PistoiaHELM / HELMWebEditor

Web browser based editor for drawing HELM macromolecules.
MIT License
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Repeating single CHEM monomer is incorrectly invalid #188

Closed ClairePA closed 6 years ago

ClairePA commented 6 years ago

Single monomers with brackets are valid and accepted by the webeditor.

PEPTIDE1{A'11'}$$$$V2.0 image

but I draw the following image

the correct HELM is generated CHEM1{[Az]'11'}$$$$V2.0 and the HELM a molecule properties are calculated.

However, if I clear the editor and paste in the HELM string CHEM1{[Az]'11'}$$$$V2.0 and click Apply, only one monomer is displayed: image and the HELM string is changed to CHEM1{[Az]}$$$$V2.0

The webservices state that CHEM1{[Az]'11'}$$$$V2.0 is invalid HELM.

MarkusWeisser commented 6 years ago

Repeating units cannot be used with CHEM monomers, only with RNA or PEPTIDE monomers. The reason for that is that CHEM monomers have not a defined connection order (R1 goes to R2) for automatically creating polymers. This should be mentioned in the HELM specification and the Editor should show the parser error.

ClairePA commented 6 years ago

Thanks Markus - you are completely right.

I have updated the spec. The issue about the editor showing the parser error is wider than just this issue and will be taken up elsewhere.