Closed ClairePA closed 6 years ago
Web Editor depends on HELM Web Service to convert the smiles into molfile. But the web services doesn't return R1/R2. The web service is:
http://54.91.164.146/WebService/service/Conversion/Molfile
And it returns:
` CDK 0222181427
8 7 0 0 0 0 0 0 0 0999 V2000 0.0000 0.0000 0.0000 0 0 0 0 0 0 0 0 0 0 0 0 1.2990 -0.7500 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1.2990 -2.2500 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0 2.5981 -0.0000 0.0000 C 0 0 2 0 0 0 0 0 0 0 0 0 2.5981 1.5000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 3.8971 -0.7500 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0 3.8971 -2.2500 0.0000 0 0 0 0 0 0 0 0 0 0 0 0 5.1962 -0.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0 1 2 1 0 0 0 0 2 3 2 0 0 0 0 2 4 1 0 0 0 0 4 5 1 6 0 0 0 4 6 1 0 0 0 0 6 7 1 0 0 0 0 6 8 1 0 0 0 0 M END `
Hi Markus,
is this something you could look at?
Square brackets are currently mandatory around the symbol. If you paste the following HELM into the editor: `PEPTIDE1{A.[[]C(=O)C@HN([*])C |$_R2;;;;;;_R1;;;$|].A}$$$$V2.0`
this will be automaticall converted into
PEPTIDE1{A.[[[R1]]C(=O)[C@H](C)N([R2])C].A}$$$$V2.0
but editor is not able to show the structure again. I guess the two square brackets around R1 are the problem. Manually removing one square bracket around R1 gives correkt structure. Is the conversion done by toolkit?
Markus, could you wrap the HELM string in GitHub code format? Otherwise the text is escaped. Thanks.
I guess Markus is using this HELM string:
PEPTIDE1{A.[[*]C(=O)[C@H](C)N([*])C |$_R2;;;;;;_R1;;;$|].A}$$$$V2.0
It does works. Here is what I see:
PEPTIDE1{A.[[*]C(=O)[C@H](C)N([*])C |$_R2;;;;;;_R1;;;$|].A}$$$$V2.0
works for me too.
However, I go back to Roger's point that it should be valid to use with no square brackets since it is part of the SMILES definition. By the way, if I change to:
`PEPTIDE1{A.[[:2]C(=O)C@HN([*:1])C |$_R2;;;;;;_R1;;;$|].A}$$$$V2.0`
I get
which is better than the structure in the comment above.
How much effort is it to allow * with no square brackets?
Retested. The test HELM string still results in disconnected monomers.
See the examples below. When *
is used instead of [*]
it is accepted as valid, but not handled correctly meaning that the monomers are not attached in the structure. You can see this where I have used and [] in different parts of this SMILES below.
Actually all these SMILES should be acceptable.
PEPTIDE1{A.[*C(=O)[C@H](C)N(*)C |$_R2;;;;;;_R1;;;$|].A}$$$$V2.0
PEPTIDE1{A.[[*]C(=O)[C@H](C)N(*)C |$_R2;;;;;;_R1;;;$|].A}$$$$V2.0
PEPTIDE1{A.[*C(=O)[C@H](C)N*C |$_R2;;;;;;_R1;;;$|].A}$$$$V2.0
PEPTIDE1{A.[[*]C(=O)[C@H](C)N([*])C |$_R2;;;;;;_R1;;;$|].A}$$$$V2.0
The canvas view looks fine.
The example no. 3 is missing a pair of brakets: PEPTIDE1{A.[C(=O)C@HN()C |$_R2;;;;;;_R1;;;$|].A}$$$$V2.
Beside that, all examples are valid in toolkit and generated structure images look good.
I am using http://54.83.135.171/WebService/FirstPage.html and the images are still wrong.
Tony, can you check that the latest version of the webservices are being used on this site please?
Thanks.
See circulated spreadsheet for expected behaviour.
Duplicate of #210. Close here and continue the discussion on that issue.
I can enter the following HELM string
PEPTIDE1{A.[*C(=O)[C@H](C)N(*)C |$_R2;;;;;;_R1;;;$|].A}$$$$V2.0
but the in-line monomer is not connected to anything.