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Conversion from Ket to V2000 Molfile is missing SBL line for SRU polymers

Open flange-ipb opened this issue 1 year ago • 0 comments

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

  1. POST this JSON data (the struct field 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

flange-ipb avatar Aug 01 '24 15:08 flange-ipb