def score(self, design, params):
score = 100
seq = design['sequence']
for i in range(0, len(seq)):
# Pairs the same way in both states, avoiding double counting
# by only looking at the opening bases
if ((design['pairmap1'][i] == design['pairmap2'][i]) and
(design['secstruct1'][i] == design['secstruct2'][i] == '(')):
# Try swapping the sequence
bp1 = design['pairmap1'][i]
newSequence = (seq[:i] + seq[bp1] + seq[(i + 1):bp1] + seq[i] +
seq[(bp1 + 1):])
# viennaconstraint includes the binding (On state)
newSSb = inv_utils.fold(newSequence, False,
design['viennaconstraint'])
newSSnob = inv_utils.fold(newSequence)
if newSSb != design['secstruct' + str(design['on_state'])]:
score += params[0]
if newSSnob != design['secstruct' + str(design['off_state'])]:
score += params[1]
return score
def score(self, design, params):
score = 100
seq = design['sequence']
for i in range(0, len(seq)):
# Pairs the same way in both states, avoiding double counting
# by only looking at the opening bases
if((design['pairmap1'][i] == design['pairmap2'][i]) and
(design['secstruct1'][i] == design['secstruct2'][i] ==
'(')):
# Try swapping the sequence
bp1 = design['pairmap1'][i]
newSequence = (seq[:i] + seq[bp1] + seq[(i+1):bp1] +
seq[i] + seq[(bp1+1):])
# viennaconstraint includes the binding (On state)
newSSb = inv_utils.fold(
newSequence,
False,
design['viennaconstraint']
)
newSSnob = inv_utils.fold(newSequence)
if newSSb != design['secstruct' + str(design['on_state'])]:
score += params[0]
if newSSnob != design['secstruct' + str(design['off_state'])]:
score += params[1]
return score
def post_solution(puzzle, title):
sequence = puzzle.best_sequence
fold = inv_utils.fold(sequence)
design = eterna_utils.get_design_from_sequence(sequence, fold[0])
header = {'Content-Type': 'application/x-www-form-urlencoded'}
login = {
'type': 'login',
'name': 'theeternabot',
'pass': '******',
'workbranch': 'main'
}
solution = {
'type': 'post_solution',
'puznid': puzzle.id,
'title': title,
'body': 'eternabot switch v1, score %s' % puzzle.best_design_score,
'sequence': sequence,
'energy': fold[1],
'gc': design['gc'],
'gu': design['gu'],
'ua': design['ua'],
'melt': design['meltpoint'],
'pointsrank': 'false',
'recommend-puzzle': 'true'
}
url = "http://jnicol.eternadev.org"
#url = 'http://eterna.cmu.edu'
loginurl = "%s/login/" % url
posturl = "%s/post/" % url
with requests.Session() as s:
r = s.post(loginurl, data=login, headers=header)
r = s.post(posturl, data=solution, headers=header)
return
def solve(self, design): bases=inv_utils.BASES random.seed() elements = design['secstruct_elements'] target_pair = design['secstruct'] pair_map = design['pairmap'] length = len(target_pair) sequence = ['A']*length natural_pair = "" while(natural_pair != target_pair): for elem in elements: inv_utils.fill_gc(elem, pair_map , sequence, random) ret = inv_utils.fold(sequence) natural_pair = ret[0] return sequence
def get_sequence_info(self, sequence):
"""
get sequence information - native fold, bp distance, pairmap, design
for a particular sequence
"""
native = []
native_pairmap = []
for i in range(self.n_targets):
fold_sequence = self.get_fold_sequence(sequence, self.targets[i])
native.append(inv_utils.fold(fold_sequence)[0])
native_pairmap.append(
eterna_utils.get_pairmap_from_secstruct(native[i]))
bp_distance = self.score_secstructs(native)
design_score = self.get_design_score(sequence, native)
return [sequence, native, native_pairmap, bp_distance, design_score]
row_num += 1
print("Done parsing..")
for design in designs:
args = (design, )
ret = inv_utils.timeout(strategy.solve,
args,
timeout_duration=2,
default=["AAAA"])
sequence = ret[0]
t0 = ret[1]
if (t0 != "timeout"):
natural = inv_utils.fold(sequence)[0]
target = design['secstruct']
if (natural == target):
design['solve_time'] = t0
else:
design['solve_time'] = "wrong solution"
else:
design['solve_time'] = t0
## Output results
f_output.write("<strong>Title : </strong>" + strategy.title_ + "<br/>")
f_output.write("<strong>Author : </strong>" + strategy.author_ + "<br/>")
f_output.write("\n\n\n")
body_data = ""