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Incorrect S-Group count in MOL V3000 header if ImplicitH is set #1415

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AliaksandrDziarkach opened this issue Nov 22, 2023 · 0 comments · Fixed by #1416
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Incorrect S-Group count in MOL V3000 header if ImplicitH is set #1415

AliaksandrDziarkach opened this issue Nov 22, 2023 · 0 comments · Fixed by #1416
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@AliaksandrDziarkach
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Indigo
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Indigo-1.16.0-rc.2

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@AliaksandrDziarkach
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AliaksandrDziarkach commented Nov 22, 2023 •
edited

Steps to reproduce:

  1. Load smiles "C1CCC(C1)Nc1ccc2ccn(-c3ccc4[nH]ncc4c3)c2c1"
  2. Save as "MDL Molfile V3000".
    In generated file Counts Line is "M V30 COUNTS 24 28 0 0 0", which means 24 atoms, 28 bonds, 0 S-Groups, etc.
    But in end of this file one S-Group defined.

Root cause: indigo Molfile saver, write counts line, then process atoms. New S-Group generated for atoms with ImplicitH count. As result Counts Line contains wrong S-Group count - 0.
@AliaksandrDziarkach AliaksandrDziarkach added this to the Backlog milestone Nov 22, 2023
@AliaksandrDziarkach AliaksandrDziarkach self-assigned this Nov 22, 2023
@AliaksandrDziarkach AliaksandrDziarkach added this to Product Backlog in Indigo via automation Nov 22, 2023
@AliaksandrDziarkach AliaksandrDziarkach moved this from Product Backlog to In progress in Indigo Nov 22, 2023
@AliaksandrDziarkach AliaksandrDziarkach moved this from In progress to In review in Indigo Nov 22, 2023
@AliaksandrDziarkach AliaksandrDziarkach linked a pull request Nov 22, 2023 that will close this issue
Backmerge #1415 Wrong S-Group count in MOL V3000 header #1416
Merged
@AliaksandrDziarkach AliaksandrDziarkach changed the title Wrong S-Group count in MOL V3000 header Incorrect S-Group count in MOL V3000 header if ImplicitH is set Nov 22, 2023
Indigo automation moved this from In review to Done Nov 22, 2023
AlexanderSavelyev pushed a commit that referenced this issue Nov 22, 2023
@AliaksandrDziarkach
Backmerge #1415 Wrong S-Group count in MOL V3000 header (#1416)
7c571fb
AlexanderSavelyev pushed a commit that referenced this issue Nov 23, 2023
@AliaksandrDziarkach
#1415 Wrong S-Group count in MOL V3000 header (#1419)
308eaf8
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Backmerge #1415 Wrong S-Group count in MOL V3000 header
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@AlexanderSavelyev @AliaksandrDziarkach