def rna_folding(rna_data, policy, stochastically=True, render=False):
np.random.seed(int.from_bytes(os.urandom(4), byteorder='little'))
rna = RNA(rna_data['seq'], rna_data['pairs'])
mcts = MCTS(policy, 2000, False, 10)
min_energy = rna.energy()
pred_energy, _, _ = mcts.evaluate_state(rna)
if render: print(rna)
while rna.action_space and pred_energy > 1:
action, action_probs = mcts.get_action(rna, stochastically=stochastically, show_node=render)
rna.move(action)
mcts.update_with_action(action)
energy = rna.energy()
if energy < min_energy: min_energy = energy
pred_energy, _, _ = mcts.evaluate_state(rna)
if render:
print("[*] RNA pair position: %s" % (action,))
print("[*] RNA secondary structure: %s" % ''.join(rna.sec))
print("[*] Predicted energy: %.2f" % pred_energy)
print("[*] Current energy: %.2f" % energy)
print("[*] Min energy: %.2f\n" % min_energy)
print(rna)
final_energy = rna.energy()
rna_data['pred_sec'] = ''.join(rna.sec)
rna_data['pred_pairs'] = rna.find_pairs
return rna_data
def main():
problem_dataset_dir = os.path.join('Problems', 'Problem1')
solution_dir = os.path.join("Problems", "Problem1Solution")
data_reader = DataReader(problem_dataset_dir)
training_data, testing_data = data_reader.get_data()
codons_table = data_reader.get_rna_codon_table()
for sample in training_data:
rna_string = sample[0]
output = sample[1]
rna = RNA(rna_string)
rna.set_codons_table(codons_table)
amino_acid = rna.to_amino_acid()
if amino_acid != output:
raise Exception("Output not matched!\nExpecting: " + output +
"\nFound: " + amino_acid)
print("Passed training data..\n\n")
writer = DataWriter(solution_dir)
usage = Usage()
for sample in testing_data:
usage.start()
rna_string = sample[0]
rna = RNA(rna_string)
rna.set_codons_table(codons_table)
amino_acid = rna.to_amino_acid()
usage.end()
writer.write_data(rna_string, amino_acid, usage.get_execution_time(),
usage.get_memory_usage())
print("RNA:\n" + rna_string)
print("Protein:\n" + amino_acid)
print("\n\nExecution Time: " + str(usage.get_execution_time()) + " s")
print("Memory Usage: " + str(usage.get_memory_usage()) + " MB")
def setup(self):
i = IndepVarComp()
# variables
i.add_output('in_design_tsr', desc='design tip speed ratio')
i.add_output('in_tf', desc='scaling factor for laminate thickness')
i.add_output('in_chord_coefficients',
desc='coefficients of polynomial chord profile',
shape=degree_bezier)
i.add_output('in_twist_coefficients',
desc='coefficients of polynomial twist profile',
shape=degree_bezier)
# parameters
self.add_subsystem('dof', i, promotes=['*'])
self.add_subsystem('rna', RNA(), promotes=['*'])
self.add_subsystem('obj', ExecComp('f = -1 * cp / 0.4967'))
#self.add_subsystem('obj', ExecComp('f = -1 * (cp/(rm)) / (0.4967/51092.66)', rm={'units' : 'kg'}))
#self.add_subsystem('obj', ExecComp('f = -1 * (cp/(rm+hm+nm)) / (0.4967/217493.9)', rm={'units' : 'kg'}, hm={'units' : 'kg'}, nm={'units' : 'kg'}))
#self.add_subsystem('obj', ExecComp('f = -1 * (cp/crt) / (0.4967/3202937.51)', crt={'units' : 'USD'}))
self.add_subsystem('c1',
ExecComp('tip = (y/5.6964)-1.0',
tip={'units': 'm'},
y={'units': 'm'})) #, d={'units' : 'm'}))
self.add_subsystem(
'c2',
ExecComp('max_s = s/(450.0*10**6) - 1.0',
s={'units': 'Pa'},
max_s={'units': 'Pa'}))
self.connect('rotor_cp', 'obj.cp')
#self.connect('rotor_mass', 'obj.rm')
#self.connect('hub_system_mass', 'obj.hm')
#self.connect('nacelle_mass', 'obj.nm')
#self.connect('cost_rna_total', 'obj.crt')
self.connect('tip_deflection', 'c1.y')
self.connect('span_stress_max', 'c2.s')
def main(x, y, z, num_steps, u1, u2, u3, pwm_u1, pwm_u2, u1_t, u2_t,
persistence, sequence):
rna = RNA(x, y, z, sequence, persistence, pwm_u1, pwm_u2, u1_t, u2_t)
i = 0
while i < num_steps:
i += 1
rna.extend()
rna.random_flight()
u1.update()
u2.update()
u3.update()
rna.bind_snorna(u1, u2)
rna.release_snorna(u1, u2)
splice = rna.bind_u3(u3)
if splice: return i, splice
return i, False
def get_dna_to_amino_acid_candidates(self, amino_acid):
substring_length = len(amino_acid) * 3
rna = RNA()
rna.set_codons_table(self.__codon_table)
candidates = []
for i in range(0, len(self.__dna_string)):
if i + substring_length > len(self.__dna_string):
break
candidate_substring = self.__dna_string[i:(i + substring_length)]
rna_string = self.__dna_to_rna_string(candidate_substring)
rna.set_rna_string(rna_string)
current_amino_acid = rna.to_amino_acid()
if current_amino_acid == amino_acid:
candidates.append(candidate_substring)
else:
reversed_dna = self.__reverse_dna(candidate_substring)
reversed_rna = self.__dna_to_rna_string(reversed_dna)
rna.set_rna_string(reversed_rna)
current_amino_acid = rna.to_amino_acid()
if current_amino_acid == amino_acid:
candidates.append(candidate_substring)
continue
complement_dna = self.__complement_dna(candidate_substring)
complement_rna = self.__dna_to_rna_string(complement_dna)
rna.set_rna_string(complement_rna)
current_amino_acid = rna.to_amino_acid()
if current_amino_acid == amino_acid:
candidates.append(candidate_substring)
continue
reversed_complement_dna = self.__complement_dna(
self.__reverse_dna(candidate_substring))
reversed_complement_rna = self.__dna_to_rna_string(
reversed_complement_dna)
rna.set_rna_string(reversed_complement_rna)
current_amino_acid = rna.to_amino_acid()
if current_amino_acid == amino_acid:
candidates.append(candidate_substring)
continue
complement_reversed_dna = self.__reverse_dna(
self.__complement_dna(candidate_substring))
complement_reversed_rna = self.__dna_to_rna_string(
complement_reversed_dna)
rna.set_rna_string(complement_reversed_rna)
current_amino_acid = rna.to_amino_acid()
if current_amino_acid == amino_acid:
candidates.append(candidate_substring)
continue
return candidates
def get_dna_to_amino_acid_candidates(self, amino_acid):
substring_length = len(amino_acid) * 3
rna = RNA()
rna.set_codons_table(self.__codon_table)
candidates = []
for i in range(0, len(self.__dna_string)):
if i + substring_length > len(self.__dna_string):
break
candidate_substring = self.__dna_string[i:(i + substring_length)]
rna_string = self.__dna_to_rna_string(candidate_substring)
rna.set_rna_string(rna_string)
current_amino_acid = rna.to_amino_acid()
if current_amino_acid == amino_acid:
candidates.append(candidate_substring)
else:
reversed_dna = self.__reverse_dna(candidate_substring)
reversed_rna = self.__dna_to_rna_string(reversed_dna)
rna.set_rna_string(reversed_rna)
current_amino_acid = rna.to_amino_acid()
if current_amino_acid == amino_acid:
candidates.append(candidate_substring)
continue
complement_dna = self.__complement_dna(candidate_substring)
complement_rna = self.__dna_to_rna_string(complement_dna)
rna.set_rna_string(complement_rna)
current_amino_acid = rna.to_amino_acid()
if current_amino_acid == amino_acid:
candidates.append(candidate_substring)
continue
reversed_complement_dna = self.__complement_dna(self.__reverse_dna(candidate_substring))
reversed_complement_rna = self.__dna_to_rna_string(reversed_complement_dna)
rna.set_rna_string(reversed_complement_rna)
current_amino_acid = rna.to_amino_acid()
if current_amino_acid == amino_acid:
candidates.append(candidate_substring)
continue
complement_reversed_dna = self.__reverse_dna(self.__complement_dna(candidate_substring))
complement_reversed_rna = self.__dna_to_rna_string(complement_reversed_dna)
rna.set_rna_string(complement_reversed_rna)
current_amino_acid = rna.to_amino_acid()
if current_amino_acid == amino_acid:
candidates.append(candidate_substring)
continue
return candidates
#entradas = [[0,0],[0,1],[1,0],[1,1]]
#respostas_corretas = [0,0,0,1]
#pesos = [0.0, 0.0]
#taxa_aprendizagem = 0.1
#RNA.treinar(entradas, respostas_corretas, pesos, taxa_aprendizagem)
porco = 0
cachorro = 1
entradas = [[1,1,0], [1,1,0], [1,1,0], [1,1,1], [0,1,1], [0,1,1]]
respostas_corretas = [porco,porco,porco,cachorro,cachorro,cachorro]
pesos = [0.0, 0.0, 0.0]
taxa_aprendizagem = 0.1
pesos_ideal = RNA.treinar(entradas, respostas_corretas, pesos, taxa_aprendizagem)
misterioso1 = [1,1,1]
misterioso2 = [1,0,0]
misterioso3 = [0,0,1]
testes = [misterioso1, misterioso2, misterioso3]
marcacoes_teste = [0,1,0]
resultados = RNA.adivinhar(testes, pesos_ideal)
for i in range(len(resultados)):
if(resultados[i] == cachorro):
print('estou chutando: cachorro')
else:
print('estou chutando: porco')