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
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'
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
, 2014 at 6:30 PM, Gerebtzoff, Gregori
gregori.gerebtz...@roche.comjavascript:_e(%7B%7D,'cvml','gregori.gerebtz...@roche.com');
wrote:
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
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,
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 =
Hi Yingfeng,
Let me remind you some chemistry basics:
Chlorine atom has 17 electrons. In last orbit it has 7 electrons hence it
requires 1 electron to complete octet. Hence it's valency is 1.
Thus it's not a surprise that your smiles is generating an error.
In order to check for get the charge
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
there.
The only problem I see after changing dotsPerAngstrom is that font size
stays the same so again you need to do the math and scale it on your own
(and set atomLabelFontSize accordingly).
Regards,
Michal Nowotka
On Fri, Sep 6, 2013 at 8:15 AM, Gerebtzoff, Gregori
gregori.gerebtz
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
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 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
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