data = {}
# compute pdfs
dataAdded = False
for idx in range(len(pdbFiles)):
fname = pdbFiles[idx]
if fname in data: continue
dataAdded = True
print("loading frame %i out of %i --> %s" % (idx, len(pdbFiles), fname))
# create constraints
PDF = PairDistributionConstraint(engine=None,
experimentalData=expDataPath,
weighting="atomicNumber")
# create engine
ENGINE = Engine(pdb=fname, constraints=[PDF])
ENGINE.run(numberOfSteps=0)
# get pdf
output = PDF.get_constraint_value()
output["observed"] = PDF.experimentalPDF
output["observedR"] = PDF.experimentalDistances
output["computedR"] = PDF.shellsCenter
output["chiSquare"] = PDF.squaredDeviations
data[fname] = output
if dataAdded: pickle.dump(data, open(pdfDataPath, "wb"))
# plot data
idx = 0
for key in pdbFiles:
#key = pdbFiles[-1]
print(key)
def run_engine(PDF=True,
IMD=True,
B=True,
BA=True,
IA=True,
molecular=True,
nsteps=10000,
ncores=1):
ENGINE = Engine(path=None)
ENGINE.set_pdb(pdbPath)
# create experimental constraints
if PDF:
C = PairDistributionConstraint(experimentalData=expPath,
weighting="atomicNumber")
ENGINE.add_constraints(C)
# create and define molecular constraints
if IMD:
C = InterMolecularDistanceConstraint(defaultDistance=1.5)
ENGINE.add_constraints(C)
if B:
C = BondConstraint()
ENGINE.add_constraints(C)
C.create_bonds_by_definition(
bondsDefinition={
"THF": [('O', 'C1', 1.29,
1.70), ('O', 'C4', 1.29,
1.70), ('C1', 'C2', 1.29,
1.70), ('C2', 'C3', 1.29,
1.70), ('C3', 'C4', 1.29,
1.70),
('C1', 'H11', 0.58,
1.15), ('C1', 'H12', 0.58,
1.15), ('C2', 'H21', 0.58,
1.15), ('C2', 'H22', 0.58, 1.15),
('C3', 'H31', 0.58,
1.15), ('C3', 'H32', 0.58,
1.15), ('C4', 'H41', 0.58,
1.15), ('C4', 'H42', 0.58, 1.15)]
})
if BA:
C = BondsAngleConstraint()
ENGINE.add_constraints(C)
C.create_angles_by_definition(
anglesDefinition={
"THF": [
('O', 'C1', 'C4', 95, 135),
('C1', 'O', 'C2', 95, 135),
('C4', 'O', 'C3', 95, 135),
('C2', 'C1', 'C3', 90, 120),
('C3', 'C2', 'C4', 90, 120),
# H-C-H angle
('C1', 'H11', 'H12', 95, 125),
('C2', 'H21', 'H22', 95, 125),
('C3', 'H31', 'H32', 95, 125),
('C4', 'H41', 'H42', 95, 125),
# 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', 80, 123),
('C1', 'H12', 'C2', 80, 123),
('C2', 'H21', 'C1', 80, 123),
('C2', 'H21', 'C3', 80, 123),
('C2', 'H22', 'C1', 80, 123),
('C2', 'H22', 'C3', 80, 123),
('C3', 'H31', 'C2', 80, 123),
('C3', 'H31', 'C4', 80, 123),
('C3', 'H32', 'C2', 80, 123),
('C3', 'H32', 'C4', 80, 123),
('C4', 'H41', 'C3', 80, 123),
('C4', 'H42', 'C3', 80, 123)
]
})
if IA:
C = ImproperAngleConstraint()
ENGINE.add_constraints(C)
C.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()
# run engine
if molecular:
ENGINE.set_groups_as_molecules()
print 'molecular, %s atoms, %s steps, %2s cores' % (
ENGINE.numberOfAtoms, nsteps, ncores),
tic = time.time()
ENGINE.run(numberOfSteps=nsteps,
saveFrequency=2 * nsteps,
restartPdb=None,
ncores=ncores)
elapsed = float(time.time() - tic) / float(nsteps)
print ' -- > %s seconds per step' % (elapsed, )
else:
ENGINE.set_groups_as_atoms()
print 'atomic , %s atoms, %s steps, %2s cores' % (
ENGINE.numberOfAtoms, nsteps, ncores),
tic = time.time()
ENGINE.run(numberOfSteps=nsteps,
saveFrequency=2 * nsteps,
restartPdb=None,
ncores=ncores)
elapsed = float(time.time() - tic) / float(nsteps)
print ' -- > %s seconds per step' % (elapsed, )
# return elapsed time
return elapsed