class TestIVM(TestCase):
def setUp(self):
self.clf = IVM()
def test_get_params(self):
self.clf.get_params()
def test_set_params(self):
self.clf.set_params(_lambda=3)
def test_fit_precict(self):
data = datasets.load_iris()
print cross_val_score(self.clf, data.data, data.target)
potList['ANGL'].setThreshold(5)
rampedParams.append(MultRamp(0.4, 1, "potList['ANGL'].setScale(VALUE)"))
potList.append(XplorPot("IMPR"))
potList['IMPR'].setThreshold(5)
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 potList import PotList
potList = PotList()
# parameters to ramp up during the simulated annealing protocol
#
from simulationTools import MultRamp, StaticRamp, InitialParams, IVMAction
rampedParams = []
highTempParams = []
# 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()
minc = IVM() # minc used for final cartesian minimization
# initialize ivm topology for torsion-angle dynamics
#
#
#
# compare atomic Cartesian rmsd with a reference structure
# backbone and heavy atom RMSDs will be printed in the output
# structure files
#
# from posDiffPotTools import create_PosDiffPot
# refRMSD = create_PosDiffPot("refRMSD","name CA or name C or name N",
# pdbFile='g_xray.pdb', ## modify ##
potList.append(XplorPot("ANGL"))
potList['ANGL'].setThreshold(5)
rampedParams.append(MultRamp(0.4, 1, "potList['ANGL'].setScale(VALUE)"))
potList.append(XplorPot("IMPR"))
potList['IMPR'].setThreshold(5)
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.
#
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
def setUp(self):
self.clf = IVM()
hitemp_potList = PotList()
hitemp_potList.add(XplorPot("BOND"))
hitemp_potList.add(XplorPot("ANGL"))
hitemp_potList.add(XplorPot("IMPR"))
hitemp_potList.add(XplorPot("CDIH"))
hitemp_potList.add(noe)
# Give atoms uniform weights, except for the anisotropy axis
AtomSel("all ").apply(SetProperty("mass", 100.))
AtomSel("all ").apply(SetProperty("fric", 10.))
#
# IVM setup
#
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()
hitemp_potList = PotList()
hitemp_potList.add( XplorPot("BOND") )
hitemp_potList.add( XplorPot("ANGL") )
hitemp_potList.add( XplorPot("IMPR") )
hitemp_potList.add( XplorPot("CDIH") )
hitemp_potList.add( noe )
# Give atoms uniform weights, except for the anisotropy axis
AtomSel("all ").apply( SetProperty("mass",100.) )
AtomSel("all ").apply( SetProperty("fric",10.) )
#
# IVM setup
#
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()
potList['ANGL'].setThreshold(5)
rampedParams.append(MultRamp(0.4, 1, "potList['ANGL'].setScale(VALUE)"))
potList.append(XplorPot("IMPR"))
potList['IMPR'].setThreshold(5)
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()
#don't yet have proper top/par values for ACD
dyn.group("segid B")
protocol.torsionTopology(dyn)
# minc used for final cartesian minimization
#
minc = IVM()
protocol.initMinimize(minc)
minc.group("segid B")
