<commit_before># Running 2 generations with a tanimoto filter

from minedatabase.pickaxe import Pickaxe

# Where are the input rxns coming from and coreactants
# Compounds that are going to be expanded
input_cpds = './pickaxe_tests/in_cpds_mid.csv'

# Cofactors used in the rules
coreactant_list = './minedatabase/data/EnzymaticCoreactants.tsv'
# The reaction rules themselves
rule_list = './minedatabase/data/EnzymaticReactionRules.tsv'

# Outputs if you are writing the results locally
write_local = False
pickaxe_rxns = './pickaxe_result/test_rxns.tsv'
pickaxe_cpds = './pickaxe_result/test_cpds.tsv'

# Database to write results to
write_db = True
database = 'tani_2gen'

# Pickaxe Options
generations = 2
racemize = False
verbose = False
bnice = True<commit_msg>fixed input compounds<commit_after># Running 2 generations with a tanimoto filter

from minedatabase.pickaxe import Pickaxe

# Where are the input rxns coming from and coreactants
# Compounds that are going to be expanded
input_cpds = './data/in_cpds_mid.csv'

# Cofactors used in the rules
coreactant_list = './minedatabase/data/EnzymaticCoreactants.tsv'
# The reaction rules themselves
rule_list = './minedatabase/data/EnzymaticReactionRules.tsv'

# Outputs if you are writing the results locally
write_local = False
pickaxe_rxns = './pickaxe_result/test_rxns.tsv'
pickaxe_cpds = './pickaxe_result/test_cpds.tsv'

# Database to write results to
write_db = True
database = 'tani_2gen'

# Pickaxe Options
generations = 2
racemize = False
verbose = False
bnice = True
{'fraction_non_alphanumeric': 0.07566862361382909, 'fraction_numerical': 0.003913894324853229, 'mean_word_length': 5.160642570281125, 'pattern_counts': {'":': 0, '<': 3, '<?xml version=': 0, '>': 3, 'https://': 0, 'lorem ipsum': 0, 'www.': 0, 'xml': 0}, 'pii_count': 0, 'substrings_counts': 0, 'word_list_counts': {'cursed_substrings.json': 0, 'profanity_word_list.json': 0, 'sexual_word_list.json': 0, 'zh_pornsignals.json': 0}}
{'dir': 'git-commits-cleaned', 'id': '323265', 'n_tokens_mistral': 524, 'n_tokens_neox': 516, 'n_words': 153}