Hey guys,
I'm still trying to generate the .rxn files. Problem now is, that in my
.rxn bond blocks I always have bonds labeld 6 instead of 1. So basically
during the transformation to a .rxn file the function is not anymore sure
if the bonds are aromatic or single bonds.
I can fix this easily with a script but can someone explain me why this
happens?
Here the code:
rxn =
AllChem.ReactionFromSmarts('ClC1=CC=C2C(=C1)C(=C([NH]2)C(=O)NCCC3=CC=C(C=C3)N4CCCCC4)CC.[N]6(C5=CC=C(C=C5C(=C6)C(=O)C(C)C)C(=O)O)CC(O)COC7=CC=C(C=C7)OC8=CC=CC=C8>>ClC1=CC=C2C(=C1)C(=C([NH]2)C(=O)N4CCC3=CC=C(C=C3C4(C5=C[N](C6=CC=C(C=C56)C(=O)O)CC(O)COC7=CC=C(C=C7)OC8=CC=CC=C8)C(C)C)N9CCCCC9)CC')
reactions_string = AllChem.ReactionToRxnBlock(rxn)
print(reactions_string)
$RXN
RDKit
2 1
$MOL
RDKit 2D
29 32 0 0 0 0 0 0 0 0999 V2000
3.0000 0.0000 0.0000 Cl 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
-1.5000 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
-1.7537 2.4138 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.1240 1.8037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.9672 0.3119 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-4.4231 2.5537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.4231 4.0537 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-5.7221 1.8037 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-7.0211 2.5537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-8.3202 1.8037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.6192 2.5537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-9.6192 4.0537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-10.9182 4.8037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-12.2173 4.0537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-12.2173 2.5537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-10.9182 1.8037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-13.5163 4.8037 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-13.5163 6.3037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-14.8154 7.0537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-16.1144 6.3037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-16.1144 4.8037 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-14.8154 4.0537 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4418 3.8810 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5565 4.8847 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 6 0
2 3 2 0
3 4 6 0
4 5 2 0
5 6 6 0
6 7 2 0
6 8 6 0
10 9 6 0
9 11 6 0
11 12 2 0
11 13 6 0
13 14 6 0
14 15 6 0
15 16 6 0
16 17 2 0
17 18 6 0
18 19 2 0
20 21 2 0
20 19 6 0
19 22 6 0
22 23 6 0
23 24 6 0
24 25 6 0
25 26 6 0
26 27 6 0
8 9 2 0
8 28 6 0
28 29 6 0
7 2 6 0
10 5 6 0
21 16 6 0
27 22 6 0
V 1 Cl
V 2 C
V 3 C
V 4 C
V 5 C
V 6 C
V 7 C
V 8 C
V 9 C
V 10 [N&H1]
V 11 C
V 12 O
V 13 N
V 14 C
V 15 C
V 16 C
V 17 C
V 18 C
V 19 C
V 20 C
V 21 C
V 22 N
V 23 C
V 24 C
V 25 C
V 26 C
V 27 C
V 28 C
V 29 C
M END
$MOL
RDKit 2D
35 38 0 0 0 0 0 0 0 0999 V2000
1.2135 -2.7256 0.0000 N 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
-1.5000 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
-1.2135 -2.7256 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.0000 -3.6073 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.6401 -3.1891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.7548 -2.1855 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.9520 -4.6564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.3786 -5.1199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.8373 -5.6601 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 3.8971 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-3.0000 2.5981 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
2.6401 -3.1891 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.9520 -4.6564 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.8373 -5.6601 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
4.3786 -5.1199 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
4.6904 -6.5871 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
6.1170 -7.0506 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
6.4289 -8.5179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.8555 -8.9814 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.9702 -7.9777 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
8.6583 -6.5105 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
7.2317 -6.0469 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
10.3968 -8.4412 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
10.7086 -9.9084 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.5939 -10.9121 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
9.9058 -12.3794 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
11.3324 -12.8429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.4471 -11.8392 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
12.1352 -10.3720 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2 3 2 0
3 4 6 0
4 5 2 0
6 7 2 0
7 8 6 0
8 9 2 0
8 10 6 0
10 11 2 0
10 12 6 0
13 12 6 0
12 14 6 0
6 5 6 0
5 15 6 0
15 16 2 0
15 17 6 0
2 1 6 0
1 18 6 0
18 19 6 0
20 19 6 0
19 21 6 0
21 22 6 0
22 23 6 0
23 24 2 0
24 25 6 0
25 26 2 0
27 28 2 0
27 26 6 0
26 29 6 0
29 30 6 0
30 31 2 0
31 32 6 0
32 33 2 0
33 34 6 0
34 35 2 0
7 2 6 0
9 1 6 0
28 23 6 0
35 30 6 0
V 1 N
V 2 C
V 3 C
V 4 C
V 5 C
V 6 C
V 7 C
V 8 C
V 9 C
V 10 C
V 11 O
V 12 C
V 13 C
V 14 C
V 15 C
V 16 O
V 17 O
V 18 C
V 19 C
V 20 O
V 21 C
V 22 O
V 23 C
V 24 C
V 25 C
V 26 C
V 27 C
V 28 C
V 29 O
V 30 C
V 31 C
V 32 C
V 33 C
V 34 C
V 35 C
M END
$MOL
RDKit 2D
63 71 0 0 0 0 0 0 0 0999 V2000
3.6517 -11.1192 0.0000 Cl 0 0 0 0 0 0 0 0 0 0 0 0
2.3527 -10.3692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0537 -11.1192 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2454 -10.3692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.2454 -8.8692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.0537 -8.1192 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
2.3527 -8.8692 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
0.7418 -6.6520 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 -6.4952 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.3601 -7.8655 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 -5.1962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.2735 -5.3890 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 -3.8971 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
0.7500 -3.8971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.5000 -2.5981 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
-1.5000 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
-1.5000 -2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.6491 -3.5623 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5444 -5.0586 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.9352 -5.6205 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-4.8994 -4.4714 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.3985 -4.4191 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.1027 -3.0947 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-6.3078 -1.8226 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.8087 -1.8750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.1045 -3.1994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-7.0120 -0.4982 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-8.5111 -0.4458 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-6.2171 0.7739 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-4.2981 -7.0760 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.2191 -8.1179 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7200 -8.0657 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-3.5820 -9.5734 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.5030 -10.6154 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.8658 -12.0708 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.7868 -13.1128 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1497 -14.5683 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.5916 -14.9817 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.6706 -13.9397 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.3077 -12.4843 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.9545 -16.4372 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
-2.8755 -17.4791 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.4336 -17.0657 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.3546 -18.1077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-0.7175 -19.5631 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.1593 -19.9766 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.2384 -18.9346 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.6491 -1.6339 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-2.3886 -0.1567 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-4.0586 -2.1469 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 2.5981 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
-0.7500 3.8971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-1.5000 5.1962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0000 5.1962 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.7500 3.8971 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
-3.0000 2.5981 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1.7455 -5.5373 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
3.2127 -5.8491 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 6 0
2 3 2 0
3 4 6 0
4 5 2 0
5 6 6 0
6 7 2 0
6 8 6 0
10 9 6 0
9 11 6 0
11 12 2 0
11 13 6 0
13 14 6 0
14 15 6 0
15 16 6 0
16 17 2 0
17 18 6 0
18 19 2 0
20 21 2 0
21 22 6 0
23 24 2 0
24 25 6 0
26 27 2 0
27 28 6 0
28 29 2 0
30 31 2 0
30 29 6 0
29 32 6 0
32 33 2 0
32 34 6 0
26 25 6 0
25 35 6 0
35 36 6 0
37 36 6 0
36 38 6 0
38 39 6 0
39 40 6 0
40 41 2 0
41 42 6 0
42 43 2 0
44 45 2 0
44 43 6 0
43 46 6 0
46 47 6 0
47 48 2 0
48 49 6 0
49 50 2 0
50 51 6 0
51 52 2 0
23 22 6 0
22 53 6 0
54 53 6 0
53 55 6 0
20 19 6 0
19 56 6 0
56 57 6 0
57 58 6 0
58 59 6 0
59 60 6 0
60 61 6 0
8 9 2 0
8 62 6 0
62 63 6 0
7 2 6 0
10 5 6 0
21 16 6 0
22 13 6 0
31 23 6 0
31 26 6 0
45 40 6 0
52 47 6 0
61 56 6 0
V 1 Cl
V 2 C
V 3 C
V 4 C
V 5 C
V 6 C
V 7 C
V 8 C
V 9 C
V 10 [N&H1]
V 11 C
V 12 O
V 13 N
V 14 C
V 15 C
V 16 C
V 17 C
V 18 C
V 19 C
V 20 C
V 21 C
V 22 C
V 23 C
V 24 C
V 25 N
V 26 C
V 27 C
V 28 C
V 29 C
V 30 C
V 31 C
V 32 C
V 33 O
V 34 O
V 35 C
V 36 C
V 37 O
V 38 C
V 39 O
V 40 C
V 41 C
V 42 C
V 43 C
V 44 C
V 45 C
V 46 O
V 47 C
V 48 C
V 49 C
V 50 C
V 51 C
V 52 C
V 53 C
V 54 C
V 55 C
V 56 N
V 57 C
V 58 C
V 59 C
V 60 C
V 61 C
V 62 C
V 63 C
M END
On Tue, Sep 3, 2019 at 3:22 PM Markus Grimm <[email protected]>
wrote:
> Yes, thank you very much!
>
> On Tue, Sep 3, 2019 at 2:57 PM Hongbin Yang <[email protected]> wrote:
>
>> Hi Makrus,
>>
>> Code:
>> ```
>>
>> reaction = AllChem.ReactionFromSmarts('[C:1]-[O:2]>>[C:1](=[O:3])-[O:2]’)
>>
>> print(AllChem.ReactionToRxnBlock(reaction))
>>
>> ```
>>
>> Output:
>>
>> ```
>>
>> $RXN
>>
>> RDKit
>>
>> 1 1
>> $MOL
>>
>> RDKit 2D
>>
>> 2 1 0 0 0 0 0 0 0 0999 V2000
>> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0
>> 1.2990 0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 2 0 0
>> 1 2 1 0
>> V 1 [C:1]
>> V 2 [O:2]
>> M END
>> $MOL
>>
>> RDKit 2D
>>
>> 3 2 0 0 0 0 0 0 0 0999 V2000
>> 0.0000 0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 1 0 0
>> 1.2990 0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 3 0 0
>> -1.2990 0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 2 0 0
>> 1 2 2 0
>> 1 3 1 0
>> V 1 [C:1]
>> V 2 [O:3]
>> V 3 [O:2]
>> M END
>>
>> ```
>>
>> Does it help?
>>
>>
>> Best,
>>
>> Hongbin Yang 杨弘宾, Ph.D.
>> Research: Toxicophore and Chemoinformatics
>> Pharmaceutical Science, School of Pharmacy
>> East China University of Science and Technology
>>
>> On 09/3/2019 17:59，Markus Grimm via
>> Rdkit-discuss<[email protected]>
>> <[email protected]> wrote：
>>
>> Dear all,
>>
>> I'm trying to generate .rxn files or one single .rdf file from a csv file
>> where I have a bunch of reactions smiles stored.
>> I know how to instantiate a rxn object but I no idea how to safe this to
>> several .rxn files or a RDF file.
>>
>> I already asked this question last Friday but unfortunately I did not
>> receive any answer. So I'm wondering is it even possible?
>>
>> Thank you very much for your support.
>>
>> Best regards,
>> Markus
>>
>>
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