Re: [Rdkit-discuss] Inconsistency between Cartridge and Python

Dear Jan and Greg, many thanks for clearing that up. Best, Daniel Von: Greg Landrum [mailto:greg.land...@gmail.com] Gesendet: Donnerstag, 24. April 2014 05:29 An: rdkit-discuss@lists.sourceforge.net Betreff: Re: [Rdkit-discuss] Inconsistency between Cartridge and Python Hi, On Wed, Apr 23,

[Rdkit-discuss] Sanitization Errors

Hi all, I'm having a dozen of compounds, where some of them have a charged atom (see the attached SMILES file). When I parse the file I get sanitization errors on the compounds with the charged atoms. But when I view them with MarvinView 6.2.0 all goes fine. I'm using an RDKit build from

Re: [Rdkit-discuss] Sanitization Errors

It looks like the problem here is a covalent bond to the counter ion. Pat On Thu, Apr 24, 2014 at 6:04 AM, Christos Kannas chriskan...@gmail.comwrote: Hi all, I'm having a dozen of compounds, where some of them have a charged atom (see the attached SMILES file). When I parse the file I

Re: [Rdkit-discuss] RDKit pharmacophore features

OK, Adding: AllChem.EmbedMolecule(m1) AllChem.UFFOptimizeMolecule(m1) Fixed the problem. Now to work out what it all means! From: Greg Landrum [mailto:greg.land...@gmail.com] Sent: 24 April 2014 04:39 To: Stephen O'hagan Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss]

Re: [Rdkit-discuss] Sanitization Errors

Hi Patrick, Thanks. So the correct would be, sodium should not have an explicit bond with the oxygen. From O=S(c1ccc(C(CCC))cc1)(O-[Na+])=O I should have O=S(c1ccc(C(CCC))cc1)([O-])=O.[Na+] Similar to the rest of my compounds. And regarding nitrogen it already has 4 bonds with

Re: [Rdkit-discuss] RDKit pharmacophore features

On Thursday, April 24, 2014, Stephen O'hagan soha...@manchester.ac.uk wrote: OK, Adding: AllChem.EmbedMolecule(m1) AllChem.UFFOptimizeMolecule(m1) Fixed the problem. Now to work out what it all means! That part is left as an exercise for the reader. ;-) *From:* Greg Landrum

[Rdkit-discuss] [Announcement] 2014 RDKit UGM: October 22nd-24th in Darmstadt

Dear all, I'm very happy to announce the 3rd RDKit User Group Meeting. The meeting, which is being hosted by Paul Czodrowski, will take place October 22nd-24th at Merck in Darmstadt, Germany. Last year's format seemed to work pretty well and the feedback was positive, so we will stick to the

Re: [Rdkit-discuss] Sanitization Errors

Yes, exactly On Thu, Apr 24, 2014 at 7:19 AM, Christos Kannas chriskan...@gmail.comwrote: Hi Patrick, Thanks. So the correct would be, sodium should not have an explicit bond with the oxygen. From O=S(c1ccc(C(CCC))cc1)(O-[Na+])=O I should have

[Rdkit-discuss] ReducedGraphs - now, where is this code ?

Hi Rdkitters, A colleague of mine has stumbled upon this page: http://www.rdkit.org/Python_Docs/rdkit.Chem.rdReducedGraphs-module.html And so he asked me how to use it, because he couldn't find it. Neither can I, not even in the latest git version. Is this a special secret feature :-) ?

Re: [Rdkit-discuss] ReducedGraphs - now, where is this code ?

On Thursday, April 24, 2014, Jan Holst Jensen j...@biochemfusion.com wrote: Hi Rdkitters, A colleague of mine has stumbled upon this page: http://www.rdkit.org/Python_Docs/rdkit.Chem.rdReducedGraphs-module.html Weird, that shouldn't be there. I wonder how that happened. And so he asked

[Rdkit-discuss] change behaviour of mailing list

Hi, I don't find a propties or options for the mailing list. Is it possible to get the mails forwarded and not combined in one email as attachments? best Soren -- Start Your Social Network Today - Download eXo Platform

Re: [Rdkit-discuss] change behaviour of mailing list

Hi Soren, On Fri, Apr 25, 2014 at 3:25 AM, Soren Wacker swac...@ucalgary.ca wrote: I don't find a propties or options for the mailing list. Is it possible to get the mails forwarded and not combined in one email as attachments? If you go here: