epam / epam/Indigo

The structure with AH from Atom Generics is rendered incorrectly after saving in Daylight SMARTS format

Open
#3,891 1 comment 0 reactions 0 assignees View on GitHub
Dominant language
C++
Stars
406
Forks
134
Avg merge
2d 11h
Merged PRs (30d)
24

Description

**Steps to reproduce**

1. Create any structure, for example, chain.
2. Click Periodic table.
3. Open Extended tab.
4. Click the "AH" button in the Atom Generics section, click the OK button and click any structure atom.
5. Click "Save as" button. Select Daylight SMART format. Click OK.
6. Clear the canvas.
7. Open the structure saved at 5th step.

**Actual result**
The structure is rendered incorrectly - all atoms except the terminal ones are replaced with diradicals (singlets), terminal atoms display with minus charge.
![image](https://user-images.githubusercontent.com/7427808/92368354-49487200-f100-11ea-9f7b-b4b073fc14ae.png)

**Expected result**
The structure should display in the same way as before saving.

Contributor guide

No contributing guide indexed for this repository

Research direction

Reproduce the issue by applying the AH atom generic, saving as Daylight SMARTS, clearing the canvas, and reopening the structure. Start by tracing the SMARTS save and load handling for atom generics and compare the reopened structure with the original; done means the AH structure renders identically after the round trip.

Written by the indexing model from the issue text.

Assessment

Tech stack
cpp
Domain
computer-graphics, tooling
Issue type
Bug
Difficulty
4/5
Estimated time
3-5 days
Activity status
Stale
Clarity
Mostly clear
Newbie friendliness
35/100

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