def test_fit(self):
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
trajnew = mdio.load("./data/md1_prod.fit_to_first.Tc5b.x", "./data/Tc5b.top")
# make sure 0-th frame does not change
frame0 = traj[0]
frame0new = trajnew[0]
assert (frame0.coords == frame0new.coords) == True
print frame0[:10]
print frame0new[:10]
frame1 = traj[1]
frame1new = trajnew[1]
print frame1[:10]
print frame1new[:10]
assert (frame1.coords == frame1new.coords) == False
# try do-fitting from Python
# not right yet
rmsd, mat, v1, v2 = frame1.rmsd(frame0, get_mvv=True)
print rmsd
frame1.trans_rot_trans(v1, mat, v2)
#frame1.trans_rot_trans(v1, mat, Vec3(0, 0, 0))
#assert frame1[:10] == frame1new[:10]
print frame1.rmsd_nofit(frame1new)
print arr_rmsd(np.asarray(frame1.coords), np.asarray(frame1new.coords))
print frame1.rmsd(frame1new)
assert frame1.rmsd(frame1new) < 1E-3
assert frame1new.rmsd(frame1, top=trajnew.top, mask="@CA") < 1E-3
def test_load_and_save_0(self):
print "test_load_and_save"
# need to load to FrameArray to save
traj = mdio.load(filename="./data/md1_prod.Tc5b.x",
top="./data/Tc5b.top")[:]
trajiter = mdio.iterload(filename="./data/md1_prod.Tc5b.x",
top="./data/Tc5b.top",
chunk=100)
print trajiter
print traj.size
indices = range(20, 30, 5) + [103, 78, 90, 82]
print type(indices)
print indices
mdio.writetraj(filename="./output/test_io_saved_.x",
traj=traj[:],
top="./data/Tc5b.top",
indices=indices,
overwrite=True)
# check frames
traj2 = mdio.load(filename="./output/test_io_saved_.x",
top="./data/Tc5b.top")
print "test_load_and_save_0"
print traj2.size
print traj2.is_empty()
print len(indices)
assert traj2.size == len(indices)
def test_0(self):
flist = glob("./data/Test_RemdTraj/rem.nc.*")
trajlist = []
for fh in flist:
topfile = "./data/Test_RemdTraj/ala2.99sb.mbondi2.parm7"
trajlist.append(mdio.load(fh, topfile))
Tset = Set([])
f4922 = FrameArray()
f4922.resize(trajlist[0].n_frames)
print f4922.n_frames
f4922.top = trajlist[0].top.copy()
for traj in trajlist:
for idx, frame in enumerate(traj):
if frame.temperature == 492.2:
f4922[idx] = frame
print f4922.temperatures
print f4922[0, 0, :]
# make sure we reproduce cpptraj output
cpptraj = mdio.load("./data/Test_RemdTraj/temp0.crd.492.20", topfile)
for idx, framepy in enumerate(f4922):
assert_almost_equal(framepy.coords, cpptraj[idx].coords)
print "YES"
def test_fancy_save(self):
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
traj[10:20].save("test_fancy_save_frame11_21.x", overwrite=True)
fanew = mdio.load("./test_fancy_save_frame11_21.x", traj.top)
for idx, f0 in enumerate(traj[10:20]):
f0new = fanew[idx]
assert_almost_equal(f0.coords, f0new.coords)
def test_0(self):
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
frame0 = traj[0]
frame0.save(filename="test_saveFrame.pdb",
top=traj.top,
overwrite=True)
fnew = mdio.load("test_saveFrame.pdb", traj.top)[0]
print frame0.coords[:20]
print fnew.coords[:20]
assert_almost_equal(frame0.coords, fnew.coords)
def test_blindload(self):
top = mdio.load("./data/Tc5b.top")
assert isinstance(top, Topology) == True
traj = mdio.load(filename="./data/md1_prod.Tc5b.x",
top="./data/Tc5b.top")
print traj
# TODO : add more classes here
is_traj = (isinstance(traj, TrajReadOnly)
or isinstance(traj, FrameArray))
assert is_traj == True
def test_1(self):
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
trajnew = mdio.load("./data/md1_prod.fit_to_first.Tc5b.x",
"./data/Tc5b.top")
frame0 = traj[0]
assert frame0[0, 2] == frame0.atoms(0)[2]
assert_almost_equal(frame0[0, :], frame0.atoms(0))
print frame0[0, :]
print frame0.atoms(0)
print frame0[:, 2]
framesub = frame0.get_subframe("@CA", traj.top)
assert framesub.n_atoms == 20
print framesub[19, :]
def test_save_traj_from_file(self):
Trajout().help()
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")[:5]
print traj.size
mdio.writetraj(filename="test_0.binpos",
traj=traj,
top="./data/Tc5b.top",
fmt="BINPOS",
overwrite=True)
savedtraj = mdio.load("./test_0.binpos", traj.top)
print "test_0.binpos size = ", savedtraj.size
print traj.size
assert savedtraj.size == traj.size
def test_readpdb(self):
print "test_readpdb +++++++++++++++++++++++++++++++"
pdbtop = mdio.readparm("./test_0_after.pdb")
assert pdbtop.n_atoms == 304
print pdbtop.n_atoms
top2 = pdbtop.copy()
top2.strip_atoms("!@CA")
print top2.n_atoms
assert top2.n_atoms == 20
# make sure that making Topology instance from pdb file is FINE
traj0 = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
traj1 = mdio.load("./data/md1_prod.Tc5b.x", "./test_0_after.pdb")
assert traj0[0].coords == traj1[0].coords
assert traj0[999].coords == traj1[999].coords
def main():
# set frame index
IDX0 = 99
IDX1 = 98
# load traj
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
# write pdb files for TMalign program so we can compare our results to TMalign
# ./TMalign -A test_gdt_0.pdb -B test_gdt_1.pdb
# turn off those if you don't like
mdio.writetraj(filename="test_gdt_0.pdb",
traj=traj[IDX0],
top=traj.top,
overwrite=True)
mdio.writetraj(filename="test_gdt_1.pdb",
traj=traj[IDX1],
top=traj.top,
overwrite=True)
# do our calculation
# option:
# score = 'gdtscore', 'tmscore' or 'maxsub'
# "@CA" : follow AMBER mask, change it if needed
score = 'tmscore'
print '%s = %s ' % (
score, calc_score(traj[IDX0], traj[IDX1], "@CA", traj.top,
score=score) / 1000.)
print calc_score(traj[IDX1], traj[IDX0], "@CA", traj.top,
score=score) / 1000.
def test_0(self):
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")[:]
arr0 = traj[:, :, :]
print arr0.shape
arr0[0, 0, 0] = 105.
print traj
print traj[0, 0, 0]
def test_0(self):
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")[:]
traj2 = traj.get_frames(indices=(1, 3, 5, 4, 8),
copy=True,
update_top=True)
print traj2
print traj2[0, 0, :]
def test_0(self):
farray = FrameArray(filename="./data/tz2.truncoct.nc", top="./data/tz2.truncoct.parm7")[:2]
fold = farray.copy()
print "old file: ", fold[0, 0, :]
act = allactions.Action_Image()
ptrajin = """
center :2-11
image center familiar com :6
"""
act.read_input(ptrajin, farray.top)
act.process(farray.top)
f2 = FrameArray()
f2.top = farray.top.copy()
act.do_action(0, farray)
print farray[0, 0, :]
print fold[0, 0, :]
if file_exist("./CpptrajTest/Test_Image/image4.crd"):
fnew = mdio.load("./CpptrajTest/Test_Image/image4.crd",
"./data/tz2.truncoct.parm7")
assert fnew.size == 2
# make sure that pycpptraj reproduce cpptraj outputo
# TODO : not yet. double-check
print fnew[0].same_coords_as(farray[0])
print fnew[0, 0, :]
print fold[0].same_coords_as(farray[0])
print fnew[0].rmsd(farray[0])
def test_0(self):
IDX0 = 99
IDX1 = 98
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
# write pdb files for TMalign program so we can compare our result to TMalign
# ./TMalign -A test_gdt_0.pdb -B test_gdt_1.pdb
mdio.writetraj(filename="test_gdt_0.pdb",
traj=traj[IDX0],
top=traj.top,
overwrite=True)
mdio.writetraj(filename="test_gdt_1.pdb",
traj=traj[IDX1],
top=traj.top,
overwrite=True)
# do our calculation
# score = 'gdtscore', 'tmscore' or 'maxsub'
score = 'tmscore'
print '%s = %s ' % (
score,
calc_score(traj[IDX0], traj[IDX1], "@CA", traj.top, score=score) /
1000.)
print calc_score(traj[IDX1], traj[IDX0], "@CA", traj.top,
score=score) / 1000.
# calculate RMSD
print "rmsd = ", traj[IDX0].rmsd(traj[IDX1])
def get_frames_same_T():
# create a list of all remd trajs
flist = glob("../tests/data/Test_RemdTraj/rem.nc.*")
# make a list of TrajReadOnly instances
trajlist = []
for fh in flist:
topfile = "../tests/data/Test_RemdTraj/ala2.99sb.mbondi2.parm7"
# load trajectory and append to trajlist
trajlist.append(mdio.load(fh, topfile))
# make FrameArray instance that holds 492.2 T frames
# we need to reserve n_frames to hold the data
f4922 = FrameArray(n_frames=trajlist[0].n_frames)
assert f4922.n_frames == trajlist[0].n_frames
f4922.top = trajlist[0].top.copy()
# extract frames having T = 492.2
# use iteration for nested loops
for traj in trajlist:
for idx, frame in enumerate(traj):
if frame.temperature == 492.2:
# we don't use `append` method since we want to make sure
# frames are in the order of simulation time
f4922[idx] = frame
# make sure f4922 only hold frames having T = 492.2 K
arr0 = array(
'd',
[492.2, 492.2, 492.2, 492.2, 492.2, 492.2, 492.2, 492.2, 492.2, 492.2])
assert f4922.temperatures == arr0
# make sure we reproduce cpptraj output
cpptraj = mdio.load("../tests/data/Test_RemdTraj/temp0.crd.492.20",
topfile)
for idx, framepy in enumerate(f4922):
assert_almost_equal(framepy.coords, cpptraj[idx].coords)
print "rmsd between pycpptraj Frame and cpptraj Frame = %s " % framepy.rmsd(
cpptraj[idx])
print f4922[5].coords[:10]
print cpptraj[5].coords[:10]
print "YES, we can reproduce cpptraj output"
def randions():
# get `traj` instance (FrameArray)
traj = load(filename="./Test_RandomizeIons/adh206.tip3p.rst7.gz",
top="./Test_RandomizeIons/adh206.ff10.tip3p.parm7.gz")
# get 1st frame from `traj`
frame0 = traj[0]
# randomize ions for frame0
randomize_ions(
frame0,
traj.top,
command="randomizeions @Na+ around :1-16 by 5.0 overlap 3.0",
)
# make sure to reproduce cpptraj output
savedframe = load(filename="./Test_RandomizeIons/random.crd.save",
top="./Test_RandomizeIons/adh206.ff10.tip3p.parm7.gz")[0]
assert frame0.rmsd(savedframe) < 1E-3
def test_1(self):
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
frame0 = traj[0]
print frame0[1:5, 2]
print np.asarray(frame0.buffer3d[1:5, :])
frame0[1:5, 2] = range(100, 104)
frame0[0, :] = range(3)
print frame0.buffer3d[1:5, :]
print np.asarray(frame0[1:5, :])
print list(frame0[1:5, :])
def test_load_and_save_0(self):
traj = mdio.load(filename="./data/md1_prod.Tc5b.x",
top="./data/Tc5b.top")[:110]
indices = range(20, 30, 5) + [103, 78, 90, 82]
print indices
#for i in indices:
# print traj[i]
mdio.writetraj(filename="./output/test_io_saved_.x",
traj=traj,
top="./data/Tc5b.top",
indices=indices,
overwrite=True)
# check frames
traj2 = mdio.load(filename="./output/test_io_saved_.x",
top="./data/Tc5b.top")
# TODO : check error
assert traj2.size == len(indices)
def test_0(self):
# TODO : not right yet.
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
# this command actually write Amber restart file
#mdio.writetraj("test_1.pdb", traj[0], top=traj.top, fmt='CHARMM')
print dir(Trajout)
print Trajout.writeframe
#with Trajout("test_1.pdb", fmt='PDBFILE', overwrite=True) as trajout:
#with Trajout("test_1.x", fmt='MOL2FILE', overwrite=True) as trajout:
with Trajout("test_1", fmt="PDBFILE", overwrite=True) as trajout:
trajout.writeframe(frame=traj[0], top=traj.top)
def test_0(self):
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
# FrameArray()
fa = traj[:]
fname = "test_savemethod.x"
fname2 = "test_savemethod_2.x"
fa.save(fname, overwrite=True)
traj.save(fname2, overwrite=True)
# load
fanew = mdio.load(fname, fa.top)
fanew2 = mdio.load(fname2, fa.top)
assert fanew.size == fa.size == fanew2.size
for idx, f0 in enumerate(fa):
f0new = fanew[idx]
f0new2 = fanew2[idx]
assert_almost_equal(f0.coords, f0new.coords)
assert_almost_equal(f0.coords, f0new2.coords)
def test_2(self):
"""test write FrameArray"""
farray = FrameArray("data/md1_prod.Tc5b.x",
"./data/Tc5b.top",
indices=range(10))
writetraj("test_write_output.x", farray, farray.top, overwrite=True)
writetraj("test_pdb_1.dummyext",
farray[0],
farray.top,
overwrite=True,
fmt='pdb')
# test 'save'
print farray
farray.save("test_write_output_save_method.x", overwrite=True)
# reproduce result?
f0 = mdio.load("test_write_output.x", "./data/Tc5b.top")
f1 = mdio.load("test_write_output_save_method.x", "./data/Tc5b.top")
from numpy.testing import assert_almost_equal as assert_ae
assert_ae(f0[:, :, :], f1[:, :, :])
def test_load_and_save_1(self):
traj = mdio.load(filename="./data/md1_prod.Tc5b.x",
top="./data/Tc5b.top")
trajiter = mdio.iterload(filename="./data/md1_prod.Tc5b.x",
top="./data/Tc5b.top",
chunk=100)
print trajiter
indices = range(20, 30, 5) + [103, 78, 90, 82]
mdio.writetraj(filename="./output/test_io_saved.pdb",
traj=traj,
top="./data/Tc5b.top",
fmt='pdbfile',
indices=indices,
overwrite=True)
# check frames
traj = mdio.load(filename="./output/test_io_saved.pdb",
top="./data/Tc5b.top")
assert traj.size == len(indices)
assert traj.top.n_atoms == 304
def test_0(self):
trajcpp = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
farray = trajcpp[:]
print farray[0, 0, 0]
# bugs: trajcpp[0, 0, 0] != farray[0, 0, 0] (must be equal)
assert farray[0][0, 0] == trajcpp[0][0, 0]
farray[0, 0, 0] = 100.10
print farray
print farray[0, 0, 0]
assert farray[0, 0, 0] == 100.10
farray[0, 0, :] = [100.10, 101.1, 102.1]
assert_almost_equal(farray[0, 0, :], [100.10, 101.1, 102.1])
def test_0(self):
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
frame0 = traj[0]
assert frame0.has_box() == False
box = frame0.get_box()
print box
assert frame0.get_box().btype == 'nobox'
print box.bname
bview = frame0.boxview
bview[3:] = np.asarray([109.471220634, 109.471220634, 109.471220634])
print frame0.has_box()
print frame0.get_box().btype
assert frame0.get_box().btype == 'truncoct'
assert frame0.get_box().bname == 'Trunc. Oct.'
print frame0.get_box().help()
def test_0(self):
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
# we could generate new traj.top from pdb file too
#traj.top = Topology("./test_0_after.pdb")
tm_0 = tm_score(traj[0], traj[1])
#print tm_0
#print tm_score(traj[0], traj[0]) # == 1.
#print tm_score(traj[0], traj[1], mask="!@CA", top=traj.top)
for idx, frame in enumerate(traj[490:501] + traj[-1:-10:-1]):
score = tm_score(frame,
traj[0],
mask1="!:2-10@CA",
top1=traj.top,
mask2="!:2-10@CA",
top2=traj.top)
print "%s : %s" % (idx, score)
def test_0(self):
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
frame0 = traj[0]
#arr0 = np.asarray(frame0)
print frame0[0, :]
assert frame0.buffer3d[0, 0] == frame0[0, 0]
assert frame0.buffer3d[0, 1] == frame0[0, 1]
assert frame0.buffer3d[0, 2] == frame0[0, 2]
assert frame0.buffer3d[1, 0] == frame0[1, 0]
assert frame0.buffer3d[19, 0] == frame0[19, 0]
frame0.buffer3d[19, 0] = 1000.
# make sure changing buffer3d will update frame0.coords too
assert frame0.buffer3d[19, 0] == frame0[19, 0]
arr0 = np.asarray(frame0.buffer3d)
print arr0.shape
arr0[19] = [200, 300, 400.]
assert frame0.buffer3d[19, 0] == frame0[19, 0] == arr0[19, 0]
# try to strip atoms
frame1 = frame0.copy()
frame1.strip_atoms("!@CA", traj.top)
print frame1.buffer3d.shape
CA_2 = frame0.get_subframe("@CA", traj.top)[2, :]
assert_almost_equal(CA_2, frame1[2, :])
assert_almost_equal(frame1.coords[6:9], frame1[2, :])
frame0[:] == frame0.coords
print frame0.buffer3d[:, 2]
print array('d', frame0.buffer3d[2:4, 0])
print array('d', frame0.buffer3d[2:4, 1])
#print CA_2
assert frame0.buffer1d.shape == (912, )
assert frame0.buffer3d.shape == (304, 3)
assert frame0.buffer1d.is_c_contig() == True
print array('d', frame0.buffer3d[0, :])
frame0.buffer3d[1:3, 0] = array('d', [1., 2.])
#assert frame0[1:3, 0] == array('d', frame0.buffer3d[1:3, 0])
print array('d', frame0.buffer3d[1:3, 0])
print frame0[1:3, 0]
assert_almost_equal(frame0[1:3, 0], array('d', frame0.buffer3d[1:3,
0]))
assert_almost_equal(frame0.buffer3d[1:3, 0],
array('d', frame0.buffer3d[1:3, 0]))
def test_0(self):
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
s = AtomSelect(traj=traj, top=traj.top, frameidx=500)
# make sure to use `property` properly
assert s.frameidx == 500
s.frameidx = 10
print s.selected_frame[:1]
assert s.frameidx == s._frameidx == 10
s.frameidx = 100
assert s.frameidx == s._frameidx == 100
print s.selected_frame.coords[:10]
print traj[100].coords[:10]
assert_almost_equal(s.selected_frame.coords, traj[100].coords)
s.frameidx = 999
for i in xrange(999):
s.frameidx = i
assert_almost_equal(s.selected_frame.coords, traj[i].coords)
def test_action(self):
action_help()
action_help("PairDist")
print
action_help("Dihedral")
dslist = DataSetList()
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
act = allactions.Action_Dihedral()
act.read_input("dihedral :4@C :5@N :5@CA :5@C range360 mass ",
current_top=traj.top,
dslist=dslist)
print traj.top
act.process(current_top=traj.top)
print act.process.__doc__
for i, frame in enumerate(traj):
act.do_action(i, frame)
d0 = cast_dataset(dslist[0])
print d0[:10]
def main():
traj = FrameArray("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
top = traj.top
frame = traj[0]
# indexing frame
print frame[top("@CA")]
# using AtomMask instance
atm = AtomMask("@CA")
top.set_integer_mask(atm)
print frame[atm]
# using AtomSelect
asl = AtomSelect()
asl.top = traj.top
asl.selected_frame = frame
print asl.select("@CA")
# timing
# TODO : not reproduce cpptraj output
from time import time
t0 = time()
ref = mdio.load("./data/Tc5b.crd",
"./data/Tc5b.top")[0].get_subframe(":2-12@CA :12-16@H",
top=traj.top)
arrrmsd = np.empty(traj.size)
for idx, frame in enumerate(traj):
arr0 = frame[top(":2-12@CA :12-16@H")]
framenew = Frame(arr0.shape[0])
framenew.set_from_crd(arr0.flatten())
arrrmsd[idx] = ref.rmsd(framenew)
print "time = %s" % (time() - t0)
print len(arrrmsd)
print arrrmsd[:10]
def test_strip_atoms(self):
traj = mdio.load("./data/md1_prod.Tc5b.x", "./data/Tc5b.top")
frame0 = traj[0]
frame1 = traj[1]
frame2 = traj[2]
frame3 = traj[3]
frame1 = frame0.strip_atoms("!@CA", traj.top, copy=True)
frame2 = Frame(frame0)
print frame2.n_atoms
print frame1.n_atoms
print frame1
assert frame1.n_atoms == 20
assert frame0.n_atoms == 304
frame0.strip_atoms("!@CA", traj.top, copy=False)
assert frame0.n_atoms == 20
_, mat, v1, v2 = frame2.rmsd(frame3, get_mvv=True)
print mat, v1, v2
print frame2[:10]
print mdio.writetraj("./test_0_before.pdb", traj=frame2, top=traj.top, overwrite=True)
frame2.trans_rot_trans(v1, mat, v2)
print frame2[:10]
print mdio.writetraj("./test_0_afeter.pdb", traj=frame2, top=traj.top, overwrite=True)
print Trajout().help()
