GLaDOS
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Published
20 hours ago •
chembl
chembl
SMILES searches in search bar versus structure search
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
@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.
