def agitate_both():
print "Agitate both"
# agitate all
ENGINE.set_groups_as_molecules()
groups = [g for g in ENGINE.groups]
for idx in range(0,ENGINE.pdb.numberOfAtoms,3):
groups.append(np.array([idx, idx+1]))
groups.append(np.array([idx, idx+2]))
ENGINE.add_groups(groups)
# set move generator
for g in ENGINE.groups:
if len(g)==2:
g.set_move_generator(DistanceAgitationGenerator(amplitude=0.1, agitate=(False,True)))
elif len(g)==3:
g.set_move_generator(AngleAgitationGenerator(amplitude=5))
else:
raise
# set ordered selector
ENGINE.set_group_selector(DefinedOrderSelector(ENGINE, order=None) )
# set ordered selector
ENGINE.set_group_selector(DefinedOrderSelector(ENGINE, order=None) )
# run engine
xyzPath="both.xyz"
if os.path.isfile(xyzPath): os.remove(xyzPath)
nsteps = 250*len(ENGINE.groups)
xyzFrequency = len(ENGINE.groups)
# run engine
ENGINE.run(numberOfSteps=nsteps, saveFrequency=2*nsteps, xyzFrequency=xyzFrequency, xyzPath=xyzPath, restartPdb=None)
def along1(ENGINE, rang=5, recur=100, refine=False, explore=True):
ENGINE.set_groups_as_molecules()
[
g.set_move_generator(
TranslationAlongSymmetryAxisGenerator(axis=1, amplitude=0.1))
for g in ENGINE.groups
]
# set selector
centers = [
np.sum(ENGINE.realCoordinates[g.indexes], axis=0) / len(g)
for g in ENGINE.groups
]
distances = [np.sqrt(np.add.reduce(c**2)) for c in centers]
order = np.argsort(distances)
recur = 200
gs = RecursiveGroupSelector(DefinedOrderSelector(ENGINE, order=order),
recur=recur,
refine=refine,
explore=explore)
ENGINE.set_group_selector(gs)
# number of steps
nsteps = recur * len(ENGINE.groups)
for stepIdx in range(rang):
LOGGER.info("Running 'along1' mode step %i" % (stepIdx))
ENGINE.run(numberOfSteps=nsteps, saveFrequency=nsteps)
def shrink(ENGINE, newDim):
ENGINE.set_groups_as_molecules()
[
g.set_move_generator(
MoveGeneratorCollector(collection=[
TranslationGenerator(amplitude=0.2),
RotationGenerator(amplitude=5)
],
randomize=True)) for g in ENGINE.groups
]
# get groups order
centers = [
np.sum(ENGINE.realCoordinates[g.indexes], axis=0) / len(g)
for g in ENGINE.groups
]
distances = [np.sqrt(np.add.reduce(c**2)) for c in centers]
order = np.argsort(distances)
# change boundary conditions
bcFrom = str([list(bc) for bc in ENGINE.boundaryConditions.get_vectors()])
ENGINE.set_boundary_conditions(newDim)
bcTo = str([list(bc) for bc in ENGINE.boundaryConditions.get_vectors()])
LOGGER.info("boundary conditions changed from %s to %s" % (bcFrom, bcTo))
# set selector
recur = 200
gs = RecursiveGroupSelector(DefinedOrderSelector(ENGINE, order=order),
recur=recur,
refine=True)
ENGINE.set_group_selector(gs)
# number of steps
nsteps = recur * len(ENGINE.groups)
for stepIdx in range(10):
LOGGER.info("Running 'shrink' mode step %i" % (stepIdx))
ENGINE.run(numberOfSteps=nsteps, saveFrequency=nsteps)
fname = "shrink_" + str(newDim).replace(".", "p")
def agitate_bonds():
print("Agitate bonds")
# agitate bonds
groups = []
for idx in range(0, ENGINE.pdb.numberOfAtoms, 3):
groups.append(np.array([idx, idx + 1]))
groups.append(np.array([idx, idx + 2]))
ENGINE.set_groups(groups)
[
g.set_move_generator(
DistanceAgitationGenerator(amplitude=0.1, agitate=(False, True)))
for g in ENGINE.groups
]
# set ordered selector
ENGINE.set_group_selector(DefinedOrderSelector(ENGINE, order=None))
# run engine
xyzPath = "bonds.xyz"
if os.path.isfile(xyzPath): os.remove(xyzPath)
nsteps = 250 * len(ENGINE.groups)
xyzFrequency = len(ENGINE.groups)
ENGINE.run(numberOfSteps=nsteps,
saveFrequency=2 * nsteps,
xyzFrequency=xyzFrequency,
xyzPath=xyzPath,
restartPdb=None)
def agitate_angles():
print "Agitate angles"
# agitate angles
ENGINE.set_groups_as_molecules()
[g.set_move_generator(AngleAgitationGenerator(amplitude=5)) for g in ENGINE.groups]
# set ordered selector
ENGINE.set_group_selector(DefinedOrderSelector(ENGINE, order=None) )
# run engine
xyzPath="angles.xyz"
if os.path.isfile(xyzPath): os.remove(xyzPath)
nsteps = 250*len(ENGINE.groups)
xyzFrequency = len(ENGINE.groups)
ENGINE.run(numberOfSteps=nsteps, saveFrequency=2*nsteps, xyzFrequency=xyzFrequency, xyzPath=xyzPath, restartPdb=None)