def test_run(self):
print "test_process_input"
state2 = CpptrajState()
toplist = state2.toplist
toplist.add_parm("./data/Tc5b.top")
state2.add_trajin("./data/md1_prod.Tc5b.x")
state2.add_reference("./data/Tc5b.nat.crd")
state2.add_trajout("./output/test.out")
state2.add_action(
allactions.Action_Distance(),
ArgList("distance :2@CA :10@CA out ./output/dist_test.txt"))
state2.add_action(allactions.Action_Distance(),
ArgList("distance :4@CA :10@CA"))
state2.framelist.set_active_ref(0)
print "test framelist.list()"
state2.run()
dslist = state2.datasetlist
d0 = dslist[0]
print "d0 is empty? ", d0.is_empty()
d1 = cast_dataset(d0, dtype="general")
print "d1 is empty? ", d1.is_empty()
print d1.data[0:10]
def test_0(self):
dslist = DataSetList()
dslist2 = DataSetList()
act = allactions.Action_Distance()
act_radgyr = allactions.Action_Radgyr()
act.master(command="distance :1@CA :2@CA",
current_frame=farray,
current_top=farray.top, dslist=dslist)
act_radgyr.master(command="radgyr @CA",
current_frame=farray,
current_top=farray.top, dslist=dslist2)
d1 = cast_dataset(dslist[0], dtype="general")
d2 = cast_dataset(dslist2[0], dtype="general")
print d1.data[:10]
print d2.data[:10]
def test_distance_frames(self):
traj = FrameArray(filename="./data/md1_prod.Tc5b.x",
top="./data/Tc5b.top")
dslist = DataSetList()
act = allactions.Action_Distance()
act.master(command="distance :1@CA :2@CA",
current_frame=traj,
current_top=traj.top,
dslist=dslist)
d1 = cast_dataset(dslist[0], dtype="general")
print d1.data[:10]
frame0 = traj[0]
frame0.strip_atoms("!@CA", traj.top)
frame1 = traj[1]
frame1.strip_atoms("!@CA", traj.top)
print "dist_rmsd = ", frame0.dist_rmsd(frame1)
distframes = distance_frames(frame0, frame1)
print distframes.__len__()
xyz0_0 = frame0.atoms(0)
xyz0_1 = frame0.atoms(1)
assert distance(xyz0_1, xyz0_0) == d1.data[0]
def test_action(self):
distaction = allactions.Action_Distance()
boxaction = allactions.Action_Box()
boxaction.help()
toplist = TopologyList()
framelist = FrameList()
dsetlist = DataSetList()
dflist = DataFileList()
# add stuff
toplist.add_parm("./data/Tc5b.top")
framelist.add_reference(ArgList("./data/Tc5b.nat.crd"), toplist)
distaction.read_input(ArgList(":2@CA :10@CA"), toplist, framelist,
dsetlist, dflist, 0)
boxaction.read_input(ArgList("x 1000. y 1000. alpha 500."), toplist,
framelist, dsetlist, dflist, 0)
distaction.process(toplist[0])
idx = 0
farray = FrameArray("./data/Tc5b.nat.crd", "./data/Tc5b.top")
distaction.do_action(0, farray[idx])
frame0 = farray[idx]
# update Frame instance with new Box info
boxaction.do_action(idx, frame0)
print frame0.get_box()
mdio.writetraj(filename="test_withbox.r",
traj=frame0,
top=farray.top,
fmt='AMBERRESTART',
overwrite=True)
frame0.set_nobox()
print frame0.get_box()
mdio.writetraj(filename="test.r",
traj=frame0,
top=farray.top,
fmt='AMBERRESTART',
overwrite=True)
def run_0():
# load traj
farray = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
# create 'strip' action
stripact = allactions.Action_Strip()
# creat datasetlist to hold distance data
dsetlist = DataSetList()
# creat datafilelist to hold filenames and do writing later
dflist = DataFileList()
# creat ActionList to hold all actions
alist = ActionList()
# creat TopologyList to hold Topology instances
toplist = TopologyList()
# add parm
toplist.add_parm(farray.top)
# add actions: Action_Strip, Action_Distance and Action_Rmsd
alist.add_action(stripact, ArgList("@H*"), toplist, None, dsetlist, dflist)
alist.add_action(allactions.Action_Distance(),
ArgList(":2@CA :3@CA out _distance.dat"), toplist, None,
dsetlist, dflist)
alist.add_action(allactions.Action_Rmsd(),
ArgList("rms first @CA out _rmsd.dat"), toplist, None,
dsetlist, dflist)
#
print "test setup_actions"
print "number of actions = ", alist.n_actions
# do checking
alist.process(toplist[0])
farray2 = FrameArray()
# creat frame0 as data holder to avoid free memory twices
# TODO : fix this
frame0 = Frame()
# testing how fast to do the actions
t0 = time()
# loop all frames
# use iterator to make faster loop
# don't use "for i in range(farray.size)"
for frame in farray:
# perform actions for each frame
frame0 = frame.copy()
alist.do_actions(frame=frame0)
#alist.do_actions(frame)
# we need to keep the modified frame in farray2
#farray2.append(frame)
farray2.append(frame0)
print time() - t0
# make sure that Action_Strip does its job in stripping
print farray2.size
assert farray2.n_frames == farray.n_frames
assert farray2[0].n_atoms != farray[0].n_atoms
# it's time to retrieve the data
# get distance data
# we need to explicitly cast_dataset
# future : automatically cast data
# get distance
ds0 = cast_dataset(dsetlist[0], dtype='general')
# get rmsd data
ds1 = cast_dataset(dsetlist[1], dtype='general')
print ds0[:10]
print ds1[:10]
# reproduce cpptraj's output?
import numpy as np
rmsdcpp = np.loadtxt("./data/rmsd_to_firstFrame_CA_allres.Tc5b.dat",
skiprows=1).transpose()[1][:10]
# YES
assert_almost_equal(rmsdcpp, ds1[:10])
# write output for rmsd and distance (stored in dflist)
# datatfile: ./_rmsd.dat, _distance.dat
dflist.write_all_datafiles()
print dir(dflist)
def test_run_0(self):
# load traj
farray = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
# create 'strip' action
stripact = allactions.Action_Strip()
# creat datasetlist to hold distance data
dsetlist = DataSetList()
dflist = DataFileList()
# creat ActionList to hold actions
alist = ActionList()
# creat TopologyList
toplist = TopologyList()
# add parm
toplist.add_parm(farray.top)
# add two actions: Action_Strip and Action_Distance
alist.add_action(stripact, ArgList("@H*"), toplist, None, dsetlist,
dflist)
alist.add_action(allactions.Action_Distance(),
ArgList(":2@CA :3@CA out test_df.dat"), toplist, None,
dsetlist, dflist)
#
print "test setup_actions"
print alist.n_actions
# do checking
alist.process(toplist[0])
farray2 = FrameArray()
frame0 = Frame()
# testing how fast to do the actions
t0 = time()
# loop all frames
# use iterator to make faster loop
# don't use "for i in range(farray.size)"
for frame in farray:
# perform actions for each frame
frame0 = frame.copy()
alist.do_actions(frame=frame0)
#alist.do_actions(frame)
# we need to keep the modified frame in farray2
#farray2.append(frame)
farray2.append(frame0)
print time() - t0
# make sure that Action_Strip does its job in stripping
print farray2.size
assert farray2.n_frames == farray.n_frames
assert farray2[0].n_atoms != farray[0].n_atoms
# it's time to retrieve the data
ds = cast_dataset(dsetlist[0], dtype='general')
print ds[:10]
print dir(dflist)
dflist.write_all_datafiles()