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_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_DatasetDouble(self):
dslist = CpptrajDatasetList()
d = dslist.add(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 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 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 test_add_for_CpptrajDatasetList(self):
dslist = CpptrajDatasetList()
# integer
dslist.add(dtype='integer', name='my_int')
dslist[-1].data = [2, 3]
aa_eq(dslist[-1].values, [2, 3])
# double
dslist.add(dtype='double', name='my_double')
dslist[-1].data = [2, 3]
aa_eq(dslist[-1].values, [2, 3])
# float
dslist.add(dtype='float', name='my_float')
dslist[-1].data = [2, 3]
aa_eq(dslist[-1].values, [2, 3])
# string
dslist.add(dtype='string', name='my_string')
dslist[-1].data = ['H', 'T']
assert dslist[-1].values.tolist() == ['H', 'T'], 'string must be equal'
# reference
dslist.add(dtype='reference', name='my_reference')
dslist[-1].data = self.traj[-2]
aa_eq(dslist[-1].xyz, self.traj[-2].xyz)
# matrix3x3
dslist.add(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(dtype='traj', name='my_traj')
dslist[-1].top = self.traj.top
dslist[-1]._load(self.traj.filename)
traj_new = dslist[-1]
# CRD
dslist.add(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(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(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(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)
