Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

When saving a structure with set up Implicit H count and any other atom attribute then an error appears #1321

Closed
urszula-gawlowska opened this issue Oct 12, 2023 · 0 comments · Fixed by #1336
Assignees
Projects

Comments

@urszula-gawlowska
Copy link
Collaborator

urszula-gawlowska commented Oct 12, 2023

Steps to Reproduce

  1. Launch "Ketcher"
  2. Draw Benzene on the canvas
  3. Add Atom Properties from the "Query specific" section to any atom:
  • Implicit H count,
  • any other atom attribute, e.g. aromacity
  1. Click on the "Save as" button
  2. Select the "Daylight SMARTS" file format

Expected behavior
There is no error on the screen and in the Console. The structure can be saved in the "Daylight SMARTS" file format

Actual behavior
The error appears on the screen and in the Console ("Convert error! struct data not recognized as molecule, query, reaction or reaction query")
At network appears 'convert' request with 400 status code
Payload:

{
  "struct": "{\n    \"root\": {\n        \"nodes\": [\n            {\n                \"$ref\": \"mol0\"\n            }\n        ]\n    },\n    \"mol0\": {\n        \"type\": \"molecule\",\n        \"atoms\": [\n            {\n                \"label\": \"C\",\n                \"location\": [\n                    8.884849152128567,\n                    -5.425074417174608,\n                    0\n                ]\n            },\n            {\n                \"label\": \"C\",\n                \"location\": [\n                    10.615150847871433,\n                    -5.424589229177204,\n                    0\n                ]\n            },\n            {\n                \"label\": \"C\",\n                \"location\": [\n                    9.751637509491239,\n                    -4.924966888850188,\n                    0\n                ],\n                \"substitutionCount\": 6,\n                \"unsaturatedAtom\": true,\n                \"queryProperties\": {\n                    \"aromaticity\": \"aliphatic\"\n                },\n                \"implicitHCount\": 3\n            },\n            {\n                \"label\": \"C\",\n                \"location\": [\n                    10.615150847871433,\n                    -6.425532067822149,\n                    0\n                ]\n            },\n            {\n                \"label\": \"C\",\n                \"location\": [\n                    8.884849152128567,\n                    -6.4300200567981385,\n                    0\n                ]\n            },\n            {\n                \"label\": \"C\",\n                \"location\": [\n                    9.753820855479558,\n                    -6.925033111149814,\n                    0\n                ]\n            }\n        ],\n        \"bonds\": [\n            {\n                \"type\": 2,\n                \"atoms\": [\n                    2,\n                    0\n                ]\n            },\n            {\n                \"type\": 1,\n                \"atoms\": [\n                    0,\n                    4\n                ]\n            },\n            {\n                \"type\": 2,\n                \"atoms\": [\n                    4,\n                    5\n                ]\n            },\n            {\n                \"type\": 1,\n                \"atoms\": [\n                    5,\n                    3\n                ]\n            },\n            {\n                \"type\": 2,\n                \"atoms\": [\n                    3,\n                    1\n                ]\n            },\n            {\n                \"type\": 1,\n                \"atoms\": [\n                    1,\n                    2\n                ]\n            }\n        ]\n    }\n}",
  "output_format": "chemical/x-daylight-smarts",
  "options": {
    "smart-layout": true,
    "ignore-stereochemistry-errors": true,
    "mass-skip-error-on-pseudoatoms": false,
    "gross-formula-add-rsites": true,
    "aromatize-skip-superatoms": true,
    "dearomatize-on-load": false,
    "ignore-no-chiral-flag": false,
    "gross-formula-add-isotopes": true
  }
}

Response:

{
    "error": "struct data not recognized as molecule, query, reaction or reaction query"
}

Attachments
convert_error

Indigo/Bingo version
Version 1.11.0-rc.1.85-g17cea6ce8-x86_64-linux-gnu-11.4.0

Additional context
It can be related to #1312 and #1309
Now, for case from #1309 error changed also to "Convert error! struct data not recognized as molecule, query, reaction or reaction query"

@urszula-gawlowska urszula-gawlowska added this to Product Backlog in Indigo via automation Oct 12, 2023
@urszula-gawlowska urszula-gawlowska changed the title When saving a structure with Atom Properties from the "Query specific" section in the "Daylight SMARTS" file format, an error appears When saving a structure with set up Implicit H count and any other atom attribute then an error appears Oct 13, 2023
Indigo automation moved this from Product Backlog to Done Oct 17, 2023
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Projects
Indigo
  
Done
Development

Successfully merging a pull request may close this issue.

3 participants