def create_dbs(self):
self.logger_freshs.debug(cc.c_magenta + __name__ + ': create_dbs' + cc.reset)
try:
if self.algo_name == 'ffs' or self.algo_name == 'perm_ffs':
import configpoints
# create instance of DB for configpoint-handling / open existing DB
confdbfile = self.timestamp + '_configpoints.sqlite'
self.storepoints=configpoints.configpoints(self, self.folder_db + confdbfile)
# create instance of DB for pre-runs:
ghostdbfile = self.timestamp + '_ghost.sqlite'
self.ghostpoints=configpoints.configpoints(self, self.folder_db + ghostdbfile)
# Symlink DBs
try:
os.remove(self.folder_db + 'configpoints.sqlite')
os.remove(self.folder_db + 'ghostpoints.sqlite')
except:
pass
try:
os.symlink(confdbfile, self.folder_db + 'configpoints.sqlite')
os.symlink(ghostdbfile, self.folder_db + 'ghostpoints.sqlite')
except:
pass
elif self.algo_name == 'spres':
##open or create a DB with the correct timepoint
confdbfile = self.timestamp + '_configpoints.sqlite'
if self.configfile.has_option('spres_control','use_multDB'):
if self.configfile.getint('spres_control','use_multDB') > 0:
import configpoints_spres_multDB
self.storepoints=configpoints_spres_multDB.configpoints(self, self.folder_db + confdbfile, self.epoch)
else:
import configpoints_spres
self.storepoints=configpoints_spres.configpoints(self, self.folder_db + confdbfile)
else:
self.logger_freshs.warn(cc.c_red + 'No option use_multDB in spres_control!' + cc.reset)
self.logger_freshs.warn(cc.c_red + 'Defaulting to use multiple DBs anyway.' + cc.reset)
import configpoints_spres_multDB
self.storepoints=configpoints_spres_multDB.configpoints(self, self.folder_db + confdbfile, self.epoch)
elif self.algo_name == 'nsffs':
import configpoints
# create instance of DB for configpoint-handling / open existing DB
confdbfile = self.timestamp + '_configpoints.sqlite'
self.storepoints=configpoints.configpoints(self, self.folder_db + confdbfile)
except Exception as e:
self.logger_freshs.debug(cc.c_red + __name__ + 'Error!:' + str(e) + cc.reset)
raise SystemExit(1)
def getP(dbFile):
###DB handler
try:
cfph = configpoints.configpoints('none', dbFile)
except:
print("NoDBFile:" + dbFile)
exit(1)
###Get a list of nucleating pathways by endpoint.
cfpcand = cfph.return_points_on_last_interface()
tracecount = 0
maxtr = len(cfpcand)
w_list = []
##backtrace each suvvessful trace to find its Rosenbluth weight
for cfp in cfpcand:
weight = 1.0
op = cfph.return_origin_point_by_id(cfp[2])
while True:
cfph.cur.execute(
'select usecount from configpoints where myid = ?', [op[8]])
result = cfph.cur.fetchone()
if result:
siblings = int(result[0])
else:
print("Error backtracing for rates")
exit(1)
weight = weight / float(siblings)
if 'escape' in op[2]:
break
op = cfph.return_origin_point_by_id(op[2])
w_list.append(weight)
print("cfp: " + cfp[8] + " has weight: " + str(weight))
p_B_given_A = np.sum(np.asarray(w_list))
return p_B_given_A
def getP( dbFile ):
###DB handler
try:
cfph = configpoints.configpoints('none',dbFile)
except:
print("NoDBFile:"+dbFile)
exit(1)
###Get a list of nucleating pathways by endpoint.
cfpcand = cfph.return_points_on_last_interface()
tracecount = 0
maxtr = len(cfpcand)
w_list = []
##backtrace each suvvessful trace to find its Rosenbluth weight
for cfp in cfpcand:
weight = 1.0
op = cfph.return_origin_point_by_id(cfp[2])
while True:
cfph.cur.execute('select usecount from configpoints where myid = ?', [op[8]])
result = cfph.cur.fetchone()
if result:
siblings = int(result[0])
else:
print("Error backtracing for rates")
exit(1)
weight = weight / float(siblings)
if 'escape' in op[2]:
break
op = cfph.return_origin_point_by_id(op[2])
w_list.append(weight)
print("cfp: "+cfp[8]+" has weight: "+str(weight))
p_B_given_A = np.sum(np.asarray(w_list))
return p_B_given_A
#if int(op[0]) != 0:
if not 'escape' in op[2]:
visit(op)
# check usage
if len(sys.argv) < 2:
print("Usage:", sys.argv[0], "<../server/DB/configpoint-DB-file>")
exit(1)
# construct timestamp out of DB filename
timestamp = re.sub('.*/', '', re.sub('_configpoints.*', '', sys.argv[1]))
datadir = datadir_base + '/' + timestamp
# configpoint handler
cfph = configpoints.configpoints('none', sys.argv[1])
# Prepare directories
outdir_base = 'OUTPUT'
outdir = outdir_base + '/' + timestamp
# backtrace plotfile
plotfile_trace = outdir + '/tree_success.gnuplot'
tmkdir(outdir_base)
tmkdir(outdir)
# ----------------------------------------------------------------------------
# Backtrace successful trajectories
# ----------------------------------------------------------------------------
sys.path.append('../server/modules')
sys.path.append('../server/modules/ffs')
# custom
import configpoints
def extract_customdata(interface, dbhandle):
customdata = dbhandle.return_customdata(interface)
floatdata = []
for el in customdata:
for el2 in el.split():
floatdata.append(float(el2))
return floatdata
if len(sys.argv) < 2:
print("Usage:", sys.argv[0], "<../server/DB/configpoint-DB-file>")
exit(1)
cfph = configpoints.configpoints('none', sys.argv[1])
maxlam = cfph.biggest_lambda()
for i in range(maxlam + 1):
print("Interface", i)
print(extract_customdata(i, cfph))
# TODO: build histograms
if el <= bin_max and el > bin_min:
tmphisto[iq] += 1
return tmphisto
# check usage
if len(sys.argv) < 2:
print("Usage:", sys.argv[0], "<configpoints.sqlite>")
exit(1)
dbfwd = sys.argv[1]
# construct timestamp out of DB filename
timestampfwd = re.sub('.*/', '', re.sub('_configpoints.*', '', dbfwd))
# configpoint handler
fcfph = configpoints.configpoints('none', dbfwd)
# Prepare directories
outdir_base = 'OUTPUT'
outdir = outdir_base + '/' + timestampfwd
tmkdir(outdir_base)
tmkdir(outdir)
# get endpoint candidates
print("Reading forward probabilities")
fprobs, fN, fnonsuccess, fM = fcfph.return_probabilities(1)
print(fprobs)
#ninterfaces = cfphfwd.biggest_lambda()
print("Reading forward lambdas")
if el <= bin_max and el > bin_min:
tmphisto[iq] += 1
return tmphisto
# check usage
if len(sys.argv) < 2:
print("Usage:", sys.argv[0], "<configpoints.sqlite>")
exit(1)
dbfwd = sys.argv[1]
# construct timestamp out of DB filename
timestampfwd = re.sub('.*/', '', re.sub('_configpoints.*', '', dbfwd))
# configpoint handler
fcfph = configpoints.configpoints('none', dbfwd)
# Prepare directories
outdir_base = 'OUTPUT'
outdir = outdir_base + '/' + timestampfwd
tmkdir(outdir_base)
tmkdir(outdir)
# get endpoint candidates
print("Reading forward probabilities")
fprobs, fN, fnonsuccess, fM = fcfph.return_probabilities(1)
print(fprobs)
#ninterfaces = cfphfwd.biggest_lambda()
print("Reading forward lambdas")
def create_dbs(self):
self.logger_freshs.debug(cc.c_magenta + __name__ + ": create_dbs" + cc.reset)
try:
if self.algo_name == "ffs" or self.algo_name == "perm_ffs":
import configpoints
# create instance of DB for configpoint-handling / open existing DB
confdbfile = self.timestamp + "_configpoints.sqlite"
self.storepoints = configpoints.configpoints(self, self.folder_db + confdbfile)
# create instance of DB for pre-runs:
ghostdbfile = self.timestamp + "_ghost.sqlite"
self.ghostpoints = configpoints.configpoints(self, self.folder_db + ghostdbfile)
# Symlink DBs
try:
os.remove(self.folder_db + "configpoints.sqlite")
os.remove(self.folder_db + "ghostpoints.sqlite")
except:
pass
try:
os.symlink(confdbfile, self.folder_db + "configpoints.sqlite")
os.symlink(ghostdbfile, self.folder_db + "ghostpoints.sqlite")
except:
pass
elif self.algo_name == "spres":
##open or create a DB with the correct timepoint
confdbfile = self.timestamp + "_configpoints.sqlite"
if self.configfile.has_option("spres_control", "use_multDB"):
if self.configfile.getint("spres_control", "use_multDB") > 0:
import configpoints_spres_multDB
self.storepoints = configpoints_spres_multDB.configpoints(
self, self.folder_db + confdbfile, self.epoch
)
else:
import configpoints_spres
self.storepoints = configpoints_spres.configpoints(self, self.folder_db + confdbfile)
else:
self.logger_freshs.warn(cc.c_red + "No option use_multDB in spres_control!" + cc.reset)
self.logger_freshs.warn(cc.c_red + "Defaulting to use multiple DBs anyway." + cc.reset)
import configpoints_spres_multDB
self.storepoints = configpoints_spres_multDB.configpoints(
self, self.folder_db + confdbfile, self.epoch
)
elif self.algo_name == "nsffs":
import configpoints
# create instance of DB for configpoint-handling / open existing DB
confdbfile = self.timestamp + "_configpoints.sqlite"
self.storepoints = configpoints.configpoints(self, self.folder_db + confdbfile)
except Exception as e:
self.logger_freshs.debug(cc.c_red + __name__ + "Error!:" + str(e) + cc.reset)
raise SystemExit(1)