def writeTrajectory(self, trajectory_name, block_size=1):
trajectory = Trajectory(self.universe, trajectory_name, 'w',
self.title, block_size=block_size)
actions = [TrajectoryOutput(trajectory, ["all"], 0, None, 1)]
snapshot = SnapshotGenerator(self.universe, actions=actions)
conf = self.universe.configuration()
vel = self.universe.velocities()
grad = ParticleVector(self.universe)
try:
while 1:
line = self.history.readline()
if not line:
break
data = FortranLine(line, history_timestep_line)
step = data[1]
natoms = data[2]
nvectors = data[3]+1
pbc = data[4]
dt = data[5]
step_data = {'time': step*dt}
if nvectors > 2:
step_data['gradients'] = grad
if pbc:
data = FortranLine(self.history.readline(), history_pbc_line)
box_x = data[0]*Units.Ang
#if data[1] != 0. or data[2] != 0.:
# raise ValueError, "box shape not supported"
data = FortranLine(self.history.readline(), history_pbc_line)
box_y = data[1]*Units.Ang
#if data[0] != 0. or data[2] != 0.:
# raise ValueError, "box shape not supported"
data = FortranLine(self.history.readline(), history_pbc_line)
box_z = data[2]*Units.Ang
#if data[0] != 0. or data[1] != 0.:
# raise ValueError, "box shape not supported"
self.universe.setSize((box_x, box_y, box_z))
for i in range(natoms):
self.history.readline()
conf.array[i] = map(float,
string.split(self.history.readline()))
if nvectors > 1:
vel.array[i] = map(float,
string.split(self.history.readline()))
if nvectors > 2:
grad.array[i] = map(float,
string.split(self.history.readline()))
Numeric.multiply(conf.array, Units.Ang, conf.array)
if nvectors > 1:
Numeric.multiply(vel.array, Units.Ang/Units.ps, vel.array)
if nvectors > 2:
Numeric.multiply(grad.array, -Units.amu*Units.Ang/Units.ps**2,
grad.array)
snapshot(data=step_data)
finally:
trajectory.close()
def _writeToTrajectory(self, filename, comment, path):
trajectory = Trajectory(self.universe, filename, "w", comment)
snapshot = SnapshotGenerator(self.universe,
actions = [TrajectoryOutput(trajectory,
["all"],
0, None, 1)])
for step in path:
self.universe.setConfiguration(step.conf)
snapshot()
trajectory.close()
def finalize(self):
"""Finalizes the calculations (e.g. averaging the total term, output files creations ...).
"""
if self.architecture == 'monoprocessor':
t = self.trajectory
else:
# Load the whole trajectory set.
t = Trajectory(None, self.trajectoryFilename, 'r')
comsUniverse = t.universe.__copy__()
comsUniverse.removeObject(comsUniverse.objectList()[:])
orderedAtoms = sorted(t.universe.atomList(), key = operator.attrgetter('index'))
groups = [Collection([orderedAtoms[ind] for ind in g]) for g in self.group]
comp = 1
for g in groups:
comAtom = Atom('H', name = 'COM'+str(comp))
comAtom._mass = g.mass()
comsUniverse.addObject(comAtom)
comp += 1
# traj_new is the filtered trajectory
outputFile = Trajectory(comsUniverse, self.output, "w")
outputFile.jobinfo = self.information + '\nOutput file written on: %s\n\n' % asctime()
# Each time |snapshot| is called, the universe contents i flushed into the output file.
snapshot = SnapshotGenerator(comsUniverse,\
actions = [TrajectoryOutput(outputFile, ["configuration","time"], 0, None, 1)])
# Loop over the output frames.
for comp in range(self.nFrames):
frameIndex = self.frameIndexes[comp]
t.universe.setFromTrajectory(t, frameIndex)
comsUniverse.setCellParameters(t.universe.cellParameters())
aComp = 0
for at in comsUniverse.atomList():
at.setPosition(self.comsTrajectory[frameIndex][aComp])
aComp += 1
snapshot(data = {'time': self.times[comp]})
# The output COM trajectory is closed.
outputFile.close()
self.toPlot = None
def test_snapshot(self):
initial = self.universe.copyConfiguration()
transformation = Translation(Vector(0.,0.,0.01)) \
* Rotation(Vector(0.,0.,1.), 1.*Units.deg)
trajectory = Trajectory(self.universe,
"test.nc",
"w",
"trajectory test",
double_precision=self.double_precision)
snapshot = SnapshotGenerator(
self.universe,
actions=[TrajectoryOutput(trajectory, ["all"], 0, None, 1)])
snapshot()
for i in range(100):
self.universe.setConfiguration(
self.universe.contiguousObjectConfiguration())
self.universe.applyTransformation(transformation)
self.universe.foldCoordinatesIntoBox()
snapshot()
trajectory.close()
self.universe.setConfiguration(initial)
trajectory = Trajectory(None, "test.nc")
t_universe = trajectory.universe
for i in range(101):
configuration = self.universe.configuration()
t_configuration = trajectory[i]['configuration']
max_diff = N.maximum.reduce(
N.ravel(N.fabs(configuration.array - t_configuration.array)))
self.assert_(max_diff < self.tolerance)
if configuration.cell_parameters is not None:
max_diff = N.maximum.reduce(
N.fabs(configuration.cell_parameters -
t_configuration.cell_parameters))
self.assert_(max_diff < self.tolerance)
self.universe.setConfiguration(
self.universe.contiguousObjectConfiguration())
self.universe.applyTransformation(transformation)
self.universe.foldCoordinatesIntoBox()
trajectory.close()
def writeTrajectory(self, trajectory_name, block_size=1):
trajectory = Trajectory(self.universe,
trajectory_name,
'w',
self.title,
block_size=block_size)
actions = [TrajectoryOutput(trajectory, ["all"], 0, None, 1)]
snapshot = SnapshotGenerator(self.universe, actions=actions)
conf = self.universe.configuration()
vel = self.universe.velocities()
grad = ParticleVector(self.universe)
nvectors = N_VECTORS
natoms = N_ATOMS
self._setSize()
try:
while True:
vline = self.velfile.readline()
pline = self.posfile.readline()
if not vline:
break
vdata = vline.split()
pdata = pline.split()
if len(pdata) == 2: # Example: ["10", "0.00120944"]
step = int(vdata[0])
step_data = {'time': step * DT}
for i in range(natoms):
conf.array[i] = map(float,
string.split(self.posfile.readline()))
vel.array[i] = map(float,
string.split(self.velfile.readline()))
conf.array = Units.Ang * conf.array
if nvectors > 1:
vel.array = Units.Ang / Units.ps * vel.array
snapshot(data=step_data)
finally:
trajectory.close()
def interpreteInputParameters(self):
"""Parse the input parameters for the analysis.
"""
# Parses the parameters that are common to different analysis.
Analysis.interpreteInputParameters(self)
self.buildTimeInfo()
self.subset = self.selectAtoms(self.subsetDefinition)
self.nSelectedAtoms = len(self.subset)
orderedAtoms = sorted(self.trajectory.universe.atomList(), key = operator.attrgetter('index'))
selectedAtoms = Collection([orderedAtoms[ind] for ind in self.subset])
# traj_new is the filtered trajectory
self.outputFile = Trajectory(selectedAtoms, self.output, "w")
# Create the snapshot generator
self.snapshot = SnapshotGenerator(self.trajectory.universe, actions = [TrajectoryOutput(self.outputFile, ["all"], 0, None, 1)])
def finalize(self):
"""Finalizes the calculations (e.g. averaging the total term, output files creations ...).
"""
if self.architecture == 'monoprocessor':
t = self.trajectory
else:
# Load the whole trajectory set.
t = Trajectory(None, self.trajectoryFilename, 'r')
orderedAtoms = sorted(t.universe.atomList(), key = operator.attrgetter('index'))
selectedAtoms = Collection([orderedAtoms[ind] for ind in self.subset])
targetAtoms = Collection([orderedAtoms[ind] for ind in self.target])
# traj_new is the filtered trajectory
outputFile = Trajectory(targetAtoms, self.output, "w")
outputFile.jobinfo = self.information + '\nOutput file written on: %s\n\n' % asctime()
# Create the snapshot generator
snapshot = SnapshotGenerator(t.universe, actions = [TrajectoryOutput(outputFile, ["configuration"], 0, None, 1)])
# Loop over the output frames.
for comp in range(self.nFrames):
frameIndex = self.frameIndexes[comp]
t.universe.setFromTrajectory(t, frameIndex)
for at in targetAtoms:
at.setPosition(Vector(self.filteredTrajectory[frameIndex][at.index]))
snapshot(data = {'time': self.times[comp]})
outputFile.close()
t.close()
self.toPlot = None
time += delta_t
snapshot(data={'time': time,
'potential_energy': energy})
if equilibration_temperature is not None \
and step % equilibration_frequency == 0:
universe.scaleVelocitiesToTemperature(equilibration_temperature)
# Define system
universe = InfiniteUniverse(Amber99ForceField())
universe.protein = Protein('bala1')
# Create trajectory and snapshot generator
trajectory = Trajectory(universe, "md_trajectory.nc", "w",
"Generated by a Python integrator")
snapshot = SnapshotGenerator(universe,
actions = [TrajectoryOutput(trajectory,
["all"], 0, None, 1)])
# Initialize velocities
universe.initializeVelocitiesToTemperature(50.*Units.K)
# Heat and equilibrate
for temperature in [50., 100., 200., 300.]:
doVelocityVerletSteps(delta_t = 1.*Units.fs, nsteps = 500,
equilibration_temperature = temperature*Units.K,
equilibration_frequency = 1)
doVelocityVerletSteps(delta_t = 1.*Units.fs, nsteps = 500,
equilibration_temperature = 300*Units.K,
equilibration_frequency = 10)
# Production run
doVelocityVerletSteps(delta_t = 1.*Units.fs, nsteps = 5000)
trajectory.close()
def finalize(self):
"""Finalizes the calculations (e.g. averaging the total term, output files creations ...).
"""
if self.architecture == 'monoprocessor':
t = self.trajectory
else:
# Load the whole trajectory set.
t = Trajectory(None, self.trajectoryFilename, 'r')
selectedAtoms = Collection()
orderedAtoms = sorted(t.universe.atomList(),
key=operator.attrgetter('index'))
groups = [[
selectedAtoms.addObject(orderedAtoms[index])
for index in atomIndexes
] for atomIndexes in self.group]
# Create trajectory
outputFile = Trajectory(selectedAtoms, self.output, 'w')
# Create the snapshot generator
snapshot = SnapshotGenerator(
t.universe,
actions=[
TrajectoryOutput(outputFile, ["configuration", "time"], 0,
None, 1)
])
# The output is written
for comp in range(self.nFrames):
frameIndex = self.frameIndexes[comp]
t.universe.setFromTrajectory(t, frameIndex)
for atom in selectedAtoms:
atom.setPosition(self.RBT['trajectory'][atom.index][comp, :])
snapshot(data={'time': self.times[comp]})
outputFile.close()
outputFile = NetCDFFile(self.output, 'a')
outputFile.title = self.__class__.__name__
outputFile.jobinfo = self.information + '\nOutput file written on: %s\n\n' % asctime(
)
outputFile.jobinfo += 'Input trajectory: %s\n\n' % self.trajectoryFilename
outputFile.createDimension('NFRAMES', self.nFrames)
outputFile.createDimension('NGROUPS', self.nGroups)
outputFile.createDimension('QUATERNIONLENGTH', 4)
# The NetCDF variable that stores the quaternions.
QUATERNIONS = outputFile.createVariable(
'quaternion', N.Float, ('NGROUPS', 'NFRAMES', 'QUATERNIONLENGTH'))
# The NetCDF variable that stores the centers of mass.
COM = outputFile.createVariable('com', N.Float,
('NGROUPS', 'NFRAMES', 'xyz'))
# The NetCDF variable that stores the rigid-body fit.
FIT = outputFile.createVariable('fit', N.Float, ('NGROUPS', 'NFRAMES'))
# Loop over the groups.
for comp in range(self.nGroups):
aIndexes = self.group[comp]
outputFile.jobinfo += 'Group %s: %s\n' % (
comp + 1, [index for index in aIndexes])
QUATERNIONS[comp, :, :] = self.RBT[comp]['quaternions'][:, :]
COM[comp, :, :] = self.RBT[comp]['com'][:, :]
FIT[comp, :] = self.RBT[comp]['fit'][:]
outputFile.close()
self.toPlot = None
def fit(pdb_file, map_file, energy_cutoff, label, trajectory_freq):
dmap = load(map_file)
universe = InfiniteUniverse(CalphaForceField(2.5))
universe.protein = Protein(pdb_file, model='calpha')
set_distances(universe.protein)
modes = calc_modes(universe, 3 * universe.numberOfAtoms())
for nmodes in range(6, len(modes)):
if modes[nmodes].frequency > energy_cutoff * modes[6].frequency:
break
if trajectory_freq > 0:
trajectory_filename = 'fit_%s_m%d.nc' % (label, nmodes)
print "Fit trajectory:", trajectory_filename
trajectory = Trajectory(
universe, trajectory_filename, 'w',
'Density fit %s using %d modes' % (label, nmodes))
actions = [
TrajectoryOutput(trajectory, ["configuration", "fit_error"], 0,
None, 1)
]
snapshot = SnapshotGenerator(universe, actions=actions)
snapshot.available_data.append('fit_error')
amplitude = 0.1
i = 0
fit = []
windex = 0
protocol_filename = 'fit_%s_m%d_fiterror.txt' % (label, nmodes)
print "Fit error protocol file:", protocol_filename
protocol = file(protocol_filename, 'w')
nmc = 2 * nmodes
modes = calc_modes(universe, nmc)
windows = N.arange(10.) * modes[nmodes].frequency / 10.
while 1:
f, gradient = dmap.fitWithGradient(universe)
fit.append(f)
print >> protocol, i, fit[-1]
protocol.flush()
if len(fit) > 1 and fit[-1] > fit[-2]:
amplitude /= 2.
random_width = gradient.norm()*(random/100.) \
/ N.sqrt(universe.numberOfAtoms())
random_vector = randomParticleVector(universe, random_width)
gradient = gradient + random_vector
displacement = ParticleVector(universe)
for n in range(nmodes):
m = modes[n]
if n < 6:
weight = 5. * weight_function(modes[6], windows[windex])
else:
weight = weight_function(m, windows[windex])
displacement = displacement + \
weight*m.massWeightedDotProduct(gradient)*m
displacement = displacement * amplitude / displacement.norm()
universe.setConfiguration(universe.configuration() + displacement)
fix_structure(universe.protein)
if trajectory_freq > 0 and i % trajectory_freq == 0:
snapshot(data={'fit_error': fit[-1]})
i = i + 1
if i % 20 == 0:
modes = calc_modes(universe, nmc)
if i % 10 == 0 and i > 50:
convergence = (fit[-1] - fit[-11]) / (fit[30] - fit[20])
if convergence < 0.05:
break
if convergence < 0.2:
windex = min(windex + 1, len(windows) - 1)
if convergence < 0.1:
amplitude = 0.5 * amplitude
protocol.close()
if trajectory_freq > 0:
trajectory.close()
pdb_out = 'fit_%s_m%d.pdb' % (label, nmodes)
print "Writing final structure to", pdb_out
universe.writeToFile(pdb_out)
chain = protein[i]
chain_calpha = protein_calpha[i]
for j in range(len(chain)):
r = conf[chain[j].peptide.C_alpha]
chain_calpha[j].peptide.C_alpha.setPosition(r)
chain_calpha[j].peptide.C_alpha.index = index
map.append(chain[j].peptide.C_alpha.index)
index = index + 1
universe_calpha.configuration()
# Open the new trajectory for just the interesting objects.
trajectory_calpha = Trajectory(universe_calpha, 'calpha_trajectory.nc', 'w')
# Make a snapshot generator for saving.
snapshot = SnapshotGenerator(universe_calpha,
actions = [TrajectoryOutput(trajectory_calpha,
None, 0, None, 1)])
# Loop over all steps, eliminate rigid-body motion with reference to
# the initial configuration, and save the configurations to the new
# trajectory.
first = 1
for step in trajectory:
conf = universe.contiguousObjectConfiguration(proteins,
step['configuration'])
conf_calpha = Configuration(universe_calpha, N.take(conf.array, map),
None)
universe_calpha.setConfiguration(conf_calpha)
if first:
initial_conf_calpha = copy(conf_calpha)
first = 0
def shrinkUniverse(universe, temperature=300.*Units.K, trajectory=None,
scale_factor=0.95):
"""
Shrinks the universe, which must have been scaled up by
:class:`~MMTK.Solvation.addSolvent`, back to its original size.
The compression is performed in small steps, in between which
some energy minimization and molecular dynamics steps are executed.
The molecular dynamics is run at the given temperature, and
an optional trajectory can be specified in which intermediate
configurations are stored.
:param universe: a finite universe
:type universe: :class:`~MMTK.Universe.Universe`
:param temperature: the temperature at which the Molecular Dynamics
steps are run
:type temperature: float
:param trajectory: the trajectory in which the progress of the
shrinking procedure is stored, or a filename
:type trajectory: :class:`~MMTK.Trajectory.Trajectory` or str
:param scale_factor: the factor by which the universe is scaled
at each reduction step
:type scale_factor: float
"""
# Set velocities and initialize trajectory output
universe.initializeVelocitiesToTemperature(temperature)
if trajectory is not None:
if isinstance(trajectory, basestring):
trajectory = Trajectory(universe, trajectory, "w",
"solvation protocol")
close_trajectory = True
else:
close_trajectory = False
actions = [TrajectoryOutput(trajectory, ["configuration"], 0, None, 1)]
snapshot = SnapshotGenerator(universe, actions=actions)
snapshot()
# Do some minimization and equilibration
minimizer = SteepestDescentMinimizer(universe, step_size = 0.05*Units.Ang)
actions = [VelocityScaler(temperature, 0.01*temperature, 0, None, 1),
TranslationRemover(0, None, 20)]
integrator = VelocityVerletIntegrator(universe, delta_t = 0.5*Units.fs,
actions = actions)
for i in range(5):
minimizer(steps = 40)
integrator(steps = 200)
# Scale down the system in small steps
i = 0
while universe.scale_factor > 1.:
if trajectory is not None and i % 1 == 0:
snapshot()
i = i + 1
step_factor = max(scale_factor, 1./universe.scale_factor)
for object in universe:
object.translateTo(step_factor*object.position())
universe.scaleSize(step_factor)
universe.scale_factor = universe.scale_factor*step_factor
for i in range(3):
minimizer(steps = 10)
integrator(steps = 50)
del universe.scale_factor
if trajectory is not None:
snapshot()
if close_trajectory:
trajectory.close()
# Open the input trajectory.
full = Trajectory(None, 'full_trajectory.nc')
# Collect the items you want to keep. Here we keep everything but
# water molecules.
universe = full.universe
keep = Collection()
for object in universe:
try:
is_water = object.type.name == 'water'
except AttributeError:
is_water = 0
if not is_water:
keep.addObject(object)
# Open the new trajectory for just the interesting objects.
subset = Trajectory(keep, 'subset_trajectory.nc', 'w')
# Make a snapshot generator for saving.
snapshot = SnapshotGenerator(
universe, actions=[TrajectoryOutput(subset, None, 0, None, 1)])
# Loop over all steps and save them to the new trajectory.
for configuration in full.configuration:
universe.setConfiguration(configuration)
snapshot()
# Close both trajectories.
full.close()
subset.close()