https://gist.github.com/greglandrum/914ae66fd2f97addbbd472ae726567b1
>
> -greg
>
>
> On Thu, Jul 25, 2019 at 4:45 PM Gianluca Sforna wrote:
>>
>> Hi all,
>> is it possible to manually add molecules to a pandas dataframe? I am
>> reading a bunch of mol2 files, adding some properties (includ
and examples I found around always assume you have a
SMILES string to start with.
Any pointers?
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't have time now to track it down, so any help is
appreciated.
Regards
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HTH
Gianluca
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Check out the vibrant tech community on one of th
v1-Linux-Extras.rpm
> RDKit-2018.03.1.dev1-Linux-Python.rpm
> RDKit-2018.03.1.dev1-Linux-Runtime.rpm
Sorry guys, I got back on the list mid-thread so I really need to ask:
is there a reason why you are trying to use cpack to build RPMs,
instead of the standard rpmbuild tools?
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x86_64 only for Fedora 26, Fedora 27 and RHEL/CentOS 7
Hope that helps
Gianluca
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On Thu, Jun 1, 2017 at 12:03 AM, Samo Turk <samo.t...@gmail.com> wrote:
> Thanks! It seems to work, but it's still compiling. Rockchip CPU in my
> Chromebook is not very fast..
>
How did it turn out? According to my Fedora builds, compiling is fine
but tests are going to fail :
nd
its regular production phase period on March 31; I do hope your admins
have an upgrade path for your cluster because it will stop receiving
security updates very soon now.
https://access.redhat.com/support/policy/updates/errata
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On Fri, Dec 2, 2016 at 6:29 PM, Tim Dudgeon wrote:
> 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 limit. If I try at a quiet time I can sometimes get them to
>
://bugzilla.redhat.com/show_bug.cgi?id=1359402
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;
> rdkit_headers(MolDraw2D.h
>MolDraw2DSVG.h
>MolDraw2Dwx.h
>MolDraw2DUtils.h
> )
>
> needs added: DEST GraphMol/MolDraw2D
>
> (the current git master has the same)
I could not find this change, so I went ahead and created the patch.
Testing it in a new build rig
sion match
and use the correct one.
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On Fri, Aug 19, 2016 at 1:52 PM, Greg Landrum wrote:
> Nice suggestion. It seems logical to me, though I would probably go with
> RDKit instead of RD as the prefix.
> It's not a small change for people who are using the C++ libs without cmake
> (I wouldn't change the
On Mon, Aug 8, 2016 at 11:20 AM, Greg Landrum wrote:
> As Paolo points out, this really just integrates the cartridge tests into
> the rest of the test suite.
Ok, so basically I was not seeing this before because I was not
running it with the old style build
>
>
Thanks for the patch Paolo.
Is test 97 new? It seems it wants to use the Postgres server and
fails, I am afraid it is not easy to have it working at build time.
On Fri, Aug 5, 2016 at 11:45 AM, Gianluca Sforna <gia...@gmail.com> wrote:
> Anyone ever tested this combo?
>
> I am cu
the CMakeFile is hardcoding the "Inchi" name as library to
search for
Maybe it should be using the "FindInchi" macro and avoid putting the
explicit name there?
Not sure how to patch it.
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in Fedora 24 and rawhide (aka Fedora 25) has
been patched, so it can be used to build rdkit.
https://bodhi.fedoraproject.org/updates/FEDORA-2016-fff5d70162
Regards
G.
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on that: I just finished testing the code with v1.61 of boost
> and everything works fine.
So we still need to skip 1.60? I think that's what Fedora 24 is shipping
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Tinker Gara
On Tue, Apr 12, 2016 at 11:51 AM, Gianluca Sforna <gia...@gmail.com> wrote:
> On Mon, Apr 11, 2016 at 1:20 PM, Greg Landrum <greg.land...@gmail.com> wrote:
>> This could be the issue fixed by this PR from Matt Swain:
>> https://github.com/rdkit/rdkit/pull/856
On Mon, Apr 11, 2016 at 1:20 PM, Greg Landrum <greg.land...@gmail.com> wrote:
> This could be the issue fixed by this PR from Matt Swain:
> https://github.com/rdkit/rdkit/pull/856
Yeah, that's it. Thanks!
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On Thu, Apr 7, 2016 at 6:24 AM, Greg Landrum wrote:
> I have tagged a beta of the next RDKit release here:
> https://github.com/rdkit/rdkit/releases/tag/Release_2016_03_1b1
Tried to rebuild the RPMs but got this right on cmake:
-- Found INCHI: /usr/lib64/libinchi.so
which is what I'm after.
In this case, you probably want to install the librdkit-dev package
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not see coming :) Congratulations and all the
best for this new adventure!
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azing mobile app experiences with Intel(R) XDK.
> Use one codebase in this all-in-one HTML5 development environment.
> Design, debug & build mobile apps & 2D/3D high-impact games for multiple
> OSs.
> http://pubads.g
On Wed, Nov 18, 2015 at 3:24 AM, Greg Landrum wrote:
>
> Gianluca's binary RPMs for Fedora 20, 21 and RHEL/Centos 6, 7 will be
> available from
> this repository:
> https://copr.fedoraproject.org/coprs/giallu/rdkit/
2015_09_1 is already there for Fedora 21, 22 and 23, I'm
found that if you run java with the -cp option (as we do in
tests) then the CLASSPATH env variable is ignored. I think this can be
the reason why I have missing symbols. I hope to find a way to
workaround this.
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/lib:
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Widest out
:
/builddir/build/BUILD/rdkit-Release_2015_03_1beta1/Code/JavaWrappers/gmwrapper/libGraphMolWrap.so:
undefined symbol: _ZTVN5RDKi
t9MolDraw2DE
Any idea?
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.
binary RPMs for Fedora 20, 21 and RHEL/Centos 6, 7 are available from:
https://copr.fedoraproject.org/coprs/giallu/rdkit/
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RPMs.
Not critical, but this tag misses the Release_ prefix so my download
script broke :)
Other than that, it builds correctly on Fedora 20 and 21 (64bit)
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On Tue, May 27, 2014 at 9:36 AM, GALLY Jose Manuel
jose.manuel.ga...@gmail.com wrote:
Do you think you could fix this?
Yeah, I got it fixed. Thanks for noticing.
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receive the update as soon as it finish building.
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The best possible search technologies are now
on
that server.
For a start, you can make your life easier by adding the EPEL
repository and pulling python26 package from there.
IIRC the only real blocker that prevented me from building RDKit
against CentOS5 + EPEL was flex
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Before I go digging the repository, can anyone tell me if the test
suite includes stuff for the postgres cartridge?
I am particularly interested in comparing results and performance with
a custom solution I have here.
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. So,
I have the most recent version of RDKit built and everything has passed the
tests.
Great!
Is there something else
in the environment I need to set up to get through the UnsatisfiedLinkError?
Sorry, I can't help there as I don't use Java. I hope someone else can chime in.
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rebuild rdkit in copr and you can
find the resulting binary RPMs here:
http://copr.fedoraproject.org/coprs/giallu/rdkit/
Regards
Gianluca
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:
http://techcrunch.com/2013/09/19/dotcloud-pivots-and-wins-big-with-docker-the-cloud-service-now-part-of-red-hat-openshift/
As enthusiast openshift user I will probably try to get rdkit running
there using docker
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source software, so I tend to trust it more
than many other things like, hard disks
http://spritesmods.com/?art=hddhack
:)
/offtopic
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On Thu, Sep 12, 2013 at 12:25 AM, Greg Landrum greg.land...@gmail.com wrote:
Glad the problem is solved.
And without disabling SELinux :)
http://stopdisablingselinux.com/
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On Fri, Aug 16, 2013 at 8:30 PM, greg landrum greg.land...@gmail.com wrote:
I definitely haven't tried it with bison 3.0 (and am kind of amazed that such
a version exists!)
And then they mock Fedora for being too bleeding edge... :P
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On Fri, Aug 2, 2013 at 9:35 PM, Richard West r.h.w...@gmail.com wrote:
1) Is there any hope of getting a version with InChI into the Ubuntu
repositories?
You can probably report a bug against the package and let the
maintainer rebuild it with inchi suppot.
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.
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rebase
git push rdkit@github master
having commit access to SVN it would be possible to push commits from
git to svn, but I have no such access and honestly I just hope we drop
svn at some point and just use git :)
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Hi all,
I just updated the rdkit packages in my fedorapeople space:
http://giallu.fedorapeople.org/rdkit-2012.12/
to include support for the inchi library.
As usual, feel free to contact me for any question about these packages
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namespace, I have surely nothing against :)
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://rdkit.googlecode.com/files/RDKit_2012_12_1beta1.tgz
RPM packages builds correctly in Fedora 17/18. CentOS/RHEL 6 builds
fails because postgres 9.1 or newer is now required.
If this is the case also for the final release, I will disable the
cartridge in the EL builds.
Thanks for the notice
G.
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:)
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. In the local instances, I got a report of
python crashing during those tests but I never got around determining
what the cause could be.
I will come back with the results of the new build.
Thanks
G.
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to be read
by humans show atom indexes starting from 1.
No one except RMS counts from 0 :)
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in there is failing? Some expect a
failure so I can't readily tell from the log which ones are
problematic.
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On Fri, Oct 5, 2012 at 7:36 AM, Greg Landrum greg.land...@gmail.com wrote:
I mentioned at the UGM that Gianluca Sforna has set up a mirror of the
RDKit subversion repository.
The repository is here: https://github.com/rdkit/rdkit
Thanks Greg, I really looked forward to join you for the UGM
the recompilation dance at each release.
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Exclusive live event will cover all the ways
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so it has cairo/pycairo included in the build.
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Exclusive
.x to build RDKit -- I am using v4.5.3. That is a
source of mishap and doom.
As I noted earlier, the compiler should not be an issue anymore, just
make sure you have gcc-4.1.2-49.el5 or newer.
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://giallu.fedorapeople.org/rdkit/
They are all 64bit; 32 bit and F16 packages available upon request.
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isomorphism techniques, is
there some out-of-the-box functionality for this?
Does anyone have some pointers on this subject?
Maybe you missed this recent item?
http://www.dalkescientific.com/writings/diary/archive/2012/05/12/mcs_background.html
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it with the
purpose of matching it against some other molecule (the query part),
I'm just not sure how RDKit could do that, if there is already an API
availiable, etc.
HTH
Gianluca
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now, but IIRC there are two different
cartridges, one for 8.x and another one for 9.x.
Just to be sure, I'd double check you are installing the right one in there.
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: W: shared-lib-calls-exit
/usr/lib64/libSLNParse.so.1.2012.03.1 exit@GLIBC_2.2.5
Cheers
G.
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no more spare time to bring it on.
* Is python 2.7 really required? I know 2.4 is getting pretty old but
if we can manage to keep it supported it would be very nice.
Alternatively, EPEL ships a python26 package that I would use rather
than compiling from sources.
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not
affect libpython).
I think the easiest solution would be to use the dynamic library
libpython2.7.so instead, which I hope is included in the ROCKS
distribution.
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that helps
G.
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alternate type of highlighting (changing the backbone color is not
always suitable).
Can't sign off any timing though, it mostly depend about whether I'll
need those at work
Cheers
G.
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bindings are
basically unusable right now unless you also activate Inchi support.
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.
Is having a black variant enough?
that would imply just swapping the background color with the default bond color
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the archive file names as well?
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On Fri, Jul 2, 2010 at 10:31 AM, Greg Landrum greg.land...@gmail.com wrote:
Do any of you have experience of this?
I'm a Fedora package maintainer so I guess I can have a look at it.
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On Mon, Mar 1, 2010 at 9:26 PM, Greg Landrum greg.land...@gmail.com wrote:
On Mon, Mar 1, 2010 at 11:24 AM, Gianluca Sforna gia...@gmail.com wrote:
Sorry for resurrecting this topic, but I just realized the Q4 2009
release tarball do not compile out of the box due to the previously
discussed
REQUIRED)
include_directories(${PYTHON_NUMPY_INCLUDE_PATH})
to let the build proceed as expected.
HTH
Gianluca
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On Thu, Jan 21, 2010 at 8:58 AM, Gianluca Sforna gia...@gmail.com wrote:
On Wed, Jan 20, 2010 at 7:59 PM, Greg Landrum greg.land...@gmail.com wrote:
The reason for the hackery is to allow an alternate python
installation to be used on systems that have more than one. This was
the only way I
with the python versions.
sorry for mixing up the two topics.
For python, it seems you need to set PYTHON_INCLUDE_PATH and
PYTHON_LIBRARY in order to use your own version
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On Thu, Jan 21, 2010 at 2:23 PM, Greg Landrum greg.land...@gmail.com wrote:
On Thu, Jan 21, 2010 at 11:32 AM, Gianluca Sforna gia...@gmail.com wrote:
For python, it seems you need to set PYTHON_INCLUDE_PATH and
PYTHON_LIBRARY in order to use your own version
exactly, and that's what
the patch I proposed and report if
things improves
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(${PYTHON_LIBRARIES})
+
find_package(NumPy REQUIRED)
include_directories(${PYTHON_NUMPY_INCLUDE_PATH})
Cheers
G.
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the paths to your preferred
boost installation?
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On Sun, Jan 17, 2010 at 10:14 AM, Greg Landrum greg.land...@gmail.com wrote:
I have successfully specified an alternate
boost directory using cmake v2.8.0, but I guess Fedora 12 comes with
v2.6.
Yes, for the records it's 2.6.4.
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