[Rdkit-devel] the RDKit and thread safety

Dear all, One of the joys of working with knime is that it makes it really easy to run RDKit code in parallel. One of the pains is that this is done using multi-threading, which quickly reveals that some of the RDKit code is not quite as thread safe as I had hoped that it was. In order to address

Re: [Rdkit-devel] 2011.12 (Q4 2011) RDKit release

Dear Michael, On Sun, Mar 4, 2012 at 8:59 PM, Michael Banck wrote: > On Sun, Jan 15, 2012 at 10:12:03AM +0100, Greg Landrum wrote: >> I'm very happy to announce that the next version of the RDKit -- >> 2011.12 (a.k.a Q4 2011) -- is released. > > I have uploaded 201

Re: [Rdkit-devel] 2011.12 (Q4 2011) RDKit release

On Wed, Mar 7, 2012 at 1:16 AM, Michael Banck wrote: > >> I'm not sure what you mean here. If you're doing an out-of-source >> build (which it sounds like you are), then you need to do a "make >> install" to get the built .so files copied into the $RDBASE/rdkit >> directory so that the python test

Re: [Rdkit-devel] Writing Fingerprints

On Thu, Mar 8, 2012 at 6:04 PM, Nicholas Firth 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 > > SparseIntVect *finger; > mol=SmilesToMol(line); > fin

Re: [Rdkit-devel] Fingerprint Reading

Dear Nick, On Mon, Mar 12, 2012 at 4:32 PM, Nicholas Firth 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. "01…", >

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

On Mon, Mar 12, 2012 at 10:48 AM, Gianluca Sforna wrote: > On Mon, Mar 12, 2012 at 10:31 AM, Gianluca Sforna wrote: >> >> According to the gcc manual,  -fexcess-precision defaults to "fast". >> Is there a specific reason to deviate from that? > > Uhm... I assumed this was something coming from rd

Re: [Rdkit-devel] the RDKit and thread safety

On Mon, Mar 5, 2012 at 8:40 AM, Greg Landrum wrote: > > One of the joys of working with knime is that it makes it really easy > to run RDKit code in parallel. One of the pains is that this is done > using multi-threading, which quickly reveals that some of the RDKit > code is not

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

Gianluca, On Tue, Mar 13, 2012 at 11:41 AM, Gianluca Sforna wrote: > On Tue, Mar 13, 2012 at 4:56 AM, Greg Landrum 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

On Wed, Mar 21, 2012 at 5:58 PM, Nicholas Firth 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, however I've seen that > r

[Rdkit-devel] Beta of Q1 2012 release available

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: http://code.google.com/p/rdkit/downloads/detail?name=RDKit

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

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 googl

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

Hi Michael, On Sun, May 20, 2012 at 3:00 PM, Michael Banck wrote: > > I have uploaded 2012.03 to Debian now.  Unfortunately, it still fails to > build on some architectures, see http://buildd.debian.org/rdkit I still need to get debian running under qemu on my ubuntu linux box. I started to set

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

On Sun, Jun 3, 2012 at 6:33 PM, Paul Emsley 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 that I'm really not

[Rdkit-devel] some nice performance improvements

Dear all, I've been making some changes to the SMILES canonicalization code (more on this later) that have also led to some nice (IMO) performance improvements. Here are the numbers. My usual benchmarking operations (http://code.google.com/p/rdkit/wiki/Benchmarking) don't really help here: 1000 m

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

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, mor

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

On Fri, Jun 29, 2012 at 7:45 AM, Greg Landrum wrote: > > The test I devised was the following : > > 1) Read a molecule from the sdf > 2) generate canonical smiles csmi > 3) Parse csmi to give a new molecule > 4) generate a new canonical smiles and make sure it matches cs

[Rdkit-devel] Beta of Q2 2012 release available

Today I tagged the beta for the 2012.06 (Q3 2012 in the old numbering) release in svn: http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_2012_06_1beta1/ and uploaded a source distribution to the google code site: http://code.google.com/p/rdkit/downloads/detail?name=RDKit_2012_06_1beta1.tg

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

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 googl

Re: [Rdkit-devel] RHEL/CentOS 5 RPM in the works

Dear Gianluca, On Fri, Jul 27, 2012 at 9:26 AM, Gianluca Sforna wrote: > I'm preparing a rpm for Centos 5 (so we can keep more build questions > away from the ML :) ) and I'm quite near a good result. Thanks for this. Any Centos-related build pain we can prevent is a very good thing. :-) > In f

Re: [Rdkit-devel] New MolDrawing.h

Hi Dave, On Tue, Aug 7, 2012 at 11:32 AM, David Cosgrove wrote: > > As discussed with Greg, I've tweaked > $RDBASE/Code/Demos/RDKit/Draw/MolDrawing.h so that for acyclic double and > triple bonds the offset is symmetrical about the bond, which I think looks > neater. The two PNGs attached show th

Re: [Rdkit-devel] New MolDrawing.h

Dave, On Tue, Aug 14, 2012 at 1:20 PM, David Cosgrove wrote: > > Thanks for the reply. I'll try and find time to have a crack at wedged > bonds in the C++ drawings. That would be very cool. > When does the next version freeze? I'll try and > get it done for then. I'm going to try to get at le

[Rdkit-devel] updating the rdkit project on sourceforge

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 (un

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

ll need 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 wrote: > Dear all, > > Sourceforge has new backend software that they are encouraging > everyone to switch their p

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

diff $RDBASE > rdk.patch - mv $RDBASE $RDBASE.old - , 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 wrote: > Ok, the change I mentioned below has been made; we're now using the > new sourc

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 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.

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

Hi James, On Fri, Aug 24, 2012 at 1:24 AM, James Swetnam wrote: > Ironically, I just ran into this same issue with our internal gcc build > today. I've attached a patch that removes the platform-specific -O0 flag > for Dict.cpp and replaces the force_types() method with the following, which > is

[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 rea

Re: [Rdkit-devel] New MolDrawing.h

On Wed, Aug 15, 2012 at 6:04 AM, Greg Landrum wrote: > > On Tue, Aug 14, 2012 at 1:20 PM, David Cosgrove > 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 the copyright tra

Re: [Rdkit-devel] fmcs in RDKit

On Sat, Sep 1, 2012 at 1:28 AM, Andrew Dalke wrote: > I've started to add the fmcs MCS search code to RDKit. > By that I mean it does not include the command-line driver > which is part of the fmcs distribution; just the MCS search code. I would have no objection to the command-line driver being

Re: [Rdkit-devel] fmcs in RDKit

On Tue, Sep 25, 2012 at 4:30 AM, Andrew Dalke wrote: > The next quarter release is coming soon, which was good incentive for me to > work on the new MCS code for RDKit. This is great news. Andrew's MCS code fills an important gap in the current RDKit functionality. > Here's the API and document

Re: [Rdkit-devel] RDKit on Github

On Fri, Oct 5, 2012 at 9:27 AM, Gianluca Sforna 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. What is in

[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 googl

[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

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

Dear Nick, On Mon, Oct 29, 2012 at 10:57 AM, Nicholas Firth wrote: > 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. The code is a 'working'

[Rdkit-devel] C# wrappers for the RDKit

Dear all, After some key assistance from a colleague (thanks Nico!), I've managed to build C# wrappers for the RDKit that are useable from within Visual Studio projects. These use the same SWIG configuration as the RDKit java wrappers, so the API should be more or less the same in both Java and C#

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

Dear all, On Mon, Oct 29, 2012 at 10:57 AM, Nicholas Firth wrote: > 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. The code is a 'working'

[Rdkit-devel] Rethinking the RDKit's implicit hydrogen handling

Hi, This is an unusually long email for me, so here's the TL;DR version: The RDKit handling of implicit hydrogens is confusing. This leads to needlessly complicated code and, almost certainly, bugs. I'm proposing to fix it, but doing so requires an API change. This work will be done on a branch un

Re: [Rdkit-devel] Rethinking the RDKit's implicit hydrogen handling

On Mon, Dec 10, 2012 at 4:51 PM, Andrew Dalke wrote: > On Dec 8, 2012, at 7:01 AM, Greg Landrum wrote: > > It's a pretty small API change, but there's a huge amount of code that > needs to be changed in the back and lots and lots of testing that has to be > done, so this

[Rdkit-devel] Getting ready for the Q4 2012 release

Dear all, I'd like to get the beta of the next RDKit release out in the next week or so. If there's anything important/major still hanging/missing, please let me know so I can try to get it fixed/integrated. -greg -- Mas

[Rdkit-devel] Beta of Q4 2012 release

Dear all, Today I tagged the beta for the 2012.12 release in svn: http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_2012_12_1beta1/ and uploaded a source distribution to the google code site: *http://rdkit.google

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

I'm very happy to announce that the next version of the RDKit -- 2012.12 (a.k.a Q4 2012) -- is released. The release notes are below. The source release is on the sourceforge downloads page: http://sourceforge.net/projects/rdkit/files/rdkit/Q4_2012/ The files can also be downloaded from the googl

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

Thanks Gianluca! On Tue, Jan 22, 2013 at 10:26 AM, Gianluca Sforna wrote: > On Tue, Jan 22, 2013 at 6:00 AM, Greg Landrum 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 can o

Re: [Rdkit-devel] VF2 subgraph isomorphism algorithm now in Boost

Yeah I saw that this morning. I will definitely do the experiment in the not too distant future. On Feb 5, 2013, at 5:04 PM, Andrew Dalke wrote: > I just read the new Boost 1.53 release notes: > > • Added VF2 subgraph isomorphism algorithm (contributed by Flavio De > Lorenzi). > > I though

[Rdkit-devel] Beta of Q1 2013 release

Dear all, Today I tagged the beta for the 2013.03 release in svn: https://sourceforge.net/p/rdkit/code/HEAD/tree/tags/Release_2013_03_1beta1/ and uploaded a source distribution to the google code site: https://rdkit.googlecode.com/files/RDKit_2013_03_1beta1.tgz There's still some documentation w

[Rdkit-devel] 2013.03 (Q1 2013) RDkit release

I'm pleased to announce that the next version of the RDKit -- 2013.03 (a.k.a Q1 2013) -- is released. The release notes are below. The source release is on the sourceforge downloads page: http://sourceforge.net/projects/rdkit/files/rdkit/Q1_2013/ The files can also be downloaded from the google p

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

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 ful

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

some kinks with mirroring the github repo back to the sourceforge svn, but these will eventually be resolved so that we have a live svn mirror for those who do not want to use git. Best Regards, -greg On Fri, May 17, 2013 at 5:41 AM, Greg Landrum wrote: > Dear all, > > We had a dis

[Rdkit-devel] Beta of Q2 2013 release

Dear all, Today I tagged the beta for the 2013.06 release in git: *https://github.com/rdkit/rdkit/releases/tag/Release_2013_06_1beta1* Thanks to the magic of github, this automatically creates a download link: https://github.com/rdkit/rdkit/archive/Release_2013_06_1beta1.tar.gz If no show-stoppe

[Rdkit-devel] Beta of Q3 2013 release available

mplementation has been updated See Jameed Hussain's tutorial from the 2013 UGM for details: https://github.com/rdkit/UGM_2013/tree/master/Tutorials/mmpa_tutorial [Jameed Hussain] - An implementation of Ertl and Schuffenhauer's Synthetic Accessibility score is available in Contr

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

On Thu, Oct 24, 2013 at 11:35 AM, Gianluca Sforna 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 -mtune=generic -Wno-u

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

On Fri, Oct 25, 2013 at 9:20 AM, Gianluca Sforna wrote: > On Thu, Oct 24, 2013 at 1:26 PM, Greg Landrum > wrote: > > > > > > Is the source actually present in > > /builddir/build/BUILD/Release_2013_09_1beta1/Code? > > Got it. The beta tar.gz extracts code in

[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 direct

[Rdkit-devel] Beta of Q1 2014 release available

Dear all, >From the "better late than never" files... ;-) Today I tagged the beta for the 2014.04 release in git: https://github.com/rdkit/rdkit/releases/tag/Release_2014_03_1beta1 Here's the github download link: https://github.com/rdkit/rdkit/archive/Release_2014_03_1beta1.tar.gz I haven't do

[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

Re: [Rdkit-devel] Charged atoms in SMARTS and SMILES

Hi Christos, On Mon, May 12, 2014 at 12:35 PM, Christos Kannas wrote: > > I've noticed the following: > >>> m = Chem.MolFromSmarts("[O]=[O+]-[O-]") > >>> print Chem.MolToSmarts(m) > O=[O&+]-[O&-] > >>> print Chem.MolToSmiles(m) > O=OO > > In order to have a correct SMILES for it I do: > >>> smile

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

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 wrote: > Hi All, > > As

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

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. Unles

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

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 wrote: > Dear all, > > In preparat

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

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

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

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 down

[Rdkit-devel] 2014.09.2 RDKit patch release

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: https://github.com/rdkit/rd

Re: [Rdkit-devel] polymers

Hi Igor, On Mon, Dec 29, 2014 at 3:43 AM, Igor Filippov 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 skipped > The RDKit doesn't

Re: [Rdkit-devel] polymers

On Mon, Dec 29, 2014 at 12:42 PM, Igor Filippov 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 accept polymers and t

[Rdkit-devel] new C++ drawing code

Dear all, I just created a pull request for integration of some new C++ drawing code into the RDKit: https://github.com/rdkit/rdkit/pull/412 This is a big one, so I will leave the PR active until the weekend for people to look at and comment on before I merge onto the master. The new code suppor

Re: [Rdkit-devel] new C++ drawing code

I merged the pull request this morning. The new C++ drawing code is now available on master. Best, -greg On Thu, Jan 15, 2015 at 5:20 AM, Greg Landrum wrote: > Dear all, > > I just created a pull request for integration of some new C++ drawing code > into the RDKit: > https://g

Re: [Rdkit-devel] new C++ drawing code

2015 at 2:41 AM, Greg Landrum > wrote: > >> I merged the pull request this morning. The new C++ drawing code is now >> available on master. >> >> Best, >> -greg >> >> >> On Thu, Jan 15, 2015 at 5:20 AM, Greg Landrum >> wrote: >> >

[Rdkit-devel] Enhancements to the 2D drawing API

Dear all, I created an issue to track some enhancements I want to make to the C++ 2D drawing API: https://github.com/rdkit/rdkit/issues/417 I'm doing the changes themselves on this branch; https://github.com/rdkit/rdkit/tree/Issue417 Here's the current state: - [x] add drawPolygon() Mandatory i

Re: [Rdkit-devel] Enhancements to the 2D drawing API

he new functions already > available? If so, I can take a look how easy it is to translate to > wxWidgets api. > > Igor > > On Wed, Jan 28, 2015 at 12:17 AM, Greg Landrum > wrote: > >> Dear all, >> >> I created an issue to track some enhancements I want t

Re: [Rdkit-devel] Install RDKit

Hi Soren, On Thu, Jan 29, 2015 at 2:03 AM, Soren Wacker wrote: > > I would highly appreciate a > conda install rdkit > > way of doing it, but that is probably not so easy to realize. > It wasn't easy to realize but fortunately Riccardo has already done the work: https://github.com/rdkit/conda-r

Re: [Rdkit-devel] Install RDKit

I believe you need to install the version of the rdkit you just built in your conda environment with conda install and make sure that environment is active. It looks like it's finding a different build. You can confirm this by doing: python -c 'import rdkit;print(rdkit.__file__)' and looking at t

Re: [Rdkit-devel] Canonical atom order

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 wrote: > Hello RDKiters, > > I'd like someh

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

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 O

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

tion python libraries), boost, etc… are rearing the > ugly head and I’m not quite sure where to begin trying to fix things. > Suggestions? > > thanks, > > Cyrus > > On Mar 9, 2015, at 10:37 PM, Greg Landrum wrote: > > Hi Cyrus, > > That's something we misse

[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 rele

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

The URL in the email below is incorrect (copy-paste bug!), it should be: https://github.com/rdkit/rdkit/releases/tag/Release_2015_03_1beta1 Apologies for the mistake. -greg On Fri, Apr 17, 2015 at 4:32 AM, Greg Landrum wrote: > Dear all, > > I have tagged a beta of the next RDKit rel

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

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 and

[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

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 wrote: > Ok, I think I've solved (or at least worked around)

Re: [Rdkit-devel] SVG font size problem

Cyrus, When you generate a PDF with the RDKit drawing code, it attempts to find installed versions of cairo and aggdraw. If these both fail, then it uses an old (and buggy) cross-platform drawing library called sping (which is included with the RDKit). It looks like the problem you are having is d

[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

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

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

[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] [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

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] 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] 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] 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

[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] 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

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

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

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] 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] 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

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

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

; 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

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

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

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