# save the emat to disk so we don't have to calculate it again later
cacheFile = 'sofea.%s.emat' % state.name,
# correct overly optimistic energy bounds with triples to get even tighter energy bounds!
tripleCorrectionThreshold = 0.0
),
confEcalc = confEcalc
)
# configure the SOFEA algorithm
sofea = osprey.SOFEA(
confSpace = confSpace,
configFunc = config,
fringedbLowerPath = 'sofea.lower.fringedb',
fringedbLowerMiB = 100,
fringedbUpperPath = 'sofea.upper.fringedb',
fringedbUpperMiB = 10,
rcdbPath = 'rc.db', # set a path to collect the residue conformation (RC) info
seqdbPath = 'sofea.seqdb'
)
# start new databases if this is the first time running this script
if not osprey.jvm.toFile('sofea.seqdb').exists():
sofea.init()
# otherwise, keep the existing databases
# if you're resuming a previous design, don't call init().
# SOFEA will try to delete your databases if you do!
# choose a termination criterion for SOFEA
# ie, what are we trying to compute?
# make a LUTE energy calculator from the trained LUTE model
luteEcalc = osprey.LUTE_ConfEnergyCalculator(
state.confSpace, osprey.LUTE_read('sofea.%s.lute' % state.name))
# read the pruning matrix
pmat = osprey.DEE_read(state.confSpace, 'sofea.%s.pmat' % state.name)
# make the SOFEA config
return osprey.SOFEA_StateConfig(luteEcalc, pmat)
# configure the SOFEA algorithm
sofea = osprey.SOFEA(confSpace=confSpace,
configFunc=config,
parallelism=parallelism,
fringeDBPath='sofea.fringedb',
fringeDBSizeMiB=100,
seqDBPath='sofea.seqdb')
# start new databases if this is the first time running this script
if not osprey.jvm.toFile('sofea.fringedb').exists():
sofea.init()
# otherwise, keep the existing databases
# if you're resuming a previous design, don't call init().
# SOFEA will try to delete your databases if you do!
# choose a termination criterion for SOFEA
# ie, what are we trying to compute?
criterion = osprey.SOFEA_MinLMFE(
emat=osprey.EnergyMatrix(
confEcalc,
# save the emat to disk so we don't have to calculate it again later
cacheFile='sofea.%s.emat' % state.name,
# correct overly optimistic energy bounds with triples to get even tighter energy bounds!
tripleCorrectionThreshold=0.0),
confEcalc=confEcalc)
# configure the SOFEA algorithm
sofea = osprey.SOFEA(confSpace=confSpace,
configFunc=config,
fringedbLowerPath='sofea.lower.fringedb',
fringedbLowerMiB=100,
fringedbUpperPath='sofea.upper.fringedb',
fringedbUpperMiB=10,
seqdbPath='sofea.seqdb')
# start new databases if this is the first time running this script
if not osprey.jvm.toFile('sofea.seqdb').exists():
sofea.init()
# otherwise, keep the existing databases
# if you're resuming a previous design, don't call init().
# SOFEA will try to delete your databases if you do!
# choose a termination criterion for SOFEA
# ie, what are we trying to compute?
criterion = osprey.SOFEA_MinLMFE(