def __init__(self,options):
#
# Read the dir
#
import large_dataset_manager
self.DM=large_dataset_manager.data_manager(options.dir)
#
# Read all datasets
#
matrix={}
count=0
data=self.DM(count)
while data:
count=count+1
data=self.DM(count)
if count>1000:
data=None
print '\b.',
import sys
sys.stdout.flush()
#
if data:
sum_intpkadiff,sum_intene,tit_fit,pHact_fit=self.analyze_point(data)
if not matrix.has_key(sum_intpkadiff):
matrix[sum_intpkadiff]={}
if not matrix[sum_intpkadiff].has_key(sum_intene):
matrix[sum_intpkadiff][sum_intene]=[0,0]
matrix[sum_intpkadiff][sum_intene][0]=matrix[sum_intpkadiff][sum_intene][0]+tit_fit
matrix[sum_intpkadiff][sum_intene][1]=matrix[sum_intpkadiff][sum_intene][1]+pHact_fit
#
# Calculate ratio
#
minS=9999.9
maxS=-9999.9
for ip in matrix.keys():
for ie in matrix[ip].keys():
minS=min(minS,ie)
maxS=max(maxS,ie)
#
vals=matrix[ip][ie]
matrix[ip][ie]=vals[0]
# Fill in empty values
minF=min(matrix.keys())
maxF=max(matrix.keys())
print minF,maxF
print minS,maxS
#stop
for ip in np.arange(minF,maxF+1,1):
if not matrix.has_key(ip):
matrix[ip]={}
for ie in range(minS,maxS+1,1):
if not matrix[ip].has_key(ie):
matrix[ip][ie]=0.0
import TwoDplots
TwoDplots.heatmap(matrix,firstkey='sum intpka diff',secondkey='sum intene (kT)')
print 'I found %7.2e datasets' %count
return
def construct_permutations(self):
"""Construct the specification for all possible permutations specified in __init__"""
#
# Make pickled files for each configuration
#
import large_dataset_manager, os
self.options.dir = os.path.join(os.getcwd(), options.dir)
if not os.path.isdir(self.options.dir):
os.mkdir(options.dir)
self.Data = large_dataset_manager.data_manager(self.options.dir)
print 'Constructing system permutations'
print '000.00 perc done',
perm = 0
last_perc = 0
#
# Init the counters
#
import time
start = time.time()
#
# Start the loop
#
while perm < self.tot_perms:
#
# Get the specification
#
spec = self.get_specs(perm)
#print spec
self.Data.put(perm, {
'configuration': spec,
'numgroups': self.number_of_groups
})
#
# Get the time to completion
#
now = time.time()
time_passed = now - start
perc = float(perm) / float(
self.tot_perms) * 100.0 + 0.00001 # To avoid zerodivision error
total_time = time_passed / (perc / 100.0)
time_to_completion = total_time - time_passed
text = '%5.2f perc done. Complete in %.2f minutes (= %.2f hours or %.2f days) ' % (
perc, time_to_completion / 60.0, time_to_completion / 60.0 /
60.0, time_to_completion / 60.0 / 60.0 / 24.0)
text = (len(text) + 4) * '\b' + text
print text,
#
# Calculate titration curves for this permutation
#
new_data = self.do_one_pKa_calc(perm)
self.Data.put(perm, new_data)
perm = perm + 1
return
def construct_permutations(self):
"""Construct the specification for all possible permutations specified in __init__"""
#
# Make pickled files for each configuration
#
import large_dataset_manager, os
self.options.dir=os.path.join(os.getcwd(),options.dir)
if not os.path.isdir(self.options.dir):
os.mkdir(options.dir)
self.Data=large_dataset_manager.data_manager(self.options.dir)
print 'Constructing system permutations'
print '000.00 perc done',
perm=0
last_perc=0
#
# Init the counters
#
import time
start=time.time()
#
# Start the loop
#
while perm<self.tot_perms:
#
# Get the specification
#
spec=self.get_specs(perm)
#print spec
self.Data.put(perm,{'configuration':spec,'numgroups':self.number_of_groups})
#
# Get the time to completion
#
now=time.time()
time_passed=now-start
perc=float(perm)/float(self.tot_perms)*100.0+0.00001 # To avoid zerodivision error
total_time=time_passed/(perc/100.0)
time_to_completion=total_time-time_passed
text='%5.2f perc done. Complete in %.2f minutes (= %.2f hours or %.2f days) ' %(perc,time_to_completion/60.0,time_to_completion/60.0/60.0,
time_to_completion/60.0/60.0/24.0)
text=(len(text)+4)*'\b'+text
print text,
#
# Calculate titration curves for this permutation
#
new_data=self.do_one_pKa_calc(perm)
self.Data.put(perm,new_data)
perm=perm+1
return
