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")