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()
