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
from fullrmc.Constraints.BondConstraints import BondConstraint from fullrmc.Constraints.AngleConstraints import BondsAngleConstraint ########################################################################################## ################################## SHUT DOWN LOGGING ################################### 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={
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