# load the conformation spaces
complex = osprey.readConfSpace("4tu5.complex.ccsx")
dhfr = osprey.readConfSpace("4tu5.DHFR.ccsx")
nadph06w = osprey.readConfSpace("4tu5.NADPH.06W.ccsx")
# more cores is more faster
parallelism = osprey.Parallelism(cpuCores=4)
tasks = parallelism.makeTaskExecutor()
# configure K*
kstar = osprey.KStar(
dhfr,
nadph06w,
complex,
epsilon=0.68,
writeSequencesToConsole=True,
# turn this one off when you get tired of the log spam
showPfuncProgress=True
)
# configure K* inputs for each conf space
for info in kstar.confSpaceInfos():
# TODO: make python API for constructor? using parallelism?
ecalc = osprey.c.energy.compiled.CPUConfEnergyCalculator(info.confSpace, tasks)
# compute reference energies
# TODO: make python API
eref = osprey.jvm.getInnerClass(osprey.c.ematrix.compiled.ErefCalculator, 'Builder')(ecalc) \
.build() \
# how should we compute energies of molecules?
# (give the complex conf space to the ecalc since it knows about all the templates and degrees of freedom)
parallelism = osprey.Parallelism(cpuCores=4)
ecalc = osprey.EnergyCalculator(complexConfSpace,
ffparams,
parallelism=parallelism)
# MARK* needs a rigid energy calculator too
ecalcRigid = osprey.SharedEnergyCalculator(ecalc, isMinimizing=False)
# configure K*
kstar = osprey.KStar(
proteinConfSpace,
ligandConfSpace,
complexConfSpace,
epsilon=
0.95, # you proabably want something more precise in your real designs
writeSequencesToConsole=True,
writeSequencesToFile='kstar.results.tsv')
# configure K* inputs for each conf space
for info in kstar.confSpaceInfos():
# how should we define energies of conformations?
eref = osprey.ReferenceEnergies(info.confSpace, ecalc)
info.confEcalc = osprey.ConfEnergyCalculator(info.confSpace,
ecalc,
referenceEnergies=eref)
# compute the minimized energy matrix
ematMinimized = osprey.EnergyMatrix(info.confEcalc,
# make the conf space for the ligand
ligandConfSpace = osprey.ConfSpace(ligand)
# make the conf space for the protein+ligand complex
complexConfSpace = osprey.ConfSpace([protein, ligand])
# how should we compute energies of molecules?
# (give the complex conf space to the ecalc since it knows about all the templates and degrees of freedom)
parallelism = osprey.Parallelism(cpuCores=4)
ecalc = osprey.EnergyCalculator(complexConfSpace,
ffparams,
parallelism=parallelism,
isMinimizing=True)
# configure K*
kstar = osprey.KStar(proteinConfSpace, ligandConfSpace, complexConfSpace)
# configure K* inputs for each conf space
for info in kstar.confSpaceInfos():
# how should we define energies of conformations?
eref = osprey.ReferenceEnergies(info.confSpace, ecalc)
info.confEcalc = osprey.ConfEnergyCalculator(info.confSpace,
ecalc,
referenceEnergies=eref)
# compute the energy matrix
emat = osprey.EnergyMatrix(info.confEcalc,
cacheFile='emat.%s.dat' % info.id)
# how should confs be ordered and searched? (don't forget to capture emat by using a defaulted argument)
import osprey
osprey.start()
# run this example AFTER you've trained the three LUTE models using LUTE.train.py
# import our conf spaces from another file
execfile('LUTE.confSpaces.py')
# configure K*
kstar = osprey.KStar(confSpaces['protein'],
confSpaces['ligand'],
confSpaces['complex'],
epsilon=0.01,
writeSequencesToConsole=True,
writeSequencesToFile='kstar.results.tsv')
# configure K* inputs for each conf space
for (id, confSpace) in confSpaces.items():
# read the trained LUTE model
pmat = osprey.DEE_read(confSpace, 'LUTE.pmat.%s.dat' % id)
model = osprey.LUTE_read('LUTE.%s.dat' % id)
# make a LUTE energy calculator from the model
luteEcalc = osprey.LUTE_ConfEnergyCalculator(confSpace, model)
# how should confs be ordered and searched? (don't forget to capture pmat,luteEcalc by using defaulted arguments)
def makeAStar(rcs, pmat=pmat, luteEcalc=luteEcalc):
return osprey.LUTE_AStar(rcs, pmat, luteEcalc, showProgress=False)
complexConfSpace = confspaces['complex']
# how should we compute energies of molecules?
# (give the complex conf space to the ecalc since it knows about all the templates and degrees of freedom)
parallelism = osprey.Parallelism(cpuCores=4)
ecalc = osprey.EnergyCalculator(complexConfSpace,
ffparams,
parallelism=parallelism)
# MARK* needs a rigid energy calculator too
ecalcRigid = osprey.SharedEnergyCalculator(ecalc, isMinimizing=False)
# configure K*
kstar = osprey.KStar(proteinConfSpace,
ligandConfSpace,
complexConfSpace,
epsilon=0.683,
writeSequencesToConsole=True,
writeSequencesToFile='kstar.results.tsv')
# configure K* inputs for each conf space
for info in kstar.confSpaceInfos():
# how should we define energies of conformations?
eref = osprey.ReferenceEnergies(info.confSpace, ecalc)
info.confEcalc = osprey.ConfEnergyCalculator(info.confSpace,
ecalc,
referenceEnergies=eref)
# compute the minimized energy matrix
ematMinimized = osprey.EnergyMatrix(info.confEcalc,
cacheFile='emat.%s.dat' % info.id)