No structure preview with inline SMILES

[MarkusWeisser]

Using inline smiles shows a symbol #1 on the canvas. No structure is displayed on mouse over.

[scilligence]

HELM Editor itself cannot parse SMILES, so it has to use web service to call server side to convert SMILES into molfile. The lookupurl parameter is used for this purpose

[scilligence]

            var args = {
                // ...
                cleanupurl: "??????" // web service to clean up structures
            };

            org.helm.webeditor.Adapter.startApp("div1", args);

[ClairePA]

This is not quattro's responsibility to fix. If the editor needs this function then Scilligence needs to write it. I do not mind whether it is a front or backend function but it is Scilligence's responsibility in either case.

[scilligence]

HELM web editor won't be able to parse SMILES - it is huge amount work to re-implement this using javascript.

The editor is ready to call a web service to convert SMILES into molfile. We can demo this using our web service.

[ClairePA]

OK, thanks. I look forward to seeing your new webservice in action. I assume you will combine the changes with the HELM webservice?

It is good to get this sorted out since the structure view is also affected.

[scilligence]

Need the backend web service to convert smiles into molfile

[scilligence]

Using new WAR file, and it is working now.

[ClairePA]

The tool tip looks good now.

However when I select the two monomer molecule to display in the structure view, I get an error.

[scilligence]

Fixed now

[ClairePA]

It does not crash now, and does display the structures, but the monomers are not connected together.

[scilligence]

I cannot reproduce it. Could you upload the HELM notation you are using?

[ClairePA]

PEPTIDE1{[C@HCc1ccc(cc1)F |$;;;_R2;;;;;;;;$|].[Hse]}$$$$V2.0

[scilligence]

This is ChemAxon smiles, and I don't think CDK can read it.

[ClairePA]

Something is reading it since the structure is displayed. It looks more like there is an issue with the connection points not being understood.

[scilligence]

Fixed in 2018-01-08 update. It converts the ChemAxon SMILES into CDK acceptable smiles.

[ClairePA]

Now I get the following error using the HELM above:

[scilligence]

Remember to copy the HELM string in editing mode:

PEPTIDE1{[[C@H](C(=O)*)Cc1ccc(cc1)F |$;;;_R2;;;;;;;;$|].[Hse]}$$$$V2.0

[ClairePA]

OK, looks fine.