In-line HELM defined using ChemAxon SMILES not connected to other monomers

[ClairePA]

If I use the following HELM strings in the HELM webeditor:

PEPTIDE1{A.[C(=O)[C@H](C)N(*)C |$_;;;;;;;_R1;;;$]}$$$$ PEPTIDE1{A.[C(=O)[C@H](C)N([*])C |$_;;;;;;;_R1;;;$]}$$$$

then it generates disconnected fragments for the structure.

The webeditor should connect the monomer structures to each other.

[scilligence]

1. When display inline monomer, it needs coordinates, which is not implemented in HELM Web Editor in javascript.

2. Currently it calls Web Service to convert SMILES into Molfile. It looks like the web service cannot read R1 from the ChemAxon smiles. If this issue is fixed in web service, could you let us know which version it is fixed. So we can update it.

[scilligence]

I just updated WebService to

Monomerservice 1.1.5 https://oss.sonatype.org/content/repositories/releases/org/pistoiaalliance/helm/helm2-monomerservice/1.1.5/helm2-monomerservice-1.1.5.war Webservice 3.0.2 https://oss.sonatype.org/content/repositories/releases/org/pistoiaalliance/helm/helm2-webservice/3.0.2/helm2-webservice-3.0.2.war

but it still cannot parse R1 correctly. Here is ajax return value: {"SMILES":"C(=O)C@HN([])C |$_;;;;;;;R1;;;$","Molfile":"|$;;;;;;;_R1;;;$\n CDK 11231816022D\n\n 7 6 0 0 1 0 0 0 0 0999 V2000\n 1.2990 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.0000 0.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 2.5981 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0\n 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.8971 -0.7500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 3.8971 -2.2500 0.0000 0 0 0 0 0 0 0 0 0 0 0 0\n 5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 2 0 0 0 0 \n 1 3 1 0 0 0 0 \n 3 4 1 6 0 0 0 \n 3 5 1 0 0 0 0 \n 5 6 1 0 0 0 0 \n 5 7 1 0 0 0 0 \nM END\n"}

[ClairePA]

Markus - could you have a look at this please? I thought CDK supported ChemAxon extended SMILES, so the R groups should be transferred?

[TianhongZhang]

The input cxsmiles is invalid. If you use the following HELM notation, it worked.

PEPTIDE1{A.[CC@@HN(C)[*] |$;;;;;;_R1$|]}$$$$

[ClairePA]

Ah. My bad. Close.