def test_actionlist(self):
'''test_actionlist
'''
dslist = DatasetList()
actlist = ActionList()
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
mask_list = ['@CB @CA', '@CA @H']
for mask in mask_list:
actlist.add(CA.Action_Vector(),
mask,
traj.top,
dslist=dslist)
actlist.compute(traj)
dslist2 = pt.calc_vector(traj, mask_list)
dslist4 = va.vector_mask(traj, mask_list)
dslist3_0 = pt.calc_vector(traj, mask_list[0])
dslist3_1 = pt.calc_vector(traj, mask_list[1])
aa_eq(dslist3_0, dslist2[0])
aa_eq(dslist3_1, dslist2[1])
aa_eq(dslist3_0, dslist4[0])
aa_eq(dslist3_1, dslist4[1])
aa_eq(dslist3_0, dslist[0].values)
aa_eq(dslist3_1, dslist[1].values)
def test_constructor_from_command_list_Trajectory(self):
'''mutable Trajectory'''
# use `load` method rather `iterload`
traj = pt.load("data/tz2.ortho.nc", "data/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_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_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_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_run_5(self):
traj = pt.iterload("./data/Tc5b.x", "./data/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 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 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_rmsd_actlist(input_traj):
from pytraj.c_action.c_action import Action_Rmsd
from pytraj import ActionList
from pytraj.datasets import DatasetList
alist = ActionList()
dslist = DatasetList()
act = Action_Rmsd()
alist.add(act,
'first @CA',
top=input_traj.top,
dslist=dslist)
for frame in input_traj:
alist.compute(frame)
return (dslist.values)
def test_modify_frame(self):
traj = pt.iterload("data/tz2.ortho.nc", "data/tz2.ortho.parm7")
dslist = CpptrajDatasetList()
dslist.add_new('topology', name='mytop')
# add a new topology
dslist[0].data = pt.strip(traj.top, ':WAT')
commands = ['autoimage', 'strip :WAT', 'createcrd mycrd', ]
actlist = ActionList(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_no_DatasetList(
self):
traj = pt.iterload(tc5b_trajin, tc5b_top)
commands = [
'rmsd @CA', 'distance :3 :7', 'distance :3 :7', 'vector :2 :3'
]
actlist = ActionList(commands, top=traj.top)
for frame in traj:
actlist.compute(frame)
aa_eq(pt.rmsd(traj, mask='@CA'), actlist.data[0])
aa_eq(pt.distance(traj, ':3 :7'), actlist.data[1])
aa_eq(pt.distance(traj, ':3 :7'), actlist.data[2])
aa_eq(pt.vector.vector_mask(traj(rmsfit=(0, '@CA')), ':2 :3'),
actlist.data[3].values)
def test_modify_frame(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 = ActionList(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_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 test_constructor_from_command_list_TrajectoryIterator_no_DatasetList(
self):
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
commands = ['rmsd @CA', 'distance :3 :7', 'distance :3 :7',
'vector :2 :3']
actlist = ActionList(commands, top=traj.top)
for frame in traj:
actlist.compute(frame)
aa_eq(pt.rmsd(traj, mask='@CA'), actlist.data[0])
aa_eq(pt.distance(traj, ':3 :7'), actlist.data[1])
aa_eq(pt.distance(traj, ':3 :7'), actlist.data[2])
aa_eq(
pt.vector.vector_mask(
traj(rmsfit=(0, '@CA')),
':2 :3'),
actlist.data[3].values)
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 test_actionlist(self):
'''test_actionlist
'''
dslist = DatasetList()
actlist = ActionList()
traj = pt.iterload("./data/Tc5b.x", "./data/Tc5b.top")
mask_list = ['@CB @CA', '@CA @H']
for mask in mask_list:
actlist.add(CA.Action_Vector(), mask, traj.top, dslist=dslist)
actlist.compute(traj)
dslist2 = pt.calc_vector(traj, mask_list)
dslist4 = va.vector_mask(traj, mask_list)
dslist3_0 = pt.calc_vector(traj, mask_list[0])
dslist3_1 = pt.calc_vector(traj, mask_list[1])
aa_eq(dslist3_0, dslist2[0])
aa_eq(dslist3_1, dslist2[1])
aa_eq(dslist3_0, dslist4[0])
aa_eq(dslist3_1, dslist4[1])
aa_eq(dslist3_0, dslist[0].values)
aa_eq(dslist3_1, dslist[1].values)
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_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 test_run_1(self):
# load traj
traj = pt.iterload("./data/Tc5b.x", "./data/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 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 test_rmsd_actlist(input_traj):
from pytraj.analysis.c_action.c_action import Action_Rmsd
from pytraj import ActionList
from pytraj.datasets import DatasetList
alist = ActionList()
dslist = DatasetList()
act = Action_Rmsd()
alist.add(act, 'first @CA', top=input_traj.top, dslist=dslist)
for frame in input_traj:
alist.compute(frame)
return (dslist.values)
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 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_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())