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The structures with atoms with valences rendering incorrectly after saving #46

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AlexanderSavelyev opened this issue Sep 7, 2020 · 2 comments · Fixed by #164
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@AlexanderSavelyev
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AlexanderSavelyev commented Sep 7, 2020

Steps to reproduce

  1. Launch application
  2. Create any structure, for example, chain.
  3. Double click any structure carbon atom.
  4. In the opened "Atom properties" window select Valence 0 (zero). Click OK.
  5. Click "Save as" button.
  6. In the Format field set "Daylight SMILE". Click "Save to file" button.
  7. Clear the canvas.
  8. Open saved in 6th step file.

Actual result
The atom with added valence is replaced with diradical (singlet).
Other variants show in the table:

Valence\Format MOL Daylight Smile Extended Smile Daylight SMART Inchi Inchi Auxinfo CML
0 OK is replaced with diradical disappears Can't be saved disappears disappears disappears
1 OK is replaced with diradical disappears Can't be saved disappears disappears OK
2 OK is replaced with diradical is replaced with diradical Can't be saved is replaced with triplet is replaced with diradical OK
3 OK is replaced with monoradical is replaced with monoradical Can't be saved is replaced with monoradical is replaced with monoradical OK
4 OK disappears disappears Can't be saved disappears disappears OK
5 OK OK OK Can't be saved OK OK OK
6 OK OK OK Can't be saved OK OK OK
7 OK OK OK Can't be saved OK OK OK
8 OK OK OK Can't be saved OK OK OK

This table is about carbon atom. For other atoms it can be different behavior.

Expected result:
The structures with added valences should saved and opened as they were created. In the case if such structure can't be saved the warning message should appear and warn user that the valences can be lost after saving.

@Aniuta907 Aniuta907 self-assigned this Nov 16, 2020
AndreiMazol pushed a commit that referenced this issue Dec 14, 2020
…er saving (#164)

* structures with valences rendering incorrectly

* fix the output of multiple messages

* fix warnings layout

Co-authored-by: Anna Kuznetsova1 <anna_kuznetsova1@epam.com>
@Aniuta907 Aniuta907 removed their assignment Dec 21, 2020
@Ksanjara Ksanjara self-assigned this Dec 21, 2020
@Ksanjara
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Ksanjara commented Dec 21, 2020

Warning message:"In Daylight SMILES valence is not supported" appears, but if User save structure in .smi or .inchi format (according to the table) and then open it - atom with valence rendering still incorrectly as at actual result description.

@AlexanderSavelyev
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it make sense to revalidate the task and return warning messages for specific formats if explicit valence is not supported

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5 participants