] Error 2
make: *** [all] Error 2
Can you help?
Thanks,
TJ O'Donnell
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-929e-f4fff3a11e9f
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Last Changed Rev: 1450
Last Changed Date: 2010-07-08 21:15:09 -0700 (Thu, 08 Jul 2010)
Thanks,
TJ O'Donnell, Ph.D.
President, gNova, Inc.
from rdkit import Chem
import sys
mb = sys.stdin.read()
mol
...@gmail.com wrote:
Hi TJ,
2010/12/24 TJ O'Donnell t...@acm.org:
I have a mol file that causes MolFromMolBlock to get stuck.
I reproduced this problem with this simple python script (below).
I've attached the problem input molfile. I got the file
from the chembl08 download. Another large
Hi Greg-
No objection here. I've been using 1024 with 2 bits here.
Are you still using 2048 for the default size?
TJ O'Donnell
On Tue, Dec 28, 2010 at 11:33 PM, Greg Landrum greg.land...@gmail.com wrote:
Dear all,
As I mentioned in an earlier message
(http://www.mail-archive.com/rdkit
=Chem.MolFromMolBlock(molblock)
E.g. mol.GetPropNames() returns a null array (or just the private and
computed props if mol.GetPropNames(True,True)
Can you give me some hints on how I might get the property tag data
from a string molblock?
TJ O'Donnell
: https://rdkit.svn.sourceforge.net/svnroot/rdkit
Repository UUID: 19320e9b-7711-0410-929e-f4fff3a11e9f
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Last Changed Date: 2011-01-05 00:45:35 -0800 (Wed, 05 Jan 2011)
Thanks,
TJ O'Donnell
on the entire set of 600K molecules.
TJ
On Sun, Jan 9, 2011 at 10:51 PM, Greg Landrum greg.land...@gmail.com wrote:
Hi TJ,
On Mon, Jan 10, 2011 at 2:37 AM, TJ O'Donnell t...@acm.org wrote:
Thanks Greg. I compiled in the changes and that molfile works fine
now, but.
Here are four new examples
I am willing and able to do consulting and contract programming using RDKit,
using either Python or C++
http://gnova.com
TJ
TJ O'Donnell, Ph.D.
President, gNova, Inc.
t...@gnova.com
On Sat, Mar 19, 2011 at 10:46 PM, Greg Landrum greg.land...@gmail.com wrote:
Dear
There are binaries available at http://www.postgresql.org/download/
and a nice wiki at http://wiki.postgresql.org/wiki/Main_Page
The postgres community is great - check out the mailing lists
at http://www.postgresql.org/community/
TJ
-
TJ O'Donnell, Ph.D.
President, gNova Inc.
t
: ring stereochemistry detected. The output SMILES
is not canonical.
Any help or input on this?
Some offending smiles are below along with the code
I used to test this. I can provide a file of 512 if you'd like.
I'm using 2012.09.1, freshly compiled from svn
and passing all tests
TJ O'Donnell
Hi JP
I use this file from PDB Europe:
ftp://ftp.ebi.ac.uk/pub/databases/msd/pdbechem/files/pdb.tar.gz
Useful links followed from
http://www.ebi.ac.uk/pdbe-srv/pdbechem/
The pdb.tar.gz file has the standard residues and LOTS of others
with specific CONNECT records.
TJ
On Mon, Jan 13, 2014 at
and useage better, probably using github.
TJ O'Donnell
On Sat, Feb 22, 2014 at 10:53 PM, Greg Landrum greg.land...@gmail.comwrote:
On Fri, Feb 21, 2014 at 5:45 PM, Jan Holst Jensen
j...@biochemfusion.comwrote:
Hi Greg,
It would be great to gain the experience. I am working on a registration
Babel can read and write both pdbqt and mol2 files. I'm not sure how the
atom ordering might be accomplished though.
TJ
On May 9, 2014 2:43 PM, Jan Domanski jan...@gmail.com wrote:
Thanks for the quick reply Christos!
I found the pdbqt_to_pdb script that you mentioned but a google search for
I've implemented a suite of rdkit functions
for postgres using plpython
https://github.com/tjod/rdchord
and the overhead is minimal
since most of the heavy lifting of substructure searching
is done by rdkit.
I think the same would be true of oracle.
---
TJ O'Donnell
On Thu, Mar
How about including a link on sourceforge to this:
https://help.github.com/articles/support-for-subversion-clients/
so that folks without git clients can get started.
TJ
On Fri, Mar 20, 2015 at 9:48 PM, Greg Landrum greg.land...@gmail.com
wrote:
The mailing lists and one form of the downloads
Tim,
I have a set of postgres python (PL/Python) functions using rdkit.
It is available at
https://github.com/tjod/rdchord
and some docs at
https://github.com/tjod/rdchord/wiki
TJ O'Donnell
On Fri, Sep 25, 2015 at 6:54 AM, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
> Jan,
&
I would suggest setting PYTHONPATH in
config or ini files for
Apache or Django or uwsgi
Not sure which is required.
On Tue, Jun 21, 2016 at 11:15 AM, Téletchéa Stéphane <
stephane.teletc...@univ-nantes.fr> wrote:
> Le 21/06/2016 20:05, Bennion, Brian a écrit :
> > What is the actual problem that
listen_addresses='*'. You can
tailor that to be more specific, but try this first.
2. The file pg_hba.conf also controls access. Look at this:
https://www.postgresql.org/docs/9.3/static/auth-pg-hba-conf.html
Be sure to restart the server after you make changes to these files.
Hope this helps,
TJ
://www.postgresql.org/docs/9.5/static/sql-insert.html#SQL-ON-CONFLICT
TJ O'Donnell
On Wed, Sep 13, 2017 at 3:13 AM, Wandré <wandrevel...@gmail.com> wrote:
> Hi,
>
> My name is Wandré and I'm from Brazil.
> I'm trying to do a big database of molecules, but, I want to eliminate all
> the redun
Try either of these:
[N,n](C)-,:[C,c](=[O])
C[N,n]-,:[C,c](=[O])
TJ O'Donnell
On Mon, Sep 18, 2017 at 4:26 PM, James T. Metz via Rdkit-discuss <
rdkit-discuss@lists.sourceforge.net> wrote:
> Hello,
>
> Given the following aromatic structure
>
> m = Chem.MolFromSmi
Try using [O;H0;D2;r6] lower-case r. Sorry I'm not at a computer to check
this.
R6 means in 6 rings.
r6 means in ring of size 6.
http://www.daylight.com/dayhtml/doc/theory/theory.smarts.html
TJ O'Donnell
On Wed, Sep 6, 2017 at 4:34 PM, James T. Metz via Rdkit-discuss <
rdkit-disc
0},{27},{34},{41}}
(1 row)
Here's an image showing the atom numbers corresponding to the list_matches
output.
TJ
[image: Inline image 2]
On Wed, Sep 6, 2017 at 6:04 PM, TJ O'Donnell <t...@acm.org> wrote:
> Try using [O;H0;D2;r6] lower-case r. Sorry I'm not at a computer to
> chec
Hi Andrew
ChEMBL 24 has compound properties in the table compound_properties. I
think the alogp
is computed using (Crippen) atom types and the acd_logp is uses ACD labs
methods.
TJ
On Wed, Aug 29, 2018 at 5:52 AM Andrew Dalke
wrote:
> Hi all,
>
> I am starting to put together materials for
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