def test_01_get_outcomes(self):
t = retro_trans.RetroTransformer()
t.load(chiral=True, refs=False, rxns=True)
outcomes = t.get_outcomes(
'CCOC(=O)[C@H]1C[C@@H](C(=O)N2[C@@H](c3ccccc3)CC[C@@H]2c2ccccc2)[C@@H](c2ccccc2)N1',
100, (gc.relevanceheuristic, gc.relevance))
precursors = outcomes.precursors
precursors_result = [precursor.smiles_list for precursor in precursors]
expected_precursors = [[
'C=CC(=O)N1[C@@H](c2ccccc2)CC[C@@H]1c1ccccc1',
'CCOC(=O)C/N=C/c1ccccc1'
]]
self.assertEqual(expected_precursors, precursors_result)
def test_09_get_outcomes_cache(self):
t = retro_trans.RetroTransformer(load_all=False, use_db=True)
t.load()
outcomes = t.get_outcomes(
'CCOC(=O)[C@H]1C[C@@H](C(=O)N2[C@@H](c3ccccc3)CC[C@@H]2c2ccccc2)[C@@H](c2ccccc2)N1',
max_num_templates=100)
precursors = outcomes[0].precursors
precursors_result = [precursor.smiles_list for precursor in precursors]
expected_precursors = [[
'C=CC(=O)N1[C@@H](c2ccccc2)CC[C@@H]1c1ccccc1',
'CCOC(=O)C/N=C/c1ccccc1'
]]
self.assertEqual(expected_precursors, precursors_result)
# Setting logging low
from rdkit import RDLogger
lg = RDLogger.logger()
lg.setLevel(RDLogger.CRITICAL)
from database import db_client
from django.conf import settings
import makeit.utilities.io.pickle as pickle
import os
import makeit.global_config as gc
# Chiral Retro Transformer
import makeit.retrosynthetic.transformer as transformer
RetroTransformer = transformer.RetroTransformer(lookup_only=True)
RetroTransformer.load(chiral=True, refs=True, rxns=False)
RETRO_CHIRAL_FOOTNOTE = 'Using {} chiral retrosynthesis templates (mincount {} if achiral, mincount {} if chiral) from {}/{}'.format(
gc.Relevance_Prioritization['output_size'],
gc.RETRO_TRANSFORMS_CHIRAL['mincount'],
gc.RETRO_TRANSFORMS_CHIRAL['mincount_chiral'],
gc.RETRO_TRANSFORMS_CHIRAL['database'],
gc.RETRO_TRANSFORMS_CHIRAL['collection'])
### Databases
db = db_client[settings.REACTIONS['database']]
REACTION_DB = db[settings.REACTIONS['collection']]
# RETRO_LIT_FOOTNOTE = 'Searched {} known reactions from literature'.format(REACTION_DB.count())
db = db_client[settings.INSTANCES['database']]
INSTANCE_DB = db[settings.INSTANCES['collection']]
db = db_client[settings.CHEMICALS['database']]
CHEMICAL_DB = db[settings.CHEMICALS['collection']]
def test_02_apply_one_template_by_idx(self):
t = retro_trans.RetroTransformer()
t.load(chiral=True, refs=False, rxns=True)
outcomes_result = t.apply_one_template_by_idx(
1,
'CCOC(=O)[C@H]1C[C@@H](C(=O)N2[C@@H](c3ccccc3)CC[C@@H]2c2ccccc2)[C@@H](c2ccccc2)N1',
109659)
expected_outcomes = [(
1,
'CCOC(=O)[C@H]1C[C@@H](C(=O)N2[C@@H](c3ccccc3)CC[C@@H]2c2ccccc2)[C@@H](c2ccccc2)N1',
109659, [('C=CC(=O)N1[C@@H](c2ccccc2)CC[C@@H]1c1ccccc1', [
0.2523617446422577, 0.1969166249036789, 0.15234193205833435,
0.13455800712108612, 0.030202925205230713,
0.024427464231848717, 0.023061120882630348,
0.018903391435742378, 0.017541231587529182,
0.01372396107763052, 0.013607553206384182,
0.012942434288561344, 0.01270198542624712,
0.012236274778842926, 0.00939953699707985,
0.008472910150885582, 0.0059701986610889435,
0.0048681264743208885, 0.004287674557417631,
0.0042765019461512566, 0.004114005248993635,
0.003224626649171114, 0.003134896280243993,
0.00310404016636312, 0.002972274785861373,
0.002696158131584525, 0.0026850011199712753,
0.0021682260558009148, 0.002018335508182645,
0.001683939597569406, 0.0014018624788150191,
0.0012026543263345957, 0.001027433667331934,
0.0010042842477560043, 0.0009036235860548913,
0.0008185449405573308, 0.0006995245930738747,
0.0005884007550776005, 0.0005666478537023067,
0.000491276616230607, 0.0004684898303821683,
0.00045587049680761993, 0.00043441925663501024,
0.0003655038308352232, 0.0003575180599000305,
0.0003510901879053563, 0.00034910428803414106,
0.00030314744799397886, 0.00029094854835420847,
0.000254554208368063, 0.00024915405083447695,
0.00022937390895094723, 0.0001904226082842797,
0.0001790589012671262, 0.00017418322386220098,
0.00016860727919265628, 0.00015959763550199568,
0.00015663796511944383, 0.00015368156891781837,
0.0001446626556571573, 0.00014138488040771335,
0.00013653609494213015
], [
922, 33433, 11500, 7263, 4005, 3581, 5541, 150347, 62514,
54396, 10503, 115523, 26842, 67342, 39406, 7421, 121814, 44003,
104591, 54496, 12802, 17425, 29358, 40183, 89253, 17054, 17142,
14952, 4909, 155144, 73901, 95665, 3419, 17528, 155365, 47886,
31303, 974, 70550, 50432, 97960, 36674, 114062, 108, 6776,
21165, 130595, 81282, 7635, 52, 82107, 95674, 1065, 74925,
88017, 92158, 37880, 9606, 6613, 49535, 16476, 94670
], 1),
('CCOC(=O)C/N=C/c1ccccc1', [
0.9659425020217896, 0.01252610795199871,
0.005059113260358572, 0.0038746828213334084,
0.0022534450981765985, 0.001429172931239009,
0.0008012531325221062, 0.0007077240734361112,
0.000661780999507755, 0.0006321603432297707,
0.0006210291176103055, 0.0005571309011429548
], [
1287, 186, 128290, 2120, 129604, 1910, 17747, 70579,
303, 713, 113217, 8087
], 1)], 0.9996535778045654)]
self.assertEqual(expected_outcomes, outcomes_result)
# Setting logging low
from rdkit import RDLogger
lg = RDLogger.logger()
lg.setLevel(RDLogger.CRITICAL)
from database import db_client
from django.conf import settings
import makeit.utilities.io.pickle as pickle
import os
import makeit.global_config as gc
# Chiral Retro Transformer
import makeit.retrosynthetic.transformer as transformer
RetroTransformer = transformer.RetroTransformer(template_prioritizer=None,
precursor_prioritizer=None,
fast_filter=None)
RetroTransformer.load()
RETRO_CHIRAL_FOOTNOTE = 'Using {} chiral retrosynthesis templates from {}/{}'.format(
gc.RELEVANCE_TEMPLATE_PRIORITIZATION['reaxys']['output_size'],
gc.RETRO_TEMPLATES['database'], gc.RETRO_TEMPLATES['collection'])
### Databases
db = db_client[gc.REACTIONS['database']]
REACTION_DB = db[gc.REACTIONS['collection']]
db = db_client[gc.CHEMICALS['database']]
CHEMICAL_DB = db[gc.CHEMICALS['collection']]
db = db_client[gc.BUYABLES['database']]
BUYABLE_DB = db[gc.BUYABLES['collection']]
db = db_client[gc.SOLVENTS['database']]
# Setting logging low
from rdkit import RDLogger
lg = RDLogger.logger()
lg.setLevel(RDLogger.CRITICAL)
from database import db_client
from django.conf import settings
import makeit.utilities.io.pickle as pickle
import os
import makeit.global_config as gc
# Retro transformer
import makeit.retrosynthetic.transformer as transformer
RetroTransformer = transformer.RetroTransformer(
mincount=gc.RETRO_TRANSFORMS['mincount'])
RetroTransformer.load(chiral=False, refs=True, rxns=False)
RetroTransformer.reorder()
RETRO_FOOTNOTE = 'Using {} retrosynthesis templates (mincount {}) from {}/{}'.format(
len(RetroTransformer.templates), settings.RETRO_TRANSFORMS['mincount'],
settings.RETRO_TRANSFORMS['database'],
settings.RETRO_TRANSFORMS['collection'])
# Chiral Retro Transformer
import makeit.retrosynthetic.transformer as transformer
RetroTransformerChiral = transformer.RetroTransformer()
RetroTransformerChiral.load(chiral=True, refs=True, rxns=False)
RetroTransformerChiral.reorder()
RETRO_CHIRAL_FOOTNOTE = 'Using {} chiral retrosynthesis templates (mincount {} if achiral, mincount {} if chiral) from {}/{}'.format(
len(RetroTransformerChiral.templates),
settings.RETRO_TRANSFORMS_CHIRAL['mincount'],
settings.RETRO_TRANSFORMS_CHIRAL['mincount_chiral'],
settings.RETRO_TRANSFORMS_CHIRAL['database'],
}
project_root = os.path.dirname(os.path.dirname(__file__))
template_name = '{}_{}_{}_{}'.format(
RETRO_TRANSFORMS_CHIRAL['database'],
RETRO_TRANSFORMS_CHIRAL['collection'],
RETRO_TRANSFORMS_CHIRAL['mincount'],
RETRO_TRANSFORMS_CHIRAL['mincount_chiral'],
)
# Get templates and their refs
database = db_client[RETRO_TRANSFORMS_CHIRAL['database']]
RETRO_DB = database[RETRO_TRANSFORMS_CHIRAL['collection']]
import makeit.retrosynthetic.transformer as transformer
RetroTransformerChiral = transformer.RetroTransformer(
mincount=RETRO_TRANSFORMS_CHIRAL['mincount'],
mincount_chiral=RETRO_TRANSFORMS_CHIRAL['mincount_chiral'],
)
RetroTransformerChiral.load(chiral=True, refs=True, rxns=False)
RetroTransformerChiral.reorder()
RETRO_CHIRAL_FOOTNOTE = 'Using {} chiral retrosynthesis templates (mincount {} if achiral, mincount {} if chiral) from {}/{}'.format(
len(RetroTransformerChiral.templates), RETRO_TRANSFORMS_CHIRAL['mincount'],
RETRO_TRANSFORMS_CHIRAL['mincount_chiral'],
RETRO_TRANSFORMS_CHIRAL['database'], RETRO_TRANSFORMS_CHIRAL['collection'])
print('Loaded {} templates'.format(len(RetroTransformerChiral.templates)))
## Create map from reaction ID to template ID
reaction_id_to_template_num = {}
template_num_to_template_id = {}
for tmp_num, template in enumerate(RetroTransformerChiral.templates):
template_num_to_template_id[tmp_num] = template['_id']
