def calcOneStructure(loopInfo):
""" this function calculates a single structure, performs analysis on the
structure, and then writes out a pdb file, with remarks.
"""
# initialize parameters for high temp dynamics.
InitialParams(rampedParams)
# high-temp dynamics setup - only need to specify parameters which
# differfrom initial values in rampedParams
InitialParams(highTempParams)
# high temp dynamics
#
protocol.initDynamics(
dyn,
potList=potList, # potential terms to use
bathTemp=init_t,
initVelocities=1,
finalTime=10, # stops at 10ps or 5000 steps
numSteps=5000, # whichever comes first
printInterval=100)
dyn.setETolerance(init_t / 100) #used to det. stepsize. default: t/1000
dyn.run()
# initialize parameters for cooling loop
InitialParams(rampedParams)
# initialize integrator for simulated annealing
#
protocol.initDynamics(
dyn,
potList=potList,
numSteps=100, #at each temp: 100 steps or
finalTime=.2, # .2ps, whichever is less
printInterval=100)
# perform simulated annealing
#
cool.run()
# final torsion angle minimization
#
protocol.initMinimize(dyn, printInterval=50)
dyn.run()
# final all- atom minimization
#
protocol.initMinimize(minc, potList=potList, dEPred=10)
minc.run()
#do analysis and write structure when this function returns
toIUPAC()
from simulationTools import analyze
protocol.writeCIF(loopInfo.filename() + ".cif", remarks=analyze(potList))
fromIUPAC()
pass
dSymm = create_DistSymmPot(
'dSymm',
genDimerRestraints(segids=['A', 'B'],
resids=range(minResid, maxResid, 5)))
potList.append(dSymm)
# ``NCS'' term - keep dimer subunits identical
from posDiffPotTools import create_PosDiffPot
ncs = create_PosDiffPot("ncs", "segid A", "segid B")
ncs.setScale(10)
potList.append(ncs)
pass
fromIUPAC()
# gyration volume term
#
# gyration volume term
#
#from gyrPotTools import create_GyrPot
#gyr = create_GyrPot("Vgyr",
# "resid 1:56") # selection should exclude disordered tails
#potList.append(gyr)
#rampedParams.append( MultRamp(.002,1,"gyr.setScale(VALUE)") )
# HBPot - knowledge-based hydrogen bond term
#
from hbPotTools import create_HBPot
hb = create_HBPot('hb')