Re: [Rdkit-discuss] ReactionFromSmarts and RunReactants

Hi Monica, As Greg stated, why do you expect your product not to be fragmented? I suggest you to have a careful look at the SMARTS definition (for instance from Daylight: http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html) In SMARTS patterns, the dot indicates disconnected fragments.

Re: [Rdkit-discuss] ?==?utf-8?q? Similarity maps using machine learning

Hi, Getting the similarity maps for multiple structures should be straightforward, just add the function call in your loop. Concerning the export of the generated images to a web service, I did the following: (assuming the figure returned by the SimilarityMaps.GetSimilarityMapForModel()

Re: [Rdkit-discuss] ?==?utf-8?q? Doing substructure search as quickly as possible...

Hi Alexis, Knowing what you want to achieve, I would take the problem the other way around. Instead of matching your many fragments to your input structure, I would rather apply the same transformation(s) you apply to your fragments to your input structure. I know that you replace all

Re: [Rdkit-discuss] Getting the list of descriptors

Hi Noel, You might try also the following: dir(Descriptors) The dir() function returns an alphabetized list of names. You can also have a look at the inspect module, especially the getdoc and getargspec functions; these will give you more information on each function. The inspect.isroutine or

[Rdkit-discuss] Capturing warnings

Hi List, Is there a clean way to capture the warnings generated by RDKit, for instance Warning: ring stereochemistry detected. The output SMILES is not canonical? I tried several approaches (the warnings python module, by redirecting the stderr with os.devnull, or try/except) but none of them

[Rdkit-discuss] RDKit cartridge speed issue

Hi RDKitters, I'm facing some performance issue using the RDKit cartridge; the database contains roughly 170k small molecules, I use the cartridge version 0.20.0 on PostgreSQL 8.4.7, and the tanimoto_threshold is set to 0.5 A simple similarity search takes at least 30 seconds to complete. The

Re: [Rdkit-discuss] Size of drawn molecules

Thanks Michal for the hint; I'm currently using the 2013.06.1 version; I'll give a try with the github version. Gregori On 6 September 2013 10:25, Michał Nowotka mmm...@gmail.com wrote: Did you check latest (github) version of RDKit? This problem (respecting dotsPerAngstrom) should be solved

[Rdkit-discuss] Transparency and enhanced molecular depiction

Hello RDKitters, I'm happy to advertise the improved molecular depiction which has just been pulled back in the main RDKit repository. I want to thank Paul Emsley for the preliminary work during the hackathon at the RDKit UGM, and Greg who helped me finalizing the changes, especially for other

Re: [Rdkit-discuss] Compound Neutralization

/GettingStartedInPython.html Best, Gregori -- Rapidly troubleshoot problems before they affect your business. Most IT organizations don't have a clear picture of how application performance affects their revenue. With AppDynamics, you get

Re: [Rdkit-discuss] Possible rotatable bonds replacement

Hi, I would also go for the second option (i.e. replace the current SMART): I also see it as a bug fix. What you could do is to highlight in the release notes or somewhere else the call one would have to do to mimic the behavior of previous releases: Lipinski.RotatableBondSmarts =

[Rdkit-discuss] Problem reading a specific smiles with the cartridge

Hi guys, I've been having problem reading this particular smiles string with the PostgreSQL cartridge: C12CC(C1)C2 I don't know if I'm running the latest version of the cartridge though... Thanks for your help! Grégori cursor.execute(select rdkit_version()) cursor.fetchone() ['0.70.0']

Re: [Rdkit-discuss] Problem reading a specific smiles with the cartridge

Hi Greg, It's just that particular smiles, I don't have any problem reading thousands of other smiles and loading them in the cartridge. Which version of the cartridge do you use? Gregori On Saturday, March 22, 2014, Greg Landrum greg.land...@gmail.com wrote: Hi Grégori, It doesn't seem

Re: [Rdkit-discuss] Problem reading a specific smiles with the cartridge

I got subsequent warnings like null argument to internal routine. Sorry to have bothered you with that! Grégori On 23 March 2014 10:30, Greg Landrum greg.land...@gmail.com wrote: On Saturday, March 22, 2014, Gerebtzoff, Gregori gregori.gerebtz...@roche.com wrote: Hi Greg, It's just

Re: [Rdkit-discuss] Chem.PandasTools

Hi Paul, The Draw modules also contains a ReactionToImage function; Your MMP can be read as a reaction. Hope this helps further! Grégori Date: Thu, 8 May 2014 16:31:32 +0200 From: paul.czodrow...@merckgroup.com Subject: [Rdkit-discuss] Chem.PandasTools To: rdkit-discuss@lists.sourceforge.net

Re: [Rdkit-discuss] Chem.PandasTools

Hi Paul, You first have to read the MMP into a reaction object (Chem.ReactionFromSmarts). Greg On Friday, May 9, 2014, paul.czodrow...@merckgroup.com wrote: Dear Gregori Samo, thanks for your hints. I just tried running Draw.ReactionToImage([*:1][H][*:1]C) = AttributeError: 'str