def test_write_pdb():
# TODO: get absolute path so we can use `tempfolder`
# if not: wrong dir if using TrajectoryIterator
traj = pt.iterload(tc5b_trajin, tc5b_top)[:]
TrajectoryWriter()
# multiple pdb in multiple files, using `save` method in traj
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = pt.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in multiple files, using `pt.write_traj`
with tempfolder():
basename = "test_pdb_files_pt_write_traj.pdb"
pt.write_traj(basename, traj, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = pt.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
with pytest.raises(IOError):
# write files again, raise if file exists
pt.write_traj(basename, traj, overwrite=False, options="multi")
# keepext
with tempfolder():
basename = 'test_pdb_files_pt_write_traj.pdb'
basename2 = 'test_pdb_files_pt_write_traj'
pt.write_traj(basename, traj, overwrite=True, options="multi keepext")
for i in range(10):
fname = "{}.{}.pdb".format(basename2, i + 1)
frame = pt.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
with pytest.raises(IOError):
pt.write_traj(basename,
traj,
overwrite=False,
options="multi keepext")
# multiple pdb in SINGLE file
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True)
traj2 = pt.load(basename, traj.top)
aa_eq(traj.xyz, traj2.xyz)
# multiple pdb in SINGLE file with `model` keyword
# write to output so we can manually check
basename = "test_pdb_files_model.pdb"
with tempfolder():
traj.save(basename, overwrite=True, options='model')
traj3 = pt.load(basename, traj.top)
aa_eq(traj.xyz, traj3.xyz)
def test_split_and_write_traj(self):
traj = pt.iterload([fn('Tc5b.x'), fn('Tc5b.x')], fn('Tc5b.top'))
# duplcate
assert traj.n_frames == 20
top = traj.top
with tempfolder():
# test TrajectoryIterator object
pt.tools.split_and_write_traj(traj,
n_chunks=4,
root_name='trajiterx',
overwrite=True)
flist = sorted(glob("trajiterx*"))
traj4 = pt.iterload(flist, top)
aa_eq(traj4.xyz, traj.xyz)
# dcd ext
pt.tools.split_and_write_traj(traj,
4,
root_name='ts',
ext='dcd',
overwrite=True)
flist = sorted(glob("ts.*.dcd"))
traj4 = pt.iterload(flist, top)
aa_eq(traj4.xyz, traj.xyz)
def test_write_xyz(self):
xyz = self.traj.xyz
fname = 'test_xyz.nc'
with tempfolder():
pt.write_traj(fname, xyz, top=self.traj.top, overwrite=True)
t0 = pt.iterload(fname, top=self.traj.top)
aa_eq(self.traj.xyz, t0.xyz)
def test_trajectory_writer():
traj = pt.iterload(tc5b_trajin, tc5b_top)
with tempfolder():
pt.write_traj("test_1.pdb", traj[0], top=traj.top, overwrite=True)
pt.write_traj("test_1.dcd", traj[0], top=traj.top, overwrite=True)
with TrajectoryWriter("test_1", overwrite=True) as trajout:
trajout.write(traj[0])
def test_write_CRYST1():
traj = pt.datafiles.load_tz2_ortho()[:1]
print(traj.unitcells)
with tempfolder():
fn = "test.pdb"
traj.save(fn)
traj2 = pt.load(fn)
aa_eq(traj.unitcells, traj2.unitcells, decimal=3)
def test_spam():
# FIXME: assert?
peaks_xyz = os.path.join(cpptraj_test_dir, 'Test_SPAM', 'peaks.xyz')
command = """
parm {}
trajin {}
autoimage
spam {} name SPAM cut 12.0 info spam.info out spam.dat reorder \
summary summary.dat
trajout test.mdcrd onlyframes 1-2
""".format(tz2_truncoct_top, tz2_truncoct_trajin, peaks_xyz)
state = pt.load_cpptraj_state(command)
with tempfolder():
state.run()
traj = pt.iterload(tz2_truncoct_trajin, tz2_truncoct_top)
# cm = 'SPAM cut 12.0 info spam.info out spam.dat reorder summary summary.dat'
cm = 'SPAM cut 12.0 reorder'
with tempfolder():
spam_out = pt.spam(traj, peak_file=peaks_xyz, command=cm)
def example_write_pdb():
traj = pt.iterload("../tests/data/Tc5b.x", "../tests/data/Tc5b.top")
# multiple pdb in multiple files, using `save` method in traj
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True, options="multi")
# multiple pdb in multiple files, using `pt.io.write_traj`
with tempfolder():
basename = "test_pdb_files_pt.io_write_traj.pdb"
pt.io.write_traj(basename, traj, overwrite=True, options="multi")
# multiple pdb in SINGLE file
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True)
# multiple pdb in SINGLE file with `optionsl` keyword
# write to output so we can manually check
with tempfolder():
basename = "test_pdb_files_model.pdb"
traj.save(basename, overwrite=True, options='model')
def test_1(self):
# TODO: get absolute path so we can use `tempfolder`
# if not: wrong dir if using TrajectoryIterator
traj = mdio.iterload("./data/Tc5b.x", "./data/Tc5b.top")[:]
trajout = TrajectoryWriter()
# multiple pdb in multiple files, using `save` method in traj
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = mdio.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in multiple files, using `mdio.write_traj`
with tempfolder():
basename = "test_pdb_files_mdio_write_traj.pdb"
mdio.write_traj(basename, traj, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = pt.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in SINGLE file
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True)
traj2 = mdio.load(basename, traj.top)
aa_eq(traj.xyz, traj2.xyz)
# multiple pdb in SINGLE file with `model` keyword
# write to output so we can manually check
basename = "./output/test_pdb_files_model.pdb"
traj.save(basename, overwrite=True, options='model')
traj3 = mdio.load(basename, traj.top)
aa_eq(traj.xyz, traj3.xyz)
def test_1(self):
# TODO: get absolute path so we can use `tempfolder`
# if not: wrong dir if using TrajectoryIterator
traj = mdio.iterload("../tests/data/Tc5b.x",
"../tests/data/Tc5b.top")[:]
trajout = TrajectoryWriter()
# multiple pdb in multiple files, using `save` method in traj
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = mdio.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in multiple files, using `mdio.write_traj`
with tempfolder():
basename = "test_pdb_files_mdio_write_traj.pdb"
mdio.write_traj(basename, traj, overwrite=True, options="multi")
for i in range(10):
fname = basename + "." + str(i + 1) # cpptraj use `1`
frame = mdio.iterload(fname, traj.top)[0]
aa_eq(frame.xyz, traj[i].xyz)
# multiple pdb in SINGLE file
with tempfolder():
basename = "test_pdb_files.pdb"
traj.save(basename, overwrite=True)
traj2 = mdio.load(basename, traj.top)
aa_eq(traj.xyz, traj2.xyz)
# multiple pdb in SINGLE file with `optionsl` keyword
# write to output so we can manually check
basename = "./output/test_pdb_files_model.pdb"
traj.save(basename, overwrite=True, options='model')
traj3 = mdio.load(basename, traj.top)
aa_eq(traj.xyz, traj3.xyz)
def test_cluster_hieragglo():
command = """
parm {}
trajin {}
createcrd crd1
cluster crdset crd1 C0 !@H hieragglo epsilon 0.8 averagelinkage
""".format(tz2_top, tz2_trajin)
with tempfolder():
state = pt.load_cpptraj_state(command)
with capture_stdout() as (cpp_out, _):
state.run()
traj = pt.iterload(tz2_trajin, tz2_top)
data = pt.cluster.hieragglo(traj,
mask='!@H=',
options='epsilon 0.8 averagelinkage')
aa_eq(state.data[-2], data.cluster_index)
def test_cluster_dbscan():
command = """
parm {}
trajin {}
createcrd crd1
cluster crdset crd1 C0 @CA dbscan epsilon 1.7 minpoints 5
""".format(tz2_top, tz2_trajin)
with tempfolder():
state = pt.load_cpptraj_state(command)
with capture_stdout() as (out, _):
state.run()
traj = pt.iterload(tz2_trajin, tz2_top)
data = pt.cluster.dbscan(traj,
mask='@CA',
options='epsilon 1.7 minpoints 5')
aa_eq(state.data[-2], data.cluster_index)
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 test_regular(self):
traj = self.traj.copy()
assert traj[0].has_box() == True
with tempfolder():
# write traj with nobox info
fname = "traj_nobox.nc"
pt.write_traj(fname, traj, options='nobox')
t = pt.load(fname, traj.top)
assert t[0].has_box() == False
aa_eq(t.xyz, traj.xyz)
# write from frame_iter, need to provide top
fname = "traj_frame_iter.nc"
# raise ValueError if there is no Topology
pt.write_traj(fname, traj(), top=traj.top, overwrite=True)
t = pt.iterload(fname, traj.top)
aa_eq(t.xyz, traj.xyz)
def test_regular(self):
traj = self.traj.copy()
assert traj[0].has_box() == True
with tempfolder():
# write traj with nobox info
fname = "traj_nobox.nc"
pt.write_traj(fname, traj, options='nobox')
t = pt.load(fname, traj.top)
assert t[0].has_box() == False
aa_eq(t.xyz, traj.xyz)
# write from frame_iter, need to provide top
fname = "traj_frame_iter.nc"
# raise ValueError if there is no Topology
pt.write_traj(fname, traj(), top=traj.top, overwrite=True)
t = pt.iterload(fname, traj.top)
aa_eq(t.xyz, traj.xyz)
def test_superpose_trajectory_iterator_pytraj_method(self):
traj_on_disk = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
traj_on_disk2 = pt.iterload(fn('Tc5b.x'), fn('Tc5b.top'))
traj_on_mem = pt.load(fn('Tc5b.x'), fn('Tc5b.top'))
ref = pt.iterload(fn("Tc5b.crd"), fn('Tc5b.top'))[0]
pt.superpose(traj_on_mem, ref=ref, mask='@CA')
pt.superpose(traj_on_disk, ref=ref, mask='@CA')
assert traj_on_disk._being_transformed == True, '_being_transformed must be True'
aa_eq(traj_on_mem.xyz, traj_on_disk.xyz)
# test saving
with tempfolder():
traj_on_mem.save('t0.nc', overwrite=True)
traj_on_disk.save('t1.nc', overwrite=True)
aa_eq(
pt.load('t0.nc', traj_on_mem.top).xyz,
pt.load('t1.nc', traj_on_disk.top).xyz)
# turn off superpose
traj_on_disk._being_transformed = False
aa_eq(traj_on_disk.xyz, traj_on_disk2.xyz)
