Python cartesianTopology 예제들

예제 #1

파일: 6nbn_Xplor-NIH_refine.py 프로젝트: PDNALab/NEF

#
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,
                 finalTemp=25,
                 tempStep=12.5,
                 ivm=dyn,
                 rampedParams=rampedParams)


def accept(potList):
    """
    return True if current structure meets acceptance criteria

예제 #2

파일: anneal2.py 프로젝트: VuisterLab/cing

# initialize ivm topology for torsion-angle dynamics

#for m in media.values():
#    m.setFreedom("fixDa, fixRh")        #fix tensor Rh, Da, vary orientation
##    m.setFreedom("varyDa, varyRh")      #vary tensor Rh, Da, vary orientation
protocol.torsionTopology(dyn)

# minc used for final cartesian minimization
#
minc = IVM()
protocol.initMinimize(minc)

#for m in media.values():
#    m.setFreedom("varyDa, varyRh")    #allow all tensor parameters float here
#    pass
protocol.cartesianTopology(minc)



# object which performs simulated annealing
#
init_t  = 3500.     # Need high temp and slow annealing to converge
cool = AnnealIVM(initTemp =init_t,
                 finalTemp=25,
                 tempStep =12.5,
                 ivm=dyn,
                 rampedParams = rampedParams)

#cart_cool is for optional cartesian-space cooling
cart_cool = AnnealIVM(initTemp =init_t,
                  finalTemp=25,