def test_get_cvs_with_qdot_broken(self):
"""Tests get_cvs with a dummy coordinate file, include_qdot = True, and a coordinate file without velocities"""
settings = configure('../../data/atesa.config')
settings.include_qdot = True
settings.topology = '../test_data/test.prmtop'
settings.cvs = [
'pytraj.distance(traj, \'@1 @3\')[0]',
'pytraj.distance(traj, \'@2 @4\')[0]'
]
with pytest.raises(IndexError):
result = utilities.get_cvs('../test_data/test.rst7', settings)
def test_get_cvs_no_qdot_reduce(self):
"""Tests get_cvs with a dummy coordinate file, include_qdot = False, and reduce = True"""
settings = configure('../../data/atesa.config')
settings.include_qdot = False
settings.topology = '../test_data/test.prmtop'
settings.cvs = [
'pytraj.distance(traj, \'@1 @3\')[0]',
'pytraj.distance(traj, \'@2 @4\')[0]'
]
with pytest.raises(FileNotFoundError): # no as.out present yet
result = utilities.get_cvs('../test_data/test.rst7',
settings,
reduce=True)
shutil.copy('../test_data/as.out',
'as.out') # copy in the necessary file
result = utilities.get_cvs('../test_data/test.rst7',
settings,
reduce=True)
assert len(result.split(' ')) == 2
assert float(result.split(' ')[0]) == pytest.approx(0.571, 1e-2)
assert float(result.split(' ')[1]) == pytest.approx(0.326, 1e-2)
def test_get_cvs_no_qdot(self):
"""Tests get_cvs with a dummy coordinate file and include_qdot = False"""
settings = configure('../../data/atesa.config')
settings.include_qdot = False
settings.topology = '../test_data/test.prmtop'
settings.cvs = [
'pytraj.distance(traj, \'@1 @3\')[0]',
'pytraj.distance(traj, \'@2 @4\')[0]'
]
result = utilities.get_cvs('../test_data/test.rst7', settings)
assert len(result.split(' ')) == 2
assert float(result.split(' ')[0]) == pytest.approx(1.09, 1e-3)
assert float(result.split(' ')[1]) == pytest.approx(1.69, 1e-3)
def test_get_cvs_with_qdot(self):
"""Tests get_cvs with a dummy coordinate file, include_qdot = True, and a coordinate file with velocities"""
settings = configure('../../data/atesa.config')
settings.include_qdot = True
settings.topology = '../test_data/test.prmtop'
settings.cvs = [
'pytraj.distance(traj, \'@1 @3\')[0]',
'pytraj.distance(traj, \'@2 @4\')[0]'
]
result = utilities.get_cvs('../test_data/test_velocities.rst7',
settings)
assert len(result.split(' ')) == 4
assert float(result.split(' ')[0]) == pytest.approx(1.089, 1e-3)
assert float(result.split(' ')[1]) == pytest.approx(1.728, 1e-3)
assert float(result.split(' ')[2]) == pytest.approx(-0.252, 1e-2)
assert float(result.split(' ')[3]) == pytest.approx(0.282, 1e-2)
def main(working_directory, rc_definition, as_out_file, extrema=False):
"""
The main function of rc_eval.py. Accepts an aimless shooting working directory and a reaction coordinate definition,
producing in that directory a new file named 'rc.out' (overwriting if one already exists) identifying each shooting
point (files in the directory whose names end in "_init.rst7") and its corresponding reaction coordinate value in a
sorted list.
If extrema == True, skips producing rc.out and just returns the minimum and maximum RC value for a single accepted
shooting move, which is useful when preparing umbrella sampling simulations.
Parameters
----------
working_directory : str
The path to the aimless shooting working directory in which to act
rc_definition : str
A reaction coordinate definition formatted as a string of python-readable code with "CV[X]" standing in for the
Xth CV value (one-indexed); this RC definition should be in terms of reduced variables (values between 0 and 1)
as_out_file : str
Path to the aimless shooting output file used to build the reaction coordinate. Usually this should be a
decorrelated file (named with "decorr").
extrema : bool
If True, skips producing rc.out and just returns the minimum and maximum RC value for a single accepted shooting
move, which is useful when preparing umbrella sampling simulations.
Returns
-------
None
"""
# Change to working directory
os.chdir(working_directory)
# Unpickle settings object for use in utilities.get_cvs
try:
settings = pickle.load(open('settings.pkl', 'rb'))
except FileNotFoundError: # replace with more informative error message
raise FileNotFoundError(
'the working directory must contain a valid settings.pkl file, which is generated '
'automatically when running ATESA, but one was not found in the working directory: '
+ working_directory)
if not settings.job_type == 'aimless_shooting':
raise RuntimeError(
'rc_eval.py can only be called on an aimless shooting working directory, but the provided '
'directory (' + working_directory +
') contains a settings.pkl file with job_type = ' +
settings.job_type)
settings.as_out_file = as_out_file # for reducing CVs properly
settings.include_qdot = False # unnecessary for our purposes
if extrema:
from atesa.main import Thread
print(
'Evaluating final RC values of forward and backward trajectories from an accepted shooting move...'
)
result = []
allthreads = pickle.load(open('restart.pkl', 'rb'))
for thread in allthreads:
if thread.history.last_accepted > -1: # if accepted move exists in thread
for job_index in range(2):
cvs = utilities.get_cvs(thread.history.prod_trajs[
thread.history.last_accepted][job_index],
settings,
reduce=True).split(' ')
result.append(utilities.evaluate_rc(rc_definition, cvs))
print(' Shooting move name: ' + thread.history.init_coords[
thread.history.last_accepted][0])
print(' extrema: ' +
str([float('%.4f' % float(item)) for item in result]))
return None # to exit the script after returning extrema
raise RuntimeError(
'none of the shooting moves in the working directory appear to contain any accepted moves.'
)
# Obtain list of shooting point coordinate files
file_list = glob.glob('*_init.rst7')
if not file_list:
raise FileNotFoundError(
'no valid shooting point files (as given by names ending in \'_init.rst7\') were found '
'in the working directory \'' + working_directory +
'\'. Is this an aimless shooting '
'working directory?')
# Iterate through the list, calling evaluate_rc for each one and storing the result
results = []
count = 0
count_to = len(file_list)
update_progress(0, 'Evaluating RC values')
speed_data = [0, 0]
for file in file_list:
t = time.time()
cv_list = utilities.get_cvs(file, settings, reduce=True).split(' ')
results.append(
[file + ': ',
utilities.evaluate_rc(rc_definition, cv_list)])
this_speed = time.time() - t
speed_data = [
(speed_data[1] * speed_data[0] + this_speed) / (speed_data[1] + 1),
speed_data[1] + 1
]
count += 1
eta = (count_to - count) * speed_data[0]
update_progress(count / count_to, 'Evaluating RC values', eta=eta)
results = sorted(
results,
key=lambda x: abs(float(x[1]))) # sort results by absolute value of RC
# Create and write to rc.out file
open('rc.out', 'w').close()
with open('rc.out', 'a') as f:
for result in results:
f.write(result[0] + str(result[1]) + '\n')
f.close()