[Rdkit-discuss] [Open position] Cheminformatician at Sosei Heptares, Cambridge, UK
Hi all, I'll keep it short: we're currently recruiting for a Cheminformatician at Sosei Heptares. We have no specific grade in mind - you could be just finishing your PhD, or be much more experienced. Here's the link for more details: https://cezanneondemand.intervieweb.it/heptares/jobs/cheminformatician-computational-chemistry-team-37704/en/ Happy to answer questions about the position - just email me off-list. Regards, Noel ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Using Chem.WrapLogs()
Thanks Maciek,
Both of those solutions works on Linux, which is fine for my purposes.
Neither works on Windows (let me know if you want me to file a bug).
Regards,
- Noel
On 8 September 2017 at 15:05, Maciek Wójcikowski <mac...@wojcikowski.pl>
wrote:
> Hi Noel,
>
> sio.seek(0) before assert or sio.getvalue() instead read().
>
>
> Pozdrawiam, | Best regards,
> Maciek Wójcikowski
> mac...@wojcikowski.pl
>
> 2017-09-08 15:51 GMT+02:00 Noel O'Boyle <baoille...@gmail.com>:
>
>> Hi all,
>>
>> I'd like to capture error messages during SMILES parsing, but am having
>> trouble getting this to work.
>>
>> The following code raises an AssertionError, for example. Is there
>> something here I'm missing? I'm using this from a Windows 7 conda
>> environment, Python 2.7 64-bit, RDKit 2017.03.3, but a similar conda
>> environment is also failing for me on Linux.
>>
>> import sys
>> from rdkit import Chem
>> Chem.WrapLogs()
>> from StringIO import StringIO
>>
>> old_stderr = sys.stderr
>> sio = sys.stderr = StringIO()
>>
>> mol = Chem.MolFromSmiles("c1c")
>> sys.stderr = old_stderr
>>
>> assert sio.read() != ""
>>
>> Regards,
>> - Noel
>>
>>
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[Rdkit-discuss] Using Chem.WrapLogs()
Hi all,
I'd like to capture error messages during SMILES parsing, but am having
trouble getting this to work.
The following code raises an AssertionError, for example. Is there
something here I'm missing? I'm using this from a Windows 7 conda
environment, Python 2.7 64-bit, RDKit 2017.03.3, but a similar conda
environment is also failing for me on Linux.
import sys
from rdkit import Chem
Chem.WrapLogs()
from StringIO import StringIO
old_stderr = sys.stderr
sio = sys.stderr = StringIO()
mol = Chem.MolFromSmiles("c1c")
sys.stderr = old_stderr
assert sio.read() != ""
Regards,
- Noel
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Re: [Rdkit-discuss] Setting location of wedge/hashes
Great. And as regards what the bond direction means...? It tells you whether it's a wedge or dash but doesn't seem to specify which end of the bond is the thin end. Is the BeginAtom of the bond always the thin end, or is any attached chiral atom always the thin end? - Noel On 10 September 2015 at 15:03, Greg Landrum <greg.land...@gmail.com> wrote: > Agreed. If you set the bond wedging explicitly it should be preserved. > > Here's the issue, which includes links to the commits with the fix (that's > now checked in): > https://github.com/rdkit/rdkit/issues/611 > > -greg > > > On Mon, Sep 7, 2015 at 1:10 PM, Noel O'Boyle <baoille...@gmail.com> wrote: >> >> Hey Greg, >> >> I hope you had a good meeting. >> >> I was wondering whether it is possible to set the location of depicted >> wedge/hashes in a MOL file output. >> >> Right now, it seems that I can call WedgeHashBonds and that tells me >> where the wedge or hashes are via GetBondDir() (although I am still a >> bit confused as to which direction they are supposed to be). And I can >> set the BondDir fine... >> >> However, when I subsequently write out a MOL file it seems that any >> changes to the location of the BondDirs are just ignored. >> >> This is not a biggie for me, but it would be nice to be able to always >> set the same bond as the stereobond in a set of amino acids, as this >> makes it obvious which are D- versus L-. >> >> Regards, >>Noel >> >> >> -- >> ___ >> Rdkit-discuss mailing list >> Rdkit-discuss@lists.sourceforge.net >> https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > -- Monitor Your Dynamic Infrastructure at Any Scale With Datadog! Get real-time metrics from all of your servers, apps and tools in one place. SourceForge users - Click here to start your Free Trial of Datadog now! http://pubads.g.doubleclick.net/gampad/clk?id=241902991=/4140 ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Setting location of wedge/hashes
Hey Greg, I hope you had a good meeting. I was wondering whether it is possible to set the location of depicted wedge/hashes in a MOL file output. Right now, it seems that I can call WedgeHashBonds and that tells me where the wedge or hashes are via GetBondDir() (although I am still a bit confused as to which direction they are supposed to be). And I can set the BondDir fine... However, when I subsequently write out a MOL file it seems that any changes to the location of the BondDirs are just ignored. This is not a biggie for me, but it would be nice to be able to always set the same bond as the stereobond in a set of amino acids, as this makes it obvious which are D- versus L-. Regards, Noel -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Notes on building the latest RDKit
Hi Greg, It might be something at this end, but compiling the FMCS target with MSVC 11.0 and Boost 1.49 I have: C:\Boost\include\boost-1_49\boost/property_tree/detail/json_parser_read.hpp(105): error C2664: 'boost::property_tree::basic_ptreeKey,Data::push_back' : cannot convert parameter 1 from 'std::pair_Ty1,_Ty2' to 'const std::pair_Ty1,_Ty2 ' This looks like an MSVC versus Boost issue rather than anything related to RDKit. Regards, - Noel On 21 May 2015 at 03:22, Greg Landrum greg.land...@gmail.com wrote: Hi Noel, On Wed, May 20, 2015 at 10:54 AM, Noel O'Boyle baoille...@gmail.com wrote: This isn't really a bug report, just an FYI that may be helpful. I've been using Boost 1.49 until now to compile RDKit, but this is now too old. Specifically, the FMCS code chokes on it. Though we likely will start requiring a reasonably up-to-date version of boost at some point in the not-too-distant future, that hasn't happened yet. I have built the current release using boost 1.48 and a recent version of the code using v1.42, so the problem isn't boost in general. If you send me the error messages you are seeing, I may be able to help diagnose this. Also, I've been compiling on Windows with mingw-w64 (the fork of MinGW), and I needed to comment out the definition of struct timezone in the FMCS code (DebugTrace.h) as it's already present in mingw-w64's includes. I don't know if it's worth fixing but if so, maybe this link will help: http://quickgit.kde.org/?p=emerge.gita=commitdiffh=cffdf0eb0b8ed8f65c640ba33db03b8f7970a6f0hp=a3f18e16cb9fffa406de70c84b855843e10e98a7 (check_type_size(timezone HAVE_TIMEZONE_DEFINED)) Thanks for pointing that out. I'll take a look. Best, -greg -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Notes on building the latest RDKit
Hi Greg, This isn't really a bug report, just an FYI that may be helpful. I've been using Boost 1.49 until now to compile RDKit, but this is now too old. Specifically, the FMCS code chokes on it. Also, I've been compiling on Windows with mingw-w64 (the fork of MinGW), and I needed to comment out the definition of struct timezone in the FMCS code (DebugTrace.h) as it's already present in mingw-w64's includes. I don't know if it's worth fixing but if so, maybe this link will help: http://quickgit.kde.org/?p=emerge.gita=commitdiffh=cffdf0eb0b8ed8f65c640ba33db03b8f7970a6f0hp=a3f18e16cb9fffa406de70c84b855843e10e98a7 (check_type_size(timezone HAVE_TIMEZONE_DEFINED)) Regards, Noel -- One dashboard for servers and applications across Physical-Virtual-Cloud Widest out-of-the-box monitoring support with 50+ applications Performance metrics, stats and reports that give you Actionable Insights Deep dive visibility with transaction tracing using APM Insight. http://ad.doubleclick.net/ddm/clk/290420510;117567292;y ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Smiles Atom order
Hi Greg, Is there any way to retrieve the SMILES atom order after generating a SMILES string, and if not, is this something that could easily be added (I might try a patch)? This is useful to store additional information relating to particular atoms in the comment field. Regards, Noel -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Smiles Atom order
Great. So if I understand you correctly, it is currently accessible from C++. - Noel On 11 June 2013 10:26, Greg Landrum greg.land...@gmail.com wrote: Noel, On Tue, Jun 11, 2013 at 10:49 AM, Noel O'Boyle baoille...@gmail.com wrote: Is there any way to retrieve the SMILES atom order after generating a SMILES string, and if not, is this something that could easily be added (I might try a patch)? This is useful to store additional information relating to particular atoms in the comment field. There is a molecule property that is set called _smilesAtomOutputOrder that contains the atom ordering. It is unfortunately not currently accessible from python. Adding access to it is probably pretty straightforward. I have to check if I can make mol.GetProp work with this or if a special function (or optional argument to MolToSmiles) is required. This is github issue #50: https://github.com/rdkit/rdkit/issues/50 -greg -- This SF.net email is sponsored by Windows: Build for Windows Store. http://p.sf.net/sfu/windows-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Cinfony 1.1 released
Hello all, I've just released Cinfony 1.1 with support for RDKitl 2011.09. New in this release is support for Indigo and OPSIN. If you are interested in writing Python scripts that have access to several cheminformatics toolkits using the same API (CDK, Open Babel, Indigo, RDKit and OPSIN are all supported), check out http://cinfony.googlecode.com. All the best, Noel -- All the data continuously generated in your IT infrastructure contains a definitive record of customers, application performance, security threats, fraudulent activity, and more. Splunk takes this data and makes sense of it. IT sense. And common sense. http://p.sf.net/sfu/splunk-novd2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Access RDKit from Java
Hi Greg, You mentioned that there is a Jar file and associated shared library for RDKit in the KNIME repository. Unfortunately, they don't provide access except on request (see http://tech.knime.org/node/20231 for example). Could you make these available somewhere or include them in a future release? - Noel -- Achieve unprecedented app performance and reliability What every C/C++ and Fortran developer should know. Learn how Intel has extended the reach of its next-generation tools to help boost performance applications - inlcuding clusters. http://p.sf.net/sfu/intel-dev2devmay ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Build on Windows
Are you sure you installed regex? It needs to be compiled. On Windows I use the binary installer where you can tick the box for different boost components. On 28 July 2010 15:14, Evgueni Kolossov ekolos...@gmail.com wrote: Tried Run cmake with -DBoost_LIBRARYDIR=whatever but it still cannot find regex On 28 July 2010 15:07, Noel O'Boyle baoille...@gmail.com wrote: On 28 July 2010 15:04, Evgueni Kolossov ekolos...@gmail.com wrote: Dear Greg, I am trying to rebuild RDKit on Windows using boost 1_43 and cannot go through the configuration stage with CMake: CMake Error at C:/Program Files/CMake 2.8/share/cmake-2.8/Modules/FindBoost.cmake:910 (message): Unable to find the requested Boost libraries. Boost version: 1.43.0 Boost include path: C:/boost/boost_1_43_0 The following Boost libraries could not be found: boost_regex No Boost libraries were found. You may need to set Boost_LIBRARYDIR to the directory containing Boost libraries or BOOST_ROOT to the location of Boost. Call Stack (most recent call first): Code/GraphMol/SLNParse/CMakeLists.txt:4 (find_package) CMake Error: The following variables are used in this project, but they are set to NOTFOUND. Please set them or make sure they are set and tested correctly in the CMake files: Boost_REGEX_LIBRARY (ADVANCED) linked by target testSLNParse in directory C:/RDKit/Code/GraphMol/SLNParse Configuring incomplete, errors occurred! I have tried to set environmental variable Boost_LIBRARYDIR to .\boost_1_43_0\bin.v2\libs or to \boost_1_43_0\boost where regex directory is but it still cannot find it. Run cmake with -DBoost_LIBRARYDIR=whatever Please help. Regards, Evgueni -- -- The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss Mob. +44(0)7812070446 -- The Palm PDK Hot Apps Program offers developers who use the Plug-In Development Kit to bring their C/C++ apps to Palm for a share of $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] RDKit packaging issues
On 5 July 2010 21:33, Gianluca Sforna gia...@gmail.com wrote:
Hi all,
after spending some time to prepare a Fedora package I have a couple
remarks/suggestions I'd like to discuss with you in order to make the
process easier for all the distributions around.
Versioning - package manager programs (this is valid in all distros)
handle updates by comparing versions to decide which one is newer.
Having names like Q12010, Q22010 etc will break ordering next year
(Q42010 Q12011).
I suggest you revise how you do name versions; one simple way to avoid
the issue is to swap year with quarter, so 2010Q4 2011Q1. Avoiding
non numeric versions would be a nice bonus, so you could use to the
same effect something like .MM (so 2010.12 2011.04)
Installation - files installed by the make install step should
honour the DESTDIR environment variable; this is becasue packagers
need to put files under a certain build directory to be picked up
later by the packaging script; this is usually accomplished by setting
the env variable DESTDIR or running make install DESTDIR=xxx. I also
need to mention this buildroot (xxx in the example) usually translates
to / when the package is installed, so default installation
subdirectories should be picked according to common standard naming.
AFAIK, with CMAKE you set -DCMAKE_INSTALL_PREFIX for a local install.
For instance, libraries (lib*.so.*) are usually to be installed in
/usr/lib{64}, binaries in /usr/bin, header files in /usr/include and
so on; I believe cmake has all we need to use these these standard
paths, but I'd need to dig manuals and/or other projects to find out
the correct spell to cast...
I think I could uncover more packaging issues as I proceed, but I
wanted to kick off some discussions on these points early so we move
on quicker toward good linux packages.
Cheers
G.
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Re: [Rdkit-discuss] Q2 2010 Release
On 1 July 2010 13:43, Evgueni Kolossov ekolos...@gmail.com wrote: Dear Greg, I was sure bison and flex are part of cygwin installation but cannot find executables. Can you suggest anything? Run cygwin setup, and type bison into the search box. Regards, Evgueni On 1 July 2010 13:06, Greg Landrum greg.land...@gmail.com wrote: On Thu, Jul 1, 2010 at 1:38 PM, Evgueni Kolossov ekolos...@gmail.com wrote: Greg, looking like it cannot be done with cmake without python installed. I have cygwin installed but cmake cannot find BISON and FLEX and complaining about python executable. Any suggestions? The python part should be easy: after you configure the first time, untick the RDK_BUILD_PYTHON_WRAPPERS box and then configure again. flex and bison should be found if they are in your PATH. Please check that they are. -greg -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- This SF.net email is sponsored by Sprint What will you do first with EVO, the first 4G phone? Visit sprint.com/first -- http://p.sf.net/sfu/sprint-com-first ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] read 2 SDF files in the loop
On 1 July 2010 19:52, Greg Landrum greg.land...@gmail.com wrote:
Dear Cedric,
On Thu, Jul 1, 2010 at 10:52 AM, Cedric MORETTI
cedric.more...@firmenich.com wrote:
Hello all,
I have a little question.
I don’t arrive to read 2 SDF files with RDKIT when I use the for loop.
I explain
I have a first sdf files with 1 property and a second with another
properties.
I put the second SDMolSupplier instead of “suppl” and load a sdf file ( look
exemple)
I think what you want is something like the following:
suppl1 = Chem.SDMolSupplier('file1.sdf')
suppl2 = Chem.SDMolSupplier('file2.sdf')
for mol1 in suppl1:
mol2 = suppl2.next()
# do something with the two molecules
Maybe for mol1, mol2 in zip(suppl1, suppl2): ?
Best Regards,
-greg
If I replace the SDMolSupplier by a text file the program don’t have a
problem.
I just search a writer to read 2 SDF ….
Tks
Cedric
reader1 = Chem.SDMolSupplier(C:\Data\scaffold/Total/totalscaffold.sdf.sdf)
writer = Chem.SDWriter(C:\Data\scaffold/Eval/evalcount.sdf)
z = 0
for mol in reader1:
h = Chem.MolToSmiles(mol)
suppl = open('C:\Data\scaffold/Total/total.txt','r')
for a in suppl:
r = 0
r+=1
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Re: [Rdkit-discuss] Having removed old libraries and compiled boost1.43 again
You should be able to accomplish the same with cmake -DBoost_USE_STATIC_LIBS=OFF. On 25 June 2010 04:58, Kei Taneishi ktanei...@gmail.com wrote: Hi Christian, I'm using dynamic linking to libboost_regex. At first, edit $RDBASE/Code/GraphMol/SLNParse/CMakeLists.txt as below. == --- ../Code/GraphMol/SLNParse/CMakeLists.txt (revision 1440) +++ ../Code/GraphMol/SLNParse/CMakeLists.txt (working copy) @@ -1,7 +1,7 @@ FIND_PACKAGE(BISON) FIND_PACKAGE(FLEX) -set(Boost_USE_STATIC_LIBS ON) +set(Boost_USE_STATIC_LIBS OFF) find_package(Boost 1.39.0 COMPONENTS regex REQUIRED) == and delete $RDBASE/build/CMakeCache.txt to forget the previous configs, then in the $RDBASE/build directory, cmake .. make. Regards, Kei bouille wrote: Dear Greg Having removed old libraries and compiled boost1.43 again [ 80%] Built target MolCatalog [ 80%] Built target testMolCatalog [ 80%] Built target rdMolCatalog Linking CXX shared library libSLNParse.so /usr/bin/ld: /usr/local/lib/libboost_regex.a(instances.o): relocation R_X86_64_32 against `boost::object_cacheboost::re_detail::cpp_regex_traits_basechar, boost::re_detail::cpp_regex_traits_implementationchar ::do_get(boost::re_detail::cpp_regex_traits_basechar const, unsigned long)::s_data' can not be used when making a shared object; recompile with -fPIC /usr/local/lib/libboost_regex.a: could not read symbols: Bad value collect2: ld a retourné 1 code d'état d'exécution make[2]: *** [Code/GraphMol/SLNParse/libSLNParse.so] Erreur 1 make[1]: *** [Code/GraphMol/SLNParse/CMakeFiles/SLNParse.dir/all] Erreur 2 make: *** [all] Erreur 2 Best Regards Christian -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- ThinkGeek and WIRED's GeekDad team up for the Ultimate GeekDad Father's Day Giveaway. ONE MASSIVE PRIZE to the lucky parental unit. See the prize list and enter to win: http://p.sf.net/sfu/thinkgeek-promo ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Error depicting a smiles string
I'll look into this as soon as possible. On 30 April 2010 10:24, Cedric MORETTI cedric.more...@firmenich.com wrote: Tks you Greg for your answer. If my brain is good, I'm remember that Noel O'Boyle (the cinfony creator's) subscribed to RDKIT mailing-list so maybe he could answer at my question. Cedric -Original Message- From: Greg Landrum [mailto:greg.land...@gmail.com] Sent: vendredi, 30. avril 2010 11:14 To: Cedric MORETTI Cc: RDKit Discuss Subject: Re: [Rdkit-discuss] Error depicting a smiles string Hi, On Fri, Apr 30, 2010 at 5:06 AM, Cedric MORETTI cedric.more...@firmenich.com wrote: I use a Q42009 with the package Cinfony. I am in windows system ( :( ) The picture made 300x300 Size 4.75kb I can't answer questions about cinfony since I don't know know how it works. Please try using the RDKit without cinfony. Thanks, -greg ** DISCLAIMER This email and any files transmitted with it, including replies and forwarded copies (which may contain alterations) subsequently transmitted from Firmenich, are confidential and solely for the use of the intended recipient. The contents do not represent the opinion of Firmenich except to the extent that it relates to their official business. ** -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] beta of Q1 2010 release up
Since the world's attention has been drawn to this, maybe I'd better
sort this out now :-)
On 20 April 2010 19:04, Andrew Dalke da...@dalkescientific.com wrote:
On Apr 20, 2010, at 6:56 PM, Geoffrey Hutchison wrote:
Feel free to steal the CMake from Open Babel. See scripts/CMakeLists.txt.
A few weeks ago, we used CMake's SWIG support to compile and install the
Python bindings -- this was buggy.
Now, we run distutils, e.g.:
install(CODE execute_process(COMMAND ${PYTHON_EXECUTABLE}
${openbabel_SOURCE_DIR}/scripts/python/setup.py install
--prefix=${CMAKE_INSTALL_PREFIX} WORKING_DIRECTORY
${openbabel_BINARY_DIR}/scripts))
In trying to get OpenBabel to compile on my Mac last week, working with Noel
on this, I found that this part of the OB configuration for the Mac doesn't
work quite right.
I expect the default installation to go into the standard Python
site-packages directory, which for me is
/Library/Python/2.6/site-packages
However, cmake wants there to be a CMAKE_INSTALL_PREFIX, and uses the default
/usr/local. This caused OB to install the Python code into
/usr/local/lib/python2.6/site-packages . It's the only package I have
installed in that directory.
I don't have a good feeling for how setting CMAKE_INSTALL_PREFIX should
affect the install. Perhaps there should be a CMAKE_INSTALL_PYTHON_PREFIX or
something like that. My observation here is only that when nothing is
specified then the default Python installation directory should be the
default determined by Python, and not by the cmake configuration.
Noel knows about this.
Andrew
da...@dalkescientific.com
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Re: [Rdkit-discuss] beta of Q1 2010 release up
On 20 April 2010 19:20, Geoffrey Hutchison ge...@geoffhutchison.net wrote:
On Apr 20, 2010, at 2:04 PM, Andrew Dalke wrote:
In trying to get OpenBabel to compile on my Mac last week, working with Noel
on this, I found that this part of the OB configuration for the Mac doesn't
work quite right.
I expect the default installation to go into the standard Python
site-packages directory, which for me is
/Library/Python/2.6/site-packages
Yes, I need to fix Noel's CMakeLists -- it needs a special case for if(APPLE)
here. That should show up in SVN in the next 15 minutes or so.
I don't have a good feeling for how setting CMAKE_INSTALL_PREFIX should
affect the install. Perhaps there should be a CMAKE_INSTALL_PYTHON_PREFIX or
something like that. My observation here is only that when nothing is
specified then the default Python installation directory should be the
default determined by Python, and not by the cmake configuration.
Well, I haven't tried, it, but if you can give me a python script which gives
the appropriate destination directory, I can hack the CMake code. e.g.
EXECUTE_PROCESS(COMMAND ${PYTHON_EXECUTABLE} -c
import numpy; print numpy.get_include()
OUTPUT_VARIABLE NUMPY_INCLUDE_DIR)
This particular bit gives CMake the location of the numpy headers. I'm sure
there's some similar function call for distutils, right?
Please - don't edit this, right now. I'm sorting it out as we speak. I
will post the solution to openbabel-devel later today, and cc all
interested parties.
Cheers,
-Geoff
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Re: [Rdkit-discuss] Compiling boost
Ok, I had to run the following after unzipping boost: ./bootstrap.sh --with-libraries=python --prefix=/home/user/Tools/cinfony/tree ./bjam install There was no need to download or install bjam separately. The RDKit build was then configured as follows: cmake .. -DCMAKE_INSTALL_PREFIX=/home/user/Tools/cinfony/tree -DBoost_INCLUDE_DIR=/home/user/Tools/cinfony/tree/include - Noel On 31 March 2010 17:16, Greg Landrum greg.land...@gmail.com wrote: Hi Noel, Looks like the problem with the build instructions is that I assume a pre-built version of bjam; bad assumption. Your best bet is probably to follow the build instructions for boost that are in the boost docs: http://www.boost.org/doc/libs/1_42_0/more/getting_started/unix-variants.html#easy-build-and-install you only need the python library, so don't worry about building everything. Note: I haven't tested the RDKit with boost 1.42, but I don't anticipate any major problems. -greg On Wed, Mar 31, 2010 at 8:46 AM, Noel O'Boyle baoille...@gmail.com wrote: Hello Greg, I'm trying to follow the instructions at http://code.google.com/p/rdkit/wiki/BuildingWithCmake on an Ubuntu 9.04 system. (1) I downloaded a boost source version. (http://sourceforge.net/projects/boost/files/boost/1.42.0/boost_1_42_0.tar.gz/download) (2) I extracted it and tried bjam --with-python release install, but I don't have bjam. (3) I downloaded ../boost-jam-3.1.18. It said there was a precompiled version, but there wasn't so I compiled it. (4) I run bjam --with-python release install, but got u...@ubuntu904desktop:~/Tools/cinfony/boost_1_42_0$ ../boost-jam-3.1.18/bin.linuxx86/bjam Unable to load Boost.Build: could not find build system. - /home/user/Tools/cinfony/boost_1_42_0/boost-build.jam attempted to load the build system by invoking 'boost-build tools/build/v2 ;' but we were unable to find bootstrap.jam in the specified directory or in BOOST_BUILD_PATH (searching /home/user/Tools/cinfony/boost_1_42_0/tools/build/v2, /usr/share/boost-build). Please consult the documentation at 'http://www.boost.org'. What am I doing wrong? Were you using the same versions? - Noel -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Compiling boost
On 1 April 2010 14:53, Noel O'Boyle baoille...@gmail.com wrote: On 1 April 2010 14:49, Greg Landrum greg.land...@gmail.com wrote: Dear Noel, On Thu, Apr 1, 2010 at 2:09 AM, Noel O'Boyle baoille...@gmail.com wrote: Ok, I had to run the following after unzipping boost: ./bootstrap.sh --with-libraries=python --prefix=/home/user/Tools/cinfony/tree ./bjam install There was no need to download or install bjam separately. The RDKit build was then configured as follows: cmake .. -DCMAKE_INSTALL_PREFIX=/home/user/Tools/cinfony/tree -DBoost_INCLUDE_DIR=/home/user/Tools/cinfony/tree/include Thanks for this. I will update the wiki. One question: you didn't provide cmake with any information about where the boost shared libraries are located. Are you sure that things are linked against the correct version of boost? No they weren't. The truth is that I found it very difficult to convince cmake to use the new boost rather than the system one even after defining three boost related variables. In the end, I just uninstalled the system one. And I should say that the CMAKE_INSTALL_PREFIX is ignored by RDKit so there was no need to specify that. One of the core ideas behind CMake is to separate the source and build trees. However, RDKit insists on building around the source. It could be a good idea to change this in future. - Noel -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Compiling boost
Hello Greg, I'm trying to follow the instructions at http://code.google.com/p/rdkit/wiki/BuildingWithCmake on an Ubuntu 9.04 system. (1) I downloaded a boost source version. (http://sourceforge.net/projects/boost/files/boost/1.42.0/boost_1_42_0.tar.gz/download) (2) I extracted it and tried bjam --with-python release install, but I don't have bjam. (3) I downloaded ../boost-jam-3.1.18. It said there was a precompiled version, but there wasn't so I compiled it. (4) I run bjam --with-python release install, but got u...@ubuntu904desktop:~/Tools/cinfony/boost_1_42_0$ ../boost-jam-3.1.18/bin.linuxx86/bjam Unable to load Boost.Build: could not find build system. - /home/user/Tools/cinfony/boost_1_42_0/boost-build.jam attempted to load the build system by invoking 'boost-build tools/build/v2 ;' but we were unable to find bootstrap.jam in the specified directory or in BOOST_BUILD_PATH (searching /home/user/Tools/cinfony/boost_1_42_0/tools/build/v2, /usr/share/boost-build). Please consult the documentation at 'http://www.boost.org'. What am I doing wrong? Were you using the same versions? - Noel -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] datamining with RDKIT and cinfony
On 19 March 2010 13:53, Cedric MORETTI cedric.more...@firmenich.com wrote: Hi I have a question with RDKIT… There are tools of dataminning in RDKIT?? I don’t find these tools… Other question When the news version to cinfony is available? The next week??? Cinfony 1.0a is available at http://cinfony.googlecode.com. You will also find a mailing list for cinfony at that website. Any questions should be sent there. I’m really interested to use this version with the last version to OpenBabel cdk and RDKIT.. Tks Noel and Greg for your job… Cedric ** DISCLAIMER This email and any files transmitted with it, including replies and forwarded copies (which may contain alterations) subsequently transmitted from Firmenich, are confidential and solely for the use of the intended recipient. The contents do not represent the opinion of Firmenich except to the extent that it relates to their official business. ** -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] rdkit and Cinfony
Hi Cedric, There will be a new version of cinfony released in the coming week (and a talk to follow at the ACS, the following week). This supports the latest version of RDKit. I also promise to set up a proper mailing list where enquiries of this sort can be sent (sorry Greg). - Noel Original message follows: On Fri, Mar 12, 2010 at 3:23 PM, Cedric MORETTI cedric.more...@firmenich.com wrote: Hello, I would like to know if there is someone who uses utility Cinfony with RDKit. I use version 0.9 of Cinfony and an old version of RDKit (May 2008). There is no problem when using both programs. But I cannot arrive to install version Q2009P25, RDKit module is not found when I loaded. Although having only replace the contents of the directory rdkit Cinfony. I'm not a cinfony user, and it would be helpful to have the full traceback (as Andrew said), but I can make a guess about this: The package structure of the RDKit changed between the Q42008 and Q12009 release. If the older version of Cinfony is expecting the old RDKit structure, it's not going to work with newer versions. Maybe there's a newer version of cinfoy you can download? Best Regards, -greg -- Download Intel#174; Parallel Studio Eval Try the new software tools for yourself. Speed compiling, find bugs proactively, and fine-tune applications for parallel performance. See why Intel Parallel Studio got high marks during beta. http://p.sf.net/sfu/intel-sw-dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Q4 Release for Windows
2010/1/25 Greg Landrum greg.land...@gmail.com: Hi Noel, On Sun, Jan 24, 2010 at 9:45 PM, Noel O'Boyle baoille...@gmail.com wrote: Hello Greg, Just tried the Q4 .tar.gz for Windows. It seems to be missing several .pyd files. In particular, it is missing rdBase.pyd so that the following error occurs: The .tar.gz file is a source release, so the lack of .pyd files is to be expected. :-) I had forgotten to put up the windows binary of the beta for Q4 2009. Looks good to me. I'm doing that now, but be forewarned it has the same path problem (i.e. missing the RDKit_Q42009_1 base dir) as the old binaries. I'll fix this for the actual release. -greg -- Throughout its 18-year history, RSA Conference consistently attracts the world's best and brightest in the field, creating opportunities for Conference attendees to learn about information security's most important issues through interactions with peers, luminaries and emerging and established companies. http://p.sf.net/sfu/rsaconf-dev2dev ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Moving to Python 2.6
Hello Greg, Hope you had a good holiday. Looking at the download figures from OB Python since Aug 09, the vast majority of users are now using Python 2.6 (on Windows at least!). Wearing my cinfony hat, is there any chance that the next windows release of RDKit will target 2.6 (or better still, both 2.5 and 2.6)? Also, it would be nice to have a .zip file instead of a .tgz file for Windows users (.tgz is heap powerful magic for many people). - Noel
Re: [Rdkit-discuss] packaging changes moved to trunk
Yes - I was wondering how you were going to pull off the Windows release. If you want someone to bounce ideas off, get in touch... 2009/2/27 Greg Landrum greg.land...@gmail.com: Dear all, I've merged the contents of the EasyInstall branch of the RDKit code onto the trunk. This has some consequences for those using the code from Python which are detailed in this repeat of some of the contents of my previous message on this topic: Build/installation instructions for linux: http://code.google.com/p/rdkit/wiki/NewLinuxBuild and for windows: http://code.google.com/p/rdkit/wiki/NewWindowsBuild Adapting the linux build instructions for the Mac (things do work on the Mac; I did most of the development work there) is left as an exercise for the reader. :-) An important note about the new code layout, from ReleaseNotes.txt: - The directory structure of the distribution has been changed in order to make installation of the RDKit python modules more straightforward. Specifically the directory $RDBASE/Python has been renamed to $RDBASE/rdkit and the Python code now expects that $RDBASE is in your PYTHONPATH. When importing RDKit Python modules, one should now do: from rdkit import Chem instead of import Chem. Old code will continue to work if you also add $RDBASE/rdkit to your PYTHONPATH, but it is strongly suggested that you update your scripts to reflect the new organization. I had hoped to be able to do a one click (or one line) binary installer for the python modules, but that seems to be more difficult than I had expected : things are fine on linux and the mac, but don't seem to work the way I want on windows (which is probably where they are most needed). I will try to do a bit more investigation of this before the next release, but it's not high priority. Best regards, -greg -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] packaging changes moved to trunk
You need a separate procedure for Windows (if sys.platform==win32) with something along the lines of the Windows installer for OB 2.2.0 Python at: http://openbabel.svn.sf.net/viewvc/openbabel/openbabel/tags/openbabel-2-2-0/windows-vc2005/OBPythonOBF/setup.py?revision=2698view=markup The extension modules in this case are not built with distutils and yet it all works. It's also possible to set some environment variables at this time, if necessary. See the postinstall.py script in the same directory. - Noel 2009/2/27 Greg Landrum greg.land...@gmail.com: On Fri, Feb 27, 2009 at 10:08 AM, Noel O'Boyle baoille...@gmail.com wrote: Yes - I was wondering how you were going to pull off the Windows release. If you want someone to bounce ideas off, get in touch... Thanks for the offer. What I tried is to use the python distutils to create either a tar ball (linux and mac) or a clickable installer (windows). This would take care of installing the RDKit in appropriate directories. The few dependencies (numpy, pil, etc.) could be pretty easily installed using other standard python tools (e.g. setuptools). The problem is that though distutils is quite good at installing extension modules that are built using distutils, it seems to be much weaker at installing extension modules that are built using some other method (i.e. bjam, cmake, whatever). Essentially what happened is that the windows installers that I'd get would end up putting the .py files in the right place, but they'd screw up the location of the .pyd files for the RDKit extension modules. This didn't happen on linux or the mac. Unless I can find some time to look for work-arounds, I'm probably just going to abandon the simple windows installation idea and go back to a well-packaged zip archive (or tarball) that the user can just extract in the appropriate place. Alternate suggestions are very welcome, -greg
Re: [Rdkit-discuss] Canonical SMILES
2009/2/17 Andrew Dalke da...@dalkescientific.com: On Feb 17, 2009, at 9:18 AM, George Oakman wrote: Does someone know if I can assume that the canonical SMILES of RDKit are the same as the Open Babel ones? You can assume they are not the same. No attempt has been made to make them consistent. I wouldn't assume that without a lot of testing. My assumption is that canonical SMILES generation is so implementation sensitive that it's very unlikely two systems would do it the same way unless that was a deliberate goal. Which I know wasn't the case with those two implementations. I think also that RDKit pays more attention to handling stereochemistry than OpenBabel. Am I doing something wrong in responding to the mailing list, it looks like all my answers are logged as a separate message as oposed to being logged in the same thread - please let me know, I don't want to make it all untidy! I don't use a threaded mail reader so I can't tell. I use Gmail and everything is nicely threaded. Andrew da...@dalkescientific.com -- Open Source Business Conference (OSBC), March 24-25, 2009, San Francisco, CA -OSBC tackles the biggest issue in open source: Open Sourcing the Enterprise -Strategies to boost innovation and cut costs with open source participation -Receive a $600 discount off the registration fee with the source code: SFAD http://p.sf.net/sfu/XcvMzF8H ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] RDKit descriptors
Hello Greg, Am I right in saying that there are no 3D descriptors in RDKit? That they're all either 1D or 2D? - Noel
Re: [Rdkit-discuss] Building on Mac
2008/11/28 Greg Landrum greg.land...@gmail.com: On Thu, Nov 27, 2008 at 10:34 PM, Noel O'Boyle baoille...@gmail.com wrote: than installs them. The Sytem Python comes with PIL, Tkinter, wxPython, Numpy and Matplotlib. And that's it. There doesn't seem to be a package manager for Macs. So if you want any other extensions you're out of luck. For what it's worth, easy_install seems to work without problems using the system python. That, of course, doesn't help you if a package isn't available via easy_install. And fink unstable is the only choice for pycairo for MacOSX on an Intel. hmm, I wonder: ~ $ sudo easy_install pycairo Password: Searching for pycairo Reading http://pypi.python.org/simple/pycairo/ Reading http://www.cairographics.org/pycairo Reading http://cairographics.org/releases/ Best match: pycairo 1.6.4 Downloading http://cairographics.org/releases/pycairo-1.6.4.tar.gz Processing pycairo-1.6.4.tar.gz Running pycairo-1.6.4/setup.py -q bdist_egg --dist-dir /tmp/easy_install-sVFG8W/pycairo-1.6.4/egg-dist-tmp-XART3x cairo = 1.6.4 detected creating pycairo.pc zip_safe flag not set; analyzing archive contents... Adding pycairo 1.6.4 to easy-install.pth file Installed /Library/Python/2.5/site-packages/pycairo-1.6.4-py2.5-macosx-10.5-i386.egg Processing dependencies for pycairo Finished processing dependencies for pycairo ~ $ python Python 2.5.1 (r251:54863, Apr 15 2008, 22:57:26) [GCC 4.0.1 (Apple Inc. build 5465)] on darwin Type help, copyright, credits or license for more information. import cairo Seems to work. But, but, but...where did cairo come from? Was it already there? If true, then it's problem solved. Apparently it's a misnomer, but whatever, it's the only choice. It all compiles beautifully and works though. If I could just get RDKit working too... Let's see if we can diagnose it. Is it just Chem that leads to the crash, or do you see the same thing when you do the simplest possible RDKit extension module import: import rdBase If you do see a crash there, please send along the output of : 'otool -L $RDBASE/Python/rdBase.so' Otherwise, try running python -v and doing the Chem import, then at least you will see which specific piece of Chem is causing the crash. Will do. It'll be late next week though before I see the Mac again. -greg
Re: [Rdkit-discuss] Building on Mac
I now realise there is a third option for me. I could install cairo with Fink, and then try to compile pycairo for the System Python using the Fink installed libraries...hmmm... 2008/11/27 Noel O'Boyle baoille...@gmail.com: Hello Greg, To make life difficult, I've been trying to build RDKit on MacOSX 10.5 but using the Fink-installed python2.5 and numpy (note: I'm using Fink unstable): I'm a newbie to MacOSX. Fink is one of two options (also tried MacPorts - didn't work well enough) for package-managed installation of open source software. It's all installed into a new folder /sw and so doesn't interfere with anything already on the system. I'm trying to compile all components of cinfony on MacOSX; I can either figure out how to compile cairo and pycairo for the System Python, or I can install these with Fink (successfully!) and try to figure out how to compile RDKit for Fink's Python. In short, RDKit compiles fine but segfaults on import Chem. I note that there's no need to compile boost-build, as a bjam executable for mac is included in the boost source distribution. There's one loose end I want to chase up (I want to make sure it's using the boost libs I compiled myself, rather than any Fink boost libs), but apart from that I'm all out of ideas. If it compiles fine, it should work, right? If I can get cairo compiled for the system python, I won't need to chase this up, but I just thought I let you know... Regards, Noel
Re: [Rdkit-discuss] Building on Mac
Actually it builds pycairo and its dependencies on the spot, rather than installs them. The Sytem Python comes with PIL, Tkinter, wxPython, Numpy and Matplotlib. And that's it. There doesn't seem to be a package manager for Macs. So if you want any other extensions you're out of luck. And fink unstable is the only choice for pycairo for MacOSX on an Intel. Apparently it's a misnomer, but whatever, it's the only choice. It all compiles beautifully and works though. If I could just get RDKit working too... Noel 2008/11/27 Greg Landrum greg.land...@gmail.com: Noel, I'm not enough of a Mac person (yet?) to know what the compelling case is for installing/using the fink python instead of the system version. Aside from being able to install instead of build pycairo, what's the argument for it? I'm pretty conservative when it comes to installing on unstable platforms. :-) -greg On Thu, Nov 27, 2008 at 10:10 AM, Noel O'Boyle baoille...@gmail.com wrote: To make life difficult, I've been trying to build RDKit on MacOSX 10.5 but using the Fink-installed python2.5 and numpy (note: I'm using Fink unstable): I'm a newbie to MacOSX. Fink is one of two options (also tried MacPorts - didn't work well enough) for package-managed installation of open source software. It's all installed into a new folder /sw and so doesn't interfere with anything already on the system. I'm trying to compile all components of cinfony on MacOSX; I can either figure out how to compile cairo and pycairo for the System Python, or I can install these with Fink (successfully!) and try to figure out how to compile RDKit for Fink's Python. In short, RDKit compiles fine but segfaults on import Chem. I note that there's no need to compile boost-build, as a bjam executable for mac is included in the boost source distribution. There's one loose end I want to chase up (I want to make sure it's using the boost libs I compiled myself, rather than any Fink boost libs), but apart from that I'm all out of ideas. If it compiles fine, it should work, right? If I can get cairo compiled for the system python, I won't need to chase this up, but I just thought I let you know... Regards, Noel - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] PubChem Compount Info
Hmmm...sounds like something that is not specific to RDKit...I might think about adding this to cinfony. Especially if you send a patch :-) Noel 2008/8/17 markus m.koss...@tu-bs.de: Hi There, I wonder if it could be possible to access the Pubchem Power User Gateway directly via RDKit. As there is already some XML based interfacing to Pymol and Pubmed, this would be a nice additional tool. I often have several compounds for which I have to know if there's any Bioactivity documented at PubChem. Until now I have to browse the Pubchem home, search for similar mols, check out the assay-ids, IC50s :-( Could that be done in a way like the Pubmed.PubmedUtils stuff? Cheers, Markus - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Distance Matrix
Perhaps I misunderstand. Are you looking for a fast Python solution to creating a distance matrix? If so, you might want to use numpy (which uses C extensions), where the distance between two vectors x, y is simply sqrt(sum((x-y)**2)). See http://projects.scipy.org/pipermail/numpy-discussion/2007-April/027170.html for a procedure to generate a full distance matrix. Noel 2008/8/15 markus m.koss...@tu-bs.de: Dear all, as there is so much Geometry functionality within the RDKit, I wonder if it provides a function that computes the DistanceMatrix of a list of Point3D Objects. If RDKit does not have this functionality, can anyone give Ideas if the Boost Libaries themselve are capable of that? At the moment I have my own compiled version of the C Clustering Library (PyCluster) which I modified in order to get a distancematrix, but this Libraries do not out of the box calculate the spatial Distance. - This SF.Net email is sponsored by the Moblin Your Move Developer's challenge Build the coolest Linux based applications with Moblin SDK win great prizes Grand prize is a trip for two to an Open Source event anywhere in the world http://moblin-contest.org/redirect.php?banner_id=100url=/ ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Timing of C++ versus Boost.Python
2008/8/6 Greg Landrum greg.land...@gmail.com:
On 8/6/08, Noel O'Boyle baoille...@gmail.com wrote:
I'm getting some strange results when I compare the timing for using
cinfony to access RDKit, compared to writing the equivalent C++
program. Basically, for iteration over a very large SDF file, it's 50%
slower if you use cinfony (which simply calls SDMolSupplier and
'yields' the results).
That doesn't sound right at all. I expect the python stuff to be a bit
slower, but not dramatically so unless you are crossing the
python-c++ barrier frequently. An example of this slow case would be
similarity searching using X molecules against a collection of Y
molecules where Y (and possible X) is large. If you were to call the
TanimotoSimilarity function X*Y times (e.g. once for each pair), that
would be pretty slow in python relative to straight C++. If you use
the BulkTanimotoSimilarity function from Python (so that you only have
to cross over into C++ X times), the difference between Python and C++
shrinks.
I'm using an SDF file from ZINC that contains 25000 or so molecules
(the first subset of the drug-like molecules) for testing. I have C++
code like the following:
void ReadFromFile(){
ROMol* mol;
SDMolSupplier molfile = SDMolSupplier(3_p0.0.sdf);
while (!molfile.atEnd()) {
mol = molfile.next();
if (mol) delete mol;
}
}
Greg, when you have time (no pun intended), I'd appreciate if you
could compare the run time of this sort of C++ program versus the
equivalent Python script using SDMolSupplier. I'd just like
independent verification for the sort of figures I'm getting. The
thing is, while some overhead is expected, the web says that SWIG
should be worse than Boost.Python, but the SWIG overhead with
OpenBabel is of the order of 4%, not 50%.
I wasn't as patient as you, so I only used 2K molecules in my test:
-bash-3.00$ cat sample.py
import Chem
for m in Chem.SDMolSupplier('pubchem_hts.2k.sdf'):
pass
-bash-3.00$ time python sample.py
real0m4.097s
user0m4.018s
sys 0m0.079s
-bash-3.00$ cat sample.cpp
#include GraphMol/RDKitBase.h
#include GraphMol/FileParsers/MolSupplier.h
#include RDGeneral/RDLog.h
using namespace RDKit;
int
main(int argc, char *argv[])
{
RDLog::InitLogs();
ROMol* mol;
SDMolSupplier molfile(pubchem_hts.2k.sdf);
while (!molfile.atEnd()) {
mol = molfile.next();
if (mol) delete mol;
}
}
-bash-3.00$ time ./sample.exe
real0m4.034s
user0m4.003s
sys 0m0.031s
As you can see, there's little difference.
So, why are you seeing such a huge difference? Are you sure that
you're using the same C++ backend? i.e. Are the python wrappers you're
using linked against the same C++ shared libraries as your sample C++
program? The svn state of the code has some optimizations relative to
the May2008 release that might explain what you're seeing.
-greg
OK - there's some problem at my end. I'll track down the usual
suspects. Thanks for checking this...
Re: [Rdkit-discuss] new Building on Windows page
2008/7/21 Greg Landrum greg.land...@gmail.com: The problem with bjam not being able to find boost-build.jam is because your BOOST_BUILD_PATH is set incorrectly; it should be set to %BOOSTHOME%; then you won't need BOOST_ROOT. So, you're saying that I don't need anyt of the BOOST variables to point to the compiled boost stuff. They should just point to the source. You also need to set PYTHONHOME to run the tests. Which I'm afraid still don't work for me. Yes; the test suite assumes on windows that Python is in c:\python25 or that you have PYTHONHOME set properly; I need to add this to the wiki. Seems to be due to spaces in the name again. It's a pretty crazy test suite so I wasn't able to dig too deep...here's an example error message: C:\Documents and Settings\Noel\Desktop\Tools\RDKit\trunk\Codeset PYTHONHOME=C:\Program Files\Python25 C:\Documents and Settings\Noel\Desktop\Tools\RDKit\trunk\Codepython ..\Python\TestRunner.py test_list.py C:\Program: can't open file 'Files\Python25\python.exe': [Errno 2] No such file or directory C:\Program: can't open file 'Files\Python25\python.exe': [Errno 2] No such file or directory If I put quotation marks around the PYTHONHOME directory, it fouls up Python itself, and won't start up properly (the error message is cannot import os) hmm, that's irritating. It also looks to be at least partially a python problem, not an RDKit problem. Maybe this is why the default installation path for python is c:\python25? Just because they knew it'd be a problem for RDKit? :-) It's never been an issue before... BTW, it seems to import fine, so I think the compilation, etc. might have worked. -greg
[Rdkit-discuss] Fwd: [Open Babel] Hydrogen adder error?
FYI - the bug below is also exhibited by RDKit. -- Forwarded message -- From: Steve Constable steve.consta...@gmail.com Date: 2008/5/1 Subject: [Open Babel] Hydrogen adder error? To: openbabel-disc...@lists.sourceforge.net Hello, I'm working with openbabel 2.1.1, and I'm having an issue with the OBMol::AddHydrogens function. I have the structure of guandinie ( N=C(N)N ). when I run babel with the -h option, everything looks good. However, if I change to the charged version, [N+]=C(N)N the additional hydrogen required is not added. Opening the structures in jmol shows that they look exactly the same. Is this something that has been fixed in SVN already? Thanks, Steve - This SF.net email is sponsored by the 2008 JavaOne(SM) Conference Don't miss this year's exciting event. There's still time to save $100. Use priority code J8TL2D2. http://ad.doubleclick.net/clk;198757673;13503038;p?http://java.sun.com/javaone ___ OpenBabel-discuss mailing list openbabel-disc...@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/openbabel-discuss
Re: [Rdkit-discuss] Depiction
The good news is that the code you sent works, but the bad news is that I get a lot of PIL deprecation warnings: C:\Documents and Settings\AvrilNoel\Desktop\Tools\RDKit_Jan2008_1c:\Program Fi les\Python25\python draw.py C:\Documents and Settings\AvrilNoel\Desktop\Tools\RDKit_Jan2008_1\Python\sping\P IL\pidPIL.py:125: DeprecationWarning: 'setink' is deprecated; use keyword argume nts instead self._pen.setink(0) C:\Documents and Settings\AvrilNoel\Desktop\Tools\RDKit_Jan2008_1\Python\sping\P IL\pidPIL.py:137: DeprecationWarning: 'setink' is deprecated; use keyword argume nts instead self._pen.setink( (int(c.red*255), int(c.green*255), int(c.blue*255)) ) C:\Documents and Settings\AvrilNoel\Desktop\Tools\RDKit_Jan2008_1\Python\sping\P IL\pidPIL.py:331: DeprecationWarning: 'setfill' is deprecated; use keyword argum ents instead self._pen.setfill(1) C:\Documents and Settings\AvrilNoel\Desktop\Tools\RDKit_Jan2008_1\Python\sping\P IL\pidPIL.py:334: DeprecationWarning: 'setfill' is deprecated; use keyword argum ents instead self._pen.setfill(0) C:\Documents and Settings\AvrilNoel\Desktop\Tools\RDKit_Jan2008_1\Python\sping\P IL\pidPIL.py:388: DeprecationWarning: 'setink' is deprecated; use keyword argume nts instead temppen.setink( (255,255,255) ) C:\Documents and Settings\AvrilNoel\Desktop\Tools\RDKit_Jan2008_1\Python\sping\P IL\pidPIL.py:414: DeprecationWarning: 'setink' is deprecated; use keyword argume nts instead temppen.setink( (int(color.red*255), int(color.green*255), int(color.blue*255) ) ) C:\Documents and Settings\AvrilNoel\Desktop\Tools\RDKit_Jan2008_1\Python\sping\P IL\pidPIL.py:415: DeprecationWarning: 'setfill' is deprecated; use keyword argum ents instead temppen.setfill(1) If I use this in the API I'm writing (did I mention that?) I'll have users all over me complaining. So I'll be happy to see you move to using more up to date code, whether or not it looks better :-) Actually, I can't access the attachment as I'm not receiving mail from the list - you should probably cc me in future (I suffer from one-too-many mailing lists). Regards, Noel On 01/04/2008, Noel O'Boyle baoille...@gmail.com wrote: I've been looking into depiction in RDKit. It uses sping, which unfortunately looks like it's not very up to date. I know that BKChem has moved from sping to pycairo. At the moment, is it actually possible to make a PNG with RDKit? Noel
[Rdkit-discuss] Depiction
I've been looking into depiction in RDKit. It uses sping, which unfortunately looks like it's not very up to date. I know that BKChem has moved from sping to pycairo. At the moment, is it actually possible to make a PNG with RDKit? Noel
