from potList import PotList potList = PotList() # parameters to ramp up during the simulated annealing protocol # from simulationTools import MultRamp, StaticRamp, InitialParams, IVMAction rampedParams = [] highTempParams = [] # IVM setup # the IVM is used for performing dynamics and minimization in torsion-angle # space, and in Cartesian space. # from ivm import IVM dyn = IVM() minc = IVM() # minc used for final cartesian minimization # initialize ivm topology for torsion-angle dynamics # # # # compare atomic Cartesian rmsd with a reference structure # backbone and heavy atom RMSDs will be printed in the output # structure files # # from posDiffPotTools import create_PosDiffPot # refRMSD = create_PosDiffPot("refRMSD","name CA or name C or name N", # pdbFile='g_xray.pdb', ## modify ##
potList['ANGL'].setThreshold(5) rampedParams.append(MultRamp(0.4, 1, "potList['ANGL'].setScale(VALUE)")) potList.append(XplorPot("IMPR")) potList['IMPR'].setThreshold(5) rampedParams.append(MultRamp(0.1, 1, "potList['IMPR'].setScale(VALUE)")) # Give atoms uniform weights, except for the anisotropy axis # protocol.massSetup() # IVM setup # the IVM is used for performing dynamics and minimization in torsion-angle # space, and in Cartesian space. # from ivm import IVM dyn = IVM() # reset ivm topology for torsion-angle dynamics # dyn.reset() protocol.torsionTopology(dyn) # minc used for final cartesian minimization # minc = IVM() protocol.initMinimize(minc) protocol.cartesianTopology(minc) # object which performs simulated annealing
def setUp(self): self.clf = IVM()