Thanks for these. I will try to take a look in the not-too-distant future
and see if I can figure out what is going on.
-greg
On Monday, February 23, 2015, JP <jeanpaul.ebe...@inhibox.com> wrote:
> 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
> <javascript:_e(%7B%7D,'cvml','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
>>
>>
>>
>> ------------------------------------------------------------------------------
>> Download BIRT iHub F-Type - The Free Enterprise-Grade BIRT Server
>> from Actuate! Instantly Supercharge Your Business Reports and Dashboards
>> with Interactivity, Sharing, Native Excel Exports, App Integration & more
>> Get technology previously reserved for billion-dollar corporations, FREE
>>
>> http://pubads.g.doubleclick.net/gampad/clk?id=190641631&iu=/4140/ostg.clktrk
>> _______________________________________________
>> Rdkit-discuss mailing list
>> Rdkit-discuss@lists.sourceforge.net
>> <javascript:_e(%7B%7D,'cvml','Rdkit-discuss@lists.sourceforge.net');>
>> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
>>
>>
>
------------------------------------------------------------------------------
Dive into the World of Parallel Programming The Go Parallel Website, sponsored
by Intel and developed in partnership with Slashdot Media, is your hub for all
things parallel software development, from weekly thought leadership blogs to
news, videos, case studies, tutorials and more. Take a look and join the
conversation now. http://goparallel.sourceforge.net/
_______________________________________________
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
