epam / Indigo

Universal cheminformatics toolkit, utilities and database search tools
http://lifescience.opensource.epam.com
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Conversion from MDL file format to Extended SMILES format replaces R pseudoatom with R# (RGroup) #380

Open StartsevDS opened 3 years ago

StartsevDS commented 3 years ago

R_pseudoatom_ketcher.zip

Steps to reproduce:

  1. Call "convert" endpoint with output_format = "chemical/x-chemaxon-cxsmiles" and struct = "\n Ketcher 3262114322D 1 1.00000 0.00000 0\n\n 1 0 0 0 0 999 V2000\n 1.0250 -1.1500 0.0000 R 0 0 0 0 0 0 0 0 0 0 0 0\nM END\n" ("struct" value is taken from the attached MOL file);
  2. Save received response: {"format": "chemical/x-chemaxon-cxsmiles","struct": "[*]"};
  3. Call "layout" endpoint with output_format = "chemical/x-mdl-molfile" and struct = "[*]" . Note values of "struct" on this step and on previous step are equal;
  4. Examine value of "struct" in response to step 3: "\n -INDIGO-03262111472D\n\n 1 0 0 0 0 0 0 0 0 0999 V2000\n 0.0000 0.0000 0.0000 R# 0 0 0 0 0 0 0 0 0 0 0 0\nM END\n" .

Actual result: "R" label of pseudoatom in request on step 1 is replaced with "R#"

Expected result: "R" label of pseudoatom should not be replaced as a result of conversion from MDL Molfile format to Extended SMILES format.

StartsevDS commented 3 years ago

Related issue: https://github.com/epam/ketcher/issues/40