It appears that Eclipse PyDev code completion and syntax colouring was fooling
me!
Get3DDistanceMatrix is flagged as “undefined”, but code runs just fine!?
Cheers,
Steve.
From: Greg Landrum [mailto:greg.land...@gmail.com]
Sent: 08 May 2014 02:52
To: Stephen O'hagan
Cc:
Hi Sushil,
On May 8, 2014, at 12:26 PM, Sushil Mishra wrote:
MCS algorithm seems to me unable to handle chiral carbons and it can not
differentiate chiral changes in ligands.
That's correct. The MCS algorithm in RDKit doesn't consider chirality. While in
principle I think it would be
Dear All,
I have recently been spending a bit more time with the RDKit cartridge, and
have what is probably a very naïve question...
Having built some RDKit fingerprints for ChEMBL_18, I see the following
behaviour (for clarification - 'ecfp4_bv' is the column in my rdk.fps table
that has been
Hi Andrew,
Thanks a lot for the suggestions. MCS search return I am getting is similar
what you have said:
-- Forwarded message --
From: Markus Sitzmann markus.sitzm...@gmail.com
Date: Thu, May 8, 2014 at 3:27 PM
Subject: Re: [Rdkit-discuss] Tautomeric InChIs
To: Edward Pyzer-Knapp e.o.pyzerkn...@gmail.com
Hi Edward,
since your InChI is a Standard InChI (1S/): tautomeric forms are
-- Forwarded message --
From: Markus Sitzmann markus.sitzm...@gmail.com
Date: Thu, May 8, 2014 at 3:14 PM
Subject: Re: [Rdkit-discuss] RDKit cartridge similarity search speeds(?)
To: James Davidson j.david...@vernalis.com
Hi James,
I would guess, in your second query,
Hello again,
Using isotopes seems to produce something that I am unable to understand.
Sorry, I am new to python so may be I am not able to do it correctly. I
have two mol2 structures stored in mol2str_1 and mol2str_2. These two have
exactly same atom name of the MCS only. Rest of the names
Hi Sushil,
There is some information on using isotope information in MCS here:
http://rdkit.blogspot.ch/2014/01/an-interesting-mcs-use-case.html
-greg
On Thu, May 8, 2014 at 4:14 PM, Sushil Mishra sushilbioi...@gmail.comwrote:
Hello again,
Using isotopes seems to produce something that I
Dear RDKitters,
I started to play around with the great Chem.PandasTool contribution
provided by Nicholas and Samo.
Given such a data frame:
Transformation npairs
1 [*:1][H][*:1]C5
how do I depict the molecular transformation in the dataframe?
I guess that I somehow
Hi,
I'm not sure if it will work but you can try:
df['new'] = df['Transformation'].map(showLine_MMP)
Regards,
Samo
On Thu, May 8, 2014 at 4:31 PM, paul.czodrow...@merckgroup.com wrote:
Dear RDKitters,
I started to play around with the great Chem.PandasTool contribution
provided by
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
Dear Gregori Samo,
thanks for your hints.
I just tried running
Draw.ReactionToImage([*:1][H][*:1]C)
=
AttributeError: 'str' object has no attribute 'GetNumReactantTemplates'
BTW, how would I finally add a picture to a Pandas data frame?
Cheers,
Paul
Hi Paul,
The Draw modules
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'
13 matches
Mail list logo
