Re: [Rdkit-devel] 2021.03.1 RDKit Release

, 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 files are

[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:

[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

[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

[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

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

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

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

[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:

[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

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.

[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

[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

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

er 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 development of exten

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

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 Tue,

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

[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

[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:

[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

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

[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

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

ost.cmake:1332 > (_Boost_MISSING_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/

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

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

[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

[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

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

step. Only if this 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 <greg.land...@gmail.com> > wrote: > >> >> >> On Wed, Apr 4, 2018 at 11:27 AM, Markus Sitzmann < >

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

[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

Re: [Rdkit-devel] problem building rdkit

eral;/ > 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 <greg.land...@gmail.com> > wrote: > &g

Re: [Rdkit-devel] problem building rdkit

r/FilterCatalog.cpp.o >> CMakeFiles/FilterCatalog.dir/FilterCatalogEntry.cpp.o >> CMakeFiles/FilterCatalog.dir/FilterMatchers.cpp.o >> CMakeFiles/FilterCatalog.dir/FunctionalGroupHierarchy.cpp.o >> ../../../lib/libRDKitSubgraphs.so.1.2018.03.1.dev1 >> ../../../lib/libRDKitSubstructMatch.

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

[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

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

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

Re: [Rdkit-devel] travis build timeouts

and then using the artifacts (=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 <greg.land...@gmail.com> > wrote: > >> Given that the current variability is almost a factor of

Re: [Rdkit-devel] travis build timeouts

building in the root 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 <greg.land...@gmail.com> > wrote: > >> Dear all, >> &

[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

[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:

[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

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

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

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

-devel] Boost and cmake version survey To: Greg Landrum <greg.land...@gmail.com> Cc: RDKit Developers List <rdkit-devel@lists.sourceforge.net> On Wed, Nov 9, 2016 at 11:41 AM, Greg Landrum <greg.land...@gmail.com> wrote: > This decision shouldn't matter to most users since they

[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

On Fri, Apr 15, 2016 at 1:18 PM, Gianluca Sforna <gia...@gmail.com> wrote: > On Fri, Apr 15, 2016 at 11:20 AM, Greg Landrum <greg.land...@gmail.com> > wrote: > > The problem here is that the rdkit doesn't really support Python 2.6 > > anymore. I don't remember at t

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

On Friday, 15 April 2016, Gianluca Sforna <gia...@gmail.com> wrote: > On Fri, Apr 15, 2016 at 4:41 AM, Greg Landrum <greg.land...@gmail.com > <javascript:;>> wrote: > > Now that I have a Centos6 box available, I'm realizing that it has python > > 2.6 &g

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

for the java wrappers or postgreSQL yet). -greg On Fri, Apr 15, 2016 at 4:41 AM, Greg Landrum <greg.land...@gmail.com> 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 bu

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

succeded, 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 <gia...@gmail.com> > wrote: > > On Thu, Apr 14, 20

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

't merge is was the problem 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 :) > > > &g

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:

Re: [Rdkit-devel] seg faults running tests on a mac

Hi Cyrus, I'm glad you were able to find something that works. If I had to guess, I would say that the root cause of all of this was the homebrew version of python confusing things. -greg On Sat, May 16, 2015 at 7:27 PM, Cyrus Harmon cyrushar...@gmail.com wrote: Ok, I think I've solved (or at

[Rdkit-devel] The RDKit and modern C++

Dear all, I would like to start allowing the use of modern C++ (by which I mean C++ 11/14) in the RDKit. I think this is an important step both for code quality in the toolkit itself and for allowing us (the developers) to continue to learn and use modern tools. Who knows, it may even help with

[Rdkit-devel] Beta of Q1 2015 release now up

Dear all, I have tagged a beta of the next RDKit release here: https://github.com/rdkit/rdkit/releases/tag/2014_09_1beta1 The relevant section of the release notes is below. I will try to get windows binaries up in the next few days. Unless major problems are found, I plan to do the actual

[Rdkit-devel] 2014.03 (Q1 2014) RDKit release

Dear all, I'm pleased to announce that the next version of the RDKit -- 2014.03 (a.k.a Q1 2014) -- is released. This is a bit late, but it turned out that it takes longer to get a 6-month release together than it did a 3-month release. Who ever would have anticipated that? ;-) The release notes

[Rdkit-devel] 2013.09.2 (Q3 2013) RDKit release

Dear all, I've just created the files for the 2013.09.2 release of the RDKit. This is purely a bug-fix release and contains no new features. The release notes are below. The source release is on the sourceforge downloads page: http://sourceforge.net/projects/rdkit/files/rdkit/Q3_2013/ and

Re: [Rdkit-devel] Beta of Q3 2013 release available

On Thu, Oct 24, 2013 at 11:35 AM, Gianluca Sforna gia...@gmail.com wrote: Tried to rebuild the RPMs for Fedora 20, fails at the cartridge with: g++ -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector-strong --param=ssp-buffer-size=4 -grecord-gcc-switches -m64

Re: [Rdkit-devel] 2012.12 (Q4 2012) RDkit release

Thanks Gianluca! On Tue, Jan 22, 2013 at 10:26 AM, Gianluca Sforna gia...@gmail.com wrote: On Tue, Jan 22, 2013 at 6:00 AM, Greg Landrum greg.land...@gmail.com wrote: I'm very happy to announce that the next version of the RDKit -- 2012.12 (a.k.a Q4 2012) -- is released. Thanks to Greg, I

Re: [Rdkit-devel] [Rdkit-discuss] PBF Code

Dear all, On Mon, Oct 29, 2012 at 10:57 AM, Nicholas Firth nicholas.fi...@icr.ac.ukwrote: Hi Guys, I have managed to be allowed to open source the code from my paper. Greg I couldn't work if I was supposed to add this to the contrib or if you do it, so I've just attached it to the email.

[Rdkit-devel] Question: Does anyone still need the Windows python 2.6 RDKit build?

Dear all, Starting with the 2012.12 release, I would like to stop doing python 2.6 builds of the RDKit for Windows. In addition to the administrative overhead of having to do the build, package it, and upload it, having a second Python installation on my Windows machine is making the process of

[Rdkit-devel] 2012.09 (Q3 2012) RDKit release

I'm very happy to announce that the next version of the RDKit -- 2012.09 (a.k.a Q3 2012) -- is released. The release notes are below. The source release is on the sourceforge downloads page: http://sourceforge.net/projects/rdkit/files/rdkit/Q3_2012/ The files can also be downloaded from the

[Rdkit-devel] Speeding up SMILES parsing

Over the past couple of days I've spent some time doing some tuning of the RDKit's SMILES parser. I made a couple of minor changes here and there and saw some improvement before making a change in the YACC grammar used to generate the parser. This made the parser source a bit more difficult to

Re: [Rdkit-devel] New MolDrawing.h

On Wed, Aug 15, 2012 at 6:04 AM, Greg Landrum greg.land...@gmail.com wrote: On Tue, Aug 14, 2012 at 1:20 PM, David Cosgrove davidacosgrov...@gmail.com wrote: As for the Qt demo, if it's convenient for you to do so, please do add the standard licence to the top of the files. I assume

Re: [Rdkit-devel] symbol(s) not found on Mac OS X 10.7.3

Hi Andrew, On Wed, Aug 22, 2012 at 12:17 PM, Andrew Dalke da...@dalkescientific.com wrote: On Aug 17, 2012, at 11:35 AM, Greg Landrum wrote: Here is, hopefully, the last update on this topic. Apologies for the verbosity. I'm trying to build the latests from the new repository. Here's

Re: [Rdkit-devel] updating the rdkit project on sourceforge

to change their local copies. I'll send information about how to do this once the migration has finished. -greg On Thu, Aug 16, 2012 at 5:24 AM, Greg Landrum greg.land...@gmail.com wrote: Dear all, Sourceforge has new backend software that they are encouraging everyone to switch their projects

Re: [Rdkit-devel] updating the rdkit project on sourceforge

$RDBASE rdk.patch - mv $RDBASE $RDBASE.old - do a fresh rdkit checkout as directed in option 1 above, make sure it goes into the directory $RDBASE - patch -p0 ./rdk.patch Best, -greg On Fri, Aug 17, 2012 at 8:25 AM, Greg Landrum greg.land...@gmail.com wrote: Ok, the change I mentioned