Hi Greg,
I use mercurial and bitbucket as you may know, hg because I prefer its
workflow compared to git and bitbucket because of the unlimited
private repositories (and I have quite a few). I would suggest github
as host if you choose git - it has the most features of all websites
in my opinion.
Hi All,
I have just published a little paper that describes Ultrafast Shape
Recognition with Credo Atom Types (USRCAT), an extension of the USR
algorithm that includes pharmacophoric information
(http://www.jcheminf.com/content/4/1/27/abstract). The paper also
describes a database implementation
On Fri, Jul 6, 2012 at 10:27 AM, JP jeanpaul.ebe...@inhibox.com wrote:
Steifl -- that is a really crafty and less painful way how to go about it.
The SMILES is in fact, a wget call away - since I am processing PDB
deposited structures.
http://www.rcsb.org/pdb/rest/describeHet?chemicalID=NAG
On 12.04 you do not need to add the PPA, PostgreSQL 9.1 is the
official package there. In addition, the official packages are also
provided by Martin Pitt, so the packages in the PPA and in the distro
are actually the same. It only make sense on 10.04 (and those that do
not ship with 9.1).
I
Yes, I could build and install the cartridge without problems
(Release_2012.03.1) on 12.04.
On Wed, May 30, 2012 at 2:23 PM, George Papadatos gpapada...@gmail.com wrote:
Hi Jan,
Mine is exactly the same:
gcc test.c -I/usr/include/postgresql/9.1/server;./a.out
90103
So, I am back to square
Forgot to reply to the mailing list:
---
You would need to register the OID of the mol type in psycopg2, like
this for example:
def cast_cube(value, cursor):
if value:
return map(float, value[1:-1].split(','))
CUBE = psycopg2.extensions.new_type((CUBE_OID,), CUBE, cast_cube)
Hi,
I'm using the RDKit PostgreSQL cartridge on the same Ubuntu
architecture. I think it is a problem with the OpenSCG package, you
should use the following repository instead: ppa:pitti/postgresql. He
is also the official maintainer of the Ubuntu PostgreSQL packages;
with those everything works
Hi all,
I have exported the schema of my PostgreSQL version of ChEMBL10. Maybe
some of you will find it helpful. It can be downloaded here:
http://dl.dropbox.com/u/1012605/schemas/ChEMBL10.sql
Please let me know if there are any problems.
Adrian
If you want to use C++, there is ESBTL, a PDB parser and data
structure for the structural and geometric analysis of biological
macromolecules (http://esbtl.sourceforge.net), MMTK
(http://dirac.cnrs-orleans.fr/MMTK/). Open Babel can read PDB files
but the last time I checked it was not possible to
Hi Greg,
there is a typo on the page describing the creation of a database
using eMolecules:
sed in the form 's/\\//' to escape backslashes will only replace
the first occurrence of the match, the 'g' at the end is necessary to
replace all occurrences on a line.
grep '6172136'
On Wed, May 4, 2011 at 04:26, Greg Landrum greg.land...@gmail.com wrote:
Dear JP,
On Tue, May 3, 2011 at 6:29 PM, JP jeanpaul.ebe...@inhibox.com wrote:
Based on an rdkit post I read over the warm weekend I set myself to
have a look at my rdkit based queries (and ways to speed them up)...
The easiest way would be to do a substructure search as a subquery or
WITH statement first and then do a SMARTS search on the result. This
way you can keep your hydrogens and the speed (most of it).
Adrian
On Thu, Mar 17, 2011 at 19:11, JP jeanpaul.ebe...@inhibox.com wrote:
Could the API
1
Is there a way to use the files in the postgresql-server-dev-8.4
package for building the cartridge?
Adrian
On Fri, Jul 2, 2010 at 10:42, Greg Landrum greg.land...@gmail.com wrote:
Hi Adrian,
On Fri, Jul 2, 2010 at 11:24 AM, Adrian Schreyer m...@adrianschreyer.eu
wrote:
That's great news
That's great news indeed Greg!
I want to migrate from MySQL to PostgreSQL once version 9.0 is
released and the rdkit cartridge will be very useful for my future
work. SMARTS support would be great as well. Do you intend on adding
things like MACCS keys and SMIRKS for transformations/reactions in
I had the same problem on Ubuntu, download the boost source from their
web site and build according to the instructions on the RDKit wiki.
Adrian
On Fri, Jun 4, 2010 at 14:16, bouille ambin...@wanadoo.fr wrote:
Dear Greg
Using Fedora 12 with original included boost
I got 2 errors
[ 83%]
MACCS keys are a set of 166 structural key descriptors (public
version) in which each bit is associated with a SMARTS pattern. The
SMARTS pattern are somewhere defined in the RDKit distribution.
http://www.dalkescientific.com/writings/NBN/fingerprints.html
Adrian
On Tue, May 4, 2010 at 16:10,
On Tue, Apr 20, 2010 at 04:59, Greg Landrum greg.land...@gmail.com wrote:
Hi Andrew,
On Mon, Apr 19, 2010 at 12:53 AM, Andrew Dalke
da...@dalkescientific.com wrote:
On Apr 18, 2010, at 5:43 PM, Greg Landrum wrote:
As usual: if no problems come up in the next week I will go ahead and
do the
Hi Greg,
I pulled the latest version from Google Code but I cannot find any
lists file for CMake. Is there a specific branch I need to pull?
Adrian
On Sat, Jan 16, 2010 at 13:42, Greg Landrum greg.land...@gmail.com wrote:
Dear all,
It's getting to be time for the Q4 2009 release and I'd
/rdFeatSelect.so] Error 1
make[1]: *** [Code/ML/FeatureSelect/Wrap/CMakeFiles/rdFeatSelect.dir/all]
Error 2
make: *** [all] Error 2
On Sat, Jan 16, 2010 at 18:37, Greg Landrum greg.land...@gmail.com wrote:
Hi Adrian,
On Sat, Jan 16, 2010 at 6:56 PM, Adrian Schreyer
adr...@cryst.bioc.cam.ac.uk
If you want a quick visualisation of a hierarchical clustering you can just
use matplotlib / hcluster to create a dendrogram. All you need to do is to
create the condensed distance matrix using RDKit as Greg described and then
(for example)
from hcluster import *
import pylab
clustering =
I can highly recommend the pyMOL interface as well (rpc.py). It is
quite powerful once you write functions on top of it and combine it
with other python things (database access), particularly with the
CGO's (e.g. rdkit/Chem/PyMol.py).
On Wed, May 20, 2009 at 08:14, markus kossner
explicitly is designed
for
small Mols, I wonder if anyone has already loaded a Protein?
I found a post by Adrian Schreyer (*[Rdkit-discuss] Atom-level SMARTS
matching*)
mentioning SIFTs, This implies the perception of Pocket-residues.
Was that done / Can that be done by the RDKit?
Cheers Markus
I was wondering what would be the best way in RDKit to represent
molecules with a metal complex in SMILES, for instance heme.
Apparently different programs use different approaches, CACTVS uses a
non-standard notation
After a couple of hours work on comparing molecules with RDKit I
noticed that the algorithm is apparently struggling with structures
that consist of a repetitive substructure, such as linear alkanes
(azelaic acid C((=O)O)(=O)O being the worst offender) or
molecules like gentian violet
Is there a convenient way of stripping dummy atoms from RECAP fragments in
RDKit (without causing problems with sanitization)?
Hi Greg,
a beta release would be nice particularly due to the bug fixes in the
canonicalization algorithm.
Cheers,
Adrian
On Jan 12, 2008 7:15 AM, Greg Landrum greg.land...@gmail.com wrote:
Dear RDKit folks,
I had hoped to have a release of the RDKit finished in December. That
obviously
Hi Greg,
I am having problems working with biomocules such as B12 (sdf attached). If
I read the file RDKit will return an error message complaining about
valences which are greater than permitted, in this case atom # 1 N. I
suspect the problem is due to metal coordination (in this case a Cobalt
I think there might be something going wrong with the hydrophobe feature
definition, or to be more precise, with the implementation.
Using the linking amino acid Alanine as an example, the C atom will be
labelled as Hydrophobe - ChainTwoWayAttach, although it is bound to the
main-chain oxygen and
Is it somehow possible in RDKit to perform a boolean SMARTS query on
individual atoms? For example I would like to identify possible weak
hydrogen bond acceptors with a SMARTS query like this [a:a,A=A,A#A,S+0] or
weak donors with [c,CX3,CX2][H].
Adrian
Apparently the RECAP implementation in RDKit cleaves bonds within ring
motifs in the case of amines, e.g. in the case of imatinib or in the
example given in the original paper.
I tried to modify the SMARTS pattern a bit in order to reproduce the
cisapride example, without success. The original
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