def findGmec(epart):
print("\n\nFinding GMEC with energy partition: %s\n" % epart)
# configure conformation energies with the desired energy partition
confEcalc = osprey.ConfEnergyCalculator(confSpace, ecalc, energyPartition=epart)
# find the GMEC
emat = osprey.EnergyMatrix(confEcalc)
astar = osprey.AStarTraditional(emat, confSpace)
gmec = osprey.GMECFinder(astar, confEcalc).find()
def makeAStar(rcs, emat=emat):
return osprey.AStarTraditional(
emat,
rcs,
showProgress=False,
# Set a limit on the size of the conf tree so we don't use unlimited memory.
# The minimum possible value here is (num design positions + 1), but setting this too
# small can make A* search take much much longer. So pick something big enough to keep
# A* running efficiently, but not so big that all the nodes don't fit in memory.
# Keep in mind, COMETS will keep multiple conf trees in memory at the same time.
# Nodes use a variable amount of memory though, so there's no hard correspondence
# between numbers of node and amount of memory used. You might need to experiment
# to see what values work best here
# (this setting works in tandem with the minNumConfTrees setting above)
maxNumNodes=1000000)
def makeRigidAStar(rcs, emat=info.ematRigid):
return osprey.AStarTraditional(emat, rcs, showProgress=True)
def makeAStar_min(rcs, emat=info.ematMinimized):
return osprey.AStarTraditional(emat, rcs, showProgress=True)
def makeAStar(rcs, emat=emat):
return osprey.AStarTraditional(emat, rcs, showProgress=False)
def makeAStarMinimized(rcs, emat=ematMinimized):
return osprey.AStarTraditional(emat, rcs, showProgress=False)
def makePfunc(rcs, confEcalc=info.confEcalcMinimized, emat=ematMinimized):
return osprey.PartitionFunction(
confEcalc, osprey.AStarTraditional(emat, rcs, showProgress=False),
osprey.AStarTraditional(emat, rcs, showProgress=False), rcs)
def makeAStarRigid(rcs, emat=complex.ematRigid):
return osprey.AStarTraditional(complex.ematRigid,
rcs,
showProgress=False)
def makeAStar(rcs, emat=complex.emat):
return osprey.AStarTraditional(complex.emat,
rcs,
showProgress=False,
maxNumNodes=2000000)
protein = osprey.Strand(mol, residues=['A2', 'A30'])
protein.flexibility['A2'].setLibraryRotamers('ALA', 'GLY')
protein.flexibility['A3'].setLibraryRotamers(osprey.WILD_TYPE, 'VAL',
'ARG').setContinuous(10)
protein.flexibility['A4'].setLibraryRotamers(
osprey.WILD_TYPE).addWildTypeRotamers()
# make the conf space
confSpace = osprey.ConfSpace(protein)
# how should molecule energies be calculated?
ecalc = osprey.EnergyCalculator(confSpace, ffparams, parallelism=parallelism)
# how could conformation energies be calculated?
confEcalc = osprey.ConfEnergyCalculator(confSpace, ecalc)
# calculate the energy matrix
emat = osprey.EnergyMatrix(confEcalc, cacheFile='/tmp/emat.dat')
# define the conformation search
astar = osprey.AStarMPLP(emat, confSpace, numIterations=1)
# or
traditionalAstar = osprey.AStarTraditional(emat, confSpace)
energyWindow = 0.1 # kcal/mol
confs = osprey.GMECFinder(astar,
confEcalc,
printIntermediateConfs=True,
confLog='confs.txt').find(energyWindow)
