Re: [Rdkit-devel] 2021.03.1 RDKit Release

n Fri, Mar 26, 2021 at 4:13 PM Greg Landrum wrote: > Dear all, > > I'm pleased to announce that the 2021.03 version of the RDKit is released. > We actually managed to get the .03 release done during March. Shocking! ;-) > The release notes are below.[1] > > The release

[Rdkit-devel] 2021.03.1 RDKit Release

Dear all, I'm pleased to announce that the 2021.03 version of the RDKit is released. We actually managed to get the .03 release done during March. Shocking! ;-) The release notes are below.[1] The release files are on the github release page: https://github.com/rdkit/rdkit/releases/tag/Release_20

[Rdkit-devel] Beta of the 2021.03 release available

Dear all, The beta of the 2020.09 RDKit release has been tagged in github: https://github.com/rdkit/rdkit/releases/tag/Release_2021_03_1b1 I'm doing a conda build for Python 3.7 on Linux now. If you would like to test the new version and need a conda build for that, please let me know and I can t

[Rdkit-devel] 2020.09.1 RDKit Release

Dear all, I'm pleased to announce that the 2020.09 version of the RDKit is released. The release notes are below. The release files are on the github release page: https://github.com/rdkit/rdkit/releases/tag/Release_2020_09_1 Binaries have been uploaded to anaconda.org (https://anaconda.org/rdki

[Rdkit-devel] Beta of the 2020.09 release available

Dear all, The beta of the 2020.09 RDKit release has been tagged in github: https://github.com/rdkit/rdkit/releases/tag/Release_2020_09_1b1 There are a couple more bug fixes and maybe one more feature expected before the actual release, but I wanted to go ahead and get the beta out there. I've do

Re: [Rdkit-devel] SDF String Generation Include Stereo information

Hi Emanuel, The chirality bit doesn't have anything to do with double bond stereochemistry.[1] So that's not what's going on here The RDKit has the ability to pass the mol block provided directly to the InChI code without interpreting it. I believe that the ChEMBL team is using that to generate I

Re: [Rdkit-devel] PostgreSQL PGXS-style Makefile, and RDGeneral/export.h: No such file or directory

[Deleted the previous contents of the thread because it was causing formatting problems for me in gmail, sorry] One thing you might consider trying here is to build and install the RDKit (without the cartridge or Python wrappers) like a normal library using the standard RDKit build process. This s

Re: [Rdkit-devel] PostgreSQL PGXS-style Makefile, and RDGeneral/export.h: No such file or directory

On Tue, Mar 31, 2020 at 12:24 AM Finnerty, Jim via Rdkit-devel < rdkit-devel@lists.sourceforge.net> wrote: > Thank you, Paolo. I found a generated export.h in Oxygen, used that, and > got past that issue. > > > > The CMake script enforces a minimum Boost version of Boost-1.56.0, whereas > we’re o

[Rdkit-devel] 2020.03.1 RDKit Release

Dear all, I'm pleased to announce that the next version of the RDKit - 2020.03 - is released. This time we even managed to get it out during the correct month! :-) The release notes are below. The release files are on the github release page: https://github.com/rdkit/rdkit/releases/tag/Release_20

[Rdkit-devel] (no subject)

Dear all, The beta of the 2020.03 RDKit release has been tagged in github: https://github.com/rdkit/rdkit/releases/tag/Release_2020_03_1b1 I've done conda builds for Python 3.6 and 3.7 for Mac, and Linux and I'm working on the Windows builds now. These all use the beta label so that they do not i

Re: [Rdkit-devel] Fwd: [Boost-users] [Graph] Large incoming changes to Boost.Graph master.

Thanks for forwarding that Emanuel. I just tried the dev version out (as John describes) with the RDKit and everything looks good: the code builds and the tests all pass -greg On Thu, Jan 9, 2020 at 7:47 AM Emanuel Ehmki wrote: > Dear all, > > is that something to consider? > > Kind regards,

Re: [Rdkit-devel] molecular representation underlying the postgresql cartridge for rdkit

Hi Peter, On Mon, Dec 2, 2019 at 10:11 AM Peter Schmidtke < peter.schmid...@discngine.com> wrote: > > I have a question regarding the underlying molecular representation used > in the rdkit cartridge for postgresql. > I didn't dig yet too much into the underlying source code of the > cartridge. I

[Rdkit-devel] 2019.09.1 RDKit Release

Dear all, I'm pleased to announce that the next version of the RDKit - 2019.09 - is released. The release notes are below. The release files are on the github release page: https://github.com/rdkit/rdkit/releases/tag/Release_2019_09_1 Binaries have been uploaded to anaconda.org (https://anaconda

[Rdkit-devel] Beta of the 2019.09 release available

Dear all, The beta of the 2019.09 RDKit release has been tagged in github: https://github.com/rdkit/rdkit/releases/tag/Release_2019_09_1b1 There are a couple more bug fixes and hopefully one more feature expected before the actual

[Rdkit-devel] CI Update

Dear all, I just realized that I haven't really said anything here about the changes that we've been making to the CI (continuous integration) system that we're using for the RDKit. In case you have no idea what I'm talking about or use CI in a different way: every pull request or code change tha

Re: [Rdkit-devel] GSoC-2019 RDKit-Neo4J project

uring this summer will be working on RDKit-Neo4J project > <https://docs.google.com/document/d/1rXUbY3di_YSW1LWTraa3cJEapRtEOrcBc1otZV56FMc/edit#> > with > Greg Landrum, Christian Pilger and Stefan Armbruster (neo4j core > developer). > The project will be focused on devel

Re: [Rdkit-devel] [Rdkit-announce] 2019.03.1 RDKit Release

ension if not exists rdkit; > CREATE EXTENSION > chembl_25=# > > I then followed the other commands in the rdkit docs to create some > fingerprints and build the similarity search index - all seems to be > working ok. > > Cheers, Drew > > > > > > On

[Rdkit-devel] 2019.03.1 RDKit Release

Dear all, I'm pleased to announce that the next version of the RDKit - 2019.03 - is released. The release notes are below. The release files are on the github release page: https://github.com/rdkit/rdkit/releases/tag/Release_2019_03_1 Binaries have been uploaded to anaconda.org (https://anaconda

Re: [Rdkit-devel] 2019_03_1b1: lots of undefined references to libboost_iostreams functions

Hi Gabriele, I haven't tried a boost 1.70 build yet, so I can't confirm that it works. Could you please try 1.69 and see if that helps? If not, please send the exact cmake command you used and what the output was. Thanks, -greg On Sat, Apr 6, 2019 at 3:53 PM wrote: > hello, > > there seems to

[Rdkit-devel] Beta of the 2019.03 release available

Dear all, The beta of the 2019.03 RDKit release has been tagged in github: https://github.com/rdkit/rdkit/releases/tag/Release_2019_03_1b1 There are a couple more bug fixes and maybe one more feature expected before the actual release, but I wanted to go ahead and get the beta out there. I've do

[Rdkit-devel] 2018.09.1 RDKit Release

I'm pleased to announce that the next version of the RDKit - 2018.09 - is released. The release notes are below. The release files are on the github release page: https://github.com/rdkit/rdkit/releases/tag/Release_2018_09_1 Binaries have been uploaded to anaconda.org (https://anaconda.org/rdkit)

[Rdkit-devel] [Question] Ok to switch to conda-forge for RDKit builds?

Dear all, TL;DR: Now that RDKit builds are available on conda-forge, I would like to stop doing builds on the rdkit conda channel. I'm looking for feedback about that here. Thanks to the persistence of Peter St John and Matt Swain, the RDKit is now available on conda-forge: https://anaconda.org/c

[Rdkit-devel] Beta of the 2018.09 release available

Dear all, The beta of the 2018.09 RDKit release has been tagged in github: https://github.com/rdkit/rdkit/releases/tag/Release_2018_09_1b1 I will try to get some conda builds for python 3.6 up over the next day or so. These will use the beta label so that they do not install by default; you'll ne

Re: [Rdkit-devel] The RDKit Travis builds

The good news is that I didn't end up needing to do anything: after the first build failed strangely the others worked normally. Yay! So we're now migrated to travis-ci.com: https://travis-ci.com/rdkit/rdkit The bad news is that the intermittent, non-reproducible build failures seem to still be an

[Rdkit-devel] The RDKit Travis builds

Just a quick FYI that I asked the folks at Travis-CI to switch us over to their newer setup (Travis-ci.com instead of Travis-ci.org) today.[1] This has broken the build, as one would expect. :-S I will spend some time on it over the next day or so to get things working again. -greg [1] there were

Re: [Rdkit-devel] Failing tests in Visual Studio build

Hi Juuso, Thanks for letting us know about this. -greg On Wed, May 30, 2018 at 10:28 AM Juuso Lehtivarjo < juuso.lehtiva...@gmail.com> wrote: > Hi All, > > Just wanted to inform all Visual Studio users of some weirdness that > we encountered after updating Visual Studio 2017 to version 15.7.2,

Re: [Rdkit-devel] RDKit 2018.03.1 Build and Installation

136 - pythonTestDirChem (Failed) >> >> Any idea? >> >> >> >> 2018-05-16 15:08 GMT+02:00 Greg Landrum : >> >>> Yeah, the dockerfile that I pointed you to installs the ubuntu version >>> of boost. That is what ends up being used to build the

Re: [Rdkit-devel] RDKit 2018.03.1 Build and Installation

. On Wed, May 16, 2018 at 3:03 PM alb greg wrote: > The system boost? You're talking about libboost? > > > > 2018-05-16 14:54 GMT+02:00 Greg Landrum : > >> cmake is finding boost v1.67, not the system boost. >> >> >> On Wed, May 16, 2018 at

Re: [Rdkit-devel] RDKit 2018.03.1 Build and Installation

NG_DEPENDENCIES) > CMakeLists.txt:303 (find_package) > > > == Using strict rotor definition > -- Found MAEParser source in > /home/labbe/src/rdkit/rdkit/External/CoordGen/maeparser > -- Found coordgenlibs source in > /home/labbe/src/rdkit/rdkit/External/CoordGen/coordgenlibs &

Re: [Rdkit-devel] RDKit 2018.03.1 Build and Installation

On Wed, May 16, 2018 at 12:53 PM alb greg wrote: > I followed the instructions in this dockerfile but it failed with an error > 2 during "make -j3 .. install" command. > > In order to be able to help I need a bit more information than that. What was the error you encountered? What version of Ubun

Re: [Rdkit-devel] RDKit 2018.03.1 Build and Installation

For what it's worth: I put together a Dockerfile to demonstrate how to build the RDKit under Ubuntu 16.04 here: https://github.com/rdkit/rdkit_containers/blob/master/docker/ubuntu_xenial/Dockerfile Aside from the RDkit itself, this uses only software that is part of the Ubuntu distribution (includ

Re: [Rdkit-devel] bivariate_normal deprecation

Thanks Kiran! On Fri, May 4, 2018 at 5:08 PM Kiran Telukunta < kiran.teluku...@indiayouth.info> wrote: > Hello Greg, > > I have created the ticket <https://github.com/rdkit/rdkit/issues/1851>. > > Thanks, > Kiran > > On 4 May 2018 at 09:13, Greg Landrum wrote

Re: [Rdkit-devel] bivariate_normal deprecation

Hi Kira, I would rather not introduce a dependency on scipy (which is rather large) here. I think it probably makes more sense to just add an RDKit reimplementation of the function and use that. I need to check, but I would guess that the license on matplotlib would probably allow us to just grab

Re: [Rdkit-devel] RDKit 2018.03.1 Build and Installation

This is indeed almost certainly due to the version of boost being “too new” for the version of cmake. I took advantage of a new cmake feature without fully thinking through the consequences of how picky cmake is about it. I’m going to revert this change to the build system before the 2018.03.2 rel

[Rdkit-devel] Apologies for the delays processing pull requests

Dear all, There's something of a backlog of unprocessed pull requests for the RDKit. Putting (what I hope were) the final touches on the release ended up being a time consuming slog and didn't leave me much time for looking at PRs. I'm sorry for this; it's great to have the contributions coming in

[Rdkit-devel] 2018.03.1 RDKit release

I'm pleased to announce that the next version of the RDKit - 2018.03 - is released. The release notes are below. The release files are on the github release page: https://github.com/rdkit/rdkit/releases/tag/Release_2018_03_1 Binaries have been uploaded to anaconda.org (https://anaconda.org/rdkit

[Rdkit-devel] The 2018.03 release, python 2.7, and Windows

Dear all, In finalizing the details for the 2018.03.1 release, I hit a problem with python v2.7 on Windows that is likely to result in there being no conda builds available for the Windows version of python 2.7. The problem is that extension modules for python 2.7 “are supposed to be” built with

Re: [Rdkit-devel] [Rdkit-discuss] [Announcement] 7th RDKit UGM in Cambridge UK

e optional training on the day before. > > > > However, I could not see any link (on the eventbrite page) regarding this > event. There was an option for the dinner & reception, but no training.. > > > > Or is the “main UGM registration” a different place than the even

[Rdkit-devel] [Announcement] 7th RDKit UGM in Cambridge UK

Dear all, This year's RDKit User Group Meeting will take place from 19-21 September in Cambridge, UK and is being hosted by Andreas Bender at Cambridge University. Registration for the RDKit UGM is free: https://www.eventbrite.com/e/7th-rdkit-ugm-2018-tickets-44883066460 We will once again mostl

[Rdkit-devel] Beta of the 2018.03 release available

Dear all, The beta of the 2018.03 RDKit release has been tagged in github: https://github.com/rdkit/rdkit/releases/tag/Release_2018_03_1b1 I will try to get some conda builds for python 3.6 up over the next day or so. These will use the beta label so that they do not install by default; you'll n

Re: [Rdkit-devel] [Rdkit-discuss] Some larger-scale RDKit C++ code changes

but I figure there are likely to be at least a few bumps. Hopefully they aren't too large. -greg On Thu, Apr 5, 2018 at 8:46 AM, Greg Landrum wrote: > Thanks for raising this Markus. It had been on my list of things to look > into for a while and I had been kind of dreading it.[1] &g

Re: [Rdkit-devel] [Rdkit-discuss] Some larger-scale RDKit C++ code changes

is a small > concern, I would do it (I doubt it is in case of RDKit). > > Markus > > On Wed, Apr 4, 2018 at 11:56 AM, Greg Landrum > wrote: > >> >> >> On Wed, Apr 4, 2018 at 11:27 AM, Markus Sitzmann < >> markus.sitzm...@gmail.com> wrote: >>

Re: [Rdkit-devel] [Rdkit-discuss] Some larger-scale RDKit C++ code changes

On Wed, Apr 4, 2018 at 11:27 AM, Markus Sitzmann wrote: > Hi Greg, > > > Concretely what this means in github is that the current master branch > will be renamed to legacy and the modern_cxx branch will be renamed to > master. > > I hope you are not actually just renaming it - although I am not

Re: [Rdkit-devel] Where's the 2018.03 release?

another active PR where we're close to having an alternate fix (amusingly, the same number as the OB fix: https://github.com/rdkit/rdkit/pull/1807). I think we're very close. -greg > > Pozdrawiam, | Best regards, > Maciek Wójcikowski > mac...@wojcikowski.pl > > 20

[Rdkit-devel] Where's the 2018.03 release?

Dear all, As you may have noticed, the new release (2018.03) is late. This is not, as you might expect, connected to my previous email about the backend code changes. It turned out to be much more difficult than anticipated to straighten out the problems we were having with newer versions of cond

[Rdkit-devel] Some larger-scale RDKit C++ code changes

NOTE: If you don't work with the RDKit at the C++ level or build the code yourself from source, you probably don't need to read this email. TL;DR: When we do the beta for the 2018.03.1 release we're going to switch the C++ backend to use modern C++ (=C++11). For people who can't switch to use that

Re: [Rdkit-devel] problem building rdkit

eneral;/ > usr/lib/x86_64-linux-gnu/libboost_system.so;general;/ > usr/lib/x86_64-linux-gnu/libpthread.so;general;/usr/ > lib/x86_64-linux-gnu/libboost_serialization.so; > > > > > On Mon, Mar 19, 2018 at 3:27 AM, Greg Landrum > wrote: > >> Well, I don'

Re: [Rdkit-devel] problem building rdkit

e,libRDKitFilterCatalog.so.1 -o >> ../../../lib/libRDKitFilterCatalog.so.1.2018.03.1.dev1 >> CMakeFiles/FilterCatalog.dir/Filters.cpp.o >> CMakeFiles/FilterCatalog.dir/FilterCatalog.cpp.o >> CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o >> CMakeFiles/FilterC

Re: [Rdkit-devel] problem building rdkit

Hi TJ, Hrm, that's ugly. Just to confirm: Are you building the master branch from github? It looks like there's no fundamental problem with master; at least the travis builds pass: https://travis-ci.org/rdkit/rdkit To help track this down, can you please send the results of doing: VERBOSE=1 make

Re: [Rdkit-devel] Two 'Labute' descriptors seem to be always returning 0.0

Hi Jeff, On Thu, Mar 15, 2018 at 10:26 PM, jeff godden wrote: > > > First and foremost thank you for your excellent offering of a singularly > useful set of molecular descriptors! > Thanks for the kind words. :-) > As one of the authors cited by Dr Labute (http://www.chemcomp.com/journ > al/vs

[Rdkit-devel] 2017.09.1 RDKit release

I'm pleased to announce that the next version of the RDKit -- 2017.09 -- is released. The release notes are below. The release files are on the github release page: https://github.com/rdkit/rdkit/releases/tag/Release_2017_09_1 Binaries have been uploaded to anaconda.org (https://anaconda.org/rdki

[Rdkit-devel] Beta of the 2017.09 release available

Dear all, This morning I tagged the beta of the 2017.09 RDKit release in github: https://github.com/rdkit/rdkit/releases/tag/Release_2017_09_1b1 I will try to get some conda builds up over the next day or so. These will use the beta label so that they do not install by default; you'll need to run

Re: [Rdkit-devel] drawing amino acids

On Fri, Sep 8, 2017 at 2:10 PM, Igor Filippov wrote: > >> >> Could it be that you didn't generate coordinates for the molecule? >> >> The result is the same for me whether I load the molecule from an SD file > with coordinates, or generate 2D or 3D coordinates on the fly. > Does it display correc

Re: [Rdkit-devel] drawing amino acids

Hi Igor, Could it be that you didn't generate coordinates for the molecule? BTW: rdMolDraw2D.PrepareMolForDrawing() is a useful function to know about. -greg On Thu, Sep 7, 2017 at 2:16 PM, Igor Filippov wrote: > Dear Colleagues, > > I seem to remember there already was a discussion about th

Re: [Rdkit-devel] Adding RDKit::ROMol *s to a boost::python::list

It's been a while since I've seen one of these, but could it be that you either haven't imported rdkit.Chem (in Python) before calling the function that returns the RDKit molecule or that your extension module is linked against a different rdkit library than the rdkit extension module that you're u

Re: [Rdkit-devel] travis build timeouts

tifacts (=libraries) from that for the python and java builds we could shorten the individual jobs. -greg > On Tue, Jun 13, 2017 at 9:20 AM, Greg Landrum > wrote: > >> Given that the current variability is almost a factor of two I don't >> think smaller changes are goin

Re: [Rdkit-devel] travis build timeouts

conda env > 2. having only one conda install for *everything* > > If you like I can try these fixes. > > Cheers, > Brian > > On Tue, Jun 13, 2017 at 3:44 AM, Greg Landrum > wrote: > >> Dear all, >> >> We're getting more and more timeouts wi

[Rdkit-devel] travis build timeouts

Dear all, We're getting more and more timeouts with RDKit builds on travis. I'm reasonably sure that this is due to some variability in the performance of the VMs that the builds end up running on. A good demonstration of that is this particular build (on a branch where I'm playing with simplifyin

[Rdkit-devel] The RDKit and modern C++ (finally)

Dear all, Now that the 2017_03 release cycle has started, I am *finally* ready to start the modern C++ work that I've discussed before. Here's a blog post on the topic: https://medium.com/@greg.landrum_t5/the-rdkit-and-modern-c-48206b966218 To that end I created a new branch this morning: https:/

Re: [Rdkit-devel] 2017.03 (Q1 2017) RDKit Release

This is now resolved: the boost-1.56 build for python 3.6 on 64bit linux (the only python3.6 build that's currently done) is in place. -- Check out the vibrant tech community on one of the world's most engaging tech sites,

Re: [Rdkit-devel] 2017.03 (Q1 2017) RDKit Release

Right you are. I will push those too From: Maciek Wójcikowski Sent: Friday, April 21, 2017 4:37:30 PM To: Greg Landrum Cc: RDKit Discuss; rdkit-annou...@lists.sourceforge.net; RDKit Developers List Subject: Re: [Rdkit-devel] 2017.03 (Q1 2017) RDKit Release Hi

[Rdkit-devel] 2017.03 (Q1 2017) RDKit Release

I'm pleased to announce that the next version of the RDKit -- 2017.03 (a.k.a. Q1 2017) -- is released. The release notes are below. The release files are on the github release page: *https://github.com/rdkit/rdkit/releases/tag/Release_2017_03_1

[Rdkit-devel] Beta of Q1 2017 release now up

[apologies for the date of this... it's not an April Fools joke] Dear all, I have tagged a beta of the next RDKit release here: https://github.com/rdkit/rdkit/releases/tag/Release_2017_03_1b1 The release notes are on the release page linked above. Note that the list of people in the acknowledgeme

Re: [Rdkit-devel] RDKit installation

Gayathree, Those instructions are for installing a binary version of the RDKit. They are not well suited for setting up an environment where you build from source. For the purposes of getting something done quickly while you're preparing your GSoC application (there's not a lot of time left), I w

Re: [Rdkit-devel] Rdkit and ipywidget installation

Dear Gayathree, On Wed, Mar 22, 2017 at 3:46 PM, Gayathree Kaluarachchi < kalpa.ga...@gmail.com> wrote: > > I am Gayathree, a level 3 undergraduate from Faculty of Information > Technology, University of Moratuwa, Sri Lanka. I am really interested in > RDKit - 3Dmol.js Integration, a project in G

Re: [Rdkit-devel] InChI 1.05

akes a difference as far as > InChI is concerned. > > Best regards, > Igor > > > On Fri, Feb 24, 2017 at 8:43 AM, Greg Landrum > wrote: > >> Thanks Igor! I was not looking forward to getting this working, so it's >> great that someone else managed to. >&g

Re: [Rdkit-devel] InChI 1.05

Thanks Igor! I was not looking forward to getting this working, so it's great that someone else managed to. I need to do a bit more tweaking in order to get the download to work using the cmake code instead of the download_inchi.sh script, but I should be done with that pretty quickly. I'll have

Re: [Rdkit-devel] RDKit Python wrappers

My two cents:- Brian got the big one: boost allows you to produce pythonic bindings and, as long as you're doing them at the same time you are writing the original code it's not that big of a deal to write the wrappers by hand.- Back when I started this SWIG was a complete disaster in terms of h

Re: [Rdkit-devel] RDKit Python wrappers

You can always just ask... On Thu, Dec 1, 2016 at 9:14 PM +0100, "David Cosgrove" wrote: Ok, I'm convinced. I assumed there was probably a good reason, but sometimes it's worth asking the question just in case. I'm not anti boost, but, as with many of their libraries I have look

[Rdkit-devel] 2016.09 (Q3 2016) RDKit Release

Dear all, I'm pleased to announce that the next version of the RDKit -- 2016.09 (a.k.a. Q3 2016) -- is released. This one is even later than usual since the RDKit UGM was quite late this year. And then we hit some problems with the python 2.7 builds on Windows . The release notes are below. The

Re: [Rdkit-devel] GenerateDepictionMatching3DStructure

Hi Dave, On Tue, Nov 22, 2016 at 11:08 AM, David Cosgrove wrote: > > I really couldn't decide whether this should just be for you, or to the > whole list, so I decided to defer the decision to you! > Seems like it's appropriate for the -devel list, so I'm including it on the reply. > I'm look

Re: [Rdkit-devel] Boost and cmake version survey

version survey To: Greg Landrum Cc: RDKit Developers List On Wed, Nov 9, 2016 at 11:41 AM, Greg Landrum wrote: > This decision shouldn't matter to most users since they will be getting > pre-built binaries either via their OS's package manager or conda. If you want to make it eas

[Rdkit-devel] Boost and cmake version survey

The move to modern C++ is coming (at last!) and when we make it, I would like to go ahead and specify (relatively) modern minimum versions of boost and/or cmake. This is your chance to pipe up on what we do here. In case you have no idea what I'm talking about here, the relevant blog post is: https

[Rdkit-devel] Beta of Q3 2016 release now up

Dear all, I have tagged a beta of the next RDKit release here: https://github.com/rdkit/rdkit/releases/tag/Release_2016_09_1b1 The relevant section of the release notes is below. Note that the list of people in the acknowledgement section was mostly created automatically from github. If you feel

Re: [Rdkit-devel] Failing test 103 on cutting edge Fedora

quot;Gianluca Sforna" wrote: Thanks Greg, here is the new build log: https://kojipkgs.fedoraproject.org//work/tasks/9220/16199220/build.log On Tue, Oct 25, 2016 at 5:33 PM, Greg Landrum wrote: > I don't see anything obvious and there's not currently an easy way to fig

Re: [Rdkit-devel] Failing test 103 on cutting edge Fedora

I don't see anything obvious and there's not currently an easy way to figure out what the problem is (but I'm fixing that now). Using this diff as a patch (not sure what syntax you want) will provide more info about which test failed: landrum@Otter:/scratch/RDKit_git/build$ git diff ../rdkit/TestR

[Rdkit-devel] 2016.03 (Q1 2016) RDKit Release

Dear all, I'm pleased to announce that the next version of the RDKit -- 2016.03 (a.k.a. Q1 2016) -- is released. The release notes are below. The release and binary files are on the github release page: *https://github.com/rdkit/rdkit/releases/tag/Release_2016_03_1

Re: [Rdkit-devel] More build fun with RHEL 6

Great. After this next round of travis builds passes I will merge the two outstanding PRs and then do the release. -greg On Fri, Apr 15, 2016 at 7:07 PM, Gianluca Sforna wrote: > On Fri, Apr 15, 2016 at 1:36 PM, Greg Landrum > wrote: > > Would you be comfortable with me doing

Re: [Rdkit-devel] More build fun with RHEL 6

On Fri, Apr 15, 2016 at 1:18 PM, Gianluca Sforna wrote: > On Fri, Apr 15, 2016 at 11:20 AM, Greg Landrum > wrote: > > The problem here is that the rdkit doesn't really support Python 2.6 > > anymore. I don't remember at the moment which pieces we used, but there

Re: [Rdkit-devel] More build fun with RHEL 6

On Friday, 15 April 2016, Gianluca Sforna wrote: > On Fri, Apr 15, 2016 at 4:41 AM, Greg Landrum > wrote: > > Now that I have a Centos6 box available, I'm realizing that it has python > > 2.6 > > Are you also installing Python 2.7 on those machines when you build

Re: [Rdkit-devel] More build fun with RHEL 6

quirements for the java wrappers or postgreSQL yet). -greg On Fri, Apr 15, 2016 at 4:41 AM, Greg Landrum wrote: > Now that I have a Centos6 box available, I'm realizing that it has python > 2.6 > Are you also installing Python 2.7 on those machines when you build the > RDKit? >

Re: [Rdkit-devel] More build fun with RHEL 6

; with only one platform where it fails; if we think the older boost > version cannot be supported, I can just stick to an older release for > EL6 > > On Thu, Apr 14, 2016 at 11:47 AM, Gianluca Sforna > wrote: > > On Thu, Apr 14, 2016 at 11:37 AM, Greg Landrum > wrote:

Re: [Rdkit-devel] More build fun with RHEL 6

oblem with the exported defines, > however I can tie it into the boost version in the FilterCatalog header > file. We had initially thought this only affected RHEL5 so it was a lower > priority, I can have a PR by the end of the day (maybe even the Basel day :) > > > > On Thu, Apr 14

Re: [Rdkit-devel] More build fun with RHEL 6

his before in FilterCatalog, I can try to patch it > for boost 1.41 but I will say that version of boost is getting pretty long > in the tooth. > > > Brian Kelley > > On Apr 14, 2016, at 6:43 AM, Greg Landrum wrote: > > I'd like to have it work on EL6; that's

Re: [Rdkit-devel] More build fun with RHEL 6

ucceded, this leaves us > with only one platform where it fails; if we think the older boost > version cannot be supported, I can just stick to an older release for > EL6 > > On Thu, Apr 14, 2016 at 11:47 AM, Gianluca Sforna > wrote: > > On Thu, Apr 14, 2016 at 11:37 AM, Greg

Re: [Rdkit-devel] More build fun with RHEL 6

Gianluca, Which version of boost are you using? -greg On Thu, Apr 14, 2016 at 11:33 AM, Gianluca Sforna wrote: > The RPM build for Fedora worked so I moved to RHEL/CentOS and got a new > error: > > > In file included from /usr/include/boost/python/to_python_indirect.hpp:10, >

Re: [Rdkit-devel] Beta of Q1 2016 release now up

On Wed, Apr 13, 2016 at 8:43 PM, Gianluca Sforna wrote: > On Wed, Apr 13, 2016 at 12:27 PM, Greg Landrum > wrote: > > Wow, that's a "typing in the wrong buffer" bug. > > Great catch. > > :) > > Another couple points. > I noticed the RDKi

Re: [Rdkit-devel] Beta of Q1 2016 release now up

phMol/SmilesParse/smiles.ll > +++ b/Code/GraphMol/SmilesParse/smiles.ll > @@ -1,4 +1,4 @@ > -%setpropoption reentrant > +%option reentrant > %option bison-bridge > %option noyywrap > > Was it correct? > > > > On Wed, Apr 13, 2016 at 10:44 AM, Greg Landrum > w

Re: [Rdkit-devel] Beta of Q1 2016 release now up

Hi Gianluca, On Tue, Apr 12, 2016 at 1:09 PM, Gianluca Sforna wrote: > > But no joy still > > > [ 36%] Building CXX object > Code/GraphMol/SmilesParse/CMakeFiles/SmilesParse.dir/lex.yysmarts.cpp.o > cd > /builddir/build/BUILD/rdkit-Release_2016_03_1b1/python2/Code/GraphMol/SmilesParse > && /

Re: [Rdkit-devel] Beta of Q1 2016 release now up

Gianluca, This could be the issue fixed by this PR from Matt Swain: https://github.com/rdkit/rdkit/pull/856 -greg On Mon, Apr 11, 2016 at 12:32 PM, Gianluca Sforna wrote: > On Thu, Apr 7, 2016 at 6:24 AM, Greg Landrum > wrote: > > I have tagged a beta of the next RDKit

[Rdkit-devel] Beta of Q1 2016 release now up

Dear all, I have tagged a beta of the next RDKit release here: https://github.com/rdkit/rdkit/releases/tag/Release_2016_03_1b1 The relevant section of the release notes is below. Note that the list of people in the acknowledgement section was mostly created automatically from github. If you feel

Re: [Rdkit-devel] Pharm2D -- 4-point pharmacophores

Hi Ondrej, There's an illustration of the representation here: http://rdkit.org/docs/RDKit_Book.html#representation-of-pharmacophore-fingerprints Some discussion in the code of the terminology used: https://github.com/rdkit/rdkit/blob/master/rdkit/Chem/Pharm2D/Generate.py#L11 and an illustration o

Re: [Rdkit-devel] RDKit binaries available for Win32 .Net?

Hi Tom, There's never really been demand for such a thing. It ought to be doable. I will investigate and see what I can come up with. -greg On Sun, Feb 7, 2016 at 7:27 PM, Tom Hagadone wrote: > Hello All: > > We have a need to be able to call RDKit from an existing Win32 C#.Net app. > I've be

Re: [Rdkit-devel] failing with rdkit.Chem.PyMol.MolViewer()

Hi Zhenquan, Did you start PyMol with the "-R" flag so that it is running the xmlrpc server? You can verify this by looking in the PyMol console for text like this: "xml-rpc server running on host localhost, port 9123" -greg On Wed, Jan 6, 2016 at 2:16 AM, Zhenquan Hu wrote: > Dear all, > >

Re: [Rdkit-devel] last test failing with python3

Hi Gianluca, It looks like that function is not available with pycairo for Python3: http://cairographics.org/documentation/pycairo/3/reference/surfaces.html#cairo.ImageSurface.create_for_data It is (or should be) available in cairocffi: https://pythonhosted.org/cairocffi/api.html#cairocffi.ImageSu

Re: [Rdkit-devel] [Rdkit-announce] 2015.09 (Q3 2015) RDKit Release

And I have now pushed the python 2.7 and python 3.4 builds for the Mac to the rdkit channel at anaconda.org. -greg On Mon, Nov 23, 2015 at 11:04 PM, Riccardo Vianello < riccardo.viane...@gmail.com> wrote: > > ​Dear all, > > RDKit 2015.09.2 conda packages for linux and win-64 are now available fo

[Rdkit-devel] 2015.09 (Q3 2015) RDKit Release

Dear all, I'm pleased to announce that the next version of the RDKit -- 2015.09 (a.k.a. Q3 2015) -- is released. The new RDKit release theme is: Better late than never. :-) Note that this is a patch release (the version number ends in _2). We discovered a couple of problems in the original releas

Re: [Rdkit-devel] PDF Book

e the copy you have in the directory is from an old pull? -greg On Sat, Nov 7, 2015 at 4:47 AM, Greg Landrum wrote: > Thanks for pointing that out. I'll fix it. > > -greg > > > On Fri, Nov 6, 2015 at 8:42 PM, Gianluca Sforna wrote: > >> I noticed the RDKit Boo

Re: [Rdkit-devel] PDF Book

Thanks for pointing that out. I'll fix it. -greg On Fri, Nov 6, 2015 at 8:42 PM, Gianluca Sforna wrote: > I noticed the RDKit Book I find in Docs/Book after the build claims to > be from the 2013.09 release. > > Is it correct? Maybe it's just in need of a rebuild? > > Regards > > G. > > -- > G

[Rdkit-devel] Beta of Q3 2015 release now up

Dear all, I have tagged a beta of the next RDKit release here: https://github.com/rdkit/rdkit/releases/tag/Release_2015_09_1beta1 The relevant section of the release notes is below. Note that the list of people in the acknowledgement section was mostly created automatically from github. If you fe

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