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
def calcOneStructure(loopInfo):
""" this function calculates a single structure, performs analysis on the
structure, and then writes out a pdb file, with remarks.
"""
# generate a new structure with randomized torsion angles
#
from monteCarlo import randomizeTorsions
randomizeTorsions(dyn)
# set torsion angles from restraints
#
from torsionTools import setTorsionsFromTable
setTorsionsFromTable(
dihedralRestraintFilename) ## does this work if incomplete? ##
protocol.fixupCovalentGeom(maxIters=100, useVDW=1)
protocol.writePDB(loopInfo.filename() + ".init")
# 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=100, # stops at 100ps or 1000 steps
numSteps=1000, # whichever comes first
printInterval=100)
dyn.setETolerance(init_t / 100) #used to det. stepsize. default: t/1000
dyn.run()
# 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- atomic degrees of freedom minimization
#
protocol.initMinimize(minc, potList=potList, dEPred=10)
minc.run()
#do analysis and write structure when function returns
pass
# 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,
finalTemp=25,
tempStep=12.5,
ivm=dyn,
rampedParams=rampedParams)
def accept(potList):
def calcOneStructure(loopInfo):
""" this function calculates a single structure, performs analysis on the
structure, and then writes out a pdb file, with remarks.
"""
# generate a new structure with randomized torsion angles
#
randomizeTorsions(dyn)
protocol.fixupCovalentGeom(maxIters=100,useVDW=1)
# set torsion angles from restraints
#
setTorsionsFromTable("dihed_g_all.tbl")
# calc. initial tensor orientation
#
# for medium in media.values():
# calcTensorOrientation(medium)
# pass
# 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=100, # stops at 800ps or 8000 steps
numSteps=1000, # whichever comes first
printInterval=100)
# pylint: disable=E1101
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()
# optional cooling in Cartesian coordinates
#
protocol.initDynamics(minc,
potList=potList,
numSteps=100, #at each temp: 100 steps or
finalTime=.4 , # .2ps, whichever is less
printInterval=100)
#cart_cool.run()
# final all- atom minimization
#
protocol.initMinimize(minc,
potList=potList,
dEPred=10)
minc.run()
#do analysis and write structure
loopInfo.writeStructure(potList)
def calcOneStructure(loopInfo):
""" this function calculates a single structure, performs analysis on the
structure, and then writes out a pdb file, with remarks.
"""
# generate a new structure with randomized torsion angles
#
randomizeTorsions(dyn)
protocol.fixupCovalentGeom(maxIters=100, useVDW=1)
# set torsion angles from restraints
#
setTorsionsFromTable("dihed_g_all.tbl")
# calc. initial tensor orientation
#
# for medium in media.values():
# calcTensorOrientation(medium)
# pass
# 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=100, # stops at 800ps or 8000 steps
numSteps=1000, # whichever comes first
printInterval=100)
# pylint: disable=E1101
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()
# optional cooling in Cartesian coordinates
#
protocol.initDynamics(
minc,
potList=potList,
numSteps=100, #at each temp: 100 steps or
finalTime=.4, # .2ps, whichever is less
printInterval=100)
#cart_cool.run()
# final all- atom minimization
#
protocol.initMinimize(minc, potList=potList, dEPred=10)
minc.run()
#do analysis and write structure
loopInfo.writeStructure(potList)
# the IVM is used for performing dynamics and minimization in torsion-angle
# space, and in Cartesian space.
#
dyn = IVM()
# 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,
def structLoopAction(loopInfo):
#
# this function calculates a single structure.
#
#
# set some high-temp force constants
#
noe.setScale(20) #use large scale factor initially
command("parameters nbonds repel %f end end" % ini_rad)
command("parameters nbonds rcon %f end end" % ini_con)
setConstraints(ini_ang, ini_imp)
# Initial weight--modified later
command("restraints dihedral scale=5. end")
#
# high temp dynamics
# note no Van der Waals term
#
init_t = 3500
ini_timestep = 0.010
bath = init_t
timestep = ini_timestep
protocol.initDynamics(
dyn,
potList=hitemp_potList, # potential terms to use
bathTemp=bath,
initVelocities=1,
finalTime=20,
printInterval=100)
dyn.setETolerance(bath / 100) #used to det. stepsize. default: bath/1000
dyn.run()
# increase dihedral term
command("restraints dihedral scale=200. end")
#
# cooling and ramping parameters
#
global k_ang, k_imp
# MultRamp ramps the scale factors over the specified range for the
# simulated annealing.
from simulationTools import MultRamp
k_noe = MultRamp(ini_noe, 30., "noe.setScale( VALUE )")
radius = MultRamp(ini_rad, 0.8,
"command('param nbonds repel VALUE end end')")
k_vdw = MultRamp(ini_con, 4, "command('param nbonds rcon VALUE end end')")
k_ang = MultRamp(ini_ang, 1.0)
k_imp = MultRamp(ini_imp, 1.0)
protocol.initDynamics(dyn,
potList=potList,
bathTemp=bath,
initVelocities=1,
finalTime=2,
printInterval=100,
stepsize=timestep)
from simulationTools import AnnealIVM
AnnealIVM(initTemp =init_t,
finalTemp=100,
tempStep =25,
ivm=dyn,
rampedParams = [k_noe,radius,k_vdw,k_ang,k_imp],
extraCommands= lambda notUsed: \
setConstraints(k_ang.value(),
k_imp.value())).run()
#
# final torsion angle minimization
#
protocol.initMinimize(dyn, printInterval=50)
dyn.run()
#
# final all atom minimization
#
protocol.initMinimize(minc, potList=potList, printInterval=100)
minc.run()
#
# analyze and write out structure
#
print "Starting writeStructure"
loopInfo.writeStructure(potList)
#
dyn = IVM()
# Minimize in Cartesian space with only the covalent constraints.
# Note that bonds, angles and many impropers can't change with the
# 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)
def structLoopAction(loopInfo):
#
# this function calculates a single structure.
#
#
# set some high-temp force constants
#
noe.setScale( 20 ) #use large scale factor initially
command("parameters nbonds repel %f end end" % ini_rad)
command("parameters nbonds rcon %f end end" % ini_con)
setConstraints(ini_ang, ini_imp)
# Initial weight--modified later
command("restraints dihedral scale=5. end")
#
# high temp dynamics
# note no Van der Waals term
#
init_t = 3500
ini_timestep = 0.010
bath = init_t
timestep = ini_timestep
protocol.initDynamics(dyn,
potList=hitemp_potList, # potential terms to use
bathTemp=bath,
initVelocities=1,
finalTime=20,
printInterval=100)
dyn.setETolerance( bath/100 ) #used to det. stepsize. default: bath/1000
dyn.run()
# increase dihedral term
command("restraints dihedral scale=200. end")
#
# cooling and ramping parameters
#
global k_ang, k_imp
# MultRamp ramps the scale factors over the specified range for the
# simulated annealing.
from simulationTools import MultRamp
k_noe = MultRamp(ini_noe,30.,"noe.setScale( VALUE )")
radius = MultRamp(ini_rad,0.8,
"command('param nbonds repel VALUE end end')")
k_vdw = MultRamp(ini_con,4, "command('param nbonds rcon VALUE end end')")
k_ang = MultRamp(ini_ang,1.0)
k_imp = MultRamp(ini_imp,1.0)
protocol.initDynamics(dyn,
potList=potList,
bathTemp=bath,
initVelocities=1,
finalTime=2,
printInterval=100,
stepsize=timestep)
from simulationTools import AnnealIVM
AnnealIVM(initTemp =init_t,
finalTemp=100,
tempStep =25,
ivm=dyn,
rampedParams = [k_noe,radius,k_vdw,k_ang,k_imp],
extraCommands= lambda notUsed: \
setConstraints(k_ang.value(),
k_imp.value())).run()
#
# final torsion angle minimization
#
protocol.initMinimize(dyn, printInterval=50)
dyn.run()
#
# final all atom minimization
#
protocol.initMinimize(minc, potList=potList, printInterval=100)
minc.run()
#
# analyze and write out structure
#
print "Starting writeStructure"
loopInfo.writeStructure(potList)
#
dyn = IVM()
# Minimize in Cartesian space with only the covalent constraints.
# Note that bonds, angles and many impropers can't change with the
# 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)
