Re: [Rdkit-devel] Writing Fingerprints

2012-03-08 Thread Greg Landrum
On Thu, Mar 8, 2012 at 6:04 PM, Nicholas Firth nicholas.fi...@icr.ac.uk wrote: Hi All, I've run into a few more problems with Fingerprinting, I'm trying to create a database of these fingerprints, I've tried a few different methods to write the fingerprints SparseIntVectboost::uint32_t

Re: [Rdkit-devel] Fingerprint Reading

2012-03-12 Thread Greg Landrum
Dear Nick, On Mon, Mar 12, 2012 at 4:32 PM, Nicholas Firth nicholas.fi...@icr.ac.uk wrote: I've now got an issue with reading in fingerprints (now that you've helped me write them), I've tried a number of different ways. Currently I've got the fingerprints as a string made up of bits, i.e.

Re: [Rdkit-devel] Anyone building the cartrdige with GCC 4.6.2 in a 32 bit env?

2012-03-16 Thread Greg Landrum
Gianluca, On Tue, Mar 13, 2012 at 11:41 AM, Gianluca Sforna gia...@gmail.com wrote: On Tue, Mar 13, 2012 at 4:56 AM, Greg Landrum greg.land...@gmail.com wrote: You've probably tracked this down already, but I guess that it's probably the postgresql configuration. So, it turned up -fexcess

Re: [Rdkit-devel] Graph-Mol

2012-03-21 Thread Greg Landrum
On Wed, Mar 21, 2012 at 5:58 PM, Nicholas Firth nicholas.fi...@icr.ac.uk wrote: Hi All, I am hoping for a piece of advice, I have a graph (connectivity matrix with atom indexes) and I want to make a molecule from that graph. I was planning on creating an sdf and then reading in this way,

[Rdkit-devel] Beta of Q1 2012 release available

2012-04-01 Thread Greg Landrum
Dear all, This morning I tagged the beta for the 2012.03 (Q1 2012 in the old numbering) release in svn: http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_2012_03_1beta1/ and uploaded a source distribution to the google code site:

[Rdkit-devel] 2012.03 (Q1 2012) RDKit release

2012-04-12 Thread Greg Landrum
I'm very happy to announce that the next version of the RDKit -- 2012.03 (a.k.a Q1 2012) -- is released. The release notes are below. The source release is on the sourceforge downloads page: http://sourceforge.net/projects/rdkit/files/rdkit/Q1_2012/ The files can also be downloaded from the

Re: [Rdkit-devel] [Rdkit-discuss] python/c++ interface again...

2012-06-03 Thread Greg Landrum
On Sun, Jun 3, 2012 at 6:33 PM, Paul Emsley paul.ems...@bioch.ox.ac.uk wrote: OK, thanks again. I have done some reading about boost.python.  I understand now (as you imply) that the idea is not to (have to) use PyObject *s.  OK, let's try with that for the moment. Yeah, the real problem is

[Rdkit-devel] Changes in the canonicalization algorithm and tests thereof

2012-06-28 Thread Greg Landrum
Dear all, I've been making some changes to the SMILES canonicalization code. My original intent was to get the code to efficiently and correctly generate SMILES for fragments of molecules (demo of this below). Along the way I realized that I could make the canonicalization faster and, I think,

[Rdkit-devel] 2012.06 (Q2 2012) RDKit release

2012-07-10 Thread Greg Landrum
I'm very happy to announce that the next version of the RDKit -- 2012.06 (a.k.a Q2 2012) -- is released. The release notes are below. The source release is on the sourceforge downloads page: http://sourceforge.net/projects/rdkit/files/rdkit/Q2_2012/ The files can also be downloaded from the

[Rdkit-devel] updating the rdkit project on sourceforge

2012-08-15 Thread Greg Landrum
Dear all, Sourceforge has new backend software that they are encouraging everyone to switch their projects too. Based on the descriptions (https://sourceforge.net/p/allura/wiki/Features/) it sounds like a good idea to me, so I plan to go ahead and initiate the update in the next couple of days

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

2012-08-17 Thread Greg Landrum
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

2012-08-17 Thread Greg Landrum
$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

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

2012-08-23 Thread Greg Landrum
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

[Rdkit-devel] Speeding up SMILES parsing

2012-08-28 Thread Greg Landrum
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

2012-08-28 Thread Greg Landrum
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] RDKit on Github

2012-10-05 Thread Greg Landrum
On Fri, Oct 5, 2012 at 9:27 AM, Gianluca Sforna gia...@gmail.com wrote: Just one note about the repo. I'm mirroring it hourly from SVN, but this is done from my own PC so, if it is offline, there could be delays on updates. Otherwise, it should be pretty much in sync with the master SVN repo.

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

2012-10-20 Thread Greg Landrum
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] Question: Does anyone still need the Windows python 2.6 RDKit build?

2012-10-24 Thread Greg Landrum
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

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

2012-11-16 Thread Greg Landrum
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.

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

2013-01-22 Thread Greg Landrum
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

[Rdkit-devel] Switching to git/github as the primary source code repository for the RDKit

2013-05-16 Thread Greg Landrum
Dear all, We had a discussion thread about switching the RDKit project to use git and github for the primary source repository and bug tracker. Thanks to a lot of help from Gianluca Sforna, it's time to make this transition for real. We have a repository set up now on github that contains the

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

2013-10-24 Thread Greg Landrum
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

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

2014-01-27 Thread Greg Landrum
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

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

2014-05-11 Thread Greg Landrum
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

Re: [Rdkit-devel] 2D Mol Draw classes

2014-07-30 Thread Greg Landrum
Thanks for this Dave. It's a long weekend for us and, if the weather plays along, I'm not going to be around, but I will take a look through next week. Input from anyone else would, of course, also be very welcome. -greg On Wed, Jul 30, 2014 at 2:11 PM, David Cosgrove

[Rdkit-devel] Beta of Q3 2014 release now up

2014-10-19 Thread Greg Landrum
Dear all, In preparation for this week's RDKit UGM, 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 before the UGM starts on Wednesday.

Re: [Rdkit-devel] Beta of Q3 2014 release now up

2014-10-19 Thread Greg Landrum
Quick update: there are now win64 binaries for the python2.7 wrapper and java wrapper attached to that beta release. Please post if you encounter any strangeness with the release. -greg On Mon, Oct 20, 2014 at 6:11 AM, Greg Landrum greg.land...@gmail.com wrote: Dear all, In preparation

Re: [Rdkit-devel] Beta of Q3 2014 release now up

2014-10-29 Thread Greg Landrum
On Wed, Oct 29, 2014 at 10:32 PM, Gianluca Sforna gia...@gmail.com wrote: On Mon, Oct 20, 2014 at 7:50 AM, Greg Landrum greg.land...@gmail.com wrote: Quick update: there are now win64 binaries for the python2.7 wrapper and java wrapper attached to that beta release. Please post if you

[Rdkit-devel] 2014.09 (Q3 2014) RDKit Release

2014-10-30 Thread Greg Landrum
Dear all, I'm pleased to announce that the next version of the RDKit -- 2014.09 (a.k.a. Q3 2014) -- 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_2014_09_1 as well as the sourceforge

[Rdkit-devel] 2014.09.2 RDKit patch release

2014-12-12 Thread Greg Landrum
Dear all, I've just completed assembling a patch to the 2014.09 rdkit release that fixes a number of bugs, including a significant memory leak in the chemical reaction handling.. The release notes are below. The release and binary files are on the github release page:

Re: [Rdkit-devel] polymers

2014-12-28 Thread Greg Landrum
Hi Igor, On Mon, Dec 29, 2014 at 3:43 AM, Igor Filippov igor.v.filip...@gmail.com wrote: I was wondering how complicated it would be to add the ability to read polymers from molfiles. Right now I am getting something like this: Unhandled CTAB feature: S group SRU on line: 75. Molecule

Re: [Rdkit-devel] polymers

2014-12-30 Thread Greg Landrum
On Mon, Dec 29, 2014 at 12:42 PM, Igor Filippov igor.v.filip...@gmail.com wrote: Greg, Thanks for the fast reply, as always! I could imagine a couple solutions to this: 1) adding additional arguments to the mol file parser that allows calling code to specify that they are willing to

Re: [Rdkit-devel] ImportError: No module named 'pidSVG'

2015-03-09 Thread Greg Landrum
Hi Cyrus, That's something we missed when we did the Python3 port of the RDKit. It turns out that there are a few of these problems in the rdkit.sping package that need to be brought up to date. I will get those fixed and checked in the next day or so. Thanks for reporting the problem, -greg

Re: [Rdkit-devel] Canonical atom order

2015-01-29 Thread Greg Landrum
There's not currently a way to do this. It's pretty easy to add to the python wrapper though, so I will go ahead and do that. Here's the github issue: https://github.com/rdkit/rdkit/issues/421 -greg On Thu, Jan 29, 2015 at 4:57 PM, Maciek Wójcikowski mac...@wojcikowski.pl wrote: Hello

[Rdkit-devel] 2015.03 (Q1 2015) RDKit Release

2015-05-05 Thread Greg Landrum
Dear all, I'm pleased to announce that the next version of the RDKit -- 2015.03 (a.k.a. Q1 2015) -- is released. Better late than never. :-) The release notes are below. The release and binary files are on the github release page: https://github.com/rdkit/rdkit/releases/tag/Release_2015_03_1

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

2015-05-11 Thread Greg Landrum
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

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

2015-05-16 Thread Greg Landrum
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] Beta of Q1 2015 release now up

2015-04-16 Thread Greg Landrum
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] Beta of Q3 2015 release now up

2015-10-27 Thread Greg Landrum
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

Re: [Rdkit-devel] PDF Book

2015-11-06 Thread Greg Landrum
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? > >

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

2015-12-03 Thread Greg Landrum
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] More build fun with RHEL 6

2016-04-14 Thread Greg Landrum
'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] More build fun with RHEL 6

2016-04-14 Thread Greg Landrum
: > I think I have seen this 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 <greg.land...@gmail.com> wrote:

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

2016-04-14 Thread Greg Landrum
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

2016-04-15 Thread Greg Landrum
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

2016-04-15 Thread Greg Landrum
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

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

2016-04-18 Thread Greg Landrum
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

2016-04-15 Thread Greg Landrum
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] InChI 1.05

2017-02-24 Thread Greg Landrum
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] InChI 1.05

2017-02-24 Thread Greg Landrum
d), but I don't think it makes a difference as far as > InChI is concerned. > > Best regards, > Igor > > > On Fri, Feb 24, 2017 at 8:43 AM, Greg Landrum <greg.land...@gmail.com> > wrote: > >> Thanks Igor! I was not looking forward to getting this working, so it

[Rdkit-devel] Boost and cmake version survey

2016-11-09 Thread Greg Landrum
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:

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

2016-11-09 Thread Greg Landrum
-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

Re: [Rdkit-devel] GenerateDepictionMatching3DStructure

2016-11-22 Thread Greg Landrum
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

Re: [Rdkit-devel] RDKit Python wrappers

2016-12-01 Thread Greg Landrum
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

2016-12-01 Thread Greg Landrum
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] Rdkit and ipywidget installation

2017-03-22 Thread Greg Landrum
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

Re: [Rdkit-devel] RDKit installation

2017-03-26 Thread Greg Landrum
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

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

2017-03-31 Thread Greg Landrum
[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

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

2017-04-20 Thread Greg Landrum
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

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

2017-04-21 Thread Greg Landrum
Right you are. I will push those too From: Maciek Wójcikowski <mac...@wojcikowski.pl> 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.

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

2017-04-21 Thread Greg Landrum
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] Adding RDKit::ROMol *s to a boost::python::list

2017-07-16 Thread Greg Landrum
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

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

2017-04-28 Thread Greg Landrum
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:

Re: [Rdkit-devel] travis build timeouts

2017-06-13 Thread Greg Landrum
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

2017-06-13 Thread Greg Landrum
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

2017-06-13 Thread Greg Landrum
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] 2017.09.1 RDKit release

2017-10-08 Thread Greg Landrum
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

2017-09-08 Thread Greg Landrum
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

Re: [Rdkit-devel] drawing amino acids

2017-09-08 Thread Greg Landrum
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

[Rdkit-devel] Beta of the 2017.09 release available

2017-09-29 Thread Greg Landrum
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