On Tue, Aug 27, 2013 at 10:32 PM, Sergio Martinez Cuesta <
sermar...@gmail.com> wrote:
> Oc(:[nH2]):[nH2] does not seem to be in the database
>
> http://cactus.nci.nih.gov/chemical/structure/Oc(:[nH2]):[nH2]/iupac_name
>
> molcovert does not generate a name either.
>
That's not actually a stable
Oc(:[nH2]):[nH2] does not seem to be in the database
http://cactus.nci.nih.gov/chemical/structure/Oc(:[nH2]):[nH2]/iupac_name
molcovert does not generate a name either.
On 27 August 2013 18:54, Markus Sitzmann wrote:
> **
> Yes, in this direction (structure to name) the Resolver is only a d
Yes, in this direction (structure to name) the Resolver is only a database lookup, in the other direction (name to structure), it first uses OPSIN (Daniel Lowe's library)which can resolve correct IUPAC names generically, if OPSIN "fails" it does a database lookup, too.MarkusNot sure what software
OPSIN wouldn't help very much here, as it deals with the inverse problem, i.e.
name to structure.
George.
Sent from my giPhone
On 27 Aug 2013, at 19:40, Vladimir Chupakhin wrote:
> Hi,
>
> did you tried http://opsin.ch.cam.ac.uk/ ?
>
> Vladimir Chupakhin
>
>
>
> On Tue, Aug 27, 2013 a
Hi,
did you tried http://opsin.ch.cam.ac.uk/ ?
Vladimir Chupakhin
On Tue, Aug 27, 2013 at 6:48 PM, Markus Hartenfeller <
markus.hartenfel...@molecularhealth.com> wrote:
> Hi Sergio,
>
> here is a solution that uses a free web service offered by the NIH.
>
> It's independent of the rdkit but
I think this is not an actual structure to name converter but a look-up service
based on a a predefined dictionary.
If this is true, then it won't return anything for any novel/unseen structures.
Give it a try and let us know.
George.
Sent from my giPhone
On 27 Aug 2013, at 18:39, David Hal
Not sure what software is behind it, but the NCI's Chemical Identifier Resolver
may suit your needs.
For your example, the URL:
http://cactus.nci.nih.gov/chemical/structure/CC(C)O/iupac_name
returns Propan-2-ol
-David
On Aug 27, 2013, at 11:54 AM, Sergio Martinez Cuesta
wrote:
> thanks Gre
Hi Sergio,
here is a solution that uses a free web service offered by the NIH.
It's independent of the rdkit but rather slow. Anyway, if you don't need
to process too many molecules at a time or if time is not the critical
factor maybe it could serve as an intermediate solution:
import urll
thanks Greg,
indeed, I only found commercial software for it
http://www.chemaxon.com/marvin/help/applications/molconvert.html
cheers
Sergio
On 27 August 2013 16:45, Greg Landrum wrote:
> Dear Sergio,
>
>
> On Tue, Aug 27, 2013 at 5:21 PM, Sergio Martinez Cuesta <
> sermar...@gmail.com> wrote
Dear Sergio,
On Tue, Aug 27, 2013 at 5:21 PM, Sergio Martinez Cuesta wrote:
> is there any IUPAC name generator in RDKit?
>
> e.g. for transforming "CC(C)O" into "propan-2-ol" ?
>
>
There is not. In fact, I'm not aware of any open source structure->name
converters.
-greg
--
Hi,
is there any IUPAC name generator in RDKit?
e.g. for transforming "CC(C)O" into "propan-2-ol" ?
Many thanks
Sergio
--
Introducing Performance Central, a new site from SourceForge and
AppDynamics. Performance Central
Thanks to both for the fast and extremely helpful reply!
Gonzalo
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 27 August 2013 16:39
To: rdkit-discuss@lists.sourceforge.net
Cc: Gonzalo Colmenarejo-Sanchez
Subject: Re: [Rdkit-discuss] molecular descriptors in C++
Nick beat me to it (tha
Nick beat me to it (thanks Nick!)
I was going to send the suggestion that a good place to look is the testing
code:
https://github.com/rdkit/rdkit/blob/master/Code/GraphMol/Descriptors/test.cpp
-greg
On Tue, Aug 27, 2013 at 4:32 PM, Nicholas Firth wrote:
> Also to add to my previous email, whe
Hi Gonzalo,
I shamelessly only have an example using PBF. Forgive the slightly dirty C++
coding, but you can get the idea of descriptor calculation.
using namespace std;
using namespace RDKit;
int main(int argc, char *argv[]){
string fileName = argv[1];
SDMolSupplier reader(fileName,
Also to add to my previous email, when I started out with C++ RDKit I found it
really useful to dig into the source code. Especially look through the code
written to test the descriptors, more often than not you can adapt what Greg
and co. have done already to do what you want.
Best,
Nick
Nich
Hi,
I'm trying to calculate molecular descriptors in C++ with the RDKit. Does
anyone have a code example that could help in this case?
Thanks a lot,
Gonzalo Colmenarejo
--
Introducing Performance Central, a new site fr
16 matches
Mail list logo
