Re: [Rdkit-discuss] RDKit, Inchi, Stereochemistry !

2015-02-18 Thread Greg Landrum
On Wed, Feb 18, 2015 at 7:01 PM, Igor Filippov wrote: > > update the bug report and work on tracking down the wrong problem > > That's how I sometimes do it too... ;) > I'll leave it as an exercise to the reader to decide if that was intentional, the fault of auto-correct, or just because it had

Re: [Rdkit-discuss] RDKit, Inchi, Stereochemistry !

2015-02-18 Thread Igor Filippov
> update the bug report and work on tracking down the wrong problem That's how I sometimes do it too... ;) Igor On Wed, Feb 18, 2015 at 12:35 PM, Greg Landrum wrote: > Yep, you guys are right. > I diagnosed that too quickly. > Thanks for pointing out the mistake. > > I'll update the bug report

Re: [Rdkit-discuss] RDKit, Inchi, Stereochemistry !

2015-02-18 Thread Greg Landrum
Yep, you guys are right. I diagnosed that too quickly. Thanks for pointing out the mistake. I'll update the bug report and work on tracking down the wrong problem -greg On Wed, Feb 18, 2015 at 4:58 PM, Markus Sitzmann wrote: > I agree with John, the InChI for mol1 and mol2 should be > > > htt

Re: [Rdkit-discuss] Rdkit-discuss Digest, Vol 88, Issue 15

2015-02-18 Thread Jessica Krause
This message was not meant for the rdkit discussion list. Kindly ignore it and sorry for the inconvenience. On 18.02.2015 16:50, Jessica Krause wrote: > Hey, > > also du ahst es bestimmt schon selber gesehen aber deine Email ging im > RDKit Verteiler rum :) > > Hat also geklappt! > > On 17.02.20

Re: [Rdkit-discuss] RDKit, Inchi, Stereochemistry !

2015-02-18 Thread Markus Sitzmann
I agree with John, the InChI for mol1 and mol2 should be http://cactus.nci.nih.gov/chemical/structure/O=C(NCCc1c1)[C@H]1CC[C@H](Cn2c(O)nc3c3c2=O)CC1/stdinchi InChI=1S/C24H27N3O3/c28-22(25-15-14-17-6-2-1-3-7-17)19-12-10-18(11-13-19)16-27-23(29)20-8-4-5-9-21(20)26-24(27)30/h1-9,18-19H,10-16

Re: [Rdkit-discuss] Rdkit-discuss Digest, Vol 88, Issue 15

2015-02-18 Thread Jessica Krause
Hey, also du ahst es bestimmt schon selber gesehen aber deine Email ging im RDKit Verteiler rum :) Hat also geklappt! On 17.02.2015 17:21, rdkit-discuss-requ...@lists.sourceforge.net wrote: > Send Rdkit-discuss mailing list submissions to > rdkit-discuss@lists.sourceforge.net > > To subsc

Re: [Rdkit-discuss] RDKit, Inchi, Stereochemistry !

2015-02-18 Thread John M
Hi Greg, I believe it's an RDKitMol -> InChI issue rather than InChI -> RDKitMol. The correct InChI (below) is different from that in the iPython listing. InChI=1S/C24H27N3O3/c28-22(25-15-14-17-6-2-1-3-7-17)19-12-10-18(11-13-19)16-27-23(29)20-8-4-5-9-21(20)26-24(27)30/h1-9,18-19H,10-16H2,(H,25,28

Re: [Rdkit-discuss] RDKit compile is successful, but python does see RDKit?

2015-02-18 Thread Stephen O'hagan
Hi, I have it working now. Two problems were causing the errors. 1) I hadn’t fully purged the RDKit libraries from an earlier apt-get install. 2) I had assumed that LD_LIBRARY_PATH being set in the usual places (such as ~/.bashrc) would work. It seems Ubuntu has a “feature” whereby