コード例 #1
0
ファイル: 6nbn_Xplor-NIH_refine.py プロジェクト: PDNALab/NEF
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
コード例 #2
0
ファイル: testEnsemblePot.py プロジェクト: locsmith/xcamshift
 def setUp(self):
     ensembleSize=3
  
     esim = EnsembleSimulation("ensemble",ensembleSize)
     print "ensemble size", esim.size(),"running on",esim.numThreads(),"processors."
     
     dyn  = ivm.IVM(esim) 
     protocol.torsionTopology(dyn)
     
     potList = PotList("test pot list")
     pot  = PyEnsemblePot('test ensemble pot')
     potList.append(pot)
     
     protocol.initDynamics(dyn,
                   bathTemp=400,
                   initVelocities=1,
                   potList=potList,
                   finalTime=1,
                   numSteps=1,
                   printInterval=0)
     dyn.run()
コード例 #3
0
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
コード例 #4
0
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)
コード例 #5
0
ファイル: anneal2.py プロジェクト: VuisterLab/cing
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)
コード例 #6
0
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)
コード例 #7
0
ファイル: anneal.py プロジェクト: VuisterLab/cing
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)