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GLYCAM-Web / gmml

Glycam Molecular Modeling Library
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Test level caught exception: Could not find prep entry for DNeu5Ac Glycam: 0Sa #104

Closed gitoliver closed 1 year ago

gitoliver commented 2 years ago

Test level caught exception: Could not find prep entry for DNeu5Ac Glycam: 0Sa The code should not look for prep files if there is no ring form specified (f or p). The error should be something like: "Ring form not specified in input residue >>>DNeu5Ac<<<".

Lachele commented 2 years ago

Rob requested that NeuNAc and Neu5Ac be accepted as input. The rationale is that these terms are widely used and that the alternate forms (L, p, f) are not generally found in mammalian systems. One of the ideas behind a generic 'sequence' component in GMML is that these bespoke translations can happen there and the real parsing can happen later. I'm not altogether opposed to forcing folks to specify isomer and ring form, but the sequence "DNeu5Aca2-OH" is valid on Actual at glycam.org/txt.

On Fri, Oct 8, 2021 at 5:03 AM gitoliver @.***> wrote:

Test level caught exception: Could not find prep entry for DNeu5Ac Glycam: 0Sa The code should not look for prep files if there is no ring form specified (f or p). The error should be something like: "Ring form not specified in input residue >>>DNeu5Ac<<<".

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gitoliver commented 1 year ago

Not doing this. DNeupNAcb2-OH or DNeup5Acb2-OH is acceptable input, not specifying the ring form will throw an error.