Running ReactionDecoder on unbalanced reactions

[notllikethat]

Hello!

I've been using this tool to perform atom mapping and one of the reactions that I've had happened to be unbalanced. It seems that whili running ReactionDecoder changed metabolite identifiers of the participants.

The rxn file I've tried to run ReactionDecoder Tool was created automatically and looks like
R02480.rxn.txt
`
$RXN

WHATEVER blabla

1 2
$MOL
C00524
WHATEVER 0000000000

65 70 0 0 1 0 0 0 0 0999 V2000
26.4746 -25.8650 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
25.2321 -26.4070 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
26.5689 -24.5105 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0
27.8058 -26.3773 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
23.9534 -25.8965 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
27.8883 -24.1959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
28.6144 -25.3428 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
22.7474 -26.5017 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
23.7390 -24.5468 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
28.3756 -22.9767 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
23.6445 -21.6212 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0
21.7775 -25.5972 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
22.4080 -24.3266 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
27.8766 -21.7589 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
23.8171 -20.2717 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
22.2950 -21.8591 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
21.8673 -23.1261 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
28.4886 -20.5280 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
26.5329 -21.5502 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
22.5863 -19.6959 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
25.0480 -19.6132 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
21.6541 -20.6702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
27.5200 -19.5888 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
26.3136 -20.2193 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
22.5747 -18.3230 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
20.2870 -20.6702 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
27.5084 -18.2157 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
23.7584 -17.6229 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
29.8441 -20.3026 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
30.7582 -21.4129 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
27.7688 -27.8205 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
29.0096 -28.5705 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
28.9731 -30.0126 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
30.2137 -30.7626 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
27.7100 -30.7117 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
22.6923 -27.8455 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
21.4956 -28.4769 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
21.4406 -29.8206 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
20.2439 -30.4449 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
22.5755 -30.5470 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
20.3364 -25.6635 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
29.9222 -25.4060 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
25.0654 -23.0671 0.0000 Fe 0 0 0 0 0 0 0 0 0 0 0 0
21.3689 -17.6419 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
21.3552 -16.2332 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
20.1156 -15.5332 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.9275 -16.2344 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
20.1022 -14.1346 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.8582 -13.4317 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
21.2818 -13.4382 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
30.3412 -18.9756 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
31.7328 -18.7439 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
32.2236 -17.4345 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
33.6210 -17.2020 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
31.3349 -16.3545 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
34.5216 -18.2967 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
34.1110 -15.8951 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
18.9275 -17.6344 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
29.9349 -16.3545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.8582 -12.0317 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0
35.5110 -15.8951 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0
17.7151 -18.3344 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0
29.2349 -15.1421 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0
20.1399 -18.3344 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
29.2349 -17.5669 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
11 16 1 0 0 0
13 17 2 0 0 0
14 18 1 0 0 0
14 19 2 0 0 0
15 20 2 0 0 0
15 21 1 0 0 0
16 22 2 0 0 0
18 23 2 0 0 0
19 24 1 0 0 0
20 25 1 0 0 0
22 26 1 0 0 0
23 27 1 0 0 0
6 7 1 0 0 0
12 13 1 0 0 0
16 17 1 0 0 0
20 22 1 0 0 0
21 24 2 0 0 0
23 24 1 0 0 0
25 28 1 0 0 0
18 29 1 0 0 0
29 30 1 0 0 0
1 2 2 0 0 0
4 31 1 0 0 0
1 3 1 0 0 0
31 32 1 0 0 0
1 4 1 0 0 0
32 33 1 0 0 0
2 5 1 0 0 0
33 34 2 0 0 0
3 6 1 0 0 0
33 35 1 0 0 0
4 7 2 0 0 0
8 36 1 0 0 0
5 8 1 0 0 0
36 37 1 0 0 0
5 9 2 0 0 0
37 38 1 0 0 0
6 10 2 0 0 0
38 39 1 0 0 0
8 12 2 0 0 0
38 40 2 0 0 0
9 13 1 0 0 0
12 41 1 0 0 0
10 14 1 0 0 0
7 42 1 0 0 0
11 15 1 0 0 0
11 43 1 0 0 0
3 43 1 0 0 0
25 44 1 0 0 0
44 45 1 0 0 0
46 45 1 6 0 0
46 47 1 0 0 0
46 48 1 0 0 0
48 49 1 0 0 0
48 50 2 0 0 0
29 51 1 0 0 0
51 52 1 0 0 0
53 52 1 6 0 0
53 54 1 0 0 0
53 55 1 0 0 0
54 56 2 0 0 0
54 57 1 0 0 0
47 58 1 0 0 0
55 59 1 0 0 0
49 60 1 0 0 0
57 61 1 0 0 0
58 62 1 0 0 0
59 63 1 0 0 0
58 64 2 0 0 0
59 65 2 0 0 0
M END
$MOL
C02248
WHATEVER 0000000000

22 20 0 0 1 0 0 0 0 0999 V2000
13.8824 -16.5900 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0
15.0949 -17.2900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.3073 -16.5900 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
17.5197 -17.2900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.7322 -16.5900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
19.9446 -17.2900 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
21.1570 -16.5900 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0
17.5197 -18.6899 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.0949 -18.6898 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
18.7322 -15.1903 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
18.7174 -19.3814 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
13.8824 -16.5900 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0
15.0949 -17.2900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.3073 -16.5900 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
17.5197 -17.2900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.7322 -16.5900 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
19.9446 -17.2900 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
21.1570 -16.5900 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0
18.7322 -15.1903 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
17.5197 -18.6899 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
18.7174 -19.3814 0.0000 S 0 0 0 0 0 0 0 0 0 0 0 0
15.0949 -18.6898 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0
2 3 1 0 0 0
3 4 1 0 0 0
4 5 1 0 0 0
5 6 1 0 0 0
6 7 1 0 0 0
4 8 1 6 0 0
2 9 2 0 0 0
5 10 2 0 0 0
8 11 1 0 0 0
12 13 1 0 0 0
13 14 1 0 0 0
14 15 1 0 0 0
15 16 1 0 0 0
16 17 1 0 0 0
17 18 1 0 0 0
15 20 1 6 0 0
13 22 2 0 0 0
16 19 2 0 0 0
20 21 1 0 0 0
M STY 1 1 MUL
M SLB 1 1 1
M SCN 1 1 HT
M SAL 1 15 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15
M SAL 1 7 16 17 18 19 20 21 22
M SPA 1 11 1 2 3 4 5 6 7 10 8 11 9
M SDI 1 4 12.9500 -19.8800 12.9500 -14.7700
M SDI 1 4 21.8400 -14.7700 21.8400 -19.8800
M SMT 1 2
M END
$MOL
C00032
WHATEVER 0000000000

43 48 0 0 0 0 0 0 0 0999 V2000
38.3311 -24.4093 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
37.0877 -24.9517 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
38.4255 -23.0539 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0
39.6633 -24.9220 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
35.8081 -24.4409 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
39.7458 -22.7390 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
40.4724 -23.8868 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
34.6012 -25.0465 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
35.5935 -23.0902 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
40.2335 -21.5190 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
35.4990 -20.1625 0.0000 N 0 0 3 0 0 0 0 0 0 0 0 0
33.6306 -24.1414 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
34.2616 -22.8698 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
39.7341 -20.3003 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
35.6717 -18.8120 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
34.1485 -20.4006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
33.7205 -21.6685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
40.3465 -19.0685 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
38.3894 -20.0914 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0
34.4400 -18.2358 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
36.9035 -18.1530 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
33.5071 -19.2108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
39.3772 -18.1286 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
38.1700 -18.7596 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
34.4284 -16.8619 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
32.1390 -19.2108 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
39.3656 -16.7545 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
35.6129 -16.1613 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
41.7030 -18.8429 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
42.6178 -19.9540 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
39.6262 -26.3663 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
40.8679 -27.1168 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
40.8314 -28.5599 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
42.0729 -29.3105 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
39.5674 -29.2595 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
34.5461 -26.3913 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
33.3485 -27.0231 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
33.2935 -28.3678 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
32.0959 -28.9925 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
34.4292 -29.0947 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0
32.1885 -24.2077 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
41.7812 -23.9500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
36.9209 -21.6094 0.0000 Fe 0 0 0 0 0 0 0 0 0 0 0 0
11 16 1 0 0 0
13 17 2 0 0 0
14 18 1 0 0 0
14 19 2 0 0 0
15 20 2 0 0 0
15 21 1 0 0 0
16 22 2 0 0 0
18 23 2 0 0 0
19 24 1 0 0 0
20 25 1 0 0 0
22 26 1 0 0 0
23 27 1 0 0 0
6 7 1 0 0 0
12 13 1 0 0 0
16 17 1 0 0 0
20 22 1 0 0 0
21 24 2 0 0 0
23 24 1 0 0 0
25 28 2 0 0 0
18 29 1 0 0 0
29 30 2 0 0 0
1 2 2 0 0 0
4 31 1 0 0 0
1 3 1 0 0 0
31 32 1 0 0 0
1 4 1 0 0 0
32 33 1 0 0 0
2 5 1 0 0 0
33 34 2 0 0 0
3 6 1 0 0 0
33 35 1 0 0 0
4 7 2 0 0 0
8 36 1 0 0 0
5 8 1 0 0 0
36 37 1 0 0 0
5 9 2 0 0 0
37 38 1 0 0 0
6 10 2 0 0 0
38 39 1 0 0 0
8 12 2 0 0 0
38 40 2 0 0 0
9 13 1 0 0 0
12 41 1 0 0 0
10 14 1 0 0 0
7 42 1 0 0 0
11 15 1 0 0 0
11 43 1 0 0 0
3 43 1 0 0 0
M END
Initially there were supposed to be two metabolites C02248 in the rxn file. However, when I've ran Reaction Decoder with commandjava -jar ./rdt-2.4.1-jar-with-dependencies.jar -Q RXN -q ../R02480.rxn -g -j AAM -f TEXTI've got the following output: [ECBLAST_R02480_AAM.rxn.txt](https://github.com/asad/ReactionDecoder/files/7569560/ECBLAST_R02480_AAM.rxn.txt)
$RXN

EC-BLAST R02480

1 3
$MOL
C00524
RDT 11162115092D

65 70 0 0 1 0 0 0 0 0999 V2000
-8.2486 9.9843 0.0000 * 0 0 0 0 0 0 0 0 0 1 0 0
-8.2911 8.4849 0.0000 N 0 0 0 0 0 0 0 0 0 2 0 0
-7.0138 7.6984 0.0000 C 0 0 0 0 0 0 0 0 0 3 0 0
-5.6941 8.4114 0.0000 O 0 0 0 0 0 0 0 0 0 4 0 0
-7.0563 6.1990 0.0000 C 0 0 1 0 0 0 0 0 0 5 0 0
-8.3760 5.4861 0.0000 N 0 0 0 0 0 0 0 0 0 6 0 0
-9.6533 6.2726 0.0000 C 0 0 0 0 0 0 0 0 0 7 0 0
-9.6108 7.7720 0.0000 * 0 0 0 0 0 0 0 0 0 8 0 0
-10.9731 5.5597 0.0000 O 0 0 0 0 0 0 0 0 0 9 0 0
-5.7790 5.4126 0.0000 C 0 0 0 0 0 0 0 0 0 10 0 0
-5.8215 3.9132 0.0000 S 0 0 0 0 0 0 0 0 0 11 0 0
-3.3180 2.3717 0.0000 C 0 0 0 0 0 0 0 0 0 12 0 0
-0.7313 3.7690 0.0000 C 0 0 0 0 0 0 0 0 0 13 0 0
-2.5382 4.3299 0.0000 C 0 0 0 0 0 0 0 0 0 14 0 0
-2.0747 5.7565 0.0000 N 0 0 0 0 0 0 0 0 0 15 0 0
-0.8612 6.6381 0.0000 C 0 0 0 0 0 0 0 0 0 16 0 0
0.6388 6.6381 0.0000 C 0 0 0 0 0 0 0 0 0 17 0 0
1.8524 5.7565 0.0000 C 0 0 0 0 0 0 0 0 0 18 0 0
3.0659 6.6381 0.0000 C 0 0 0 0 0 0 0 0 0 19 0 0
4.2794 5.7565 0.0000 C 0 0 0 0 0 0 0 0 0 20 0 0
3.8159 4.3299 0.0000 C 0 0 0 0 0 0 0 0 0 21 0 0
4.5659 3.0299 0.0000 C 0 0 0 0 0 0 0 0 0 22 0 0
3.8159 1.7299 0.0000 C 0 0 0 0 0 0 0 0 0 23 0 0
2.3059 1.7299 0.0000 N 0 0 0 0 0 0 0 0 0 24 0 0
1.5559 0.4299 0.0000 C 0 0 0 0 0 0 0 0 0 25 0 0
0.0559 0.4299 0.0000 C 0 0 0 0 0 0 0 0 0 26 0 0
1.1024 0.5950 0.0000 C 0 0 0 0 0 0 0 0 0 27 0 0
-0.1112 -0.2866 0.0000 C 0 0 0 0 0 0 0 0 0 28 0 0
-1.3247 0.5950 0.0000 C 0 0 0 0 0 0 0 0 0 29 0 0
-0.8612 2.0216 0.0000 C 0 0 0 0 0 0 0 0 0 30 0 0
-2.0747 2.9033 0.0000 C 0 0 0 0 0 0 0 0 0 31 0 0
0.6388 2.0216 0.0000 N 0 0 0 0 0 0 0 0 0 32 0 0
1.8524 2.9033 0.0000 Fe 0 0 0 0 0 0 0 0 0 33 0 0
2.3159 4.3299 0.0000 N 0 0 0 0 0 0 0 0 0 34 0 0
-2.7513 0.1315 0.0000 C 0 0 0 0 0 0 0 0 0 35 0 0
-0.1112 -1.7866 0.0000 C 0 0 0 0 0 0 0 0 0 36 0 0
-1.4102 -2.5366 0.0000 C 0 0 0 0 0 0 0 0 0 37 0 0
-1.4102 -4.0366 0.0000 C 0 0 0 0 0 0 0 0 0 38 0 0
-0.1112 -4.7866 0.0000 O 0 0 0 0 0 0 0 0 0 39 0 0
-2.7092 -4.7866 0.0000 O 0 0 0 0 0 0 0 0 0 40 0 0
2.7828 -0.6389 0.0000 C 0 0 0 0 0 0 0 0 0 41 0 0
4.1229 0.1319 0.0000 C 0 0 0 0 0 0 0 0 0 42 0 0
5.4867 -0.4927 0.0000 C 0 0 0 0 0 0 0 0 0 43 0 0
2.6371 -2.1318 0.0000 C 0 0 0 0 0 0 0 0 0 44 0 0
3.8571 -3.0045 0.0000 C 0 0 0 0 0 0 0 0 0 45 0 0
3.7114 -4.4974 0.0000 C 0 0 0 0 0 0 0 0 0 46 0 0
2.3456 -5.1176 0.0000 O 0 0 0 0 0 0 0 0 0 47 0 0
4.9314 -5.3701 0.0000 O 0 0 0 0 0 0 0 0 0 48 0 0
5.7060 6.2200 0.0000 C 0 0 0 0 0 0 0 0 0 49 0 0
3.0659 8.1381 0.0000 C 0 0 0 0 0 0 0 0 0 50 0 0
4.3649 8.8881 0.0000 S 0 0 0 0 0 0 0 0 0 51 0 0
4.3649 10.3881 0.0000 C 0 0 0 0 0 0 0 0 0 52 0 0
5.6640 11.1381 0.0000 C 0 0 2 0 0 0 0 0 0 53 0 0
5.6640 12.6381 0.0000 N 0 0 0 0 0 0 0 0 0 54 0 0
4.3649 13.3881 0.0000 C 0 0 0 0 0 0 0 0 0 55 0 0
4.3649 14.8881 0.0000 * 0 0 0 0 0 0 0 0 0 56 0 0
3.0659 12.6381 0.0000 O 0 0 0 0 0 0 0 0 0 57 0 0
6.9630 10.3881 0.0000 C 0 0 0 0 0 0 0 0 0 58 0 0
6.9630 8.8881 0.0000 O 0 0 0 0 0 0 0 0 0 59 0 0
8.2620 11.1381 0.0000 N 0 0 0 0 0 0 0 0 0 60 0 0
8.2620 12.6381 0.0000 * 0 0 0 0 0 0 0 0 0 61 0 0
1.7669 8.8881 0.0000 C 0 0 0 0 0 0 0 0 0 62 0 0
0.2306 5.0930 0.0000 C 0 0 0 0 0 0 0 0 0 63 0 0
1.7306 5.0831 0.0000 C 0 0 0 0 0 0 0 0 0 64 0 0
-3.3604 0.8723 0.0000 C 0 0 0 0 0 0 0 0 0 65 0 0
2 1 1 0 0 0 0
3 2 1 0 0 0 0
3 4 2 0 0 0 0
5 3 1 0 0 0 0
5 6 1 6 0 0 0
10 5 1 0 0 0 0
6 7 1 0 0 0 0
7 8 1 0 0 0 0
7 9 2 0 0 0 0
11 10 1 0 0 0 0
12 11 1 0 0 0 0
13 12 1 0 0 0 0
12 65 1 0 0 0 0
14 13 1 0 0 0 0
13 63 2 0 0 0 0
15 14 2 0 0 0 0
14 31 1 0 0 0 0
16 15 1 0 0 0 0
17 16 2 3 0 0 0
16 63 1 0 0 0 0
18 17 1 0 0 0 0
18 19 2 0 0 0 0
34 18 1 0 0 0 0
19 20 1 0 0 0 0
19 50 1 0 0 0 0
21 20 2 0 0 0 0
20 49 1 0 0 0 0
22 21 1 0 0 0 0
21 34 1 0 0 0 0
23 22 2 0 0 0 0
23 24 1 0 0 0 0
42 23 1 0 0 0 0
25 24 2 0 0 0 0
26 25 1 0 0 0 0
25 41 1 0 0 0 0
27 26 2 3 0 0 0
27 28 1 0 0 0 0
27 32 1 0 0 0 0
29 28 2 0 0 0 0
28 36 1 0 0 0 0
30 29 1 0 0 0 0
29 35 1 0 0 0 0
31 30 2 0 0 0 0
30 32 1 0 0 0 0
32 33 1 0 0 0 0
34 33 1 0 0 0 0
36 37 1 0 0 0 0
37 38 1 0 0 0 0
38 39 2 0 0 0 0
38 40 1 0 0 0 0
41 42 2 0 0 0 0
41 44 1 0 0 0 0
42 43 1 0 0 0 0
44 45 1 0 0 0 0
45 46 1 0 0 0 0
46 47 2 0 0 0 0
46 48 1 0 0 0 0
50 51 1 0 0 0 0
50 62 1 0 0 0 0
51 52 1 0 0 0 0
52 53 1 0 0 0 0
53 54 1 6 0 0 0
53 58 1 0 0 0 0
54 55 1 0 0 0 0
55 56 1 0 0 0 0
55 57 2 0 0 0 0
58 59 2 0 0 0 0
58 60 1 0 0 0 0
60 61 1 0 0 0 0
63 64 1 0 0 0 0
M END
$MOL
M00001
RDT 11162115092D

43 48 0 0 0 0 0 0 0 0999 V2000
1.5995 -1.6728 0.0000 C 0 0 0 0 0 0 0 0 0 13 0 0
-1.2945 -2.8205 0.0000 C 0 0 0 0 0 0 0 0 0 35 0 0
1.4538 -3.1657 0.0000 C 0 0 0 0 0 0 0 0 0 12 0 0
-5.9849 -4.3003 0.0000 O 0 0 0 0 0 0 0 0 0 40 0 0
-6.7878 -1.8294 0.0000 O 0 0 0 0 0 0 0 0 0 39 0 0
-3.9346 -0.9024 0.0000 C 0 0 0 0 0 0 0 0 0 36 0 0
4.5227 5.1861 0.0000 C 0 0 0 0 0 0 0 0 0 50 0 0
3.0961 4.7226 0.0000 C 0 0 0 0 0 0 0 0 0 19 0 0
1.8826 5.6043 0.0000 C 0 0 0 0 0 0 0 0 0 20 0 0
0.6691 4.7226 0.0000 C 0 0 0 0 0 0 0 0 0 21 0 0
-0.5445 5.6043 0.0000 C 0 0 0 0 0 0 0 0 0 22 0 0
-2.0445 5.6043 0.0000 C 0 0 0 0 0 0 0 0 0 23 0 0
-3.2580 4.7226 0.0000 N 0 0 0 0 0 0 0 0 0 24 0 0
2.9396 -0.9019 0.0000 C 0 0 0 0 0 0 0 0 0 63 0 0
4.3034 -1.5265 0.0000 C 0 0 0 0 0 0 0 0 0 64 0 0
-3.7215 3.2960 0.0000 C 0 0 0 0 0 0 0 0 0 25 0 0
-1.9146 2.7351 0.0000 C 0 0 0 0 0 0 0 0 0 41 0 0
-1.4417 1.3116 0.0000 C 0 0 0 0 0 0 0 0 0 44 0 0
-3.6061 0.1424 0.0000 C 0 0 0 0 0 0 0 0 0 45 0 0
-6.2031 0.2160 0.0000 O 0 0 0 0 0 0 0 0 0 48 0 0
0.3726 -0.6040 0.0000 C 0 0 0 0 0 0 0 0 0 14 0 0
1.1226 0.6960 0.0000 N 0 0 0 0 0 0 0 0 0 15 0 0
2.6326 0.6960 0.0000 C 0 0 0 0 0 0 0 0 0 16 0 0
3.3826 1.9960 0.0000 C 0 0 0 0 0 0 0 0 0 17 0 0
2.6326 3.2960 0.0000 C 0 0 0 0 0 0 0 0 0 18 0 0
4.8346 6.6533 0.0000 C 0 0 0 0 0 0 0 0 0 62 0 0
-1.1274 -0.6040 0.0000 C 0 0 0 0 0 0 0 0 0 31 0 0
-0.0809 -0.4388 0.0000 C 0 0 0 0 0 0 0 0 0 30 0 0
-1.2945 -1.3205 0.0000 C 0 0 0 0 0 0 0 0 0 29 0 0
-2.0445 0.9877 0.0000 C 0 0 0 0 0 0 0 0 0 27 0 0
-3.2580 1.8694 0.0000 C 0 0 0 0 0 0 0 0 0 26 0 0
-0.5445 0.9877 0.0000 N 0 0 0 0 0 0 0 0 0 32 0 0
0.6691 1.8694 0.0000 Fe 0 0 0 0 0 0 0 0 0 33 0 0
1.1326 3.2960 0.0000 N 0 0 0 0 0 0 0 0 0 34 0 0
-2.5080 -0.4388 0.0000 C 0 0 0 0 0 0 0 0 0 28 0 0
-4.8833 0.9289 0.0000 C 0 0 0 0 0 0 0 0 0 46 0 0
-4.8409 2.4283 0.0000 O 0 0 0 0 0 0 0 0 0 47 0 0
0.5473 4.0492 0.0000 C 0 0 0 0 0 0 0 0 0 43 0 0
1.8826 7.1043 0.0000 C 0 0 0 0 0 0 0 0 0 49 0 0
-0.9527 4.0591 0.0000 C 0 0 0 0 0 0 0 0 0 42 0 0
2.6738 -4.0384 0.0000 C 0 0 0 0 0 0 0 0 0 65 0 0
-4.2465 -2.3696 0.0000 C 0 0 0 0 0 0 0 0 0 37 0 0
-5.6730 -2.8331 0.0000 C 0 0 0 0 0 0 0 0 0 38 0 0
1 3 1 0 0 0 0
1 14 2 0 0 0 0
21 1 1 0 0 0 0
29 2 1 0 0 0 0
3 41 2 0 0 0 0
43 4 1 0 0 0 0
43 5 2 0 0 0 0
35 6 1 0 0 0 0
6 42 1 0 0 0 0
8 7 1 0 0 0 0
7 26 2 0 0 0 0
8 9 1 0 0 0 0
25 8 2 0 0 0 0
10 9 2 0 0 0 0
9 39 1 0 0 0 0
11 10 1 0 0 0 0
10 34 1 0 0 0 0
12 11 2 3 0 0 0
12 13 1 0 0 0 0
40 12 1 0 0 0 0
16 13 2 0 0 0 0
14 15 1 0 0 0 0
23 14 1 0 0 0 0
16 17 1 0 0 0 0
31 16 1 0 0 0 0
17 18 1 0 0 0 0
17 40 2 0 0 0 0
18 19 1 0 0 0 0
19 36 1 0 0 0 0
36 20 1 0 0 0 0
22 21 2 0 0 0 0
21 27 1 0 0 0 0
23 22 1 0 0 0 0
24 23 2 0 0 0 0
25 24 1 0 0 0 0
34 25 1 0 0 0 0
27 28 2 3 0 0 0
28 29 1 0 0 0 0
28 32 1 0 0 0 0
29 35 2 0 0 0 0
30 31 2 0 0 0 0
30 32 1 0 0 0 0
30 35 1 0 0 0 0
32 33 1 0 0 0 0
34 33 1 0 0 0 0
36 37 2 0 0 0 0
40 38 1 0 0 0 0
42 43 1 0 0 0 0
M END
$MOL
C02248
RDT 11162115092D

11 10 0 0 1 0 0 0 0 0999 V2000
-3.2476 6.3750 0.0000 S 0 0 0 0 0 0 0 0 0 51 0 0
-1.9486 5.6250 0.0000 C 0 0 0 0 0 0 0 0 0 52 0 0
-5.8457 3.3750 0.0000 * 0 0 0 0 0 0 0 0 0 56 0 0
-4.5466 5.6250 0.0000 O 0 0 0 0 0 0 0 0 0 57 0 0
-0.6495 3.3750 0.0000 C 0 0 0 0 0 0 0 0 0 58 0 0
-0.6495 1.8750 0.0000 O 0 0 0 0 0 0 0 0 0 59 0 0
-1.9486 4.1250 0.0000 C 0 0 1 0 0 0 0 0 0 53 0 0
-3.2476 3.3750 0.0000 N 0 0 0 0 0 0 0 0 0 54 0 0
-4.5466 4.1250 0.0000 C 0 0 0 0 0 0 0 0 0 55 0 0
0.6495 4.1250 0.0000 N 0 0 0 0 0 0 0 0 0 60 0 0
1.9486 3.3750 0.0000 * 0 0 0 0 0 0 0 0 0 61 0 0
2 1 1 0 0 0 0
7 2 1 0 0 0 0
3 9 1 0 0 0 0
9 4 2 0 0 0 0
5 6 2 0 0 0 0
7 5 1 0 0 0 0
5 10 1 0 0 0 0
7 8 1 1 0 0 0
9 8 1 0 0 0 0
10 11 1 0 0 0 0
M END
$MOL
C00032
RDT 11162115092D

11 10 0 0 1 0 0 0 0 0999 V2000
1.9486 3.3750 0.0000 * 0 0 0 0 0 0 0 0 0 1 0 0
0.6495 4.1250 0.0000 N 0 0 0 0 0 0 0 0 0 2 0 0
-0.6495 3.3750 0.0000 C 0 0 0 0 0 0 0 0 0 3 0 0
-0.6495 1.8750 0.0000 O 0 0 0 0 0 0 0 0 0 4 0 0
-1.9486 4.1250 0.0000 C 0 0 1 0 0 0 0 0 0 5 0 0
-3.2476 3.3750 0.0000 N 0 0 0 0 0 0 0 0 0 6 0 0
-4.5466 4.1250 0.0000 C 0 0 0 0 0 0 0 0 0 7 0 0
-5.8457 3.3750 0.0000 * 0 0 0 0 0 0 0 0 0 8 0 0
-4.5466 5.6250 0.0000 O 0 0 0 0 0 0 0 0 0 9 0 0
-1.9486 5.6250 0.0000 C 0 0 0 0 0 0 0 0 0 10 0 0
-3.2476 6.3750 0.0000 S 0 0 0 0 0 0 0 0 0 11 0 0
2 1 1 0 0 0 0
3 2 1 0 0 0 0
3 4 2 0 0 0 0
5 3 1 0 0 0 0
5 6 1 1 0 0 0
5 10 1 0 0 0 0
7 6 1 0 0 0 0
8 7 1 0 0 0 0
7 9 2 0 0 0 0
10 11 1 0 0 0 0
M END
`

So my question is whether it is okay for ReactionDecoder to assign metabolite identifiers the way it did and whether there is a way of being notified when the reaction is unbalanced?

Thank you!