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_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_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(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(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 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_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_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_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 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)