In-line HELM monomers are not connected

[ClairePA]

I can add the following HELM to the webeditor and the monomers are displayed as connected.

PEPTIDE1{[C[C@@H](N*)C(*)=O |$;;;_R1;;_R2;;$|].[O=C(*)CN* |$;;_R2;;;_R1;$|]}$$$$V2.0

However, the properties

and structure view

show that they are not connected.,

[scilligence]

The problem is the web service drops R# information when converting SMILES into Molfile:

"http://54.83.135.171/WebService/service/Conversion/Molfile"

Input SMILES:C[C@@H](N*)C(*)=O |$;;;_R1;;_R2;;$|

Output Molfile:

{"SMILES":"C[C@@H](N*)C(*)=O |$;;;_R1;;_R2;;$|","Molfile":"\r\n CDK 0812181436\r\n\r\n 7 6 0 0 0 0 0 0 0 0999 V2000\r\n 0.0000 2.2500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n 1.2990 1.5000 0.0000 C 0 0 1 0 0 0 0 0 0 0 0 0\r\n 2.5981 2.2500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\r\n 3.8971 1.5000 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0\r\n 1.2990 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\r\n -0.0000 -0.7500 0.0000 * 0 0 0 0 0 0 0 0 0 0 0 0\r\n 2.5981 -0.7500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\r\n 2 1 1 1 0 0 0 \r\n 2 3 1 0 0 0 0 \r\n 3 4 1 0 0 0 0 \r\n 2 5 1 0 0 0 0 \r\n 5 6 1 0 0 0 0 \r\n 5 7 2 0 0 0 0 \r\nM END\r\n"}

[ClairePA]

Hi Markus, Could someone have a look at this?

[ClairePA]

It looks like there are two things going on here.

The webservices can take in SMILES without square brackets and will generate an image which has the monomers connected (albeit the free connection points are capped with H rather than being left as stars).

However, the webeditor does not use the webservices to create the atom/bond structure. It relies on the webservices to convert the SMILES to the molfile and then connect the R groups on the molfile. The conversion of SMILES to molfile results in a molfile containing *s, but not numbers therefore is not suitable for connecting up the monomers. It is as if it strips off the ChemAxon section which numbers the connection points.

So are there two choices:

• Either use the webservices to get the atom/bond structure.
• Or fix the SMILES to molfile conversion.

Could someone comment?

[ClairePA]

SMILES to molfile conversion is now fixed and webeditor displays the connected structure. Close.