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# Copyright (c) 2015, Novartis Institutes for BioMedical Research Inc.
# All rights reserved.
#
# Redistribution and use in source and binary forms, with or without
# modification, are permitted provided that the following conditions are
# met:
#
# * Redistributions of source code must retain the above copyright
# notice, this list of conditions and the following disclaimer.
# * Redistributions in binary form must reproduce the above
# copyright notice, this list of conditions and the following
# disclaimer in the documentation and/or other materials provided
# with the distribution.
# * Neither the name of Novartis Institutes for BioMedical Research Inc.
# nor the names of its contributors may be used to endorse or promote
# products derived from this software without specific prior written
# permission.
#
# THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS
# "AS IS" AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT
# LIMITED TO, THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR
# A PARTICULAR PURPOSE ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT
# OWNER OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL,
# SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT
# LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
# DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY
# THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT
# (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
# OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
#
import itertools
import os
import pickle
import sys
import time
import unittest
from rdkit import Chem, Geometry, RDConfig, rdBase
from rdkit.Chem import AllChem, rdChemReactions
test_data = [
("good", '''$RXN
ISIS 052820091627
2 1
$MOL
-ISIS- 05280916272D
2 1 0 0 0 0 0 0 0 0999 V2000
-3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
-3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0
1 2 1 0 0 0 0
V 1 halogen.bromine.aromatic
M RGP 1 2 1
M END
$MOL
-ISIS- 05280916272D
4 3 0 0 0 0 0 0 0 0999 V2000
3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0
4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0
4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0 0
1 2 1 0 0 0 0
2 4 1 0 0 0 0
V 2 boronicacid
M RGP 1 1 2
M END
$MOL
-ISIS- 05280916272D
2 1 0 0 0 0 0 0 0 0999 V2000
11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 1 0 0
11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 2 0 0
1 2 1 0 0 0 0
M RGP 2 1 1 2 2
M END'''),
("bad", '''$RXN
ISIS 052820091627
2 1
$MOL
-ISIS- 05280916272D
2 1 0 0 0 0 0 0 0 0999 V2000
-3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
-3.9875 -7.4667 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
V 1 halogen.bromine.aromatic
M RGP 1 2 1
M END
$MOL
-ISIS- 05280916272D
4 3 0 0 0 0 0 0 0 0999 V2000
3.4375 -7.7917 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0
4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0 0
1 2 1 0 0 0 0
2 4 1 0 0 0 0
V 2 boronicacid
M RGP 1 1 2
M END
$MOL
-ISIS- 05280916272D
2 1 0 0 0 0 0 0 0 0999 V2000
11.2667 -7.3417 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
11.9811 -6.9292 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
M RGP 2 1 1 2 2
M END'''),
# chemdraw style
("bad", '''$RXN
ISIS 052820091627
2 1
$MOL
-ISIS- 05280916272D
2 1 0 0 0 0 0 0 0 0999 V2000
-3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
-3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
V 1 halogen.bromine.aromatic
M END
$MOL
-ISIS- 05280916272D
4 3 0 0 0 0 0 0 0 0999 V2000
3.4375 -7.7917 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0
4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0
4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0 0
1 2 1 0 0 0 0
2 4 1 0 0 0 0
V 2 boronicacid
M END
$MOL
-ISIS- 05280916272D
2 1 0 0 0 0 0 0 0 0999 V2000
11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0
11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
M END'''),
("fail", '''$RXN
ISIS 052820091627
2 1
$MOL
-ISIS- 05280916272D
2 1 0 0 0 0 0 0 0 0999 V2000
-3.2730 -7.0542 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0
-3.9875 -7.4667 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
V 1 halogen.bromine.aromatic
M END
$MOL
-ISIS- 05280916272D
4 3 0 0 0 0 0 0 0 0999 V2000
3.4375 -7.7917 0.0000 R3 0 0 0 0 0 0 0 0 0 0 0 0
4.1520 -7.3792 0.0000 B 0 0 0 0 0 0 0 0 0 0 0 0
4.1520 -6.5542 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.8664 -7.7917 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2 3 1 0 0 0 0
1 2 1 0 0 0 0
2 4 1 0 0 0 0
V 2 boronicacid
M END
$MOL
-ISIS- 05280916272D
2 1 0 0 0 0 0 0 0 0999 V2000
11.2667 -7.3417 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0
11.9811 -6.9292 0.0000 R2 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
M END'''),
]
unused_rlabel_in_product = """$RXN
bug.rxn
ChemDraw06121709062D
1 1
$MOL
2 1 0 0 0 0 0 0 0 0999 V2000
0.1604 0.3798 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.1604 -0.3798 0.0000 R 0 0 0 0 0 0 0 0 0 1 0 0
1 2 1 0 0
M END
$MOL
2 1 0 0 0 0 0 0 0 0999 V2000
-1.2690 -1.3345 0.0000 R 0 0 0 0 0 0 0 0 0 1 0 0
1.2690 1.3345 0.0000 R1 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0
M END
"""
kekule_rxn = """$RXN
bug.rxn
ChemDraw06121709062D
1 1
$MOL
RDKit 2D
6 6 0 0 0 0 0 0 0 0999 V2000
1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 2 0
3 4 1 0
4 5 2 0
5 6 1 0
6 1 2 0
M END
$MOL
RDKit 2D
6 6 0 0 0 0 0 0 0 0999 V2000
1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 -1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 1.2990 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0
2 3 2 0
3 4 1 0
4 5 2 0
5 6 1 0
6 1 2 0
M END
"""
good_res = (0, 0, 2, 1, (((0, 'halogen.bromine.aromatic'), ), ((1, 'boronicacid'), )))
bad_res = (3, 0, 2, 1, (((0, 'halogen.bromine.aromatic'), ), ((1, 'boronicacid'), )))
class TestCase(unittest.TestCase):
def test_sanitize(self):
for status, block in test_data:
print("*" * 44)
rxna = AllChem.ReactionFromRxnBlock(block)
rxnb = AllChem.ReactionFromRxnBlock(block)
rxna.Initialize()
res = rdChemReactions.PreprocessReaction(rxna)
print(AllChem.ReactionToRxnBlock(rxna))
if status == "good":
self.assertEqual(res, good_res)
elif status == "bad":
self.assertEqual(res, bad_res)
print(">" * 44)
rxnb.Initialize()
try:
rdChemReactions.SanitizeRxn(rxnb)
res = rdChemReactions.PreprocessReaction(rxnb)
print(AllChem.ReactionToRxnBlock(rxnb))
self.assertEqual(res, good_res)
assert not status == "fail"
except Exception:
print("$RXN Failed")
if status == "fail":
continue
raise
def test_unused_rlabel_in_product(self):
rxn = AllChem.ReactionFromRxnBlock(unused_rlabel_in_product)
# test was for a seg fault
rdChemReactions.SanitizeRxn(rxn)
def test_only_aromatize_if_possible(self):
rxn = AllChem.ReactionFromRxnBlock(kekule_rxn)
# test was for a seg fault
groups = rxn.RunReactants([Chem.MolFromSmiles("c1ccccc1")])
print(groups)
self.assertFalse(len(groups))
# check normal sanitization
rdChemReactions.SanitizeRxn(rxn)
groups = rxn.RunReactants([Chem.MolFromSmiles("c1ccccc1")])
self.assertTrue(len(groups[0]))
# now check adjustparams with ONLY aromatize if possible
rxn = AllChem.ReactionFromRxnBlock(kekule_rxn)
rdChemReactions.SanitizeRxn(rxn)
groups = rxn.RunReactants([Chem.MolFromSmiles("c1ccccc1")])
self.assertTrue(len(groups[0]))
def test_github_4162(self):
rxn = rdChemReactions.ReactionFromSmarts("[C:1](=[O:2])-[OD1].[N!H0:3]>>[C:1](=[O:2])[N:3]")
rxn_copy = rdChemReactions.ChemicalReaction(rxn)
rdChemReactions.SanitizeRxn(rxn)
rdChemReactions.SanitizeRxn(rxn_copy)
pkl = rxn.ToBinary()
rxn_from_pickle = rdChemReactions.ChemicalReaction(pkl)
rdChemReactions.SanitizeRxn(rxn_from_pickle)
pkl = pickle.dumps(rxn)
rxn_from_pickle = pickle.loads(pkl)
rdChemReactions.SanitizeRxn(rxn_from_pickle)
pkl = rxn_from_pickle.ToBinary()
rxn_from_pickle = rdChemReactions.ChemicalReaction(pkl)
rdChemReactions.SanitizeRxn(rxn_from_pickle)
pkl = pickle.dumps(rxn_from_pickle)
rxn_from_pickle = pickle.loads(pkl)
rdChemReactions.SanitizeRxn(rxn_from_pickle)
if __name__ == '__main__':
unittest.main()
|
