Open Emma-Manners opened 4 years ago
@eloyfelix The error seems to be when it calls the ctab2smiles endpoint. You can reproduce it with this command:
curl 'https://www.ebi.ac.uk/chembl/api/utils/ctab2smiles' \
-H 'Connection: keep-alive' \
-H 'Pragma: no-cache' \
-H 'Cache-Control: no-cache' \
-H 'Accept: */*' \
-H 'X-Requested-With: XMLHttpRequest' \
-H 'User-Agent: Mozilla/5.0 (Macintosh; Intel Mac OS X 10_15_4) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/81.0.4044.122 Safari/537.36' \
-H 'Content-Type: multipart/form-data; boundary=----WebKitFormBoundaryOyI4BbAWuRexqLss' \
-H 'Origin: https://www.ebi.ac.uk' \
-H 'Sec-Fetch-Site: same-origin' \
-H 'Sec-Fetch-Mode: cors' \
-H 'Sec-Fetch-Dest: empty' \
-H 'Referer: https://www.ebi.ac.uk/chembl/' \
-H 'Accept-Language: es,en-GB;q=0.9,en;q=0.8,en-US;q=0.7,gl;q=0.6' \
-H 'Cookie: chembl_sketcher=marvinjs; _ga=GA1.3.12510205.1475154173; _ga=GA1.1.12510205.1475154173; marvinjs=<cml><MDocument><MChemicalStruct><molecule molID="m1"><atomArray><atom id="a1" elementType="C" x2="-1.49333332139" y2="0"/><atom id="a2" elementType="C" x2="-0.746666660693" y2="-1.29322665632"/><atom id="a3" elementType="C" x2="0.746666660693" y2="-1.29322665632"/><atom id="a4" elementType="C" x2="1.49333332139" y2="0"/><atom id="a5" elementType="C" x2="0.746666660693" y2="1.29322665632"/><atom id="a6" elementType="C" x2="-0.746666660693" y2="1.29322665632"/><atom id="a7" elementType="C" x2="2.98666664277" y2="0"/><atom id="a8" elementType="C" x2="3.73333330347" y2="-1.29322665632"/><atom id="a9" elementType="C" x2="5.22666662485" y2="-1.29322665632"/><atom id="a10" elementType="C" x2="5.97333328555" y2="0"/><atom id="a11" elementType="C" x2="5.22666662485" y2="1.29322665632"/><atom id="a12" elementType="C" x2="3.73333330347" y2="1.29322665632"/><atom id="a13" elementType="C" x2="-2.98666664277" y2="0"/><atom id="a14" elementType="C" x2="-3.73333330347" y2="1.29322665632"/><atom id="a15" elementType="C" x2="-5.22666662485" y2="1.29322665632"/><atom id="a16" elementType="C" x2="-5.97333328555" y2="0"/><atom id="a17" elementType="C" x2="-5.22666662485" y2="-1.29322665632"/><atom id="a18" elementType="C" x2="-3.73333330347" y2="-1.29322665632"/></atomArray><bondArray><bond atomRefs2="a1 a2" order="2"/><bond atomRefs2="a2 a3" order="1"/><bond atomRefs2="a3 a4" order="2"/><bond atomRefs2="a4 a5" order="1"/><bond atomRefs2="a5 a6" order="2"/><bond atomRefs2="a6 a1" order="1"/><bond atomRefs2="a7 a8" order="2"/><bond atomRefs2="a8 a9" order="1"/><bond atomRefs2="a9 a10" order="2"/><bond atomRefs2="a10 a11" order="1"/><bond atomRefs2="a11 a12" order="2"/><bond atomRefs2="a12 a7" order="1"/><bond atomRefs2="a4 a7" order="1"/><bond atomRefs2="a13 a14" order="2"/><bond atomRefs2="a14 a15" order="1"/><bond atomRefs2="a15 a16" order="2"/><bond atomRefs2="a16 a17" order="1"/><bond atomRefs2="a17 a18" order="2"/><bond atomRefs2="a18 a13" order="1"/><bond atomRefs2="a1 a13" order="1"/></bondArray></molecule></MChemicalStruct></MDocument></cml>; experimentation_subject_id=IjE0ZTlkM2ExLTc3YTQtNDQwOC04N2NhLWI1OGRmODU1ODMzNSI%3D--efad8bd2673c3b9d66dfb63fb694f9f6cd604d85; __utma=222765775.12510205.1475154173.1553781848.1579009629.8; __utmz=222765775.1579009629.8.1.utmcsr=(direct)|utmccn=(direct)|utmcmd=(none); cookies-accepted=true; cookies-accepted=true; csrftoken=kGlxsmFb6Y3FduzPJTQMcYAOXRnt6TpKqzDnOYOayVTsFyBykGjNFsv16NHs0nCZ; mywork.tab.tasks=false; chembl-website-v0.2-data-protection-accepted=true; __atuvc=0%7C12%2C0%7C13%2C0%7C14%2C0%7C15%2C1%7C16; _gid=GA1.3.2082011833.1587999822; _gat_gtag_UA_137029308_1=1' \
--data-binary $'------WebKitFormBoundaryOyI4BbAWuRexqLss\r\nContent-Disposition: form-data; name="file"; filename="molecule.mol"\r\nContent-Type: chemical/x-mdl-molfile\r\n\r\n\n MJ182100 \n\n 34 37 0 0 0 0 0 0 0 0999 V2000\n -0.4340 -1.0013 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -1.3004 -0.5019 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.3012 0.4980 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4356 0.9986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4364 1.9986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.3028 2.4980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.1684 1.9972 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -3.0348 2.4966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -3.0356 3.4966 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.1700 3.9974 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -1.3036 3.4980 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.4291 2.4994 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 0.4283 3.4994 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4380 3.9988 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -0.4388 4.9986 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n 0.4307 0.4994 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.4315 -0.5005 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2979 -0.9999 0.0000 N 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2987 -2.0000 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 0.4332 -2.5006 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 2.1651 -2.4991 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.0308 -1.9986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.8972 -2.4977 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.8980 -3.4978 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.0324 -3.9986 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 3.0332 -4.9986 0.0000 Br 0 0 0 0 0 0 0 0 0 0 0 0\n 2.1659 -3.4992 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1.2963 1.0000 0.0000 O 0 0 0 0 0 0 0 0 0 0 0 0\n -2.1660 -1.0027 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -3.0324 -0.5033 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -3.8980 -1.0041 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -3.8972 -2.0040 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -3.0308 -2.5033 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n -2.1652 -2.0025 0.0000 C 0 0 0 0 0 0 0 0 0 0 0 0\n 1 2 2 0 0 0 0\n 2 3 1 0 0 0 0\n 3 4 1 0 0 0 0\n 4 5 1 0 0 0 0\n 5 6 4 0 0 0 0\n 6 7 4 0 0 0 0\n 7 8 4 0 0 0 0\n 8 9 4 0 0 0 0\n 9 10 4 0 0 0 0\n 10 11 4 0 0 0 0\n 5 12 4 0 0 0 0\n 12 13 4 0 0 0 0\n 13 14 4 0 0 0 0\n 14 15 2 0 0 0 0\n 4 16 1 0 0 0 0\n 16 17 1 0 0 0 0\n 17 18 1 0 0 0 0\n 18 19 2 0 0 0 0\n 19 20 1 0 0 0 0\n 19 21 1 0 0 0 0\n 21 22 4 0 0 0 0\n 22 23 4 0 0 0 0\n 23 24 4 0 0 0 0\n 24 25 4 0 0 0 0\n 25 26 1 0 0 0 0\n 25 27 4 0 0 0 0\n 16 28 2 0 0 0 0\n 2 29 1 0 0 0 0\n 29 30 4 0 0 0 0\n 30 31 4 0 0 0 0\n 31 32 4 0 0 0 0\n 32 33 4 0 0 0 0\n 33 34 4 0 0 0 0\n 11 6 4 0 0 0 0\n 14 11 4 0 0 0 0\n 27 21 4 0 0 0 0\n 34 29 4 0 0 0 0\nM END\n\r\n------WebKitFormBoundaryOyI4BbAWuRexqLss\r\nContent-Disposition: form-data; name="sanitize"\r\n\r\n0\r\n------WebKitFormBoundaryOyI4BbAWuRexqLss--\r\n' \
--compressed
When I try to parse the molblock Marvin generates with RDKit it fails to kekulise. I need to check a bit more on this.
Works in the search bar but not in structure search, I'm not sure why (the vast majority of SMILES work well).
O=C(NC(C(C1=CC=CC=C12)=NNC2=O)C(N/N=C(C)/C3=CC=CC(Br)=C3)=O)C4=CC=CC=C4