Indigo
Indigo copied to clipboard
Conversion from Ket to V2000 Molfile is missing SBL line for SRU polymers
This is the continuation of epam/ketcher#2999, which hasn't been taken care of for one year. As mentioned there, I think this is an issue in Indigo and not in Ketcher itself, so I'm bringing this up here.
Summary
After drawing a SRU polymer with star atoms in Ketcher (currently v2.21.0) and converting it to a V2000 Molfile via the remote Indigo service (call ketcher.getMolfile() on the JavaScript console) the resulting Molfile is missing the SBL line.
Steps to Reproduce
- POST this JSON data (the
structfield contains a Ket serialization of polystyrene) to https://lifescience.opensource.epam.com/v2/indigo/convert and inspect the Molfile in the response.
Expected behavior The Molfile contains the SBL line. The following Molfile directly saved from Ketcher has it:
Ketcher 8 12417112D 1 1.00000 0.00000 0
11 11 0 0 0 0 0 0 0 0999 V2000
7.4000 -3.3250 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
13.1750 -6.9410 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.1750 -6.9410 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.6750 -7.8071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
20.5750 -9.7071 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
14.6750 -6.0750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.6734 -4.3447 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.1743 -5.2085 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.6743 -4.3440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.6799 -6.0743 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.1744 -5.2050 0.0000 C 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
3 6 1 0 0 0
8 6 2 0 0 0
6 10 1 0 0 0
10 11 2 0 0 0
11 9 1 0 0 0
9 7 2 0 0 0
7 8 1 0 0 0
M STY 1 1 SRU
M SLB 1 1 1
M SCN 1 1 HT
M SMT 1 n
M SAL 1 9 2 3 4 6 7 8 9 10 11
M SBL 1 2 1 4
M SDI 1 4 9.9554 -5.8055 10.6196 -4.4606
M SDI 1 4 17.9571 -8.0846 17.2929 -9.4295
M SDS EXP 1 1
M END
Actual behavior The Molfile from Indigo's conversion doesn't contain the SBL line:
-INDIGO-08012414522D
11 11 0 0 0 0 0 0 0 0999 V2000
7.4000 -3.3250 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
13.1750 -6.9410 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.1750 -6.9410 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.6750 -7.8071 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
20.5750 -9.7071 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0
14.6750 -6.0750 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.6734 -4.3447 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
14.1743 -5.2085 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.6743 -4.3440 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
15.6799 -6.0743 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
16.1744 -5.2050 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0
1 2 1 0 0 0 0
2 3 1 0 0 0 0
3 4 1 0 0 0 0
4 5 1 0 0 0 0
3 6 1 0 0 0 0
8 6 2 0 0 0 0
6 10 1 0 0 0 0
10 11 2 0 0 0 0
11 9 1 0 0 0 0
9 7 2 0 0 0 0
7 8 1 0 0 0 0
M STY 1 1 SRU
M SLB 1 1 1
M SCN 1 1 HT
M SAL 1 8 2 3 4 6 7 8 9 10
M SAL 1 1 11
M SMT 1 n
M SDI 1 4 12.8362 -6.9495 13.2791 -6.0529
M SDI 1 4 15.5389 -7.1691 15.0961 -8.0657
M END