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SMARTS saver works incorrectly for non-query entities if atom valence or radical present #1260

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mkviatkovskii opened this issue Sep 8, 2023 · 0 comments · Fixed by #1261
Closed

SMARTS saver works incorrectly for non-query entities if atom valence or radical present #1260

mkviatkovskii opened this issue Sep 8, 2023 · 0 comments · Fixed by #1261
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@mkviatkovskii
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Bug c++ Core
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Indigo
Milestone
Indigo-1.14.0-rc.5

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mkviatkovskii commented Sep 8, 2023 •
edited

Steps to Reproduce

  1. Load molecule or reaction with atom mappings from SMILES/SMARTS common subset using lndigo, e.g. [C:1]=[C:2][C:3].[C:4]=[C:5][C:6]>>[C:3][C:2]=[C:5][C:6].
  2. Clear atom mappings via automap("clear").
  3. Attempt to save it to SMARTS format.

Expected behavior
Valid SMARTS like [#6]=[#6]-[#6].[#6]=[#6]-[#6]>>[#6]-[#6]=[#6]-[#6] |^3:0,3,^1:1,4,7,8| generated.

Actual behavior
Error SMILES saver: Unknown atom attribute 9 appears.

Indigo/Bingo version
indigo-1.14.0-rc.4
@mkviatkovskii mkviatkovskii added this to Product Backlog in Indigo via automation Sep 8, 2023
@mkviatkovskii mkviatkovskii self-assigned this Sep 8, 2023
@mkviatkovskii mkviatkovskii moved this from Product Backlog to In review in Indigo Sep 8, 2023
@mkviatkovskii mkviatkovskii added this to the Indigo-1.14.0-rc.5 milestone Sep 8, 2023
mkviatkovskii added a commit that referenced this issue Sep 8, 2023
@mkviatkovskii
#1260: fix SMARTS saver for non-query entities with atom mappings
d7f69c6
@mkviatkovskii mkviatkovskii linked a pull request Sep 8, 2023 that will close this issue
#1260: fix SMARTS saver for non-query entities with atom mappings #1261
Merged
mkviatkovskii added a commit that referenced this issue Sep 8, 2023
@mkviatkovskii
#1260: fix formatting
29f7f84
mkviatkovskii added a commit that referenced this issue Sep 8, 2023
@mkviatkovskii
#1260: fix build on macOS
2b531d4
mkviatkovskii added a commit that referenced this issue Sep 8, 2023
@mkviatkovskii
#1260: fix build on macOS
935e19f
mkviatkovskii added a commit that referenced this issue Sep 8, 2023
@mkviatkovskii
#1260: fix SMARTS saver for non-query entities with atom mappings (#1261
6ed3230 
)
Indigo automation moved this from In review to Done Sep 8, 2023
mkviatkovskii added a commit that referenced this issue Sep 8, 2023
@mkviatkovskii
#1260: fix SMARTS saver for non-query entities with atom mappings (#1261
ffabd04 
)
mkviatkovskii added a commit that referenced this issue Sep 11, 2023
@mkviatkovskii
#1260: fix saving rgroups in SMARTS
058a9d8
mkviatkovskii added a commit that referenced this issue Sep 11, 2023
@mkviatkovskii
#1260: fix for saving r-sites to SMARTS (#1263)
8853f40
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Labels
Bug c++ Core
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Indigo
  
Done
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Indigo-1.14.0-rc.5
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#1260: fix SMARTS saver for non-query entities with atom mappings epam/Indigo
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@mkviatkovskii