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()
functi
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 non-hydr
>
> Dear RDKitters,
>
> I'm using Jameed's wonderful code for a matched pair analysis.
>
> Given such a transformation string "[*:1]C>>[*:1][H]"
> => How do I check if [*:1] is an aromatic or an aliphatic atom?
>
>
> I fear that this can only be done by going back into the original
> data/outp
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.
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 i
> Hi -
>
> A RDKit-based implementation of the QED measure as described by
> Richard Bickerton (Nature Chemistry, 2012, 4, 90-98) has been
> implemented and made available for download from our website (
> www.silicos-it.com > Biscu-it).
>
> Regards,
> - Hans
>
>
Hi Hans,
Thanks for the impl
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
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 data
Hi guys,
Is there an easy way to increase the maximal size of a molecule on the
canvas?
I realized that at some point increasing the canvas size won't increase the
size of the molecule anymore.
Looking at the code of MolDrawing.py the function scaleAndCenter seems to
deal with that aspect, I trie
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 wrote:
> Did you check latest (github) version of RDKit? This problem (respecting
> dotsPerAngstrom) should be sol
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 can
t.org/docs/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 AppDy
Hi Toby,
One additional note on what Greg wrote:
you can define another smarts pattern for the identification of rotatable
bonds:
Lipinski.RotatableBondSmarts = Chem.MolFromSmarts("...")
Some smarts from the literature:
Daylight:
[!$(*#*)&!D1&$(*(-[!#1])~[!#1])]-&!@[!$(*#*)&!D1&$(*(-[!#1])~[!#1])
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 =
Chem.MolFromSmar
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
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 wrote:
> Hi Grégori,
>
> It doesn't s
the DB was somehow corrupted, since 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 wrote:
>
>
> On Saturday, March 22, 2014, Gerebtzoff, Gregori <
> gregori.gerebtz...
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
Hi Paul,
You first have to read the MMP into a reaction object
(Chem.ReactionFromSmarts).
Greg
On Friday, May 9, 2014, wrote:
> Dear Gregori & Samo,
>
> thanks for your hints.
>
> I just tried running
>
> Draw.ReactionToImage("[*:1][H]>>[*:1]C")
>
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