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
markers = ["", '.', '+', '^', '|'] INTRA_STYLES = [r[0] + r[1] for r in itertools.product(['--'], colors)] INTRA_STYLES = [r[0] + r[1] for r in itertools.product(markers, INTRA_STYLES)] INTER_STYLES = [r[0] + r[1] for r in itertools.product(['-'], colors)] INTER_STYLES = [r[0] + r[1] for r in itertools.product(markers, INTER_STYLES)] trajectories = ["atomsTraj.xyz", "exploreTraj.xyz"] pdbPath = "CO2.pdb" expDataPath = "Xrays.gr" # create engine ENGINE = Engine(path=None) ENGINE.set_pdb(pdbPath) PDF_CONSTRAINT = PairDistributionConstraint(experimentalData=expDataPath, weighting="atomicNumber") ENGINE.add_constraints([PDF_CONSTRAINT]) ENGINE.initialize_used_constraints() ENGINE.set_chi_square() def create_figure(PDF, show=False, savePath=None): # get output output = PDF.get_constraint_value() # create figure FIG = plt.figure() FIG.patch.set_facecolor('white') grid = gridspec.GridSpec(nrows=2, ncols=2) grid.update(left=0.05, right=0.95, wspace=0.05) totalAx = plt.subplot(grid[0, :]) lowRAx = plt.subplot(grid[1, 0]) highRAx = plt.subplot(grid[1, 1])
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={ "TIP": [('OH2', 'H1', 0.8, 1.1), ('OH2', 'H2', 0.8, 1.1)]
NSTEPS = 10000 pdbPath = 'system.pdb' expData = 'experimental.gr' # initialize engine ENGINE = Engine(path=None) ENGINE.set_pdb(pdbPath) # create constraints PDF_CONSTRAINT = PairDistributionConstraint(experimentalData=expData, weighting="atomicNumber") EMD_CONSTRAINT = InterMolecularDistanceConstraint() B_CONSTRAINT = BondConstraint() BA_CONSTRAINT = BondsAngleConstraint() IA_CONSTRAINT = ImproperAngleConstraint() # add constraints to engine ENGINE.add_constraints([ PDF_CONSTRAINT, EMD_CONSTRAINT, B_CONSTRAINT, BA_CONSTRAINT, IA_CONSTRAINT ]) # initialize constraints definitions B_CONSTRAINT.create_bonds_by_definition( bondsDefinition={ "THF": [('O', 'C1', 1.22, 1.70), ('O', 'C4', 1.22, 1.70), ( 'C1', 'C2', 1.25, 1.90), ('C2', 'C3', 1.25, 1.90), ( 'C3', 'C4', 1.25, 1.90), ('C1', 'H11', 0.58, 1.22), ('C1', 'H12', 0.58, 1.22), ('C2', 'H21', 0.58, 1.22), ('C2', 'H22', 0.58, 1.22), ('C3', 'H31', 0.58, 1.22), ('C3', 'H32', 0.58,
sqExpPath = os.path.join(DIR_PATH, sqFileName) pdbPath = os.path.join(DIR_PATH, pdbFileName) engineFilePath = os.path.join(DIR_PATH, engineFileName) # set some useful flags FRESH_START = True # check Engine exists, if not build it otherwise load it. ENGINE = Engine(path=None) if not ENGINE.is_engine(engineFilePath) or FRESH_START: # create engine ENGINE = Engine(path=engineFilePath, freshStart=True) ENGINE.set_pdb(pdbFileName) # add G(r) constraint PDF_CONSTRAINT = PairDistributionConstraint(experimentalData=grExpPath, weighting="atomicNumber") ENGINE.add_constraints([PDF_CONSTRAINT]) # Rebin S(Q) experimental data and build constraint Sq = np.transpose(rebin(np.loadtxt(sqExpPath), bin=0.05)).astype(FLOAT_TYPE) RSF_CONSTRAINT = ReducedStructureFactorConstraint(experimentalData=Sq, weighting="atomicNumber") ENGINE.add_constraints([RSF_CONSTRAINT]) # add coordination number constraint and set to un-used ACN_CONSTRAINT = AtomicCoordinationNumberConstraint() ENGINE.add_constraints([ACN_CONSTRAINT]) ACN_CONSTRAINT.set_used(False) # add inter-molecular distance constraint EMD_CONSTRAINT = InterMolecularDistanceConstraint(defaultDistance=2.2, flexible=True) ENGINE.add_constraints([EMD_CONSTRAINT]) # save engine
from fullrmc.Constraints.DistanceConstraints import InterMolecularDistanceConstraint from fullrmc.Generators.Rotations import RotationGenerator from fullrmc.Generators.Translations import TranslationTowardsCenterGenerator ########################################################################################## ################################## 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 inter-molecular distance constraint EMD_CONSTRAINT = InterMolecularDistanceConstraint(defaultDistance=1.75) ENGINE.add_constraints([EMD_CONSTRAINT]) ########################################################################################## #################################### DIFFERENT RUNS #################################### def move_towards(): # set only one molecule group ENGINE.set_groups_as_molecules() secMolIdxs = ENGINE.groups[1].indexes ENGINE.set_groups(ENGINE.groups[0]) # set move generator for g in ENGINE.groups: t = TranslationTowardsCenterGenerator(center={'indexes': secMolIdxs}, amplitude=0.15, angle=90) r = RotationGenerator(amplitude=10)
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