Ok so I got out my test set of 6,940,083 molecules. First, I generated the
inchi using 2014_09_2. I then checked out (and built) the master (with
Greg's latest commits) from github and regenerated the inchis for all these
molecules.
3,257 molecules (of 6,940,083) gave me a different inchis between the
current production version and the development (github) one.
For these 3,257 molecules I hammered the
http://cactus.nci.nih.gov/chemical/structure/%s/stdinchi site and assumed
this to be the 'correct' inchi (those great guys will have an interesting
spike in their web traffic last Fri evening). In 6 (out of 3,257) cases we
get different Inchis from cactus.nci.nih.gov vs RDKit github development
version (2015.03.1pre).
Here is the list (first inchi is the 2014_09_2, second one is the
2015.03.1pre generated one, third inchi is the cactus.nci.nih.gov):
O=C(/N=c1/[nH]ncs1)[C@H]1CC[C@H](Cn2cnc3ccccc3c2=O)CC1
MPQBIWRBISQCLJ-BETUJISGSA-N MPQBIWRBISQCLJ-JOCQHMNTSA-N
InChI=1S/C18H19N5O2S/c24-16(21-18-22-20-11-26-18)13-7-5-12(6-8-13)9-23-10-19-15-4-2-1-3-14(15)17(23)25/h1-4,10-13H,5-9H2,(H,21,22,24)/t12-,13+
# RDKit 2014_09_2
InChI=1S/C18H19N5O2S/c24-16(21-18-22-20-11-26-18)13-7-5-12(6-8-13)9-23-10-19-15-4-2-1-3-14(15)17(23)25/h1-4,10-13H,5-9H2,(H,21,22,24)/t12-,13-
# RDKit 2015.03.1pre
InChI=1S/C18H29N5O2S/c24-16(21-18-22-20-11-26-18)13-7-5-12(6-8-13)9-23-10-19-15-4-2-1-3-14(15)17(23)25/h12-15,19-20H,1-11H2,(H,21,22,24)/t12-,13-,14?,15?
# cactus.nci.nih.gov
O=C(/N=c1\[nH]c(-c2ccccn2)cs1)[C@H]1CC[C@H](Cn2cnc3ccccc3c2=O)CC1
CZKXHWCYFFXKGH-CALCHBBNSA-N CZKXHWCYFFXKGH-QAQDUYKDSA-N
InChI=1S/C24H23N5O2S/c30-22(28-24-27-21(14-32-24)20-7-3-4-12-25-20)17-10-8-16(9-11-17)13-29-15-26-19-6-2-1-5-18(19)23(29)31/h1-7,12,14-17H,8-11,13H2,(H,27,28,30)/t16-,17+
InChI=1S/C24H23N5O2S/c30-22(28-24-27-21(14-32-24)20-7-3-4-12-25-20)17-10-8-16(9-11-17)13-29-15-26-19-6-2-1-5-18(19)23(29)31/h1-7,12,14-17H,8-11,13H2,(H,27,28,30)/t16-,17-
InChI=1S/C24H39N5O2S/c30-22(28-24-27-21(14-32-24)20-7-3-4-12-25-20)17-10-8-16(9-11-17)13-29-15-26-19-6-2-1-5-18(19)23(29)31/h16-21,25-26H,1-15H2,(H,27,28,30)/t16-,17-,18?,19?,20?,21?
CCOC(=O)Cc1cs/c(=N/C(=O)[C@H]2CC[C@H](Cn3cnc4ccccc4c3=O)CC2)[nH]1
GAXCPQSXDNGSQV-IYBDPMFKSA-N GAXCPQSXDNGSQV-WKILWMFISA-N
InChI=1S/C23H26N4O4S/c1-2-31-20(28)11-17-13-32-23(25-17)26-21(29)16-9-7-15(8-10-16)12-27-14-24-19-6-4-3-5-18(19)22(27)30/h3-6,13-16H,2,7-12H2,1H3,(H,25,26,29)/t15-,16+
InChI=1S/C23H26N4O4S/c1-2-31-20(28)11-17-13-32-23(25-17)26-21(29)16-9-7-15(8-10-16)12-27-14-24-19-6-4-3-5-18(19)22(27)30/h3-6,13-16H,2,7-12H2,1H3,(H,25,26,29)/t15-,16-
InChI=1S/C23H36N4O4S/c1-2-31-20(28)11-17-13-32-23(25-17)26-21(29)16-9-7-15(8-10-16)12-27-14-24-19-6-4-3-5-18(19)22(27)30/h15-19,24H,2-14H2,1H3,(H,25,26,29)/t15-,16-,17?,18?,19?
COCc1n[nH]/c(=N/C(=O)[C@H]2CC[C@H](Cn3cnc4ccccc4c3=O)CC2)s1
YVZJPKUMKXPZTK-OKILXGFUSA-N YVZJPKUMKXPZTK-HDJSIYSDSA-N
InChI=1S/C20H23N5O3S/c1-28-11-17-23-24-20(29-17)22-18(26)14-8-6-13(7-9-14)10-25-12-21-16-5-3-2-4-15(16)19(25)27/h2-5,12-14H,6-11H2,1H3,(H,22,24,26)/t13-,14+
InChI=1S/C20H23N5O3S/c1-28-11-17-23-24-20(29-17)22-18(26)14-8-6-13(7-9-14)10-25-12-21-16-5-3-2-4-15(16)19(25)27/h2-5,12-14H,6-11H2,1H3,(H,22,24,26)/t13-,14-
InChI=1S/C20H33N5O3S/c1-28-11-17-23-24-20(29-17)22-18(26)14-8-6-13(7-9-14)10-25-12-21-16-5-3-2-4-15(16)19(25)27/h13-17,21,23H,2-12H2,1H3,(H,22,24,26)/t13-,14-,15?,16?,17?
COC(=O)c1[nH]/c(=N\C(=O)[C@H]2CC[C@H](Cn3cnc4ccccc4c3=O)CC2)sc1C(C)C
KNDSLDLCZNAXPK-IYBDPMFKSA-N KNDSLDLCZNAXPK-WKILWMFISA-N
InChI=1S/C24H28N4O4S/c1-14(2)20-19(23(31)32-3)26-24(33-20)27-21(29)16-10-8-15(9-11-16)12-28-13-25-18-7-5-4-6-17(18)22(28)30/h4-7,13-16H,8-12H2,1-3H3,(H,26,27,29)/t15-,16+
InChI=1S/C24H28N4O4S/c1-14(2)20-19(23(31)32-3)26-24(33-20)27-21(29)16-10-8-15(9-11-16)12-28-13-25-18-7-5-4-6-17(18)22(28)30/h4-7,13-16H,8-12H2,1-3H3,(H,26,27,29)/t15-,16-
InChI=1S/C24H38N4O4S/c1-14(2)20-19(23(31)32-3)26-24(33-20)27-21(29)16-10-8-15(9-11-16)12-28-13-25-18-7-5-4-6-17(18)22(28)30/h14-20,25H,4-13H2,1-3H3,(H,26,27,29)/t15-,16-,17?,18?,19?,20?
CC(C)[C@H]1CC[C@H](C(=O)N[C@H](Cc2ccccc2)C(=O)/N=c2\[nH]ncs2)CC1
OKTRHZCAACPPLC-FGTMMUONSA-N OKTRHZCAACPPLC-KZNAEPCWSA-N
InChI=1S/C21H28N4O2S/c1-14(2)16-8-10-17(11-9-16)19(26)23-18(12-15-6-4-3-5-7-15)20(27)24-21-25-22-13-28-21/h3-7,13-14,16-18H,8-12H2,1-2H3,(H,23,26)(H,24,25,27)/t16-,17+,18-/m1/s1
InChI=1S/C21H28N4O2S/c1-14(2)16-8-10-17(11-9-16)19(26)23-18(12-15-6-4-3-5-7-15)20(27)24-21-25-22-13-28-21/h3-7,13-14,16-18H,8-12H2,1-2H3,(H,23,26)(H,24,25,27)/t16-,17-,18-/m1/s1
InChI=1S/C21H36N4O2S/c1-14(2)16-8-10-17(11-9-16)19(26)23-18(12-15-6-4-3-5-7-15)20(27)24-21-25-22-13-28-21/h14-18,22H,3-13H2,1-2H3,(H,23,26)(H,24,25,27)/t16-,17-,18-/m1/s1
I have looked at these molecules in MarvinSketch to try to figure out why
different inchis are being generated. Perhaps there is a problem in RDKit
which is always detecting one of the rings as aromatic (the Inchi doesn't
seem to agree on the aromaticity).
I hope this is helpful.
JP
-
Jean-Paul Ebejer
Early Stage Researcher
On 20 February 2015 at 08:00, Greg Landrum <greg.land...@gmail.com> wrote:
> A general comment/request:
> One of the great things about the RDKit community, including this mailing
> list, is how supportive and helpful people are. In contrast to many online
> communities it's a friendly place and I think that's great.
>
> This thread is starting to get a bit aggressive in tone... please keep an
> eye on that.
>
> -greg
>
>
>
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