def evolve(self):
try:
evolve()
except KeyboardInterrupt:
print "catched KeyboardInterrupt!"
output.PrintTimings()
output.PrintStats()
output.PrintTotalTimings()
sys.exit(0)
def signal_term_handler(signal, frame):
if signal or frame:
print 'got kill signal!'
output.PrintTimings()
output.PrintStat()
output.PrintTotalTimings()
try:
f_locals = inspect.trace()[-1][0].f_locals
DumpMols(f_locals['lib'], f_locals['gen'])
DumpMols(f_locals['pool'])
except Exception as e:
print "didn't manage to dump pool and mylib after kill signal", e
print "Error Termination"
sys.exit(0)
def evolve():
global startiter, lib, pool, _iterhead, _gridAssign
###################################################
########## ###########
########## MAIN LOOP ###########
########## ###########
###################################################
for gen in xrange(startiter, mprms.nGen):
# 0. Decide workflow for current iteration:
Tautomerizing, Filtering, GenStrucs = dr.SetIterationWorkflow(gen)
# 1. PRELOGGING
print _iterhead.format(gen)
stats.update({'gen': gen, 'nPool': len(pool), 'nLib': len(lib)})
# 2.MUTATIONS AND CROSSOVERS
newlib = dr.DriveMutations(lib)
# 3. FILTERS
newlib = dr.DriveFilters(newlib, Filtering, GenStrucs)
# 3b. Once Filtering/GenStrucs is switched on Pool has to be filtered too:
pool = dr.DrivePoolFilters(pool, Filtering, GenStrucs, Tautomerizing,
gen)
# 4. OBJECTIVE EVALUATION
if mprms.optimize:
print "acsess.py len(newlib, pool):{} {}".format(
len(newlib), len(pool))
pool = objective.EvaluateObjective(newlib + pool, gen)
else:
pool = dr.ExtendPool(pool, lib, newlib)
# 5. SELECTION
siml = None
if mprms.cellDiversity:
if mprms.optimize:
siml, lib, _gridAssign = cd.GridDiversity(lib, newlib, molgrid=_gridAssign)
else:
siml, lib, _gridAssign = cd.GridDiversity_JITFilter(lib, newlib, molgrid=_gridAssign)
else:
if mprms.optimize:
oldN = len(pool)
lib, pool = objective.SelectFittest(pool, mprms.subsetSize, gen)
stats['nUnFit'] = oldN - len(pool)
elif len(pool) > mprms.subsetSize:
lib = dr.DriveSelection(pool, mprms.subsetSize)
else:
lib = [mol for mol in pool]
FinishSelection(lib)
if len(lib) == 0:
raise RuntimeError('no molecules left')
# 6. DIVERSITY IS:
if siml is None:
if mprms._similarity:
siml = NNSimilarity(lib)
else:
# library diversity should not be assessed by normalization of only
# the lib. so either no normalization or a normalization based on
# the whole pool.
siml = AveNNDistance(lib, norm=False)
print '\nLIBRARY DIVERSITY: ', siml
# 7. POSTLOGGING
with open('mylib.smi', 'w') as f:
for i, mol in enumerate(lib):
f.write(Chem.MolToSmiles(mol) + ' {:d}\n'.format(i))
if gen % mprms.writeInterval == 0 or gen == mprms.nGen - 1:
DumpMols(lib, gen)
DumpMols(pool)
stats['diversity'] = siml
output.PrintTimings()
output.PrintStat()
output.PrintTotalTimings()
print "DONE"
return
def signal_term_handler(signal, frame):
print 'got kill signal!'
output.PrintTimings()
output.PrintStats()
output.PrintTotalTimings()
sys.exit(0)