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_matrix(self):
import numpy as np
from pytraj import ArgList
from pytraj import matrix as ma
from pytraj.externals.six import iteritems
matrix_test_dir = cpptraj_test_dir + "/Test_Matrix/"
top_file = matrix_test_dir + "/1rrb_vac.prmtop"
crd_file = matrix_test_dir + "/1rrb_vac.mdcrd"
traj = pt.iterload(crd_file, top_file)
with tempfolder():
state = pt.load_cpptraj_state(all_commands, traj)
state.run()
state_byres = pt.load_batch(traj, byres_cm)
state_byres.run()
byres_matlist = []
# no byres keyword
for idx, line in enumerate(command_list):
arg = ArgList(line)
# get function
act_key = arg.get_string_key("matrix")
slist = arg.get_string_key('out').split(".")
mask = arg.get_next_mask()
fname = ".".join((slist[0], slist[-1], slist[1]))
# get correct name
func = ma.__dict__[act_key]
# get command
command = line.split(act_key)[1]
matout = func(traj, command, dtype='ndarray')
# cpptraj output has only 3 digits after decimal
if 'byres' not in command:
aa_eq(matout.flatten(), state.data[idx + 1].values)
else:
# save data for asserting later
byres_matlist.append(matout)
byres_arr = np.array(byres_matlist, dtype='f8')
# only take byres datasets
saved_matbyres = state_byres.data[[1, 3]].values
aa_eq(byres_arr, saved_matbyres)
def load_cpptraj_output(txt, dtype=None):
"""load output from cpptraj
Parameters
----------
txt : str
cpptraj's trajin
dtype : str, return data type
Returns
-------
if dtype is 'state', return CpptrajState
if dtype is 'ndarray', return ndarray and so on
"""
from pytraj.core.c_core import _load_batch
from pytraj.datasetlist import DatasetList
from pytraj import ArgList
commands = list(filter(lambda x: x, txt.split("\n")))
for idx, line in enumerate(commands):
if 'parm' in line:
arglist = ArgList(line)
# use absolute path
fname = os.path.abspath(arglist.get_string_key('parm'))
commands[idx] = " ".join(('parm', fname))
if 'trajin' in line:
arglist = ArgList(line)
# use absolute path
relative_fname = arglist.get_string_key('trajin')
the_rest_of_line = ' '.join(line.split(relative_fname)[1:])
fname = os.path.abspath(relative_fname)
commands[idx] = " ".join(('trajin', fname, the_rest_of_line))
txt = "\n".join([line for line in commands])
state = _load_batch(txt, traj=None)
state.run()
if dtype == 'state':
out = state
else:
out = DatasetList(state.datasetlist)
return out