Incorrect structure generated for repeating units

[ClairePA]

I draw the following:

The structure is hard to see: and generates the following molfile.

   JSDraw204261815252D

 12 11  0  0  1  0              0 V2000
   16.2010   -7.4359    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5519   -8.2160    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   18.9030   -7.4361    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   17.5518   -9.7759    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   18.9031   -5.8761    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   16.2010  -10.5559    0.0000 R#  0  0  0  0  0  0  0  0  0  0  0  0
   21.6054   -5.8765    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   21.6050   -7.4366    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   22.9559   -8.2167    0.0000 C   0  0  0  0  0  0  0  0  0  0  0  0
   20.2540   -8.2161    0.0000 N   0  0  0  0  0  0  0  0  0  0  0  0
   24.3070   -7.4372    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
   22.9556   -9.7768    0.0000 O   0  0  0  0  0  0  0  0  0  0  0  0
  2  1  1  1  0  0  0
  4  2  1  0  0  0  0
  2  3  1  0  0  0  0
  3  5  2  0  0  0  0
  3 10  1  0  0  0  0
  4  6  1  0  0  0  0
  8  7  1  1  0  0  0
 10  8  1  0  0  0  0
  8  9  1  0  0  0  0
  9 11  2  0  0  0  0
  9 12  1  0  0  0  0
A    6
R1
M  RGP  1   6   1
M  END

and SMILES is C[C@H](N[H])C(=O)N[C@@H](C)C(=O)N[C@@H](C)C(=O)O.C[C@H](N*)C(=O)O

importing into PubChem Sketcher and moving the overlapping atoms gives:

So one of the repeating units is not attached.

[MarkusWeisser]

Toolkit is not able to create SMILES or Molfile from HELM with reating units.

[ClairePA]

Why not? They are exact structures and should be generated.

[MarkusWeisser]

Yes, there is no technical reason for this limitation.

[ClairePA]

Please would you change the toolkit to generate the SMILES and molfile from HELM with repeating units?

[ClairePA]

Discussed with Yohann. Novartis are interested in using repeating units and would prefer this to be fixed.

[ClairePA]

Retested and the issue is still present.

[AnneMund]

I cannot reproduce the issue; if I try out the image generation on the WebService side for PEPTIDE1{A.D'2'.C.F}$$$$V2.0, I get the following:

If I generate SMILES instead and put them into the PubChem Sketcher, I get which results in

Could it be that the re-test happended with an older version of the WebService still in place?

[ClairePA]

It looks like you are right. When I test on http://54.83.135.171/WebService/FirstPage.html I get the right structure, but if I use the webeditor on the same server I get disconnected structures. So, the conclusion is that the webservices are now working correctly, but the webeditor is creating its own structure and it is resulting in disconnected structures.

Reassigning this issue to Tony.

[ClairePA]

Actually I have retested with more examples and the webservices version works for peptides, but not for CHEM and RNA. Try the examples below: CHEM1{[Az]'11'}$$$$V2.0 RNA1{R'11'}$$$$V2.0 So both the webeditor and the webservices still need fixing.

[ClairePA]

Converting these issues into new separate issue logs as there are several things going on. Closing this log.