", traj.top,
dslist, dflist)
# using string for action 'dssp'
alist.add('dssp', "out ./output/_dssp_alist.out", traj.top, dslist,
dflist)
alist.add('matrix', "out ./output/_mat_alist.out", traj.top, dslist,
dflist)
def _toy_radgyr(traj,
mask="",
top=None,
dtype='ndarray',
nomax=True,
frame_indices=None):
'''
Examples
--------
>>> import pytraj as pt
>>> pt.mindist(traj, '@CA @H')
'''
act = c_action.Action_Radgyr()
dslist = CpptrajDatasetList()
_nomax = 'nomax' if nomax else ''
mask = ' '.join((mask, _nomax))
act(mask, traj, top=top, dslist=dslist)
return get_data_from_dtype(dslist, dtype=dtype)
def test_modify_frame_use_Pipeline(self):
traj = pt.iterload(fn("tz2.ortho.nc"), fn("tz2.ortho.parm7"))
dslist = CpptrajDatasetList()
dslist.add('topology', name='mytop')
# add a new topology
dslist[0].data = pt.strip(traj.top, ':WAT')
commands = [
'autoimage',
'strip :WAT',
'createcrd mycrd',
]
actlist = Pipeline(commands, top=traj.top, dslist=dslist)
for frame in traj:
actlist.compute(frame)
aa_eq(dslist['mycrd'].xyz,
pt.get_coordinates(traj, mask='!:WAT', autoimage=True))
def test_constructor_from_command_list_TrajectoryIterator(self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
commands = [
'rmsd @CA', 'distance :3 :7', 'distance :3 :7', 'vector :2 :3'
]
dslist = CpptrajDatasetList()
actlist = ActionList(commands, traj.top, dslist=dslist)
d0 = dslist.add('ref_frame', 'my_ref')
d0.add_frame(traj[3])
for frame in traj:
actlist.compute(frame)
aa_eq(pt.rmsd(traj, mask='@CA'), dslist[0])
aa_eq(pt.distance(traj, ':3 :7'), dslist[1])
aa_eq(pt.distance(traj, ':3 :7'), dslist[2])
aa_eq(pt.vector.vector_mask(traj(rmsfit=(0, '@CA')), ':2 :3'),
dslist[3].values)
def lifetime(data, cut=0.5, rawcurve=False, more_options='', dtype='ndarray'):
"""lifetime (adapted lightly from cpptraj doc)
Parameters
----------
data : 1D-array or 2D array-like
cut : cutoff to use when determining if data is 'present', default 0.5
more_options : str, more cpptraj's options. Check cpptraj's manual.
"""
data = np.asarray(data)
if data.ndim == 1:
data_ = [data, ]
else:
data_ = data
_outname = 'name lifetime_'
_cut = 'cut ' + str(cut)
_rawcurve = 'rawcurve' if rawcurve else ''
# do not sorting dataset's names. We can accessing by indexing them.
_nosort = 'nosort'
namelist = []
cdslist = CpptrajDatasetList()
for idx, arr in enumerate(data_):
# create datasetname so we can reference them
name = 'data_' + str(idx)
if 'int' in arr.dtype.name:
cdslist.add_set("integer", name)
else:
cdslist.add_set("double", name)
cdslist[-1].data = np.asarray(arr)
namelist.append(name)
act = CpptrajAnalyses.Analysis_Lifetime()
_cm = ' '.join(namelist)
command = " ".join((_cm, _outname, _cut, _rawcurve, _nosort, more_options))
act(command, dslist=cdslist)
for name in namelist:
cdslist.remove_set(cdslist[name])
return get_data_from_dtype(cdslist, dtype=dtype)
def test_add_new_for_CpptrajDatasetList(self):
# TODO:
dslist = CpptrajDatasetList()
# integer
dslist.add_new(dtype='integer', name='my_int')
dslist[-1].data = [2, 3]
aa_eq(dslist[-1].values, [2, 3])
# double
dslist.add_new(dtype='double', name='my_double')
dslist[-1].data = [2, 3]
aa_eq(dslist[-1].values, [2, 3])
# float
dslist.add_new(dtype='float', name='my_float')
dslist[-1].data = [2, 3]
aa_eq(dslist[-1].values, [2, 3])
# string
dslist.add_new(dtype='string', name='my_string')
dslist[-1].data = ['H', 'T']
assert dslist[-1].values.tolist() == ['H', 'T'], 'string must be equal'
# reference
dslist.add_new(dtype='reference', name='my_reference')
dslist[-1].data = self.traj[-2]
aa_eq(dslist[-1].xyz, self.traj[-2].xyz)
# matrix3x3
dslist.add_new(dtype='matrix3x3', name='my_mat3x3')
mat = pt.calc_rotation_matrix(self.traj, ref=0, mask='@CA')
# there is no assignment. Need to update by another method
dslist[-1]._append_from_array(mat)
aa_eq(dslist[-1].values, mat)
# TRAJ
dslist.add_new(dtype='traj', name='my_traj')
dslist[-1].top = self.traj.top
dslist[-1]._load(self.traj.filename)
traj_new = dslist[-1]
# FIXME: segmentation fault
# CRD
dslist.add_new(dtype='coords', name='my_crd')
dslist[-1].top = self.traj.top
dslist[-1].load(self.traj.filename)
traj_new = dslist[-1]
aa_eq(traj_new.xyz, self.traj.xyz)
aa_eq(pt.rmsd(traj_new), pt.rmsd(self.traj))
# vector
dslist.add_new(dtype='vector', name='my_vec')
vecs = pt.vector.vector_mask(self.traj, ':3 :2')
dslist[-1].data = vecs
aa_eq(dslist[-1].values, vecs)
# grid
dslist.add_new(dtype='grid', name='my_grid')
arr = np.random.rand(8, 9, 3).astype('f4')
dslist[-1].data = arr
aa_eq(dslist[-1].values, arr)
# mesh
dslist.add_new(dtype='xymesh', name='my_mesh')
arr = np.random.rand(8, 2).astype('f8')
# there is not easy method to update, use _append_from_array
dslist[-1]._append_from_array(arr)
aa_eq(dslist[-1].values, arr)
# modes
mat = pt.matrix.covar(self.traj, '@CA')
modes = pt.matrix.diagonalize(mat, n_vecs=mat.shape[0], dtype='dataset')[0]
modes2 = modes.__class__()
# dummy test to set name and scalar_type
# (prepare for pca)
modes2.name = 'test_mode'
modes2.scalar_type = 'covar'
modes2._set_modes(False, mat.shape[0], modes.eigenvectors.shape[0],
modes.eigenvalues, modes.eigenvectors.flatten())
aa_eq(modes.eigenvalues, modes2.eigenvalues)
aa_eq(modes.eigenvectors, modes2.eigenvectors)
def test_add_new_for_CpptrajDatasetList(self):
# TODO:
dslist = CpptrajDatasetList()
# integer
dslist.add_new(dtype='integer', name='my_int')
dslist[-1].data = [2, 3]
aa_eq(dslist[-1].values, [2, 3])
# double
dslist.add_new(dtype='double', name='my_double')
dslist[-1].data = [2, 3]
aa_eq(dslist[-1].values, [2, 3])
# float
dslist.add_new(dtype='float', name='my_float')
dslist[-1].data = [2, 3]
aa_eq(dslist[-1].values, [2, 3])
# string
dslist.add_new(dtype='string', name='my_string')
dslist[-1].data = ['H', 'T']
assert dslist[-1].values.tolist() == ['H', 'T'], 'string must be equal'
# reference
dslist.add_new(dtype='reference', name='my_reference')
dslist[-1].data = self.traj[-2]
aa_eq(dslist[-1].xyz, self.traj[-2].xyz)
# matrix3x3
dslist.add_new(dtype='matrix3x3', name='my_mat3x3')
mat = pt.calc_rotation_matrix(self.traj, ref=0, mask='@CA')
# there is no assignment. Need to update by another method
dslist[-1]._append_from_array(mat)
aa_eq(dslist[-1].values, mat)
# TRAJ
dslist.add_new(dtype='traj', name='my_traj')
dslist[-1].top = self.traj.top
dslist[-1]._load(self.traj.filename)
traj_new = dslist[-1]
# FIXME: segmentation fault
# CRD
dslist.add_new(dtype='coords', name='my_crd')
dslist[-1].top = self.traj.top
dslist[-1].load(self.traj.filename)
traj_new = dslist[-1]
aa_eq(traj_new.xyz, self.traj.xyz)
aa_eq(pt.rmsd(traj_new), pt.rmsd(self.traj))
# vector
dslist.add_new(dtype='vector', name='my_vec')
vecs = pt.vector.vector_mask(self.traj, ':3 :2')
dslist[-1].data = vecs
aa_eq(dslist[-1].values, vecs)
# grid
dslist.add_new(dtype='grid', name='my_grid')
arr = np.random.rand(8, 9, 3).astype('f4')
dslist[-1].data = arr
aa_eq(dslist[-1].values, arr)
# mesh
dslist.add_new(dtype='xymesh', name='my_mesh')
arr = np.random.rand(8, 2).astype('f8')
# there is not easy method to update, use _append_from_array
dslist[-1]._append_from_array(arr)
aa_eq(dslist[-1].values, arr)
# modes
mat = pt.matrix.covar(self.traj, '@CA')
modes = pt.matrix.diagonalize(mat,
n_vecs=mat.shape[0],
dtype='dataset')[0]
modes2 = modes.__class__()
# dummy test to set name and scalar_type
# (prepare for pca)
modes2.name = 'test_mode'
modes2.scalar_type = 'covar'
modes2._set_modes(False, mat.shape[0], modes.eigenvectors.shape[0],
modes.eigenvalues, modes.eigenvectors.flatten())
aa_eq(modes.eigenvalues, modes2.eigenvalues)
aa_eq(modes.eigenvectors, modes2.eigenvectors)
