})
BA_CONSTRAINT.create_angles_by_definition(
anglesDefinition={"CO2": [('C', 'O1', 'O2', 170, 180)]})
# initialize constraints data
ENGINE.initialize_used_constraints()
# save engine
ENGINE.save()
else:
ENGINE = ENGINE.load(enginePath)
# unpack constraints before fitting in case tweaking is needed
PDF_CONSTRAINT, IMD_CONSTRAINT, B_CONSTRAINT, BA_CONSTRAINT = ENGINE.constraints
# set all constraints as used. Used value is True by default!
# Now you know you can deactivate any constraint at any time though.
PDF_CONSTRAINT.set_used(True)
IMD_CONSTRAINT.set_used(True)
B_CONSTRAINT.set_used(True)
BA_CONSTRAINT.set_used(True)
##########################################################################################
##################################### DIFFERENT RUNS ###################################
def run_atoms(ENGINE, rang=None, recur=None, xyzFrequency=500):
ENGINE.set_groups(None)
# set selector
if recur is None: recur = 10
ENGINE.set_group_selector(RandomSelector(ENGINE))
# number of steps
nsteps = recur * len(ENGINE.groups)
if rang is None: rang = 20
for stepIdx in range(rang):
if allElements[g.indexes[0]] == 'ni':
g.set_move_generator(toTiSG)
elif allElements[g.indexes[0]] == 'ti':
g.set_move_generator(toNiSG)
# run
ENGINE.run(numberOfSteps=nsteps,
saveFrequency=saveFrequency,
restartPdb=None)
##########################################################################################
################################### RUN no_constraints #################################
# rename first frame set by default to '0'
ENGINE.rename_frame('0', 'no_constraints')
ACN_CONSTRAINT.set_used(False)
EMD_CONSTRAINT.set_used(False)
run_normal(nsteps=1000000, saveFrequency=1000, engineFilePath=engineFilePath)
run_swap(nsteps=100000, saveFrequency=1000, engineFilePath=engineFilePath)
run_normal(nsteps=10000, saveFrequency=1000, engineFilePath=engineFilePath)
##########################################################################################
###################################### RUN with_vdw ####################################
ENGINE.add_frames('with_vdw')
ENGINE.set_used_frame('with_vdw')
ENGINE.reinit_frame('with_vdw')
ACN_CONSTRAINT.set_used(False)
EMD_CONSTRAINT.set_used(True)
run_normal(nsteps=1000000, saveFrequency=1000, engineFilePath=engineFilePath)
run_swap(nsteps=100000, saveFrequency=1000, engineFilePath=engineFilePath)
run_normal(nsteps=10000, saveFrequency=1000, engineFilePath=engineFilePath)