2012_12_1/Contrib/M_Kossner/BaseFeatures_DIP2_NoMicrospecies.fdef")
>> ValueError: pattern->getNumAtoms() != len(feature weight vector)
>
> That was indeed a bug in the file, which is now fixed. Thanks for reporting
> it.
>
> The file itself is an attempt at building a use
ds.
@Greg:
Now that some people are interested in the code:
May this script find a save harbour in the Contrib folder?
All the best!
Markus
Christian de Bouillé wrote:
Hi Greg
I have tested the script from
Markus Kossner
Starting string
Oc1c1N1CCN(C(=S)NCc2cc3c(cc2)OCO3)CC1
Scaffold with m
Hi Greg,
exactly that was the case.
RDKit nicely installs now!
Cheers,
Markus
On 11/15/2010 10:05 AM, Greg Landrum wrote:
> HI Markus,
>
> On Mon, Nov 15, 2010 at 9:51 AM, Markus Kossner
> wrote:
>> Hi Greg,
>> I have tried to install the latest RDKit on a freshly i
Hi Greg,
I have tried to install the latest RDKit on a freshly installed Ubuntu
10.10.
After installing python-dev, sqlite3, numpy, bison, flex AND THE BOOST
LIBRARIES VIA APT (boost 1.42), I additionally installed boost 1.4.2 in
/opt/boost_1_42_0.
During the cmake step flex and bison were found
Paul Emsley wrote:
> On 17/09/10 07:57, markus kossner wrote:
>
>> some time ago I implemented a filter function during a pdb mining
>> campaign. The Idea was to exclude compounds to far away from drug like
>> chemical matter.
>>
>>
>
> As a matt
Hi James,
some time ago I implemented a filter function during a pdb mining
campaign. The Idea was to exclude compounds to far away from drug like
chemical matter.
The function I wrote is not the prettiest one, but it is somehow
complementary to your substructure matching. The filter function u
정종영 wrote:
> Hi,
> I found that the xyz coordinates in conformer class are different from
> coordinates in the original input sdf file.
> Why does the loss of original cooridinates happen?
> And how can I use Conformer with original coordinates in input file?
> Jongyoung
> -
Greg Landrum wrote:
> Dear Markus,
>
> On Thu, Jul 22, 2010 at 10:49 AM, markus kossner wrote:
>
>> after I talked to Nik at the Sheffield Conference about the difficulty of
>> defining Positive/Negative ionizable features by SMARTS he asked me to to
>> send m
Greg Landrum wrote:
Dear Markus,
On Thu, Jul 8, 2010 at 2:56 PM, markus kossner wrote:
Dear Cedric,
months ago I did some extraction of frameworks with the RDKit. I'm
neither sure, if my script follows the exact Murcko paper, nor is the
snippet well tested.
At least it could prov
Dear Cedric,
months ago I did some extraction of frameworks with the RDKit. I'm
neither sure, if my script follows the exact Murcko paper, nor is the
snippet well tested.
At least it could provide a starting point for your further work. I sent
an email to your personal address with the script at
Cedric MORETTI wrote:
>
> Hello all,
>
> I have I little problem with RDKIT( I hope :D)
>
> My program don’t arrive to close the SDwriter whereas I put the
> command “writer.close()” and Chem.SDWriter.close() in the end of programm
>
> I just let the part of the code that is import for understand
Greg, as always: Thank you very much for your help!
Greg Landrum wrote:
> Hi Markus,
>
> On Wed, Jun 9, 2010 at 8:28 AM, markus kossner wrote:
>
>> Hi Greg,
>> I just searched for a possibility to query an Atom for its van der Waals
>> Radius, but did not find
Hi Greg,
I just searched for a possibility to query an Atom for its van der Waals
Radius, but did not find a 'pythonic way' like an Atom-Property or the
like in the docu.
Do you have a hint on the best way to get this information using the RDKit?
Thank you in advance,
Markus
---
bouille wrote:
> Dear Greg
>
> How I can raise the following error ?
>
> 291475, COc1ccc(cc1)\C=C1\[S]=C(Nc2ccc(cc2)S(N)(=O)=O)NC1=O |t:11|
> Traceback (most recent call last):
> File "/home/bouille/DescriptorsCalcul/3mon3D.py", line 85, in
> sdf3D = Chem.MolToMolBlock(molH)
> ValueError: Sa
Dear Sedric,
I copied and pasted the smiles codes to a local file and used the
following python snippet:
#I don't use cynfony, so this is pure RDKit Version Q4_2009 on Ubunto 9.4
from rdkit import Chem
suppl = Chem.SmilesMolSupplier("test.smi")
for mol in suppl:
print mol.GetNumAtoms()
The o
Dear All,
I read about a CompressedSDMolSupplier (assuming it is a Supplier for
zipped sd files, isn't it?) in the release Notes for Q32009_1.
However I could neither find a function like that in the rdkit.Chem
Module nor any hint in the docs. Could anyone please give me a pointer?
Cheers, Mark
Greg Landrum wrote:
Dear Markus,
On Tue, Jan 12, 2010 at 10:28 AM, markus kossner wrote:
I recently played around with the rdkit and got an interesting behavior when
reading sd-files from different vendors:
As I scrolled through the mailing list I found the thread by Marshall
Levesque
Hi Greg,
I am currently working my way through the Pharm2D Modules and have
some Questions:
1.) A '2DPharmacophore' is the non-hashed bitstring as described in
the Gobbi Paper cited in the doc files isn't it?
2.)Does rdkit.Chem.Pharm2D.Generate.Gen2DFingerprint yield the hashed
version descr
Hi Greg,
I updated to the latest RDKit installation using boost_1_41_0 and the
compilation did not throw any error (boost as well as rdkit). However
when I run the tests, I get some errors from two scripts as follows
(The first representatives per script):
***
Hi there,
I recently noticed some unexpected behavior of the PropertyMol.
Note that I have installed the Q1_2009 installation currently.
Look at that:
>>> from rdkit import Chem
>>> mol=Chem.MolFromSmiles('c1c1')
>>> mol.SetProp('_Name','benzene')
>>> w=Chem.SDWriter('test.sdf')
>>> w.write(mo
Message: 7
Date: Tue, 19 May 2009 18:17:55 +0100
From: Peter Harley
Subject: Re: [Rdkit-discuss] GUI
To: George Oakman
Cc: rdkit-discuss@lists.sourceforge.net
Message-ID: <4a12e9c3.2000...@cam.ac.uk>
Content-Type: text/plain; charset=windows-1252; format=flowed
George Oakman wrote:
> Dear all
rdkit-discuss-requ...@lists.sourceforge.net wrote:
Send Rdkit-discuss mailing list submissions to
rdkit-discuss@lists.sourceforge.net
To subscribe or unsubscribe via the World Wide Web, visit
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
or, via email, send a message
Hi all,
yesterday I tried to test out the functionality of the Pubmed modules.
First let me explain the scene:
I want to use the RDKit Pubmed modules for Pubchem
Compound,Substance,Bioassay etc-data queries
In order to get the answer to the following question:
In which assays was 'aspirin' test
Hi there,
I'm quite new to compiled Programming languages and
as can be read here my problems occured previously.
However I dind't manage to install the Kit properly.
I modyfied the boost::random source, copied the log files as described
and was also able to do the two "bjam" commands as descri
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