Chemical Structure Conversion: SMILES to URL returns error 500

[lotharwissler]

From the following list, each SMILES receives an InternalServerError (500) when querying the SMILES to URL API method:

ClC1=C(Cl)[C@]2(Cl)C(Cl)(Cl)[C@@]1(Cl)C3C(Cl)C=CC23
Clc1cc(Cl)cc(N2C(=O)[C@]3([C@@](C2=O)(C3)C)C)c1
ClC1=C(Cl)[C@]2(Cl)C(Cl)(Cl)[C@@]1(Cl)C3C2COS(=O)OC3
O=C1NN=C(C1=Cc2ccc(N3CCCC3)cc2)C
Clc1cc(Cl)cc(NC(=O)C2(C(C(=O)O)(C2)C)C)c1
O=C1ON=C(C1=Cc2ccc(N3CCCCC3)cc2)C
O=C1ON=C(c2ccncc2)C1=Cc3ccc(N4CCCC4)cc3
O=C1ON=C(C1=Cc2ccc(N3CCCC3)cc2)Cc4ccccc4
O=C1N(N=C(C1=Cc2ccc(N3CCCC3)cc2)C)c4ccccc4
Oc1ccc(c2cc(c3ccccc3)ccc2)cc1
Oc1ccc(c2c(c3ccccc3)cccc2)cc1
S1C(C(=O)NC1=O)=Cc2cc(Oc3ccccc3)ccc2
ON1N=CC=C1C(c2ccccc2)=C(c3ccccc3)CC
ON1N=CC(C(=C(c2ccccc2)c3ccccc3)CC)=C1
Oc1ccc(c2nc(c(nc2C)c3ccc(O)cc3)C)cc1
Oc1ccc(cc1)C(c2ccc(O)cc2)=C3[C@H]4C[C@@H](C3)CC4
S1C=C(C(=C(c2ccccc2)C=3C=NN(OCCCN(C)C)C3)CC)C=C1
O=C(O)COc1ccc(cc1)C(c2cc(O)ccc2)=C(c3ccccc3)CC
Oc1ccc(c2nc(c3ccc(O)cc3)c(c(n2)Cc4ccc(O)cc4)C)cc1
Oc1ccc(c2nc(c(c(n2)CC)c3ccc(O)cc3)c4ccc(O)cc4)cc1
O=C(N1CCOCC1)C=Cc2ccc(cc2)C3N(c4ccccc4)CCc5c3ccc(O)c5
O=C(O)[C@H](NC(=CC(=O)c1ccccc1)C)Cc2ccc(OCc3ccccc3)cc2
Fc1c(O)c(F)cc([N+]([O-])=O)c1
Fc1c(O)c(F)cc(N2C=CC=C2)c1
S1C(C(=O)NC1=O)=Cc2cc(ccc2)C
S(c1c([N+]([O-])=O)cccc1)c2ccccc2
O=C(O)CC1=NN=C2N(c3c(N2)cccc3)C1=O
S1(=O)(=O)N(C(=O)c2c1c(cc3c2cccc3)C(=O)O)C

[danidi]

I checked some of them and got the following error: Results returned from ChemSpider contain warnings or errors: "Cannot do the convertion. Sorry!"

[ChemConnector]

I checked the first and received a hit on ChemSPider as shown below. The next three also gave hits on ChemSpider…

From: danidi [mailto:notifications@github.com] Sent: Wednesday, November 19, 2014 4:33 AM To: openphacts/GLOBAL Subject: Re: [GLOBAL] Chemical Structure Conversion: SMILES to URL returns error 500 (#214)

I checked some of them and got the following error: Results returned from ChemSpider contain warnings or errors: "Cannot do the convertion. Sorry!"

— Reply to this email directly or view it on GitHub https://github.com/openphacts/GLOBAL/issues/214#issuecomment-63613098 . https://github.com/notifications/beacon/AAmDD8aWJy1LWUlSEJi8g4KXdYB5YMzfks5nPFtJgaJpZM4C9mfd.gif

[karapetk]

Where do these Smiles came from? If they are not in OPS you would get that response.

[danidi]

Actually the exact structure search gives a 404 for the first SMILES. Why do we get a 500 error in SMILES to URL?

[danidi]

Also the InChIKey look up returns a 500 error code if nothing is found. It would be good to be consistent with the rest of the API calls here, which return 404 if nothing is found.

[nicklynch]

See also #7 as these might be related. Where if structure not there it returns an error

This gives ClC1=C(Cl)[C@]2(Cl)C(Cl)(Cl)[C@@]1(Cl)C3C(Cl)C=CC23 the warnings message

Use this same one to query Chemspider ClC1=C(Cl)[C@]2(Cl)C(Cl)(Cl)[C@@]1(Cl)C3C(Cl)C=CC23 you will get this one C1=CC(C2C1[C@@]3(C(=C([C@]2(C3(Cl)Cl)Cl)Cl)Cl)Cl)Cl

Then C1=CC(C2C1[C@@]3(C(=C([C@]2(C3(Cl)Cl)Cl)Cl)Cl)Cl)Cl gives the same error.

[valt]

https://rsc-solutions.atlassian.net/browse/OPS-122