search

PistoiaHELM / HELMWebEditor

Web browser based editor for drawing HELM macromolecules.
MIT License
18 stars 10 forks source link

Webservices do not cap in-line SMILES #178

Closed ClairePA closed 6 years ago

ClairePA commented 6 years ago

The following HELM

PEPTIDE1{C.G.[[*]N[C@@H](C=O)C([*])=O |$_R1;;;;;;_R2;$|]}$$$$V2.0 Does not generate the correct mol formula. The un-substituted R group is not changed into the capping group.

image

MarkusWeisser commented 6 years ago

Where is the capping group defined?

ClairePA commented 6 years ago

Ah OK, good point. Should we calculate a mol wt / formula at all in this case?

MarkusWeisser commented 6 years ago

I guess it makes sense to not calculate molecular properties from not fully defined structures. I would not recommend to use default values für capping groups. The user should modify the inline SMILES for a fully defined molecule.

ClairePA commented 6 years ago

The HELM team agreed that mol properties should not be calculated for structures with free connection points. This issue is continued via the spreadsheet of in-line HELM test structures. CLose here.