wrote:
Hi Tim,
It looks like you are missing the rpmbuild binary on the machine where
you are trying to build the RPM.
Issuing a
yum install rpm-build
as root should get it installed.
Cheers,
p.
On 11/15/17 19:00, Tim Dudgeon wrote:
So this now seems to have been merged to master so I gave
building rpms fails.
I'm probably doing something stupid here as I'm not that familiar with
cmake and cpack.
On 10/11/2017 00:03, Francois BERENGER wrote:
On 11/08/2017 08:47 PM, Tim Dudgeon wrote:
There is mention of RPM distributions of RDKit
(https://copr.fedorainfracloud.org/coprs/gi
I just hit the same problem.
Setup:
- Centos7 with postgres already present.
- Install miniconda
- conda install -y -c rdkit rdkit-postgres95
The install ran OK with no errors. However I notice that it states that
these packages are installed:
rdkit: 2017.09.1-py27_1 rdkit
There is mention of RPM distributions of RDKit
(https://copr.fedorainfracloud.org/coprs/giallu/rdkit/).
But on trying these:
1. the distro is based on the 2017_03_1 release
2. it fails due to missing libinchi.so.1 dependency.
This is presumably no longer being maintained?
Anything that can be
ions (chemfp 3.0 now supports Python 3) costs money. Both are
> distributed under the MIT license.
>
> Within a month or so I'll be making a new release of the no-cost version.
> I'll update the fingerprint type names, to reflect a change in the recent
> RDKit release.
>
> On
I think I recall Greg mentioning that RDKit can be used for very fast
similarity search (e.g. all vs. all comparisons or searches against
multi-million sized datasets).
If so, is this part the of the standard distro, or something extra
(chemfp?).
And can it run inside the cartridge?
And any
Fri, Dec 2, 2016 at 6:29 PM, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
Of course builds from source are never fast enough, and the RDKit
one is
pretty big.
So far I've lived with this and made cups of coffee.
But s
Of course builds from source are never fast enough, and the RDKit one is
pretty big.
So far I've lived with this and made cups of coffee.
But since I've been working with the Release_2016_09_2 release my Docker
image builds on Docker Hub [1] are timing out as they sometimes exceed
the 2 hour
Which Cambridge? Assume this is Cambridge MA not Cambridge UK?
On 15/09/2016 19:29, Brian Kelley wrote:
Novartis is kindly hosting an RDKit Meetup October 19th starting at
4:30pm
The first 45 minutes or so will be devoted to introducing new features
in the RDKit and also a Q and A or
Hi Gianluca
Unfortunately that doesn't work. It's still picking up junit.jar not
junit4.jar from /usr/share/java
Tim
On 26/08/2016 10:15, Gianluca Sforna wrote:
> On Thu, Aug 25, 2016 at 5:34 PM, Tim Dudgeon <tdudgeon...@gmail.com> wrote:
>> It seems that RDKit looks for j
This topic (https://sourceforge.net/p/rdkit/mailman/message/35173301/)
discussed using conformer generation as input into Open3DAlign.
One thing I noticed is that the conformer generation (using the
useExpTorsionAnglePrefs=True and
useBasicKnowledge=True options) does not generate conformers
highestConfId = i
i +=1
print "Lowest:", lowest, lowestConfId
print "Highest:", highest, highestConfId
Chem.MolToMolFile(mol1, "lowest.mol", confId=lowestConfId)
Chem.MolToMolFile(mol1, "highest.mol", confId=highestConfId)
Hi All,
I'm trying to get to grips with using Open3D Align in RDKit, but hitting
problems.
My approach is to generate random conformers of the probe molecule and
align it to the reference molecule. My example is cobbled together from
the examples in the cookbook.
from rdkit import Chem,
I'm slightly confused over the cartridge search functions.
The docs give examples like this:
select * from rdk.mols where m@>'c12c1CNCCN2'
select * from rdk.mols where m@>'c1[o,s]ncn1'::qmol
Q1: As SSS by definition uses a query mol, I'm not totally clear what's
happening in the first of
I've got molfiles that have element labels all in upper case (e.g. CL
instead of Cl).
Parsing these fails (Element 'CL' not found).
I notice that in the C++ and Python APIs there is a 'strictParsing'
option that I'm hoping makes RDKit tolerant of this, but this option
does not seem to be
Hi
I'm having problems building the java wrappers for the 2016_03_1 release
when inchi support is enabled (the -DRDK_BUILD_INCHI_SUPPORT=ON option).
If I turn inchi off or build from master it builds OK.
This is the error I get:
Scanning dependencies of target GraphMolWrap
[ 98%] Building CXX
oot,
restart the postgres service. That fixed the problem for me.
Kind regards,
p.
On 18/04/2016 09:18, Tim Dudgeon wrote:
I spoke too soon!
I'm still having problem with postgres cartridge.
psql -c 'create extension rdkit' rdkitdb
ERROR: could not load library
"/usr/lib/postgresql/9.4/lib/rd
e. That fixed the problem for me.
Kind regards,
p.
On 18/04/2016 09:18, Tim Dudgeon wrote:
I spoke too soon!
I'm still having problem with postgres cartridge.
psql -c 'create extension rdkit' rdkitdb
ERROR: could not load library
"/usr/lib/postgresql/9.4/lib/rdkit.so":
/usr/lib/post
ian Kelley
On Apr 17, 2016, at 8:28 AM, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
I've hit the same issue. Any thoughts on what the underlying issue is
(without reverting to using anaconda)?
An example that illustrates this is here:
https://github.
On Apr 17, 2016, at 8:28 AM, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
I've hit the same issue. Any thoughts on what the underlying
issue is (without reverting to using anaconda)?
An example that illustrates this is here
I've hit the same issue. Any thoughts on what the underlying issue is
(without reverting to using anaconda)?
An example that illustrates this is here:
https://github.com/InformaticsMatters/rdkit
Tim
On 20/11/2015 16:02, Greg Landrum wrote:
Hi Huw,
This is not directly responsive to your
are
properly handled, but it's difficult to assess how much work that
would be.
-greg
On Wed, Mar 30, 2016 at 2:00 PM, Tim Dudgeon <tdudgeon...@gmail.com
<mailto:tdudgeon...@gmail.com>> wrote:
Hi All,
this probably a pretty basic question, but I'm struggling to work
Hi All,
this probably a pretty basic question, but I'm struggling to work out
how to use the SDWriter from Java.
The class that SWIG has generated for SDWriter has a constructor of type:
SDWriter(SWIGTYPE_p_std__ostream outstream)
which looks like its the one I need (I need to write to a Java
Michaela
I have a Dockerfile that does this that should hopefully show what's needed:
https://github.com/InformaticsMatters/rdkit_java/blob/master/Dockerfile
Or you could even use the build Docker image:
https://hub.docker.com/r/informaticsmatters/rdkit_java/
Tim
On 25/02/2016 14:29, Michaela
usage it is worth taking a look at the rdchord
project that TJ has sent links to.
Cheers
-- Jan
On 2015-09-25 15:54, Tim Dudgeon wrote:
Jan,
thanks for that. I'll give it a try.
Are there any examples of writing RDKit functions and procedures for
postgres in python?
I see this general postgres
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 ChemAx
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 is largely independent of the quirks of
Are javadocs for the java wrappers available anywhere?
Tim
--
Monitor 25 network devices or servers for free with OpManager!
OpManager is web-based network management software that monitors
network devices and physical
variable. Here's what
I have:
declare -x JAVA_HOME=/usr/lib/jvm/java-7-openjdk-amd64
-greg
On Mon, Jun 22, 2015 at 3:55 PM, Tim Dudgeon tdudgeon...@gmail.com
mailto:tdudgeon...@gmail.com wrote:
Hi all,
I'm having problems building the java wrappers on Ubuntu with
OpenJDK7
Hi all,
I'm having problems building the java wrappers on Ubuntu with OpenJDK7.
This is the error I have:
-- Boost version: 1.55.0
-- Found the following Boost libraries:
-- regex
-- Found SWIG: /usr/bin/swig2.0 (found version 2.0.12)
-- Found Java: /usr/bin/java (found version 1.7.0.79)
CMake
at this point in time.
So, maybe this will happen sometime, but don't hold your breath.
Tim
On 12/05/2015 02:53, Greg Landrum wrote:
Hi Tim,
On Mon, May 11, 2015 at 6:25 PM, Tim Dudgeon tdudgeon...@gmail.com
mailto:tdudgeon...@gmail.com wrote:
I wondered if anyone has considered trying to get
ECFP, like all fingerprints are notoriously sensitive to trivial
structural changes so your example is no surprise (the extra carbonyl
group also affects aromaticity depending on your view of aromaticity).
But I don't think there is anything simple and fast that's better.
Maybe a clustering
It would indeed be cool, but it might be too specialised for them.
I will follow up and ask if you'd like, but I'd need a bit more
information about what would be involved.
Tim
On 12/05/2015 02:53, Greg Landrum wrote:
Hi Tim,
On Mon, May 11, 2015 at 6:25 PM, Tim Dudgeon tdudgeon
I wondered if anyone has considered trying to get the RDkit cartridge
running on Amazon Relational Database Service (RDS)? When using this you
don't get a shell on the underlying server and everything has to be done
directly at the database level.
This seems to be the most relevant information:
How to install RDKit cartridge?
The instructions here show how to use it, but not how to install it.
http://www.rdkit.org/docs/Cartridge.html
I have RDKit and PostgreSQL installed from the corresponding Debian
packages, but alas no cartridge :-(
Tim
make install
$ make installcheck
(only the second step has to be performed as root)
Kind regards,
Axel
On 04/24/2015 01:33 PM, Tim Dudgeon wrote:
How to install RDKit cartridge?
The instructions here show how to use it, but not how to install it.
http://www.rdkit.org/docs/Cartridge.html
I
Is the only way to get the java wrappers to build from source?
I'm currently using the Debian versions pulled from the Ubuntu
repositories, but if I'm right this doesn't include the java wrappers
for jython?
Tim
--
I'm trying to install on Mac with the instructions here:
https://github.com/rdkit/homebrew-rdkit
The basic install:
brew install rdkit
works fine, but I want the Java wrappers so that I can run with Jython.
And I get this:
$ brew install --with-java rdkit
== Downloading
That should give more detailed error messages in the Terminal, and
also holds off from deleting the log files right away.
Matt
On 6 Jul 2014, at 11:53, Tim Dudgeon tdudgeon...@gmail.com
mailto:tdudgeon...@gmail.com wrote:
I'm trying to install on Mac with the instructions here:
https
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