Aromatic atom list is not recognized in SMARTS query

[urszula-gawlowska]

When Indigo converts a SMARTS query with a list atoms in aromatic format (lowercase atom symbols, e.g. "c,n") into a structure, the list is not recognized properly and is interpreted as a custom query in the returned structure.

For example, the following query results in a molecule with custom query "c,n" instead of atom list with carbon and nitrogen.
c1-[#6]=[#6]-[#6]=[#6]-[c,n]=1

[vanoprenko]

https://www.daylight.com/dayhtml/doc/theory/theory.smarts.html

[vanoprenko]

Causes epam/ketcher#3455

[vanoprenko]

Technical details based on investigation:

Payload for layout request:

{
  "struct": "c1-[#6]=[#6]-[#6]=[#6]-[c,n]=1",
  "output_format": "chemical/x-indigo-ket",
  "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
  }
}

Response for layout request:

{
    "format": "chemical/x-indigo-ket",
    "original_format": "chemical/x-daylight-smiles",
    "struct": "{\"root\":{\"nodes\":[{\"$ref\":\"mol0\"}]},\"mol0\":{\"type\":\"molecule\",\"atoms\":[{\"label\":\"C\",\"location\":[0.0,0.0,0.0],\"queryProperties\":{\"aromaticity\":\"aromatic\"}},{\"label\":\"C\",\"location\":[-1.3856407403945923,-0.800000011920929,0.0]},{\"label\":\"C\",\"location\":[-1.3856406211853028,-2.4000000953674318,0.0]},{\"label\":\"C\",\"location\":[1.3987644820190327e-7,-3.200000047683716,0.0]},{\"label\":\"C\",\"location\":[1.3856407403945923,-2.3999998569488527,0.0]},{\"label\":\"C\",\"location\":[1.3856407403945923,-0.8000001907348633,0.0],\"queryProperties\":{\"customQuery\":\"c,n\"}}],\"bonds\":[{\"type\":1,\"atoms\":[0,1]},{\"type\":2,\"atoms\":[1,2]},{\"type\":1,\"atoms\":[2,3]},{\"type\":2,\"atoms\":[3,4]},{\"type\":1,\"atoms\":[4,5]},{\"type\":2,\"atoms\":[5,0]}]}}"
}