Python IVM.reset Exemples

Exemple #1

Fichier : 6nbn_Xplor-NIH_refine.py Projet : PDNALab/NEF

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
#
from simulationTools import AnnealIVM
init_t = 3000.  # Need high temp and slow annealing to converge
cool = AnnealIVM(initTemp=init_t,

Exemple #2

Fichier : anneal.py Projet : VuisterLab/cing

# internal torsion-angle dynamics
#  breaks bonds topologically - doesn't change force field

dyn.potList().add( XplorPot("BOND") )
dyn.potList().add( XplorPot("ANGL") )
dyn.potList().add( XplorPot("IMPR") )

dyn.breakAllBondsIn("all")

protocol.initMinimize(dyn,numSteps=1000)
dyn.run()

#
# reset ivm topology for torsion-angle dynamics
#
dyn.reset()
dyn.potList().removeAll()

protocol.torsionTopology(dyn)

#
# minc used for final cartesian minimization
#
minc = IVM()
protocol.initMinimize(minc)
IVM_groupRigidSidechain(minc)
minc.breakAllBondsIn("all")

def setConstraints(k_ang,k_imp):
    command("""
      constraints