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Webeditor does not connect monomers in brackets #231

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ClairePA opened this issue Nov 5, 2018 · 4 comments
Open

Webeditor does not connect monomers in brackets #231

ClairePA opened this issue Nov 5, 2018 · 4 comments
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@ClairePA
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ClairePA commented Nov 5, 2018

I enter the following HELM and click apply

PEPTIDE1{C'2'.A}$$$$V2.0

The HELM diagram is shown correctly

image

but the repeated cystine is not connected:

image

This means the mol wt and formula are wrong.

I was using http://54.83.135.171/HELM2MonomerService/hwe/examples/App.htm

@scilligence
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The problem is the web service don't return R1 in the molfile:
http://54.83.135.171/WebService/service/Conversion/Molfile

{"SMILES":"C(=O)C@HN([*])C |$_;;;;;;;R1;;;$","Molfile":"|$;;;;;;;_R1;;;$\n CDK 11201819012D\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
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Why are you converting SMILES to molfile and not picking up the molfile from the monomer definition?

@TianhongZhang
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For this particular example, can you just convert
PEPTIDE1{C'2'.A}$$$$V2.0
to
PEPTIDE1{C.C.A}$$$$V2.0
then show the structure?

@ClairePA
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I don't see why not internally, but we should see PEPTIDE1{C'2'.A}$$$$V2.0 displayed in the HELM box. Otherwise it doesn't look like we support the notation and we need to be able to generate the bracket notation from a drawing.

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