def OH_rdf_partial(output):
'''Oxygen-Hydrogen rdf for half of the trajectory'''
out, err = cfiles(
"rdf",
"--steps", "::2",
"-c", "15",
"-p", "150",
"-s", "pairs: name(#1) O and name(#2) H",
TRAJECTORY, "-o", output
)
assert(out == "")
assert(err == "")
data = read_rdf(output)
check_oh_rdf(data)
out, err = cfiles(
"rdf",
"--steps", ":50",
"-c", "15",
"-p", "150",
"-s", "pairs: name(#1) H and name(#2) O",
TRAJECTORY, "-o", output
)
assert(out == "")
assert(err == "")
data = read_rdf(output)
check_ho_rdf(data)
def OH_rdf_partial():
'''Oxygen-Hydrogen rdf for half of the trajectory'''
out, err = cfiles(
"rdf",
"--steps", "::2",
"-c", "15",
"-p", "150",
"-s", "pairs: name(#1) O and name(#2) H",
TRAJECTORY, "-o", OUTPUT
)
assert(out == "")
assert(err == "")
data = read_rdf(OUTPUT)
check_oh_rdf(data)
out, err = cfiles(
"rdf",
"--steps", ":50",
"-c", "15",
"-p", "150",
"-s", "pairs: name(#1) H and name(#2) O",
TRAJECTORY, "-o", OUTPUT
)
assert(out == "")
assert(err == "")
data = read_rdf(OUTPUT)
check_oh_rdf(data)
def correlations(output):
output_corr = output + ".autocorr"
out, err = cfiles(
"hbonds",
"--guess-bonds",
"-c", "15",
TRAJECTORY, "-o", output,
"--autocorrelation", output_corr
)
assert(out == "")
assert(err == "")
# This is only a regression test, checking that the right output is
# generated.
expected = os.path.join(
os.path.dirname(__file__), "data", "water.hbonds.autocorrelation.dat"
)
with open(output_corr) as actual:
with open(expected) as expected:
for line in actual:
expected_line = expected.readline()
if line.startswith("#"):
continue
step, value = map(float, line.split())
exp_step, exp_value = map(float, expected_line.split())
assert(step == exp_step)
assert(abs((value - exp_value) / value) < 1e-3)
os.unlink(output_corr)
def hbonds():
out, err = cfiles("hbonds", "--guess-bonds", "-c", "15", TRAJECTORY, "-o",
OUTPUT)
assert (out == "")
assert (err == "")
data, indexes = read_data(OUTPUT)
check_angles(data)
check_hbonds(indexes)
def angles(selection, output):
out, err = cfiles(
"angles", "--guess-bonds", "-c", "15", "-s", selection, TRAJECTORY, "-o", output
)
assert out == ""
assert err == ""
data = read_data(output)
check_angles(data)
def density(selection):
out, err = cfiles("density", "-c", "24:24:25.458:90:90:120", "--max=20",
"--points=200", "--radial=Z", "-s", selection,
TRAJECTORY, "-o", OUTPUT)
assert (out == "")
assert (err == "")
data = read_data(OUTPUT)
check_density(data)
return data
def OH_rdf_all():
'''Oxygen-Hydrogen rdf for the whole trajectory'''
out, err = cfiles("rdf", "-c", "15", "-p", "150", "-s",
"pairs: name(#1) O and name(#2) H", TRAJECTORY, "-o",
OUTPUT)
assert (out == "")
assert (err == "")
data = read_rdf(OUTPUT)
check_oh_rdf(data)
out, err = cfiles("rdf", "-c", "15", "-p", "150", "-s",
"pairs: name(#1) H and name(#2) O", TRAJECTORY, "-o",
OUTPUT)
assert (out == "")
assert (err == "")
data = read_rdf(OUTPUT)
check_ho_rdf(data)
def hbonds(output):
out, err = cfiles(
"hbonds",
"--guess-bonds",
"-c", "15",
TRAJECTORY, "-o", output
)
assert(out == "")
assert(err == "")
indexes = read_data(output)
check_hbonds(indexes)
def oxygen_rdf_all(output):
'''Oxygen rdf for the whole trajectory'''
out, err = cfiles(
"rdf",
"-c", "15", # Set cell
"-p", "150", # Use 150 points in the histogram
"-s", "name O", # Compute rdf between O
TRAJECTORY, "-o", output
)
assert(out == "")
assert(err == "")
data = read_rdf(output)
check_oxygen_rdf(data)
def oxygen_rdf_all():
'''Oxygen rdf for the whole trajectory'''
out, err = cfiles(
"rdf",
"-c", "15", # Set cell
"-p", "150", # Use 150 points in the histogram
"-s", "name O", # Compute rdf between O
TRAJECTORY, "-o", OUTPUT
)
assert(out == "")
assert(err == "")
data = read_rdf(OUTPUT)
check_oxygen_rdf(data)
def density(selection, output):
out, err = cfiles(
"density",
"-c", "24:24:25.458:90:90:120",
"--max=20",
"--points=200",
"--radial=Z",
"-s", selection,
TRAJECTORY, "-o", output
)
assert(out == "")
assert(err == "")
data = read_data(output)
check_density(data)
return data
pass
with open(self.name + ".pdb", "w") as fd:
fd.write(PDB_CONTENT)
def __exit__(self, type, value, traceback):
try:
os.unlink(self.name + ".pdb")
except OSError:
pass
try:
os.unlink(self.name + ".xyz")
except OSError:
pass
if __name__ == '__main__':
filename = "convert"
with isolate_files(filename):
out, err = cfiles("convert", filename + ".pdb", filename + ".xyz")
assert (out == "")
assert (err == "")
with open(filename + ".xyz") as fd:
assert (fd.read() == XYZ_CONTENT)
with isolate_files(filename):
out, err = cfiles("convert", filename + ".pdb", filename + ".xyz",
"--selection", 'atoms: type O')
assert (out == "")
assert (err == "")
with open(filename + ".xyz") as fd:
assert (fd.read() == XYZ_SEL_CONTENT)
def __exit__(self, type, value, traceback):
try:
os.unlink(self.name + ".pdb")
except OSError:
pass
try:
os.unlink(self.name + ".xyz")
except OSError:
pass
if __name__ == '__main__':
filename = "convert"
with isolate_files(filename):
out, err = cfiles("convert", filename + ".pdb", filename + ".xyz")
assert(out == "")
assert(err == "")
with open(filename + ".xyz") as fd:
assert(fd.read() == XYZ_CONTENT)
with isolate_files(filename):
out, err = cfiles(
"convert",
filename + ".pdb",
filename + ".xyz",
"--selection", 'atoms: type O'
)
assert(out == "")
assert(err == "")
with open(filename + ".xyz") as fd:
# -*- coding: utf8 -*-
from testrun import cfiles
if __name__ == '__main__':
stdout, stderr = cfiles("--version")
assert (stderr == "")
assert ("version" in stdout)
assert ("using chemfiles" in stdout)
stdout, stderr = cfiles("-V")
assert (stderr == "")
assert ("version" in stdout)
assert ("using chemfiles" in stdout)
# -*- coding: utf8 -*-
from testrun import cfiles
if __name__ == '__main__':
stdout, stderr = cfiles("--version")
assert(stderr == "")
assert("version" in stdout)
assert("using chemfiles" in stdout)
stdout, stderr = cfiles("-V")
assert(stderr == "")
assert("version" in stdout)
assert("using chemfiles" in stdout)