Example #1
0
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()
Example #2
0
strand = osprey.Strand('1CC8.ss.pdb')
strand.flexibility['A2'].setLibraryRotamers('ALA', 'GLY')
strand.flexibility['A3'].setLibraryRotamers(osprey.WILD_TYPE, 'VAL')
strand.flexibility['A4'].setLibraryRotamers(osprey.WILD_TYPE)

# make the conf space
confSpace = osprey.ConfSpace(strand)

# choose a forcefield
ffparams = osprey.ForcefieldParams()

# how should we compute energies of molecules?
ecalc = osprey.EnergyCalculator(confSpace, ffparams)

# how should we define energies of conformations?
confEcalc = osprey.ConfEnergyCalculator(confSpace, ecalc)

# compute the energy matrix
emat = osprey.EnergyMatrix(confEcalc)

# run DEE with just steric pruning
pmat = osprey.DEE(confSpace, emat, showProgress=True)

# or run DEE with Goldstein pruning
#i0 = 10.0 # kcal/mol
#pmat = osprey.DEE(confSpace, emat, showProgress=True, singlesGoldsteinDiffThreshold=i0, pairsGoldsteinDiffThreshold=i0)

# find the best sequence and rotamers
astar = osprey.AStarMPLP(emat, pmat)
gmec = osprey.GMECFinder(astar, confEcalc).find()
Example #3
0
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)
Example #4
0
	strand.flexibility[resNum].setLibraryRotamers(osprey.WILD_TYPE, 'ARG', 'LYS')

# make the conf space
confSpace = osprey.ConfSpace(strand)

# choose a forcefield
ffparams = osprey.ForcefieldParams()

# how should we compute energies of molecules?
ecalc = osprey.EnergyCalculator(confSpace, ffparams)

# how should we define energies of conformations?
confEcalc = osprey.ConfEnergyCalculator(confSpace, ecalc)
emat = osprey.EnergyMatrix(confEcalc)

# let's use an energy window so the search takes a noticeable amount of time
energyWindow = 5.0 # kcal/mol

# find the best sequence and rotamers
# and store conformations in a database
confDBFile = 'gmec.conf.db'
astar = osprey.AStarMPLP(emat, confSpace)
gmec = osprey.GMECFinder(astar, confEcalc, confDBFile=confDBFile).find(energyWindow)


# If OSPREY exits unexpectedly, the 'gmec.conf.db' file will still remain.
# running the design again using an existing confDB should be MUCH faster!
# meaning, your design should catch up to where it left off very quickly.
astar = osprey.AStarMPLP(emat, confSpace)
gmec2 = osprey.GMECFinder(astar, confEcalc, confDBFile=confDBFile).find(energyWindow)
Example #5
0
# negatively charged residues: ASP, GLUE
# polar uncharged: SER, THR, ASN, GLN, TYR, CYS

# Conversely, "deep" residues should only mutate to hydrophobic

# Fow now here are the residues in the "native pocket"
# For chain X residue number N, the residue is identified by 'XN'
strand.flexibility['A54'].setLibraryRotamers(
    osprey.WILD_TYPE, 'ASP',
    'GLU')  # Wild type means the residue is free to be unchanged
# BUT will still have it's flexibility modelled
strand.flexibility['A55'].setLibraryRotamers(osprey.WILD_TYPE, 'ASP', 'GLU')
strand.flexibility['A145'].setLibraryRotamers(osprey.WILD_TYPE, 'ASP', 'GLU')
strand.flexibility['A185'].setLibraryRotamers(osprey.WILD_TYPE, 'ASP', 'GLU')
strand.flexibility['A239'].setLibraryRotamers(osprey.WILD_TYPE, 'ASP', 'GLU')
strand.flexibility['A241'].setLibraryRotamers(osprey.WILD_TYPE, 'ASP', 'GLU')
strand.flexibility['A242'].setLibraryRotamers(osprey.WILD_TYPE, 'ASP', 'GLU')
strand.flexibility['A241'].setLibraryRotamers(osprey.WILD_TYPE, 'ASP', 'GLU')
# Now the conf space is defined
confSpace = osprey.ConfSpace(strand)

# DEFAULT CONFIG FOR NOW
ffparams = osprey.ForceFieldParams()
ecalc = osprey.EnergyCalculator(confSpace, ffparams)
confEcalc = osprey.ConfEnergyCalculator(confSpace, ecalc)
emat = osprey.EnergyMatrix(confEcalc)
astar = osprey.AStarMPLP(emat, confSpace)

# find the best sequence and rotamers
gmec = osprey.GMECFinder(confSpace, astar, ecalc).find()
Example #6
0
import osprey

osprey.start()

# define a strand
strand = osprey.Strand('1CC8.ss.pdb')
strand.flexibility['A2'].setLibraryRotamers(osprey.WILD_TYPE).setContinuous()
strand.flexibility['A3'].setLibraryRotamers(osprey.WILD_TYPE).setContinuous()
strand.flexibility['A4'].setLibraryRotamers(osprey.WILD_TYPE).setContinuous()

# make the conf space
confSpace = osprey.ConfSpace(strand)

# choose a forcefield
ffparams = osprey.ForcefieldParams()

# how to compute the energy of a conformation?
ecalc = osprey.EnergyCalculator(confSpace, ffparams)
confEcalc = osprey.ConfEnergyCalculator(confSpace, ecalc)

# configure external memory settings
osprey.initExternalMemory(64)

# how should confs be ordered and searched?
emat = osprey.EnergyMatrix(confEcalc)
astar = osprey.AStarMPLP(emat, confSpace, useExternalMemory=True)

# find the best sequence and rotamers
gmec = osprey.GMECFinder(astar, confEcalc, useExternalMemory=True).find()
Example #7
0
ffparams = osprey.ForcefieldParams()

# how should we compute energies of molecules?
ecalc = osprey.EnergyCalculator(confSpace, ffparams)

# how should we define energies of conformations?
confEcalc = osprey.ConfEnergyCalculator(confSpace, ecalc)

# how should confs be ordered and searched?
emat = osprey.EnergyMatrix(confEcalc)
astar = osprey.AStarMPLP(emat, confSpace)

# find the best sequence and rotamers
# and save all the conformations in the confdb for easier analysis later
confDBFile = 'conf.db'
gmec = osprey.GMECFinder(astar, confEcalc, confDBFile=confDBFile).find()

# get the conformation analyzer
analyzer = osprey.ConfAnalyzer(confEcalc)

# analyze the gmec
analysis = analyzer.analyze(gmec)
print('\n')
print(analysis)
osprey.writePdb(analysis.epmol, 'gmec.pdb')

# breakdown the forcefield energy by position
print('Forcefield breakdown:')
print(analysis.breakdownEnergyByPosition(osprey.BreakdownType.All))

# breakdown the forcefield energy by position and effect