appreciated :-).
Cheers
-- Jan Holst Jensen
--
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Dear Greg,
The same thing happens when I try to enable the 'rdkit' extension directly.
postgres@linux-dev-x86 ~ $ psql
psql (9.1.3)
Type help for help.
postgres=# create extension rdkit;
FATAL: failed to initialize rdkit.tanimoto_threshold to 0.5
FATAL: failed to
?
Cheers
-- Jan Holst Jensen
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will include
Meanwhile, I got RDKit_2012_03_1 running fine in Postgres
9.0.4 (the OpenSCG version) on an Ubuntu 10.04 build server.
I will try to install Postgres 9.1 on that server and see
if the error can be reproduced with that setup.
Dear Greg,
I have now installed Postgres 9.1 on the mentioned
are using a 64-bit VM. I
wonder if that is significant. I don't have a 64-bit Linux VM ready for
test building at the moment but let me see if I can establish one.
Kind regards
-- Jan Holst Jensen
--
Live Security
On 2012-04-26 08:37, Gianluca Sforna wrote:
On Thu, Apr 26, 2012 at 8:26 AM, Jan Holst Jensenj...@biochemfusion.com
wrote:
jhje@ubuntu-lynet-test:~/RDKit_2012_03_1/Code/PgSQL/rdkit$
After having installed the cartridge as the postgres user with psql
Dear Greg,
I can again reproduce the Postgres 9.1 issue, this time in a brand new
64-bit VM.
Ubuntu 10.04.2 x86_64 server installed from scratch.
gnome-desktop-environment installed, VMware tools installed.
jhje@ubuntu-x64-build:~$ cat /etc/issue
Ubuntu 10.04.2 LTS \n \l
then cause your code to break half-way through the process ?
Cheers
-- Jan Holst Jensen
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On 2012-05-30 11:28, George Papadatos wrote:
Hi Jan,
I followed your advice and I added the new repo, however the problem
still persists:
[...]
Again, _all_ the tests fail as do the create extension attempts.
I even tried explicit postgresql-9.1 and postgresql-9.2 (beta version)
but
On 2012-05-30 13:24, George Papadatos wrote:
Thanks to both of you.
I do not know how to check for the PG_VERSION_NUM.
Hi George,
I think the snippets below should do it. It shows what my Linux Mint
machine thinks. It seems to be reporting the correct version though,
even though it fails to
On 2012-05-30 13:24, George Papadatos wrote:
Thanks to both of you.
I do not know how to check for the PG_VERSION_NUM. I tried to edit to
guc.c by removing the conditional check of the PG_VERSION but with the
same results:
Adrian, is this what you meant?
DefineCustomRealVariable(
How odd. Adrian, are you using a 32-bit or 64-bit version of Ubuntu 12.04 ?
Cheers
-- Jan
On 2012-05-30 15:26, Adrian Schreyer wrote:
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
My failing Linux Mint is 32-bit like George's 12.04. Don't know if it is
significant but it could be that the problem only occurs on 32-bit.
Greg mentioned that he has successfully built and tested on Ubuntu 12.04
- was that 64-bit or 32-bit ?
Cheers
-- Jan
On 2012-05-30 15:49, Adrian
On 2012-05-31 07:52, Greg Landrum wrote:
On Wed, May 30, 2012 at 4:50 PM, Greg Landrumgreg.land...@gmail.com wrote:
On Wed, May 30, 2012 at 4:13 PM, Jan Holst Jensenj...@biochemfusion.com
wrote:
My failing Linux Mint is 32-bit like George's 12.04. Don't know if it is
significant but it
? The RDKit bitness must be the
same as the Python version you are using, which is 32-bit (EPD 7.0-2
*32 bit python* 2.7.1).
Kind regards
-- Jan Holst Jensen
--
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Exclusive live event will cover
, but I
would like to avoid setting up the Windows build process if I can -
unless a talk or tutorial at the upcoming UGM will show me that it is
quite easy :-).
Any smarter alternatives to this ?
Cheers
-- Jan Holst Jensen
On 2012-09-11 16:13, Greg Landrum wrote:
Hi,
On Tue, Sep 11, 2012 at 2:50 PM, Jan Holst Jensen j...@biochemfusion.com
wrote:
Hi all,
I would like to use RDKit from a Pascal (Delphi) program on Windows and
for that a DLL with a C-style interface would be easiest to work with.
At least
installed in C:\boost\boost_1_51\lib\ are x86
(32-bit).
Cheers
-- Jan Holst Jensen
--
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Exclusive live event will cover all the ways today's security and
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Hi,
I have now managed to produce a nice little self-contained DLL that uses
RDKit to do substructure mapping. It receives a query and a target
molecule as two MDL molfile strings. When the inputs are valid it
behaves well and returns the atom mapping to me. Yes :-).
However, when I give it
On 2012-09-15 05:40, Greg Landrum wrote:
Hi Jan,
On Sat, Sep 15, 2012 at 12:47 AM, Jan Holst Jensen
j...@biochemfusion.com wrote:
I have now managed to produce a nice little self-contained DLL that uses
RDKit to do substructure mapping. It receives a query and a target molecule
as two MDL
On 2012-10-21 21:15, Gianluca Sforna wrote:
On Sun, Oct 21, 2012 at 5:12 AM, Greg Landrum greg.land...@gmail.com wrote:
I'm very happy to announce that the next version of the RDKit --
2012.09 (a.k.a Q3 2012) -- is released.
Hi Greg,
sorry, I didn't it before but trying to rebuild the RPMs
Hi RDKitters,
Before I embark on this journey - has anyone else attempted compiling
and running the RDKit pgSQL cartridge on 64-bit Windows ? Gotchas,
success stories, and fiaskos/war stories would be equally appreciated :-).
Cheers
-- Jan Holst Jensen
Hi Riccardo,
On 2012-11-16 13:29, Riccardo Vianello wrote:
Hi Jan,
On Fri, Nov 16, 2012 at 11:54 AM, Jan Holst Jensen
j...@biochemfusion.com wrote:
[...]
../../lib/libSmilesParse.so.1.2012.09.1: undefined reference to
`boost::thread_resource_error::~thread_resource_error()'
collect2: ld
for
the cartridge, but this works OK for me - on that machine at least.
Cheers
-- Jan
__
Hi Riccardo,
On 2012-11-16 13:29, Riccardo Vianello wrote:
Hi Jan,
On Fri, Nov 16, 2012 at 11:54 AM, Jan Holst Jensen
j...@biochemfusion.com wrote:
[...]
../../lib/libSmilesParse.so
On 2012-11-14 10:30, paul.czodrow...@merckgroup.com wrote:
Dear Jan,
nope - but this reminds me on one UGM topic:
Could anyone provide a 64bit Win7 build?
Well, a couple of notes along the way to building the PostgreSQL
cartridge for Windows. This one is for building 64-bit RDKit on
Hi RDKitters,
I now have the Postgres cartridge code compiling on 64-bit Windows. I
had to add a few explicit casts to dodge C2440 compiler errors but
nothing strange there. What puzzles me are the compile errors I saw when
compiling rdkit_op.c.
rdkit.h defines SearchMolCache() like this:
Hi RDKitters,
I wonder why the InChI strings generated by RDKit differ from the ones
generated by the standard IUPAC inchi-1 executable.
I have used the IUPAC inchi-1 executable from a command line to generate
IUPAC InChI strings (the executable that comes pre-built with the InChI
1.04
Dear Greg,
On 2013-05-01 09:58, Greg Landrum wrote:
Dear Jan,
On Mon, Apr 29, 2013 at 8:03 AM, Jan Holst Jensen j...@biochemfusion.com
wrote:
Hi RDKitters,
I wonder why the InChI strings generated by RDKit differ from the ones
generated by the standard IUPAC inchi-1 executable.
At least
Hi Yingfeng,
Looks like what happened to me, when I had forgotten to set the
environment. Did you set LD_LIBRARY_PATH to $RDBASE/lib before running
the tests ?
Kind regards
-- Jan Holst Jensen
On 2013-06-05 16:09, Yingfeng Wang wrote:
Yes. I tried again. This time,
after run download
, Yingfeng Wang wrote:
Yes, I did.
export RDBASE=/opt/RDKit_latest/latest
export LD_LIBRARY_PATH=$RDBASE/lib:$LD_LIBRARY_PATH
export PYTHONPATH=$RDBASE:$PYTHONPATH
I put them on ~/.bashrc
On Wed, Jun 5, 2013 at 10:53 AM, Jan Holst Jensen
j...@biochemfusion.com mailto:j...@biochemfusion.com wrote
On 2013-12-20 04:57, Greg Landrum wrote:
Hi Jan
On Thu, Dec 19, 2013 at 11:32 PM, Jan Holst Jensen
j...@biochemfusion.com mailto:j...@biochemfusion.com wrote:
The first lines of C:/temp/big.mol are:
HERCEPTIN FAB (ANTIBODY) - LIGHT CHAIN
RDKit 3D
Hi George et al,
flexmatch(... 'all') is the most strict exact match that the
Symyx/Accelrys cartridge has. You can relax the matching behavior to
varying degrees by passing it different options, e.g. using 'tau'
instead of 'all' will make the identity check tautomer-agnostic (to the
extent
On 2014-02-21 11:04, Michal Krompiec wrote:
Hello,
We've been using the RDKit nodes in KNIME for quite a while without
any problems. But suddenly they ceased to work on some computers,
while still working on other ones. Tried with a fresh KNIME
installation with latest RDKit nodes - same
Hi Greg,
Are there any plans for a mol_*to*_ctab() function in the PG cartridge ?
Would make SD file export from the database a bit easier.
If there are no immediate plans, I can take a stab at adding it myself.
* Looks like rdkit_io.c is the place to add it ?
* Should I manually define the
(if they
are loaded from SMILES, for example), should ctabs with all zero
coordinates be generated or should depictions be generated?
-greg
On Fri, Feb 21, 2014 at 2:23 PM, Jan Holst Jensen
j...@biochemfusion.com mailto:j...@biochemfusion.com wrote:
Hi Greg,
Are there any plans for a mol_
Hi Greg,
I now have a working version of mol_to_ctab() - except when I add in
depiction generation. There is a linking issue I don't understand.
In adapter.cpp I have added this function that implements the C++ part
of mol_to_ctab():
extern C char *
makeCtabText(CROMol data, int
of the libraries (static linking can
introduce that).
Try moving the depiction lib to the beginning of the libs list
-greg
On Sunday, February 23, 2014, Jan Holst Jensen j...@biochemfusion.com
mailto:j...@biochemfusion.com wrote:
Hi Greg,
I now have a working version of mol_to_ctab() - except
github.
TJ O'Donnell
On Sat, Feb 22, 2014 at 10:53 PM, Greg Landrum greg.land...@gmail.com
mailto:greg.land...@gmail.com wrote:
On Fri, Feb 21, 2014 at 5:45 PM, Jan Holst Jensen
j...@biochemfusion.com mailto:j...@biochemfusion.com wrote:
Hi Greg,
It would be great
Hi RDKitters,
OK - CentOS 5.3 is getting ancient, but: Does anyone have an rdkit RPM
or just a binary build for CentOS 5.3 that works with its standard
Python 2.4 ? The build process doesn't look so fun on such an old OS.
I am testing if rdkit can be used from Oracle on a customer (test!)
On 2014-02-26 11:04, Greg Landrum
wrote:
On Wed, Feb 26, 2014 at 10:56 AM,
Gianluca Sforna gia...@gmail.com wrote:
On Tue, Feb 25, 2014 at 9:40 PM, Jan Holst
Jensen j
Hi RDKitters,
I have dabbled with calling RDKit from Oracle and have succeeded. It is
done via an Oracle cartridge that makes it possible to call Python
scripts from Oracle. The cartridge is not nearly as sophisticated as
Postgres' support for Python, but it gets the job done.
The cartridge
Hi,
About ready to push a changeset for implementing mol_to_ctab(), but I
would like it to play nice and preserve input depictions.
Ideally I would like the following
select mol_to_ctab(mol_from_ctab(input-molfile));
to output a molfile where the coordinates of input-molfile are
of
mol_from_ctab() in rdkit_io.c
-greg
On Wed, Mar 5, 2014 at 10:27 AM, Jan Holst Jensen
j...@biochemfusion.com mailto:j...@biochemfusion.com wrote:
Hi,
About ready to push a changeset for implementing mol_to_ctab(),
but I would like it to play nice and preserve input depictions
Hi RDKitters,
I managed to get RDKit 2013_09_2 built on CentOS 5.3. Will post a short
recipe later.
Right now, I am still left with three tests that fail, but I think
(hope) that I can live with that ? Failing tests are:
72:pythonTestDbCLI
73:pythonTestDirML
On 2014-03-19 05:54, Greg Landrum wrote:
On Tue, Mar 18, 2014 at 4:59 PM, Jan Holst Jensen
j...@biochemfusion.com mailto:j...@biochemfusion.com wrote:
Hi RDKitters,
I managed to get RDKit 2013_09_2 built on CentOS 5.3. Will post a
short recipe later.
Wow; that's an ancient
, Jan Holst Jensen j...@biochemfusion.com
wrote:
On 2014-03-19 05:54, Greg Landrum wrote:
On Tue, Mar 18, 2014 at 4:59 PM, Jan Holst Jensen j...@biochemfusion.com
wrote:
Hi RDKitters,
I managed to get RDKit 2013_09_2 built on CentOS 5.3. Will post a short
recipe later.
Wow; that's an ancient
-- Jan
On 2014-02-26 11:26, Jan Holst Jensen wrote:
On 2014-02-26 11:04, Greg Landrum wrote:
On Wed, Feb 26, 2014 at 10:56 AM, Gianluca Sforna gia...@gmail.com
mailto:gia...@gmail.com wrote:
On Tue, Feb 25, 2014 at 9:40 PM, Jan Holst Jensen
j...@biochemfusion.com mailto:j
On 2014-04-23 16:01, Daniel Moser wrote:
Hi all,
I think I found some inconsistent behaviour between the cartridge and
python. At least for NCO the cartridge function mol_hbd returns a
different value than Descriptors.NumHDonors.
[...]
I'm seeing this behaviour both with the 2013.09.2 as
Hi Rdkitters,
A colleague of mine has stumbled upon this page:
http://www.rdkit.org/Python_Docs/rdkit.Chem.rdReducedGraphs-module.html
And so he asked me how to use it, because he couldn't find it. Neither
can I, not even in the latest git version. Is this a special secret
feature :-) ?
On 2014-05-07 17:26, chemis...@gmx.de wrote:
*Gesendet:* Mittwoch, 07. Mai 2014 um 15:56 Uhr
*Von:* chemis...@gmx.de
*An:* rdkit-discuss@lists.sourceforge.net
*Betreff:* how can I test if a molecule already has 2D coordinates?
for a given molecule, how can I test if it already has 2D
On 2014-07-29 12:17, acanada wrote:
Hello,
I have a postgres table with compound names and other info. I want to save also
.mol or .sdf information associated to this compounds. I'm getting the
structure information from the chebi web service and I assume that I have to
save this info in
On 2014-08-22 10:38, Michał Nowotka wrote:
A question I have is why you want to access the bond wedging.
This is very good question so I will begin with answering this. I'm
writing a module, which converts *mrv files to molfiles, both ways. In
my case, the original mrv file looks like this:
that '4' value in my question refers to the 'bond stereo'
property, not 'bond type'.
On Fri, Aug 22, 2014 at 1:32 PM, Jan Holst Jensen j...@biochemfusion.com
wrote:
On 2014-08-22 10:38, Michał Nowotka wrote:
A question I have is why you want to access the bond wedging.
This is very good
On 2014-08-22 10:38, Michał Nowotka wrote:
A question I have is why you want to access the bond wedging.
[...] Now imagine I only have this molfile and I want to convert it back to
*mrv. I don't want to write my own parser for molfiles when I know
that RDKit can already parse it. But I need to
On 2014-08-26 17:34, Andrew Pannifer wrote:
Hi,
I have just installed rdkit on a RHEL machine (from source) together
with postgresql 9.0 (from the repo on the website). rdkit is doing
fine on the ctest results and modules import fine while postgresql is
also OK.
In contrast, attempts to
On 2014-08-28 14:34, Michal Krompiec wrote:
Hello, has anybody tried to compile a portable Windows binary of
PostgreSQL with RDKit cartridge? There is a portable PostreSQL at
http://sourceforge.net/projects/postgresqlportable/ and I wonder if it
is possible to use it with the cartridge.
Best
/p:Configuration=Release INSTALL.vcxproj
Cheers
-- Jan Holst Jensen
--
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On 2015-02-12 17:50, JP wrote:
My Makefile now looks:
# -
# Variables used and default values:
USE_INCHI=1 # enables InChI functions; requires rdkit
built with inchi support
# USE_AVALON=0 # enables avalon
the environment for the XAMMP service
via a file as JP can on Linux, then you need to reboot the server.
And... I guess you have done this, but don't forget to set the
environment variables as SYSTEM variables so the service can see them.
Cheers
-- Jan Holst Jensen
On 2015-03-05 11:13, JP wrote
Actually, you want to send your loving thoughts to MDL (now: Biovia).
They defined the SDF format :-).
Cheers
-- Jan
On 2015-04-29 13:26, Nicholas Firth wrote:
Ahh ok… Interesting way to format a file! Got to love ChemAxon...
Best,
Nick
*Nicholas C. Firth*| PhD Student | Cancer Therapeutics
Hi Michael,
I don't know what's wrong, but I can confirm the behavior on an RDKit
build based on 2013_09_2:
select id, molecule
from parents$calc_props
where molecule operator(rdkit.@)
'CC[C@H](C)C(=O)O[C@H]1C[C@@H](C)C=C2C=C[C@H](C)[C@H](CC[C@@H]3C[C@@H](O)CC(=O)O3)[C@H]21'
limit 10
id
molfile
specification, but RDKit probably accepts longer strings (I would guess,
but have not tried).
A more generic solution would be to map RDKit atom and bond properties
to molfile S-group data - but that's a bit more involved and is not
supported at the moment.
Cheers
-- Jan Holst Jensen
?
-greg
On Sat, Jul 4, 2015 at 8:08 PM, Jan Holst Jensen
j...@biochemfusion.com mailto:j...@biochemfusion.com wrote:
Hi Hitesh,
The V2000 molfile format has a feature that can be used to set a
simple text value for an atom by adding V lines to the
molfile. The RDKit molfile
On Sun, Jul 5, 2015 at 10:49 AM, Jan Holst Jensen
j...@biochemfusion.com mailto:j...@biochemfusion.com wrote:
Hi Greg,
I was running with both RDKit 2014.09.2 and 2013.09.1. V lines
accepted and read in input, but no V lines produced in mol
block output
?
Tim
On 25/09/2015 08:30, Jan Holst Jensen wrote:
On 2015-09-24 16:22, Tim Dudgeon wrote:
I'm trying to get to grips with using the RDKit cartridge, and so far
its going well.
One thing I'm concerned about is molecule standardization, along the
lines of the ChemAxon Standardizer that allows
On 2015-09-24 16:22, Tim Dudgeon wrote:
> I'm trying to get to grips with using the RDKit cartridge, and so far
> its going well.
> One thing I'm concerned about is molecule standardization, along the
> lines of the ChemAxon Standardizer that allows substructure searches to
> be done is a way that
data being added to P.
http://sourceforge.net/p/rdkit/mailman/message/34131420/
You can try out the valence change locally by adding it to
atomic_data.cpp (TAB-delimited format) and rebuilding RDKit.
Cheers
-- Jan Holst Jensen
# -
Uncomment the #USE_INCHI=0 line and change it so it reads:
USE_INCHI=1
and then rebuild and reinstall the cartridge. That should do it :-).
Cheers
-- Jan Holst Jensen
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:06 AM, Jan Holst Jensen
<j...@biochemfusion.com <mailto:j...@biochemfusion.com>> wrote:
Hi RDKitters,
I am happy to announce an open source Excel add-in that gives easy
access to the RDKit Python API. The add-in is BSD-licensed like RDKit.
https://github.com/ja
ation of this
first version.
Cheers
-- Jan Holst Jensen
--
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ckages are available.
Using conda makes the installation a lot simpler and saves me a fair
amount of time while doing the builds.
Is using the anaconda python distribution a problem for you?
On Thu, May 4, 2017 at 5:41 PM, Jan Holst Jensen
<j...@biochemfusion.com <mailto:j...@biochemfusion
Hi,
I was trying to find Python Windows binaries for the latest RDKit
release. I could find them for the older 2016_03_1 release on
SourceForge but had no luck finding anything newer on SourceForge or Github.
According to GitHub they should be there:
://github.com/janholstjensen/rdkit4excel
<https://github.com/janholstjensen/rdkit4excel>
Cheers
-- Jan Holst Jensen
--
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Hi Kovas,
Greg has precisely pointed out the major problem of collapsing fragments
into single atoms: Searching and comparing structures.
With that warning in mind: I use pseudo atoms (e.g. "Ala", "Arg",...) to
good effect to represent amino acids in peptides and proteins. My
colleague
L*
M SCN 1 1 HT
M SAL 1 2 2 3
M SDI 1 4 -4.3971 2.3134 -5.0201 1.5441
M SDI 1 4 -6.3183 1.6760 -5.6953 2.4454
M SBL 1 2 1 3
M SMT 1 *1*
M END
"
which RDKit will process and
Hi,
I have an issue with the cartridge - mol_to_svg() changes the input
molecule so I want to make MolGetSVG() to work on a copy of the input
molecule instead.
In Code/PgSQL/rdkit/adapter.cpp:
extern "C" char *MolGetSVG(CROMol i, unsigned int w, unsigned int h,
Hi Michal,
V2000 format is restricted by its specification to fixed format with 4
decimals. V3000 output is not restricted to a fixed format, but the
current code still rounds it in practice as seen below.
To get extra precision you could change the formatting of x, y, and z
coordinate
On 2019-02-05 20:38, tech tech wrote:
Hi, all,
I tried to install the cartridge for Postgres.
I am using ubuntu 18.04 and postgres 9.6
However, when I typed this commond:
/home/hat/anaconda3/envs/my-rdkit-env/bin/initdb -D /var/www/rdkit
I saw following errors. I don't know how to fix it.
eplaced with an RXN file entry. The syntax for data
fields is a bit different too. Data fields can be used to describe
agents, conditions, etc. but there is no fixed vocabulary (that I know
of) for e.g. specifying "this is an agent". Hence, exchanging and
parsing RDF files can be ... i
the
chiral information is right there.
>>> Chem.MolToSmiles(mol, isomericSmiles = True)
'C[C*@*H](N)C(=O)O'
>>> mol = Chem.MolFromSmiles("C[C@H](N)C(=O)O")
>>> Chem.FindMolChiralCenters(mol)
[(1, 'S')]
>>>
Cheers
-- Jan Holst Jensen
On 2019-09
generated by
SDF production different than earlier conformations used to calculate
InChI ?) ?
I don't know if subtle RDKit version differences between KNIME and conda
could cause it - I am not familiar enough with the KNIME nodes to be
able to judge that.
Cheers
-- Jan Holst Jensen
On 2019-11
did to overcome them, it would be much appreciated.
Cheers,
Sharang
On Thu, May 7, 2020 at 3:22 AM Jan Holst Jensen <mailto:j...@biochemfusion.com>> wrote:
Hi Sharang,
A very old version of RDKit ?
When I use your form of calling mol_to_ctab() it does preserve
coordinat
You can also cross-check with standard InChI to see if this is an RDKit
issue or a more general InChI issue. To convert InChI strings (and
optionally AuxInfo) to SDF format with the standard inchi-1 executable,
put the InChI string and AuxInfo into a text file and convert it like this.
> I could not figure out how Rdkit is guessing it as 2D structure, as
there is no such information in SDF.
Ah, but there is, just a little hidden :-). The source-and-timestamp
line of each molfile in the SDF contains that information. The line is
the second line of the molfile and you can
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