MAINT: improve error with SMILES

gruenewald-lab / CGsmiles

Coarse-Grained Smiles (CGsmiles) for representing abitrarily complex molecules using a compact line notation

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MAINT: improve error with SMILES #28

Open tylerjereddy opened 2 weeks ago

tylerjereddy commented 2 weeks ago

The error message when processing conventional SMILES strings can be confusing, as observed at: https://github.com/marrink-lab/polyply_1.0/issues/390#issuecomment-2455472121
For cases like that where there are no polymeric fragments (i.e., no use of braces), this patch improves the error message (and adds a test for it) to nudge the user to BigSMILES or CGSmiles formats.

tylerjereddy commented 2 weeks ago

I pushed a commit that attempts to resolve the first round of review comments.

Also, I noticed that test_syntax_errors wasn't actually verifying that the error message strings matched, so I went ahead and fixed that by using the canonical match=.. syntax, and that now correctly enforces matching error strings (I fixed one small issue that slipped through previously because of this).