def create_engine():
# create engine
ENGINE = Engine(path=None)
ENGINE.set_pdb(pdbPath)
# initialize constraints
B_CONSTRAINT = BondConstraint()
BA_CONSTRAINT = BondsAngleConstraint()
IA_CONSTRAINT = ImproperAngleConstraint()
# add constraints
ENGINE.add_constraints([B_CONSTRAINT])
B_CONSTRAINT.create_bonds_by_definition( bondsDefinition={"THF": [('O' ,'C1' , 1.20, 1.70),
('O' ,'C4' , 1.20, 1.70),
('C1','C2' , 1.25, 1.90),
('C2','C3' , 1.25, 1.90),
('C3','C4' , 1.25, 1.90),
('C1','H11', 0.88, 1.16),('C1','H12', 0.88, 1.16),
('C2','H21', 0.88, 1.16),('C2','H22', 0.88, 1.16),
('C3','H31', 0.88, 1.16),('C3','H32', 0.88, 1.16),
('C4','H41', 0.88, 1.16),('C4','H42', 0.88, 1.16)] })
ENGINE.add_constraints([BA_CONSTRAINT])
BA_CONSTRAINT.create_angles_by_definition( anglesDefinition={"THF": [ ('O' ,'C1' ,'C4' , 105, 125),
('C1' ,'O' ,'C2' , 100, 120),
('C4' ,'O' ,'C3' , 100, 120),
('C2' ,'C1' ,'C3' , 95 , 115),
('C3' ,'C2' ,'C4' , 95 , 115),
# H-C-H angle
('C1' ,'H11','H12', 98 , 118),
('C2' ,'H21','H22', 98 , 118),
('C3' ,'H31','H32', 98 , 118),
('C4' ,'H41','H42', 98 , 118),
# H-C-O angle
('C1' ,'H11','O' , 100, 120),
('C1' ,'H12','O' , 100, 120),
('C4' ,'H41','O' , 100, 120),
('C4' ,'H42','O' , 100, 120),
# H-C-C
('C1' ,'H11','C2' , 103, 123),
('C1' ,'H12','C2' , 103, 123),
('C2' ,'H21','C1' , 103, 123),
('C2' ,'H21','C3' , 103, 123),
('C2' ,'H22','C1' , 103, 123),
('C2' ,'H22','C3' , 103, 123),
('C3' ,'H31','C2' , 103, 123),
('C3' ,'H31','C4' , 103, 123),
('C3' ,'H32','C2' , 103, 123),
('C3' ,'H32','C4' , 103, 123),
('C4' ,'H41','C3' , 103, 123),
('C4' ,'H42','C3' , 103, 123) ] })
ENGINE.add_constraints([IA_CONSTRAINT])
IA_CONSTRAINT.create_angles_by_definition( anglesDefinition={"THF": [ ('C2','O','C1','C4', -15, 15),
('C3','O','C1','C4', -15, 15) ] })
# initialize constraints data
ENGINE.initialize_used_constraints()
# set moves generators
# set all move generators to Translation with a maximum amplutide of 0.3 A
[g.set_move_generator(TranslationGenerator(amplitude=0.3)) for g in ENGINE.groups]
# set randomly 25% of the translation amplitude to 10A
[g.set_move_generator(TranslationGenerator(amplitude=10.)) for g in ENGINE.groups if np.random.random()>0.25]
# return engine
return ENGINE
LOGGER.set_minimum_level(sys.maxint, stdoutFlag=True, fileFlag=True)
##########################################################################################
##################################### CREATE ENGINE ####################################
pdbPath = "system.pdb"
ENGINE = Engine(path=None)
ENGINE.set_pdb(pdbPath)
# add constraints
B_CONSTRAINT = BondConstraint()
BA_CONSTRAINT = BondsAngleConstraint()
ENGINE.add_constraints([B_CONSTRAINT, BA_CONSTRAINT])
B_CONSTRAINT.create_bonds_by_definition(bondsDefinition={
"TIP": [('OH2', 'H1', 0.8, 1.1), ('OH2', 'H2', 0.8, 1.1)]
})
BA_CONSTRAINT.create_angles_by_definition(
anglesDefinition={"TIP": [('OH2', 'H1', 'H2', 80, 120)]})
# set TranslationGenerator move generators amplitude
[g.moveGenerator.set_amplitude(0.025) for g in ENGINE.groups]
##########################################################################################
#################################### DIFFERENT RUNS ####################################
def run_normal(nsteps, xyzPath):
B_CONSTRAINT.create_bonds_by_definition(bondsDefinition={
"TIP": [('OH2', 'H1', 0.8, 1.1), ('OH2', 'H2', 0.8, 1.1)]
})
ENGINE.run(numberOfSteps=nsteps,
saveFrequency=nsteps * 2,
xyzFrequency=1,
xyzPath=xyzPath,
BA_CONSTRAINT.create_angles_by_definition(
anglesDefinition={
"THF": [
('O', 'C1', 'C4', 105, 125),
('C1', 'O', 'C2', 100, 120),
('C4', 'O', 'C3', 100, 120),
('C2', 'C1', 'C3', 95, 115),
('C3', 'C2', 'C4', 95, 115),
# H-C-H angle
('C1', 'H11', 'H12', 98, 118),
('C2', 'H21', 'H22', 98, 118),
('C3', 'H31', 'H32', 98, 118),
('C4', 'H41', 'H42', 98, 118),
# H-C-O angle
('C1', 'H11', 'O', 100, 120),
('C1', 'H12', 'O', 100, 120),
('C4', 'H41', 'O', 100, 120),
('C4', 'H42', 'O', 100, 120),
# H-C-C
('C1', 'H11', 'C2', 103, 123),
('C1', 'H12', 'C2', 103, 123),
('C2', 'H21', 'C1', 103, 123),
('C2', 'H21', 'C3', 103, 123),
('C2', 'H22', 'C1', 103, 123),
('C2', 'H22', 'C3', 103, 123),
('C3', 'H31', 'C2', 103, 123),
('C3', 'H31', 'C4', 103, 123),
('C3', 'H32', 'C2', 103, 123),
('C3', 'H32', 'C4', 103, 123),
('C4', 'H41', 'C3', 103, 123),
('C4', 'H42', 'C3', 103, 123)
]
})
ENGINE.add_constraints([B_CONSTRAINT, BA_CONSTRAINT, IA_CONSTRAINT])
B_CONSTRAINT.create_bonds_by_definition(
bondsDefinition={
"PFT": [
('Xe', 'F1', 1.9, 2.1),
('Xe', 'F2', 1.9, 2.1),
('Xe', 'F3', 1.9, 2.1),
('Xe', 'F4', 1.9, 2.1),
('Xe', 'F5', 1.9, 2.1),
]
})
BA_CONSTRAINT.create_angles_by_definition(
anglesDefinition={
"PFT": [
('Xe', 'F1', 'F2', 60, 80),
('Xe', 'F2', 'F3', 60, 80),
('Xe', 'F3', 'F4', 60, 80),
('Xe', 'F4', 'F5', 60, 80),
('Xe', 'F5', 'F1', 60, 80),
]
})
IA_CONSTRAINT.create_angles_by_definition(
anglesDefinition={
"PFT": [('F4', 'F2', 'F1', 'F3', -2,
2), ('F5', 'F2', 'F1', 'F3', -2,
2), ('Xe', 'F2', 'F1', 'F3', -2, 2)]
})
# set TranslationGenerator move generators amplitude
[g.moveGenerator.set_amplitude(0.1) for g in ENGINE.groups]
if not ENGINE.is_engine(enginePath) or FRESH_START:
# initialize engine
ENGINE = Engine(path=enginePath, freshStart=True)
ENGINE.set_pdb(pdbPath)
PDF_CONSTRAINT = PairDistributionConstraint(experimentalData=expDataPath,
weighting="atomicNumber")
IMD_CONSTRAINT = InterMolecularDistanceConstraint(defaultDistance=1.4)
B_CONSTRAINT = BondConstraint()
BA_CONSTRAINT = BondsAngleConstraint()
# add constraints
ENGINE.add_constraints(
[PDF_CONSTRAINT, IMD_CONSTRAINT, B_CONSTRAINT, BA_CONSTRAINT])
B_CONSTRAINT.create_bonds_by_definition(bondsDefinition={
"CO2": [('C', 'O1', 0.52, 1.4), ('C', 'O2', 0.52, 1.4)]
})
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)
('H31','H21', 2.0, 100),
('H31','H22', 2.0, 100),
('H32','H21', 2.0, 100),
('H32','H22', 2.0, 100),] })
BA_CONSTRAINT.create_angles_by_definition( anglesDefinition={"BUT": [ # C-C-C angles
('C2' ,'C1' ,'C3' , 99 , 119),
('C3' ,'C1' ,'C4' , 99 , 119),
# C-H3 angles
('C1' ,'H11','H12', 99 , 119),
('C1' ,'H11','H13', 99 , 119),
('C1' ,'H12','H13', 99 , 119),
('C4' ,'H41','H42', 99 , 119),
('C4' ,'H41','H43', 99 , 119),
('C4' ,'H42','H43', 99 , 119),
# C-H2 angles
('C2' ,'H21','H22', 99 , 119),
('C3' ,'H31','H32', 99 , 119),
# C-C-H angles
('C1' ,'C2' ,'H11', 101, 121),
('C1' ,'C2' ,'H12', 101, 121),
('C1' ,'C2' ,'H13', 101, 121),
('C4' ,'C3' ,'H41', 101, 121),
('C4' ,'C3' ,'H42', 101, 121),
('C4' ,'C3' ,'H43', 101, 121),
('C2' ,'C1' ,'H21', 97 , 117),
('C2' ,'C3' ,'H22', 97 , 117),
('C3' ,'C2' ,'H31', 97 , 117),
('C3' ,'C4' ,'H32', 97 , 117)] })
DA_CONSTRAINT.create_angles_by_definition( anglesDefinition={"BUT": [ ('C1','C2','C3','C4', 30,90, 150,210, 270,330)] })
# set TranslationGenerator move generators amplitude