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Aromacity is incorrectly marked in the SMARTS file #1329

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urszula-gawlowska opened this issue Oct 13, 2023 · 1 comment
Closed

Aromacity is incorrectly marked in the SMARTS file #1329

urszula-gawlowska opened this issue Oct 13, 2023 · 1 comment
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@urszula-gawlowska
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Steps to Reproduce

  1. Launch "Ketcher"
  2. Draw structure on the canvas
  3. Double click on any atom
  4. Go to "Query specific" section
  5. Set aromacity to 'aromatic' or 'aliphatic'
  6. Click 'Apply'
  7. Click on the "Save as" button
  8. Select the "Daylight SMARTS" file format

Expected behavior
Aromacity should be added to the SMARTS representation by 'a or lowercase' and 'A or uppercase'

Actual behavior
SMARTS is created in the incorrect way: #6(-[c])-[#6] or #6(-[C])-[#6]
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                    11.47815796013802,\n                    -5.702705231625483,\n                    0\n                ]\n            },\n            {\n                \"label\": \"C\",\n                \"location\": [\n                    12.344183363922458,\n                    -5.202705231625483,\n                    0\n                ]\n            },\n            {\n                \"label\": \"C\",\n                \"location\": [\n                    10.61213255635358,\n                    -5.202705231625483,\n                    0\n                ],\n                \"queryProperties\": {\n                    \"aromaticity\": \"aliphatic\"\n                }\n            },\n            {\n                \"label\": \"C\",\n                \"location\": [\n                    11.47815796013802,\n                    -6.702705231625483,\n                    0\n                ]\n            }\n        ],\n        \"bonds\": [\n            {\n                \"type\": 1,\n                \"atoms\": [\n                    0,\n                    1\n                ]\n            },\n            {\n                \"type\": 1,\n                \"atoms\": [\n                    0,\n                    2\n                ]\n            },\n            {\n                \"type\": 1,\n                \"atoms\": [\n                    0,\n                    3\n                ]\n            }\n        ],\n        \"stereoFlagPosition\": {\n            \"x\": 12.344183363922458,\n            \"y\": 4.202705231625483,\n            \"z\": 0\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:

{
    "format": "chemical/x-daylight-smarts",
    "original_format": "unknown",
    "struct": "[#6](-[#6])(-[C])-[#6]"
}

Attachments
aromacity_bug

Indigo/Bingo version
Version 1.15.0-dev.1.0-g5ee0dbc7d-x86_64-linux-gnu-11.2.1

@AliaksandrDziarkach
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'A or uppercase' means "[#6;A]" or "C"
So works as designed

Indigo automation moved this from Product Backlog to Done Oct 19, 2023
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