def init_grammar(self, max_num_mols):
L = get_smiles_from_database(max_num_mols)
for ind, smiles in enumerate(L):
if ind >= max_num_mols:
break
if ind > self.last_processed: # don't repeat
try:
# this causes g to remember all the rules occurring in these molecules
these_actions = self.grammar.raw_strings_to_actions(
[smiles])
this_tree = self.grammar.last_tree_processed
these_tuples = tree_with_rule_inds_to_list_of_tuples(
this_tree)
for p, nt, c in these_tuples:
if (p, nt) not in self.grammar.conditional_frequencies:
self.grammar.conditional_frequencies[(p, nt)] = {}
if c not in self.grammar.conditional_frequencies[(p,
nt)]:
self.grammar.conditional_frequencies[(p,
nt)][c] = 1
else:
self.grammar.conditional_frequencies[(p,
nt)][c] += 1
# count the frequency of the occurring rules
for aa in these_actions:
for a in aa:
if a not in self.grammar.rule_frequency_dict:
self.grammar.rule_frequency_dict[a] = 0
self.grammar.rule_frequency_dict[a] += 1
lengths = [len(x) for x in these_actions]
new_max_len = max(lengths)
self.total_len += sum(lengths)
if new_max_len > self.max_len:
self.max_len = new_max_len
print("Max len so far:", self.max_len)
except Exception as e: #TODO: fix this, make errors not happen ;)
print(e)
self.last_processed = ind
# if we discovered a new rule, remember that
if not len(self.new_rules) or self.grammar.rate_tracker[-1][
-1] > self.new_rules[-1][-1]:
self.new_rules.append(
(ind, *self.grammar.rate_tracker[-1]))
print(self.new_rules[-1])
if ind % 10 == 9:
self.save()
if ind % 100 == 0 and ind > 0:
self.stats[ind] = {
'max_len': self.max_len,
'avg_len': self.total_len / ind,
'num_rules': len(self.grammar.rules),
}
self.grammar.normalize_conditional_frequencies()
self.grammar.calc_terminal_distance()
return self.max_len # maximum observed molecule length
def count_rule_frequencies(self, trees):
for tree in trees:
these_tuples = tree_with_rule_inds_to_list_of_tuples(tree)
for p, nt, c in these_tuples:
if (p, nt) not in self.conditional_frequencies:
self.grammar.conditional_frequencies[(p, nt)] = {}
if c not in self.conditional_frequencies[(p, nt)]:
self.conditional_frequencies[(p, nt)][c] = 1
else:
self.conditional_frequencies[(p, nt)][c] += 1
these_actions = [rule.rule_id for rule in tree.rules()]
for a in these_actions:
if a not in self.rule_frequency_dict:
self.rule_frequency_dict[a] = 0
self.rule_frequency_dict[a] += 1