Re: [Rdkit-discuss] Python argument types did not match C++ signature
On Oct 14, 2014, at 8:41 PM, Greg Landrum greg.land...@gmail.com wrote: The first thing that comes to mind, and I'm not sure that this has any relevance at all, is that it could be an import order thing. Does Bill import Chem before he imports your code? The next possibility that I can come up with is that there was something different in the build of your code and the RDKit on Bill's machine. I’ve just completely rebuilt everything to ensure all are built with exactly the same compiler. The error persists. As a positive control, I can create a SMILES structure within (the same) RDKit, and manipulate (add/remove) the hydrogens. Either different compiler versions were used or different RDKit versions or different boost versions. This somehow ends up being enough to screw up the type recognition between the two extension modules. A check here is to be sure that they were built using the same environment, that Python is using the one you think it is, and that DYLD_LIBRARY_PATH is set such that the correct RDKit libs are being found. As far as I am able to tell, all of this is true (as mentioned, the paths are hard-coded, but I also tried with manually setting $DYLD_LIBRARY_PATH, just in case it mattered. It didn’t). I’ll poke around some more. Thanks. William G. Scott http://scottlab.ucsc.edu/~wgscott -- Comprehensive Server Monitoring with Site24x7. Monitor 10 servers for $9/Month. Get alerted through email, SMS, voice calls or mobile push notifications. Take corrective actions from your mobile device. http://p.sf.net/sfu/Zoho ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Python argument types did not match C++ signature
On Oct 14, 2014, at 8:41 PM, Greg Landrum greg.land...@gmail.com wrote:
Hi Paul,
On Tue, Oct 14, 2014 at 11:22 PM, Paul Emsley pems...@mrc-lmb.cam.ac.uk
wrote:
I'm a bit lost with boost::python/RDKit/MacOSX.
I have a boost::python function:
RDKit::ROMol *hydrogen_transformations(const RDKit::ROMol r);
which is exposed like this:
BOOST_PYTHON_MODULE(pyrogen) {
def(hydrogen_transformations, hydrogen_transformations,
return_value_policymanage_new_object());
}
That all looks fine.
When I run this on my computers (RHEL6, Ubuntu, Fedora), it compiles and runs
fine fine. When Bill Scott tries on his Mac, at run-time he gets:
File /sw/lib/python2.7/site-packages/coot/pyrogen.py, line 607, in
make_restraints
sane_H_mol = pyrogen_boost.hydrogen_transformations(m_H)
Boost.Python.ArgumentError: Python argument types in
pyrogen_boost.hydrogen_transformations(Mol)
did not match C++ signature:
hydrogen_transformations(RDKit::ROMol)
Where m_H is created like this:
m_H = AllChem.AddHs(m)
and has type:
class 'rdkit.Chem.rdchem.Mol'
I'm not following why a Mol is not an RDKit::ROMol.
Don't get hung up on that bit; it's the usual way that those error messages
are worded. The first bit tells you the python type name, the second the C++
type name. The problem here is that it seems to not recognize that it should
be able to translate the Mol into the ROMol.
I'd appreciate any insight.
ooof... insight's going to be tough... how about guesses? ;-)
The first thing that comes to mind, and I'm not sure that this has any
relevance at all, is that it could be an import order thing. Does Bill import
Chem before he imports your code?
The next possibility that I can come up with is that there was something
different in the build of your code and the RDKit on Bill's machine. Either
different compiler versions were used or different RDKit versions or
different boost versions. This somehow ends up being enough to screw up the
type recognition between the two extension modules. A check here is to be
sure that they were built using the same environment, that Python is using
the one you think it is, and that $DYLD_LIBRARY_PATHis set such that the
correct RDKit libs are being found.
-greg
Hi Greg:
Thanks for the feedback.
The main likely differences are
1. I am using Apple’s clang++
2. I am using (fink’s) boost1.53.python27 to build (fink’s) RDkit (vers
2014.03.1). It was kind of an ordeal to get it working, so there is a distinct
possibility I f-ed something up.
$DYLD_LIBRARY_PATH is by fink policy unset, but the library paths are all
correctly hard-coded, and (in my case at least) I don’t have any other set of
libs for it to find.
Thanks.
Bill
William G. Scott
http://scottlab.ucsc.edu/~wgscott
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[Rdkit-discuss] RDKit, Java, and Fink on OS X
Hi folks: I’ve made a second update to the Fink RDKit package for OS X. I think it has all the extras turned on now, apart from the swig wrappers. I also made an extra fink package called rdkit-postgresql93” which (if I did it correctly) gives the user the option of building rdkit with or without the database support. As Greg reported earlier, I haven’t gotten the swig wrappers to link yet (using swig 3.0.0 and and boost 1.53 dependencies). I’ll make a further update/revision to the fink package when this gets sorted. Meanwhile, if anyone happens to use this and has any suggestions for improvements, please let me know. William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA University of California at Santa Cruz Santa Cruz, California 95064 USA http://scottlab.ucsc.edu/scottlab/ -- Accelerate Dev Cycles with Automated Cross-Browser Testing - For FREE Instantly run your Selenium tests across 300+ browser/OS combos. Get unparalleled scalability from the best Selenium testing platform available Simple to use. Nothing to install. Get started now for free. http://p.sf.net/sfu/SauceLabs ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDkit, OS X 10.9 and clang++
On Oct 26, 2013, at 9:24 AM, David Hall li...@cowsandmilk.net wrote: 'm fairly confident this isn't a compiler problem, but a libc++ problem. CXXFLAGS=-stdlib=libstdc++ cmake .. gets you past the current problem. But if boost is built against libc++ , it doesn't link, so I also built boost against libstdc++ and everything built. Thanks very much for this. It didn’t ultimately solve my problem (even after rebuilding boost), but it got me a lot further, and to a kludge, which then lead to a solution. Using libstdc++ got me to the point in compiling RDkit where I previously found I could get using fink’s g++4.8 compiler, but it still failed linking the boost libraries. I do not know why. Applying a sort of idiot-logic analogy, I decided to try building boost with fink’s g++-4.8 compiler, which required doing this edit to boost’s tools (I couldn’t get it to take from the command invocation): perl -pi -e 's|g\+\+|g++-4|' tools/build/v2/tools/darwin.jam That change, and using fink’s g++4.8 again with RDkit gets it to compile on OS X 10.9. I’m not competent enough to claim that it IS the compiler, but it looks that way to me. (It may have fortuitously changed something else). In any case, thanks for the help. Hopefully at some point I will figure out how to fix it (and/or boost) properly. — Bill -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDkit, OS X 10.9 and clang++
On Oct 26, 2013, at 12:17 PM, William G. Scott wgsc...@ucsc.edu wrote: On Oct 26, 2013, at 9:24 AM, David Hall li...@cowsandmilk.net wrote: 'm fairly confident this isn't a compiler problem, but a libc++ problem. CXXFLAGS=-stdlib=libstdc++ cmake .. gets you past the current problem. But if boost is built against libc++ , it doesn't link, so I also built boost against libstdc++ and everything built. It turns out David Hall is absolutely right. Setting CXXFLAGS=-stdlib=libstdc++” allows RDkit, (as well as coot), to compile with clang++ on OS X 10.9. There is something else subtle going on with the fink boost libraries such that rdkit only compiles for me when I use vanilla g++-4.8 (available in fink) to compile the boost libraries. However, everything else, including RDkit itself, compiles with Apple’s clang++ when CXXFLAGS=-stdlib=libstdc++” I’ll shut up now and will go away and ponder, but I just want to make clear that the problem I encountered isn’t in RDkit per se. Thanks to everyone for all the help. Bill -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] RDkit, OS X 10.9 and clang++
Dear RDkit community: I’ve been maintaining a fink package for RDkit (primarily as a dependency for coot). cf: http://tinyurl.com/rdkitfink It compiles and on OSX 10.6, 10.7 and 10.8, but not 10.9. (This includes the 2013_9 pre-release, FWIW.) With 10.9, the migration to clang++ is upon us, and I’m stuck. Has anyone succeeded in getting rdkit compiled on 10.9, and if so, how? Also, if anyone has feedback or recommendations for how to improve the fink rdkit package, please let me know. Thanks in advance. Bill Scott William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDkit, OS X 10.9 and clang++
Hi Greg: I’ve just placed two log files on http://fennario.ucsc.edu/~wgscott/temp/rdkit/ One was generated using the /usr/bin/g++ compiler on 10.9, i.e., zsh-% /usr/bin/g++ --version Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) Target: x86_64-apple-darwin13.0.0 Thread model: posix which seems to be the same as zsh-% /usr/bin/clang++ --version Apple LLVM version 5.0 (clang-500.2.79) (based on LLVM 3.3svn) Target: x86_64-apple-darwin13.0.0 Thread model: posix The other one, which gets a bit further, was generated with fink’s g++ version 4.8 compiler in /sw/bin/g++, i.e., zsh-% /sw/bin/g++-4 --version g++-4 (GCC) 4.8.2 Copyright (C) 2013 Free Software Foundation, Inc. However, as a positive control, I just installed the most recently available compilers for 10.8, which still works fine to compile rdkit fennario-% /usr/bin/g++ --version Configured with: --prefix=/Applications/Xcode.app/Contents/Developer/usr --with-gxx-include-dir=/usr/include/c++/4.2.1 Apple LLVM version 5.0 (clang-500.2.76) (based on LLVM 3.3svn) Target: x86_64-apple-darwin12.5.0 Thread model: posix It looks almost the same as the one for 10.9, so I am even more stumped than before. Bill On Oct 25, 2013, at 11:23 AM, greg landrum greg.land...@gmail.com wrote: Not an easy one. Since I don't have a Mac with 10.9 installed, I can't try it out either. I have been able to build the rdkit with clang++ in the past without problems and could certainly give that a try on a Linux box. Which version of clang are you using? What are you seeing for error messages when you try a build? -greg On 25 Oct 2013, at 18:43, William G. Scott wgsc...@ucsc.edu wrote: Dear RDkit community: I’ve been maintaining a fink package for RDkit (primarily as a dependency for coot). cf: http://tinyurl.com/rdkitfink It compiles and on OSX 10.6, 10.7 and 10.8, but not 10.9. (This includes the 2013_9 pre-release, FWIW.) With 10.9, the migration to clang++ is upon us, and I’m stuck. Has anyone succeeded in getting rdkit compiled on 10.9, and if so, how? Also, if anyone has feedback or recommendations for how to improve the fink rdkit package, please let me know. Thanks in advance. Bill Scott William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135991iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Problems homebrewing RDKit
I've made a Fink package for OS X, if that helps. If you don't want to use fink, it might still be of use to look at it. http://fink.cvs.sourceforge.net/viewvc/fink/dists/10.7/stable/main/finkinfo/sci/rdkit.info?view=markup HTH, William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Oct 21, 2013, at 9:07 AM, Nathan Brown nathan.br...@icr.ac.uk wrote: Hi All, I'm having some trouble installing RDKit using Eddie's brew on my new MacBook Pro. I've attached the reported errors below. Has anyone seen these before or have any idea how complete the installation? Cheers, Nath 104876CTHLT:Library nbrown$ brew doctor Your system is ready to brew. 104876CTHLT:Library nbrown$ brew install --HEAD rdkit == Cloning https://github.com/rdkit/rdkit.git Updating /Library/Caches/Homebrew/rdkit--git == cmake -DCMAKE_INSTALL_PREFIX='/usr/local/Cellar/rdkit/HEAD' -DCMAKE_BUILD_TYPE=None -DCMAKE_FIND_FRAMEWORK=LAST -Wno-dev -DRDK_INSTALL_INTREE=OFF -DRDK_INSTALL_STATIC_LIBS=OFF -DPYTHON_LIBRARY='/Syste used as include directory in directory /tmp/rdkit-oc3C/Code/ChemicalFeatures/Wrap -- Configuring incomplete, errors occurred! See also /tmp/rdkit-oc3C/CMakeFiles/CMakeOutput.log. See also /tmp/rdkit-oc3C/CMakeFiles/CMakeError.log. READ THIS: https://github.com/mxcl/homebrew/wiki/troubleshooting The Institute of Cancer Research: Royal Cancer Hospital, a charitable Company Limited by Guarantee, Registered in England under Company No. 534147 with its Registered Office at 123 Old Brompton Road, London SW7 3RP. This e-mail message is confidential and for use by the addressee only. If the message is received by anyone other than the addressee, please return the message to the sender by replying to it and then delete the message from your computer and network. -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135031iu=/4140/ostg.clktrk___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- October Webinars: Code for Performance Free Intel webinars can help you accelerate application performance. Explore tips for MPI, OpenMP, advanced profiling, and more. Get the most from the latest Intel processors and coprocessors. See abstracts and register http://pubads.g.doubleclick.net/gampad/clk?id=60135031iu=/4140/ostg.clktrk ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] DYLD_LIBRARY_PATH: RDKit + MacPorts compatibility problem
Hi Christian: I ran into a series of such problems while making the fink package for this a few weeks ago. Fink has the same edict (which is a good idea by the way) not to use DYLD_LIBRARY_PATH. My work-around was to use install_name_tool to properly hard-code the correct paths into the libraries after compiling. You can see how I did it here: http://fink.cvs.sourceforge.net/viewvc/fink/dists/10.7/stable/main/finkinfo/sci/rdkit.info?view=markup Feel free to use any or all of it for making a macports package. Bill William G. Scott Professor Department of Chemistry and Biochemistry and The Center for the Molecular Biology of RNA 228 Sinsheimer Laboratories University of California at Santa Cruz Santa Cruz, California 95064 USA On Mar 26, 2013, at 1:57 AM, Christian Kramer ck171...@gmail.com wrote: Dear all, I write this Email to report a bug/problem for the combination RDKit MacPorts that has kept me busy for two days. After recompiling a new version of boost I managed to install rdkit on my OS X 10.8 mac, otherwise using the libraries provided by MacPorts. As far as I can tell, RDKit works, but a lot of the other python modules that provide graphical output like matplotlib, Tkinter etc. do not work any more. For example, when trying to import Tkinter into python I get the following error: ## In [1]: import Tkinter --- ImportError Traceback (most recent call last) ipython-input-1-a0c812564da3 in module() 1 import Tkinter /opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/lib-tk/Tkinter.py in module() 37 # Attempt to configure Tcl/Tk without requiring PATH 38 import FixTk --- 39 import _tkinter # If this fails your Python may not be configured for Tk 40 tkinter = _tkinter # b/w compat for export 41 TclError = _tkinter.TclError ImportError: dlopen(/opt/local/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/_tkinter.so, 2): Symbol not found: __cg_jpeg_resync_to_restart Referenced from: /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO Expected in: /opt/local/lib/libJPEG.dylib in /System/Library/Frameworks/ImageIO.framework/Versions/A/ImageIO ## After a long search, it turned out that this is because I have to set the DYLD_LIBRARY_PATH for RDKit, which is incompatible with MacPorts. When I remove the DYLD_LIBRARY_PATH statement from my ~/.bash_profile and /etc/bashrc, Tkinter an matplotlib work, but RDKit does not work any more. Also, RDKit does not work using the DYLD_LIBRARY_FALLBACK_PATH instead. When googling for the DYLD_LIBRARY_PATH issue, I find quite a number of comments that suggest to not use this variable. So here is my question: Is it possible to remove the necessity to have the DYLD_LIBRARY_PATH set for rdkit in a future version? Or this there another workaround to get RDKit and matplotlib installed via MacPorts running? Cheers from Innsbruck, Christian -- Own the Future-Intelreg; Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Own the Future-Intelreg; Level Up Game Demo Contest 2013 Rise to greatness in Intel's independent game demo contest. Compete for recognition, cash, and the chance to get your game on Steam. $5K grand prize plus 10 genre and skill prizes. Submit your demo by 6/6/13. http://p.sf.net/sfu/intel_levelupd2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] rdkit OS X fink package
On Feb 9, 2013, at 7:23 AM, Greg Landrum greg.land...@gmail.com wrote: It certainly could be. I normally dynamically link against the boost python lib. It's worth trying using the dynamically linked version and seeing if it helps. I will do that. Out of curiosity, why did you decide not to use whatever boost version fink normally installs? -greg Fink has boost version 1.35, which I understood to be too old, and boost1.46.1.cmake, which I never was able to get rdkit to compile against (very possibly my ignorance). So I thought the most expedient thing was to use the latest boost and then if it works, nag the maintainer of boost 1.35 to update it. I think I'm far enough along to ask now. -Bill -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] rdkit OS X fink package
On Feb 9, 2013, at 8:10 AM, Greg Landrum greg.land...@gmail.com wrote: On Sat, Feb 9, 2013 at 4:36 PM, William G. Scott wgsc...@ucsc.edu wrote: Out of curiosity, why did you decide not to use whatever boost version fink normally installs? -greg Fink has boost version 1.35, which I understood to be too old, and boost1.46.1.cmake, which I never was able to get rdkit to compile against (very possibly my ignorance). So I thought the most expedient thing was to use the latest boost and then if it works, nag the maintainer of boost 1.35 to update it. I think I'm far enough along to ask now. 1.35? Wow... that's 5 years old. That's almost as bad as CentOS 5! [1] -greg [1] Problems building the RDKit on CentOS 5 caused by either buggy compilers or old Boost versions were a recurring theme here for a while, so that's a sort of bad joke. I suspect they wanted to migrate to boost.cmake. Will rdkit build with that (I couldn't get it to work, but that doesn't mean a whole lot…). If so, what is the minimum version that is compatible? -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] rdkit OS X fink package
On Feb 9, 2013, at 8:28 AM, Greg Landrum greg.land...@gmail.com wrote: On Sat, Feb 9, 2013 at 5:13 PM, William G. Scott wgsc...@ucsc.edu wrote: I suspect they wanted to migrate to boost.cmake. Will rdkit build with that (I couldn't get it to work, but that doesn't mean a whole lot…). boost.cmake is kind of a strange beast. I was pretty excited when it first appeared, but it seems to have never been accepted/taken up by the boost community. I thought it was kind of languishing, but from the wiki (https://svn.boost.org/trac/boost/wiki/CMakeModularizationStatus) it seems there is actually something going on. Interesting. If so, what is the minimum version that is compatible? CMakeLists.txt in $RDBASE looks for at least 1.39. I don't think that I have added anything since then that would change that. -greg Switching to the dylib enabled me to discover the underlying problem, which was (my) boost was linking to the wrong python. My after-the-fact repair, i.e., install_name_tool -change /System/Library/Frameworks/Python.framework/Versions/2.7/Python /sw/lib/python2.7/config/libpython2.7.dylib libboost_python.dylib fixed it! Thank you for setting me in the right direction. I'll probably have to annoy you some more as I ready the package for prime time. Again, many thanks for your help. Bill -- Free Next-Gen Firewall Hardware Offer Buy your Sophos next-gen firewall before the end March 2013 and get the hardware for free! Learn more. http://p.sf.net/sfu/sophos-d2d-feb ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] rdkit OS X fink package
Hi RDKit community:
First post.
I'm trying to make a rdkit package for Fink on OS X. (Fink is a debian-like
package management system for OS X). My initial reasons for doing this is
rdkit is a new dependency for a Fink package I currently maintain (the
molecular graphics display program coot), but I also am interested, being a
chemist.
I've compiled it and its dependencies, and am trying a few basic tests, and am
running into some problems. I am using Ubuntu's rdkit package as a positive
control.
If I do a simple test on Ubuntu, I get this uneventful response:
from rdkit import Chem
m = Chem.MolFromSmiles('Cc1c1')
Chem.MolToSmiles(m)
'Cc1c1'
If I do the same on the OS X version I compiled (using fink's python2.7 and
other dependencies, not the OS X system python), I get an error:
m = Chem.MolFromSmiles('Cc1c1')
Chem.MolToSmiles(m)
Traceback (most recent call last):
File stdin, line 1, in module
Boost.Python.ArgumentError: Python argument types in
rdkit.Chem.rdmolfiles.MolToSmiles(Mol)
did not match C++ signature:
MolToSmiles(RDKit::ROMol mol, bool isomericSmiles=False, bool
kekuleSmiles=False, int rootedAtAtom=-1, bool canonical=True, bool
allBondsExplicit=False)
I get errors of this form in other instances as well. I have no idea what it
means. Any suggestions where to start? (I had to compile a newer version of
boost than what is in fink, but it statically linked, so I was hoping to avoid
version mismatch errors. Could this be the source of the error?)
Thanks in advance.
Bill
William G. Scott
Professor
Department of Chemistry and Biochemistry
and The Center for the Molecular Biology of RNA
228 Sinsheimer Laboratories
University of California at Santa Cruz
Santa Cruz, California 95064
USA
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