Re: [Rdkit-discuss] Contractors working with the RDKit?
We can do this kind of work at Scientific Software Solutions Ltd. ( www.scisoftpro.com), especially with C++ Regards, Evgueni On 20 March 2011 05:46, Greg Landrum greg.land...@gmail.com wrote: Dear all, I was recently asked if there was anyone out there who was able to do contract development work with or on the RDKit. It's a good question, but I didn't have a good answer handy. So I'm asking here. If you currently do, or are willing to do, contract development work either extending the RDKit or developing new tools based on the RDKit, please reply to this thread. It would be helpful if you indicate your comfort level on both the C++ or Python sides. If there's sufficient interest/response, I'd be happy to include a section either on rdkit.org or on the wiki with names/links. Thanks, -greg -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss -- Colocation vs. Managed Hosting A question and answer guide to determining the best fit for your organization - today and in the future. http://p.sf.net/sfu/internap-sfd2d___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Build on Windows
Hi Greg, Actually 1.43 version is in CMakeLists. So I have repeated the whole process but... with the same result. I have tried to edit file FindBoost.cmake from CMake because there was no boost version 1.43 for some reason (I cannot understand how you build it without this changes) and this helped a little - no complains about not finding boost any more. But it still cannot find regex for some reason and i do not understand why I do not have .dll built. May be RDKit now cannot be build without Python at all? Regards, Evgueni On 29 July 2010 20:12, Greg Landrum greg.land...@gmail.com wrote: Hi Evgueni, On Thu, Jul 29, 2010 at 9:08 PM, Evgueni Kolossov ekolos...@gmail.com wrote: - I am sure I included install in the bjam command line - I have only /c/boost/lib/libboost_regex-vc90-mt-1_43.lib and /c/boost/lib/libboost_regex-vc90-mt.lib -and I have not added 1.43 to the Boost_ADDITIONAL_VERSIONS line So, will add it and try again that should clear it up. I'm not sure the software will actually run without being able to find the dll (and I'm also not sure why it's not present), but hopefully you'll be able to link. -greg -- 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] Build on Windows
Greg, I do not understand: .\bjam.exe toolset=msvc link=shared --with-regex release install or .\bjam.exe toolset=msvc link=static --with-regex release install? Regards, Evgueni On 30 July 2010 09:44, Greg Landrum greg.land...@gmail.com wrote: On Fri, Jul 30, 2010 at 9:55 AM, Evgueni Kolossov ekolos...@gmail.com wrote: Actually 1.43 version is in CMakeLists. So I have repeated the whole process but... with the same result. I have tried to edit file FindBoost.cmake from CMake because there was no boost version 1.43 for some reason (I cannot understand how you build it without this changes) You shouldn't need to do this since the changes to CMakeLists.txt provide all the additional information that's required. and this helped a little - no complains about not finding boost any more. But it still cannot find regex for some reason and i do not understand why I do not have .dll built. Maybe you need to be more explicit about it (though I'm not clear why this should be). I just modified the bjam command on the wiki to add a link=shared parameter to it. For you the command is probably : .\bjam.exe toolset=msvc link=shared --with-regex release install I left out python and thread since I don't think you need either of them. Try that one and see if the dll gets built. For reasons I don't completely understand, you still also need the regex static library, so if you start from scratch with boost, you need to also do: .\bjam.exe toolset=msvc link=static --with-regex release install May be RDKit now cannot be build without Python at all? The RDKit build options don't have anything to do with how boost builds itself, so I don't think that's it. -greg -- 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] Build on Windows
Ok this way it works... Regards, Evgueni On 30 July 2010 09:52, Greg Landrum greg.land...@gmail.com wrote: On Fri, Jul 30, 2010 at 10:50 AM, Evgueni Kolossov ekolos...@gmail.com wrote: Greg, I do not understand: .\bjam.exe toolset=msvc link=shared --with-regex release install or .\bjam.exe toolset=msvc link=static --with-regex release install? for the moment, please do both. Once I have this figured out we should be able to drop the second one. -greg 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] Build on Windows
Hi Greg, I have done exactly as you described it now and build boost with regex Unfortunately I have the same problems as before: Boost version: 1.43.0 Found BISON: C:/cygwin/bin/bison.exe Found FLEX: C:/cygwin/bin/flex.exe 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! Regards, Evgueni On 29 July 2010 05:50, Greg Landrum greg.land...@gmail.com wrote: Dear all, On Wed, Jul 28, 2010 at 4:04 PM, Evgueni Kolossov ekolos...@gmail.com wrote: I am trying to rebuild RDKit on Windows using boost 1_43 and cannot go through the configuration stage with CMake: There's been a lot of activity on this thread (thanks to everyone for pitching in), and a lot of the problem was caused by the fact that the windows build instructions online in the wiki not correct/complete. I've just update the instructions at http://code.google.com/p/rdkit/wiki/BuildingOnWindows and now hopefully they are more helpful. Two likely problems: - The build instructions for boost in the wiki were not complete. This has been fixed. - The RDKit as released (and in SVN) probably would not find boost 1.43 using cmake. This is a simple configuration change in $RDBASE/CMakeLists.txt (described in the wiki). I just did a clean build with boost 1.43 using the wiki instructions and I believe they should be ok. Evgueni; it would be great if you could let us know if you still encounter problems. Best Regards, -greg -- 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] Build on Windows
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] Build on Windows
Done but it still cannot find libraries On 28 July 2010 15:17, Peter Schmidtke pschmid...@ub.edu wrote: did you erase all content in the build directory before running cmake again? I sometimes noticed some strange behaviour when some old cmake stuff was still in the dir. On 28/07/2010, at 16:14, Evgueni Kolossov 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 Peter Schmidtke - PhD Student Department of Physical Chemistry School of Pharmacy University of Barcelona Barcelona, Spain -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Scientific Software Solutions Ltd. www.scisoftpro.com Tel. +44(0)1628 647 333 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 $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Build on Windows
No, what is this for? On 28 July 2010 15:31, Peter Schmidtke pschmid...@ub.edu wrote: Did you ./boostrap boost with regex using : ./bootstrap.sh --prefix=$HOME/pool --libdir=$HOME/pool/lib --with-libraries=python,regex ? On 28/07/2010, at 16:28, Evgueni Kolossov wrote: Yes this is set in environmental variables and I am using CMake 2.8 On 28 July 2010 15:24, Peter Schmidtke pschmid...@ub.edu wrote: BOOST_ROOT=/pathToBoost where pathToBoost is the directory containing the include and lib directory of your boost install... what cmake version are you using? If it's the 2.6, go for the 2.8 instead! On 28/07/2010, at 16:20, Evgueni Kolossov wrote: Done but it still cannot find libraries On 28 July 2010 15:17, Peter Schmidtke pschmid...@ub.edu wrote: did you erase all content in the build directory before running cmake again? I sometimes noticed some strange behaviour when some old cmake stuff was still in the dir. On 28/07/2010, at 16:14, Evgueni Kolossov 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 Peter Schmidtke - PhD Student Department of Physical Chemistry School of Pharmacy University of Barcelona Barcelona, Spain -- Peter Schmidtke - PhD Student Department of Physical Chemistry School of Pharmacy University of Barcelona Barcelona, Spain Mob. +44(0)7812070446 Peter Schmidtke - PhD Student Department of Physical Chemistry School of Pharmacy University of Barcelona Barcelona, Spain -- 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 $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Build on Windows
Thanks, I think I will install 1_42 from install package and rebuild all with 1_42 until installation package will be available for 1_43 Regards, Evgueni On 28 July 2010 15:38, Peter Schmidtke pschmid...@ub.edu wrote: Ah sorry mea culpa this was for unix based systems. However, on windows you should use : .\bjam.exe --toolset=msvc --with-python --with-regex release install instead I think to build boost. I'm not 100% sure about this as the rkdit build documentation for windows says something different. Try to build boost with this and build rdkit again. On 28/07/2010, at 16:34, Evgueni Kolossov wrote: No, what is this for? On 28 July 2010 15:31, Peter Schmidtke pschmid...@ub.edu wrote: Did you ./boostrap boost with regex using : ./bootstrap.sh --prefix=$HOME/pool --libdir=$HOME/pool/lib --with-libraries=python,regex ? On 28/07/2010, at 16:28, Evgueni Kolossov wrote: Yes this is set in environmental variables and I am using CMake 2.8 On 28 July 2010 15:24, Peter Schmidtke pschmid...@ub.edu wrote: BOOST_ROOT=/pathToBoost where pathToBoost is the directory containing the include and lib directory of your boost install... what cmake version are you using? If it's the 2.6, go for the 2.8 instead! On 28/07/2010, at 16:20, Evgueni Kolossov wrote: Done but it still cannot find libraries On 28 July 2010 15:17, Peter Schmidtke pschmid...@ub.edu wrote: did you erase all content in the build directory before running cmake again? I sometimes noticed some strange behaviour when some old cmake stuff was still in the dir. On 28/07/2010, at 16:14, Evgueni Kolossov 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 Peter Schmidtke - PhD Student Department of Physical Chemistry School of Pharmacy University of Barcelona Barcelona, Spain -- Peter Schmidtke - PhD Student Department of Physical Chemistry School of Pharmacy University of Barcelona Barcelona, Spain Mob. +44(0)7812070446 Peter Schmidtke - PhD Student Department of Physical Chemistry School of Pharmacy University of Barcelona Barcelona, Spain Peter Schmidtke - PhD Student Department of Physical Chemistry School of Pharmacy University of Barcelona Barcelona, Spain -- The Palm PDK Hot Apps Program offers developers who use the Plug
Re: [Rdkit-discuss] Q2 2010 Release
Thank you very much Regards, Evgueni On 2 July 2010 07:11, Greg Landrum greg.land...@gmail.com wrote: Hi Evgueni, On Fri, Jul 2, 2010 at 8:06 AM, Evgueni Kolossov ekolos...@gmail.com wrote: Thank you very much. I understood I need to rebuild again to have all libraries in one place or copy them manually? If you get the new version of $RDBASE/Code/cmake/Modules/RDKitUtils.cmake from here: http://rdkit.svn.sourceforge.net/viewvc/rdkit/trunk/Code/cmake/Modules/RDKitUtils.cmake?revision=1444 then rerun cmake and re-open the rdkit solution, you should have an INSTALL target. Building that target will copy the libraries to $RDBASE/lib for you. Alternatively you can copy them manually, whichever you find easier. -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
Re: [Rdkit-discuss] Q2 2010 Release
Dear Greg, I was sure bison and flex are part of cygwin installation but cannot find executables. Can you suggest anything? 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
Re: [Rdkit-discuss] Q2 2010 Release
Dear Noel, Thank you very much - done upgrade anyway and now can find bison and flex Regards, Evgueni On 1 July 2010 13:45, Noel O'Boyle baoille...@gmail.com wrote: 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
[Rdkit-discuss] Installation on Windows
Hi Greg, I have decided now to move into latest version and got couple of questions: - What the latest boost version you can recommend? - I believe before it was requirement to install some additional boost libraries. Is it still required or not? Regards, Evgueni -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Scientific Software Solutions Ltd. www.scisoftpro.com -- 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] about building RDKit on VS 2008
Dear Jongyoung , You need to add to your project: - Additional include directories for C++ section and Additional library directories section for linker: - C:\RDKit\External\Lapack\win32 - C:\RDkit\Code - C:\boost\boost_1_39 - C:\RDKit\External\vflib-2.0\ - C:\RDKit\External\vflib-2.0\include Depend on your installation directories can be different from the above - For Linker add to Additional Dependencies section - all RDKit libraries with .lib extension should be listed here Regards, Evgueni 2010/4/19 정종영 lis...@yonsei.ac.kr Dear Dr. Kolossov, I am trying to build and set up RDKit c++ library in Visual studion 2008. I did this according to Greg's wiki manual http://code.google.com/p/rdkit/wiki/BuildingOnWindows After completing all buliding steps, I lost my way to use it on VS. I think that I have problems to add dependency on external projects on VS 2008. Could you give me some tips about how to add RDKit library to VS 2008 develop projects on it? Best regards, Jongyoung Joung -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Scientific Software Solutions Ltd. www.scisoftpro.com Tel. +44(0)1628 647 333 Mob. +44(0)7812070446 -- 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] about building RDKit on VS 2008
Dear Greg, Thanks for suggestion - I am still on the old version. It just making it easier... Regards, Evgueni On 19 April 2010 10:39, Greg Landrum greg.land...@gmail.com wrote: Dear Evgueni, 2010/4/19 Evgueni Kolossov ekolos...@gmail.com: You need to add to your project: - Additional include directories for C++ section and Additional library directories section for linker: - C:\RDKit\External\Lapack\win32 - C:\RDkit\Code - C:\boost\boost_1_39 - C:\RDKit\External\vflib-2.0\ - C:\RDKit\External\vflib-2.0\include NOTE: in newer releases of the RDKit (and it looks like Jongyoung is using a newer version) neither lapack nor vflib are required. In fact, neither of those directories exist anymore. Best Regards, -greg -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Scientific Software Solutions Ltd. www.scisoftpro.com Tel. +44(0)1628 647 333 Mob. +44(0)7812070446 -- 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] MOL_SPTR_VECT
Dear Greg, I am very sorry - I have found the problem: the code is inside the loop and pointer have been deleted after push_back into vector and for this reason pointer in vector was not valid any more Regards, Evgueni On 11 February 2010 05:22, Greg Landrum greg.land...@gmail.com wrote: Hi Evgueni, On Wed, Feb 10, 2010 at 11:02 AM, Evgueni Kolossov ekolos...@gmail.com wrote: Dear Greg, I just cannot understand what's going on - please take a look below: std::string strSmiles = [*]; RDKit::RWMol *fragMol = new RDKit::RWMol(); fragMol = RDKit::SmilesToMol(strSmiles); RDKit::ROMOL_SPTR msp((RDKit::ROMol *)fragMol); //TESTING std::string strTest = RDKit::MolToSmiles(*msp.get()); //TEST RESULT: strTest is the same as strSmiles RDKit::MOL_SPTR_VECT m_vF; m_vF.push_back(msp); //TESTING std::string strTest2 = RDKit::MolToSmiles(*m_vF[0].get()); //TEST RESULT: EXCEPTION Can you help please!! The code above looks fine to me. To test, I compiled it and ran it just now and everything worked without problems. Does the exact code above lead to an exception when you run it? If so, please let me know operating system and compiler version so we can start trying to track it down. -greg -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Scientific Software Solutions Ltd. www.scisoftpro.com Tel. +44(0)1628 647 333 Mob. +44(0)7812070446 -- SOLARIS 10 is the OS for Data Centers - provides features such as DTrace, Predictive Self Healing and Award Winning ZFS. Get Solaris 10 NOW http://p.sf.net/sfu/solaris-dev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] MOL_SPTR_VECT
Dear Greg,
Thank you very much for quick answer.
I think the problem is in the copying from one vector to another:
for (unsigned int i=9; i m_vF.size(); i++)
vNew.push_back(m_vF[i]);
Can this corrupt the content of new vector?
Regards,
Evgueni
On 5 February 2010 05:13, Greg Landrum greg.land...@gmail.com wrote:
Hi Evgueni,
On Thu, Feb 4, 2010 at 5:25 PM, Evgueni Kolossov ekolos...@gmail.com
wrote:
I have a vector RDKit::MOL_SPTR_VECT m_vF.
Vector is populated Ok.
Now i am trying to get mols from this vector:
nCount = 0;
RDKit::ROMol *fMol = new RDKit::ROMol(*m_vF[nCount]);
This will compile OK but will throw an exception on execution in
T * operator- () const
{
BOOST_ASSERT(px != 0);
return px;
}
which called from ROMol::initFromOther()
Can you please suggest what is wrong with vector elements access by this
way?
There's nothing in principle wrong with it. Here's a little sample I
just did that works without problems:
{
RWMol *m=new RWMol();
m-addAtom(new Atom(6));
m-addAtom(new Atom(6));
m-addBond(0,1,Bond::SINGLE);
ROMOL_SPTR msp((ROMol *)m);
RDKit::MOL_SPTR_VECT m_vF;
m_vF.push_back(msp);
ROMol *nm = new ROMol(*m_vF[0]);
}
are you 100% certain that the molecules in your vector are ok? You
could test like this:
nCount = 0;
RDKit::ROMol *tMol = m_vF[nCount].get();
tMol-debugMol(std::cerr);
-greg
--
Dr. Evgueni Kolossov (PhD)
ekolos...@gmail.com
Scientific Software Solutions Ltd.
www.scisoftpro.com
Tel. +44(0)1628 647 333
Mob. +44(0)7812070446
--
The Planet: dedicated and managed hosting, cloud storage, colocation
Stay online with enterprise data centers and the best network in the business
Choose flexible plans and management services without long-term contracts
Personal 24x7 support from experience hosting pros just a phone call away.
http://p.sf.net/sfu/theplanet-com___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] MOL_SPTR_VECT
Hi Greg,
I have a vector RDKit::MOL_SPTR_VECT m_vF.
Vector is populated Ok.
Now i am trying to get mols from this vector:
nCount = 0;
RDKit::ROMol *fMol = new RDKit::ROMol(*m_vF[nCount]);
This will compile OK but will throw an exception on execution in
T * operator- () const
{
BOOST_ASSERT(px != 0);
return px;
}
which called from ROMol::initFromOther()
Can you please suggest what is wrong with vector elements access by this
way?
Regards,
Evgueni
--
The Planet: dedicated and managed hosting, cloud storage, colocation
Stay online with enterprise data centers and the best network in the business
Choose flexible plans and management services without long-term contracts
Personal 24x7 support from experience hosting pros just a phone call away.
http://p.sf.net/sfu/theplanet-com___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] SubstructMatch
Dear Greg, Leaving cycle/non-cycle atoms aside let's try to figure out how to reduce the number of maps allowing only 1 overlap between matches: Can you please suggest the best approach to do that? Example: vMatches: [0][5]((0,1),(1,2),(2,3),(3,4),(4,5)) [1][5]((0,1),(1,2),(2,3),(3,8),(4,7)) [2][5]((0,2),(1,3),(2,4),(3,5),(4,6)) [3][5]((0,2),(1,3),(2,8),(3,7),(4,6)) [4][5]((0,3),(1,4),(2,5),(3,6),(4,7)) [5][5]((0,3),(1,8),(2,7),(3,6),(4,5)) [6][5]((0,4),(1,3),(2,8),(3,7),(4,6)) [7][5]((0,4),(1,5),(2,6),(3,7),(4,8)) [8][5]((0,5),(1,4),(2,3),(3,8),(4,7)) [9][5]((0,6),(1,5),(2,4),(3,3),(4,8)) [10][5]((0,9),(1,1),(2,2),(3,3),(4,4)) [11][5]((0,9),(1,1),(2,2),(3,3),(4,8)) [12][5]((0,9),(1,10),(2,11),(3,12),(4,13)) [13][5]((0,9),(1,10),(2,11),(3,12),(4,18)) [14][5]((0,9),(1,19),(2,18),(3,12),(4,11)) [15][5]((0,9),(1,19),(2,18),(3,12),(4,13)) [16][5]((0,10),(1,11),(2,12),(3,18),(4,19)) I need actually to get finally for this example: [1][5]((0,1),(1,2),(2,3),(3,8),(4,7)) [12] [5]((0,9),(1,10),(2,11),(3,12),(4,13)) in all other matches overlap is over 1. Regards, Evgueni 2009/12/1 Evgueni Kolossov ekolos...@gmail.com I will repeat myself: please provide a specific match that you consider to be wrong. I can investigate if it make sense Comments like this do not improve my motivation to continue to be helpful. I am sorry - I have no intention to offend you. I just cannot understand the purpose of this function with current limitations Regards, Evgueni 2009/12/1 Greg Landrum greg.land...@gmail.com On Tue, Dec 1, 2009 at 12:31 PM, Evgueni Kolossov ekolos...@gmail.com wrote: I can investigate but even without this cyclic/non-cyclic problem there cannot be 17 matches! Especially with uniquify set to true. I will repeat myself: please provide a specific match that you consider to be wrong. So, this function is actually useless. Comments like this do not improve my motivation to continue to be helpful. -greg -- Join us December 9, 2009 for the Red Hat Virtual Experience, a free event focused on virtualization and cloud computing. Attend in-depth sessions from your desk. Your couch. Anywhere. http://p.sf.net/sfu/redhat-sfdev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] SubstructMatch
Hi Greg, I have enclosed 2 files - images for structure and fragment. When using unsigned int SubstructMatch() I am getting value = 17!!! Looking like function is not taking in account atom types and flag uniquify is not working at all - or may be I am missing something? Can you please comment on this behaviour? Regards, Evgueni attachment: frag.pngattachment: Thioperamide.png-- Join us December 9, 2009 for the Red Hat Virtual Experience, a free event focused on virtualization and cloud computing. Attend in-depth sessions from your desk. Your couch. Anywhere. http://p.sf.net/sfu/redhat-sfdev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] SubstructMatch
Yes, Greg, I believe that result 17 matches for this fragment does not make any sense 2009/12/1 Greg Landrum greg.land...@gmail.com Dear Evgueni, On Tue, Dec 1, 2009 at 10:21 AM, Evgueni Kolossov ekolos...@gmail.com wrote: I have enclosed 2 files - images for structure and fragment. When using unsigned int SubstructMatch() I am getting value = 17!!! Looking like function is not taking in account atom types and flag uniquify is not working at all - or may be I am missing something? Can you please comment on this behaviour? I guess I don't really see anything particularly unusual. Have you tried looking at the values you get for the matches? Is there a particular result you see that doesn't make sense? -greg -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446 -- Join us December 9, 2009 for the Red Hat Virtual Experience, a free event focused on virtualization and cloud computing. Attend in-depth sessions from your desk. Your couch. Anywhere. http://p.sf.net/sfu/redhat-sfdev2dev___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Fwd: SubstructMatch
-- Forwarded message --
From: Evgueni Kolossov ekolos...@gmail.com
Date: 2009/12/1
Subject: Re: [Rdkit-discuss] SubstructMatch
To: Greg Landrum greg.land...@gmail.com
Fragment: *
Structure: S=C(CC1C1)N1CCC(c2nc[nH]c2)CC1
Code
//
void CFragmentation::ReplaceDummies(RDKit::RWMol * frag)
{
RDKit::QueryAtom *qat = new RDKit::QueryAtom();
qat-setQuery(RDKit::makeAtomNullQuery());
for(unsigned int i=0; ifrag-getNumAtoms(); i++)
{
if(frag-getAtomWithIdx(i)-getAtomicNum()==0)
frag-replaceAtom(i,qat);
}
delete qat;
}
//
std;:string strSmilesFrag = *, strSmilesStruct =
S=C(CC1C1)N1CCC(c2nc[nH]c2)CC1;
std::vector RDKit::MatchVectType vMatches;
RDKit::RWMol *frag = new RDKit::RWMol();
frag = RDKit::SmilesToMol(iter-strSmilesFrag);
SciDB::CFragmentation::ReplaceDummies(frag);
RDKit::ROMol *mol = new RDKit::ROMol();
mol = RDKit::SmilesToMol(strSmilesStruct);
int nMap = RDKit::SubstructMatch(*mol, *frag,vMatches);
I believe nMap = 17 does not make sense!
Regards,
Evgueni
2009/12/1 Greg Landrum greg.land...@gmail.com
If you've looked at the matches and found specific ones that don't
make sense, please post them, the exact query and molecule you used
(including the atom numbering), and the code you are using to do the
matching and I will take a look.
-greg
On Tue, Dec 1, 2009 at 10:52 AM, Evgueni Kolossov ekolos...@gmail.com
wrote:
Yes, Greg,
I believe that result 17 matches for this fragment does not make any
sense
2009/12/1 Greg Landrum greg.land...@gmail.com
Dear Evgueni,
On Tue, Dec 1, 2009 at 10:21 AM, Evgueni Kolossov ekolos...@gmail.com
wrote:
I have enclosed 2 files - images for structure and fragment. When
using
unsigned int SubstructMatch() I am getting value = 17!!! Looking like
function is not taking in account atom types and flag uniquify is not
working at all - or may be I am missing something? Can you please
comment on
this behaviour?
I guess I don't really see anything particularly unusual. Have you
tried looking at the values you get for the matches? Is there a
particular result you see that doesn't make sense?
-greg
--
--
Dr. Evgueni Kolossov (PhD)
ekolos...@gmail.com
Tel. +44(0)1628 627168
Mob. +44(0)7812070446
--
Join us December 9, 2009 for the Red Hat Virtual Experience,
a free event focused on virtualization and cloud computing.
Attend in-depth sessions from your desk. Your couch. Anywhere.
http://p.sf.net/sfu/redhat-sfdev2dev___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Substructure search
Thanks Greg, I have calculated it will slow down on about 30% using this replacement which is significant for big datasets. The substructure matching uses atoms and bonds, and returns the results as lists of atom indices; how (and why) would you propose to ignore an atom but not a bond? I mean take bond in account as it is but use match any for dummy atom Regards, Evgueni 2009/11/7 Greg Landrum greg.land...@gmail.com Combining two answers into one: On Fri, Nov 6, 2009 at 7:59 AM, Evgueni Kolossov ekolos...@gmail.com wrote: Hi Greg, Yes, this is solution I been thinking about as well but there is 2 problems: 1. It will slow dawn mapping process which is slow already 2. What atom to use for replacement? I'm not sure I understand what you mean about slowing down the mapping process. If you replace the dummies in your fragments with query atoms, as I proposed in the sample code in my earlier message, the substructure search should not be substantially slower. The replacement itself also won't take that long, unless you really have a *lot* of fragments. On Fri, Nov 6, 2009 at 9:03 AM, Evgueni Kolossov ekolos...@gmail.com wrote: I think you should distinguish between dummy atoms and connection points - for fragments it is connection points we are talking about. The code doesn't understand anything about connection points... it just has atoms. Dummy atoms are atoms with atomic number zero. The substructure matching code applied to normal Atoms (i.e. not QueryAtoms) compares two atoms by checking to see if their atomic numbers match, so dummies match dummies. Additionally, when isotopes are specified, it checks that the specified isotopes match. QueryAtoms, on the other had, allow client code to specify the function that's used for matching. The example I provided showed how to use a function that matches any atom; which I think is what you are looking for. So, it suppose to ignore this atom (but not bond!) during matching process. May be just add another bool flag to allow user select different behavior? The substructure matching uses atoms and bonds, and returns the results as lists of atom indices; how (and why) would you propose to ignore an atom but not a bond? -greg -- Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day trial. Simplify your report design, integration and deployment - and focus on what you do best, core application coding. Discover what's new with Crystal Reports now. http://p.sf.net/sfu/bobj-july___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Substructure search
Greg,
I think you should distinguish between dummy atoms and connection points -
for fragments it is connection points we are talking about. So, it suppose
to ignore this atom (but not bond!) during matching process. May be just add
another bool flag to allow user select different behavior?
Regards,
Evgueni
2009/11/6 Evgueni Kolossov ekolos...@gmail.com
Hi Greg,
Yes, this is solution I been thinking about as well but there is 2
problems:
1. It will slow dawn mapping process which is slow already
2. What atom to use for replacement?
What if I will just remove this atom(s)?
Regards,
Evgueni
2009/11/6 Greg Landrum greg.land...@gmail.com
On Wed, Nov 4, 2009 at 7:54 PM, Greg Landrum greg.land...@gmail.com
wrote:
On Wed, Nov 4, 2009 at 3:26 PM, Evgueni Kolossov ekolos...@gmail.com
wrote:
I found that SubstructMatch would not work if query is a fragment (with
*
atoms).
Can you suggest solution for this problem?
That's a bug. Dummy atoms (things with atomic number zero) that do not
have an isotope specification should match anything. If you have a
sourceforge account, please enter the bug, otherwise let me know and I
will enter it.
After going back through the code and thinking about this for a while
I'm going to change my original answer: it's not a bug that standard
dummy atoms only match other dummy atoms. When I saw the * in the
original message I started thinking about the QueryAtoms produced by a
* in SMARTS, which definitely should (and do) match other dummies.
The behavior with standard Atoms is useful for things like flagging
attachment points of R groups on a scaffold. Here's an example:
[5] f= Chem.MolFromSmiles('c1cccnc1*')
[6] p = Chem.MolFromSmarts('c1cccnc1*')
[9] m = Chem.MolFromSmiles('c1ccc(C)nc1*')
Matching using f, which has dummy Atoms only gives one match:
[10] m.GetSubstructMatches(f)
Out[10]: ((0, 1, 2, 3, 5, 6, 7),)
But matching using p, which has a QueryAtom built from * matches twice:
[11] m.GetSubstructMatches(p)
Out[11]: ((0, 1, 2, 3, 5, 6, 7), (2, 1, 0, 6, 5, 3, 4))
For your use case, I'd suggest replacing the dummies in your fragments
with QueryAtoms that have the appropriate query, something like this
(not tested):
//-
#include GraphMol/RDKitQueries.h
void replaceDummies(RWMol *frag){
QueryAtom *qat = new QueryAtom();
qat-setQuery(makeAtomNullQuery());
for(unsigned int i=0;ifrag-getNumAtoms();++i){
if(frag-getAtomWithIdx(i)-getAtomicNum()==0){
frag-replaceAtom(i,qat);
}
}
delete qat;
}
//-
I hope this helps,
-greg
--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now. http://p.sf.net/sfu/bobj-july___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Substructure search
Hi Greg,
Yes, this is solution I been thinking about as well but there is 2 problems:
1. It will slow dawn mapping process which is slow already
2. What atom to use for replacement?
What if I will just remove this atom(s)?
Regards,
Evgueni
2009/11/6 Greg Landrum greg.land...@gmail.com
On Wed, Nov 4, 2009 at 7:54 PM, Greg Landrum greg.land...@gmail.com
wrote:
On Wed, Nov 4, 2009 at 3:26 PM, Evgueni Kolossov ekolos...@gmail.com
wrote:
I found that SubstructMatch would not work if query is a fragment (with
*
atoms).
Can you suggest solution for this problem?
That's a bug. Dummy atoms (things with atomic number zero) that do not
have an isotope specification should match anything. If you have a
sourceforge account, please enter the bug, otherwise let me know and I
will enter it.
After going back through the code and thinking about this for a while
I'm going to change my original answer: it's not a bug that standard
dummy atoms only match other dummy atoms. When I saw the * in the
original message I started thinking about the QueryAtoms produced by a
* in SMARTS, which definitely should (and do) match other dummies.
The behavior with standard Atoms is useful for things like flagging
attachment points of R groups on a scaffold. Here's an example:
[5] f= Chem.MolFromSmiles('c1cccnc1*')
[6] p = Chem.MolFromSmarts('c1cccnc1*')
[9] m = Chem.MolFromSmiles('c1ccc(C)nc1*')
Matching using f, which has dummy Atoms only gives one match:
[10] m.GetSubstructMatches(f)
Out[10]: ((0, 1, 2, 3, 5, 6, 7),)
But matching using p, which has a QueryAtom built from * matches twice:
[11] m.GetSubstructMatches(p)
Out[11]: ((0, 1, 2, 3, 5, 6, 7), (2, 1, 0, 6, 5, 3, 4))
For your use case, I'd suggest replacing the dummies in your fragments
with QueryAtoms that have the appropriate query, something like this
(not tested):
//-
#include GraphMol/RDKitQueries.h
void replaceDummies(RWMol *frag){
QueryAtom *qat = new QueryAtom();
qat-setQuery(makeAtomNullQuery());
for(unsigned int i=0;ifrag-getNumAtoms();++i){
if(frag-getAtomWithIdx(i)-getAtomicNum()==0){
frag-replaceAtom(i,qat);
}
}
delete qat;
}
//-
I hope this helps,
-greg
--
Let Crystal Reports handle the reporting - Free Crystal Reports 2008 30-Day
trial. Simplify your report design, integration and deployment - and focus on
what you do best, core application coding. Discover what's new with
Crystal Reports now. http://p.sf.net/sfu/bobj-july___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] fragments aromaticity
Hi Greg, I got a small problem with the fragments - aromatic cycles coming with all bonds as double. If I save it into SDF and open SDF than it all Ok. I believe I saw somewhere fix for this. Can you please point me to the right place? Regards, Evgueni -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] fragments aromaticity
Yes, it is reproducible every time... Actually code is quite simple: iterate through the rings, bonds, atoms for each bond and add atoms and bonds to a new mol like: Atom *begAtom = mol.getAtomWithIds(begIdx)-copy(); newBegIdx = fragMol-AddAtom(begAtom, false, true); the same for an endAtom etc... Bond *pNewBond = pBond-copy(); pNewBond-setOwningMol(fragMol); pNewBond -setBeginAtomIdx(newBegIdx); pNewBond -setEndAtomIdx(newEndIdx); int nNewBondIdx = fragMol-addBond(pNewBond, true); Regards, Evgueni 2009/10/19 Greg Landrum greg.land...@gmail.com On Mon, Oct 19, 2009 at 12:06 PM, Evgueni Kolossov ekolos...@gmail.com wrote: I got a small problem with the fragments - aromatic cycles coming with all bonds as double. If I save it into SDF and open SDF than it all Ok. I believe I saw somewhere fix for this. Can you please point me to the right place? hmm, that's weird; it's not really sounding familiar. Do you have a reproducible example of it happening? -greg -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446 -- Come build with us! The BlackBerry(R) Developer Conference in SF, CA is the only developer event you need to attend this year. Jumpstart your developing skills, take BlackBerry mobile applications to market and stay ahead of the curve. Join us from November 9 - 12, 2009. Register now! http://p.sf.net/sfu/devconference___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Fragmentation
Some more fixes 2009/8/13 Greg Landrum greg.land...@gmail.com Dear Evgueni, Thanks for the contribution. I am travelling at the moment, but I will try to find some time review the code over the next few days. Best Regards, -greg attachment: salts.zip
Re: [Rdkit-discuss] Fragmentation
Sorry - forgot that anion in nitro group and perchlorate can be affected - fixed now. Regards, Evgueni 2009/8/13 Evgueni Kolossov ekolos...@gmail.com Hi Greg, I have enclosed files for class CSalts which is doing salt stripping. The main function (StripSalt) taking a few arguments: - RDKit::ROMol mol - the molecule of interest - std::vectorstd::string vSalts - smiles strings from the salt dictionary - bool bRemoveSmallest - if it true than only biggesrt fragment will be left (some customers like it that way) - bool bSuppressCharges - if true will call static function SuppressCharges(RDKit::RWMol mol) which will suppress charges by add/remove 'H+'. This way it should not affect any special cases like nitro groups, etc.because they do not have protons to remove. Please take a look if it require any corrections and give me your feedback. You can modify it freely and can add to RDKit if you wish as my small contribution. Regards, Evgueni 2009/8/12 Greg Landrum greg.land...@gmail.com On Wed, Aug 12, 2009 at 11:54 AM, Evgueni Kolossovekolos...@gmail.com wrote: Greg, Am I right that the function std::vectorboost::shared_ptrROMol getMolFrags(const ROMol mol, bool sanitizeFrags=true, INT_VECT *frags=0) will return the vector of fragments as ROMol's? yes, that is correct. -greg attachment: salts.zip
Re: [Rdkit-discuss] Fragmentation
Bug found and fixed. 2009/8/13 Evgueni Kolossov ekolos...@gmail.com Sorry - forgot to fix one more things. Now it's final. Regards, Evgueni 2009/8/13 Evgueni Kolossov ekolos...@gmail.com Sorry - forgot that anion in nitro group and perchlorate can be affected - fixed now. Regards, Evgueni 2009/8/13 Evgueni Kolossov ekolos...@gmail.com Hi Greg, I have enclosed files for class CSalts which is doing salt stripping. The main function (StripSalt) taking a few arguments: - RDKit::ROMol mol - the molecule of interest - std::vectorstd::string vSalts - smiles strings from the salt dictionary - bool bRemoveSmallest - if it true than only biggesrt fragment will be left (some customers like it that way) - bool bSuppressCharges - if true will call static function SuppressCharges(RDKit::RWMol mol) which will suppress charges by add/remove 'H+'. This way it should not affect any special cases like nitro groups, etc.because they do not have protons to remove. Please take a look if it require any corrections and give me your feedback. You can modify it freely and can add to RDKit if you wish as my small contribution. Regards, Evgueni 2009/8/12 Greg Landrum greg.land...@gmail.com On Wed, Aug 12, 2009 at 11:54 AM, Evgueni Kolossovekolos...@gmail.com wrote: Greg, Am I right that the function std::vectorboost::shared_ptrROMol getMolFrags(const ROMol mol, bool sanitizeFrags=true, INT_VECT *frags=0) will return the vector of fragments as ROMol's? yes, that is correct. -greg attachment: salts.zip
Re: [Rdkit-discuss] Fragmentation
Thanks - this actually doing what we need at once Regards, Evgueni 2009/8/12 Greg Landrum greg.land...@gmail.com On Wed, Aug 12, 2009 at 11:54 AM, Evgueni Kolossovekolos...@gmail.com wrote: Greg, Am I right that the function std::vectorboost::shared_ptrROMol getMolFrags(const ROMol mol, bool sanitizeFrags=true, INT_VECT *frags=0) will return the vector of fragments as ROMol's? yes, that is correct. -greg -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
Re: [Rdkit-discuss] Fragmentation
Greg, You probably doing some fixes for nitro groups, etc. somewhere (probably in MolFromSmiles). I think this can be useful to identify exceptions. Can you please point me where this staff is? Regards, Evgueni 2009/8/10 Greg Landrum greg.land...@gmail.com On Mon, Aug 10, 2009 at 12:43 PM, Evgueni Kolossovekolos...@gmail.com wrote: One more question about salts stripping - is there way to suppress charges? Let's say you will remove [Na+] but the negative charge will be on anion. How we can remove it? The same if you say removing [Cl-] and there will be for example (R)3-NH+ we need to remove H+ from it. Any thought about this? You could loop through the molecule and set the formal charges to zero. You'll have to be figure out some way to solve the problems this will cause with nitro groups (and related substructures) though. -greg -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
Re: [Rdkit-discuss] Fragmentation
Hi Greg, One more question about salts stripping - is there way to suppress charges? Let's say you will remove [Na+] but the negative charge will be on anion. How we can remove it? The same if you say removing [Cl-] and there will be for example (R)3-NH+ we need to remove H+ from it. Any thought about this? Regards, Evgueni 2009/7/20 Greg Landrum greg.land...@gmail.com Hi Evgueni On Mon, Jul 20, 2009 at 7:05 PM, Evgueni Kolossovekolos...@gmail.com wrote Another related question: is there any way to strip salts or I need to implement it myself? There is a deleteSubstructs() function in ChemTransforms that does the work, but it needs to be fed with a set of substructure definitions for the salts. There isn't currently such a thing distributed with the RDKit. -greg -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
Re: [Rdkit-discuss] Fragmentation
Thank you very much 2009/7/21 Greg Landrum greg.land...@gmail.com On Tue, Jul 21, 2009 at 8:09 AM, Evgueni Kolossovekolos...@gmail.com wrote: One more question - is there function to get how many structures is in mol? MolOps::getMolFrags()
Re: [Rdkit-discuss] Fragmentation
Thanks Greg, This is the best (on my opinion) way to do salt stripping - to have a library of salts... Another question - is there function to map fragment to structure (to get how many times this fragment appeared in structure)? Regards, Evgueni 2009/7/20 Greg Landrum greg.land...@gmail.com Hi Evgueni On Mon, Jul 20, 2009 at 7:05 PM, Evgueni Kolossovekolos...@gmail.com wrote Another related question: is there any way to strip salts or I need to implement it myself? There is a deleteSubstructs() function in ChemTransforms that does the work, but it needs to be fed with a set of substructure definitions for the salts. There isn't currently such a thing distributed with the RDKit. -greg -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
Re: [Rdkit-discuss] Fragmentation
Hi Greg, What's the best way to check for duplicate in this smart pointers vector of fragments when adding a new fragment to the vector? Regards, Evgueni -Original Message- From: Greg Landrum [mailto:greg.land...@gmail.com] Sent: 26 June 2009 19:45 To: Evgueni Kolossov Subject: Re: Fragmentation Hi Evgueni, storing molecules in an std::vector just isn't going to work. Use smart pointers (RDKit::ROMOL_SPTR) instead. On Fri, Jun 26, 2009 at 10:50 AM, Evgueni Kolossov wrote: Hi Greg, No, the solution you suggested is not working. I have found the problem but I need your help to sort it out: I am storing fragments in the std::vectorRDKit::ROMol m_vFrags Looking like near all operation with this vector causing the problem with operator '=': m_vFrags.clear() -problem RDKit::ROMol *mol; mol = RDKit::SmilesToMol(strSmi); m_vFrags.push_back(*mol) -problem etc. What you can suggest? Regards, Evgueni
Re: [Rdkit-discuss] beta of Q2 release available
Dear Greg, Can you please explain the usage of atom labels Q, A, and *. I know that * used in fragments. Where you using Q and A? Regards, Evgueni 2009/6/21 Greg Landrum greg.land...@gmail.com Dear all, It's getting to be time for the next RDKit release. Yesterday I tagged the Q2 2009 release: http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_Q22009_1beta1/ and put a source tar ball up on the google code site: http://code.google.com/p/rdkit/downloads/list I'm going to continue to work on the code, particularly on the documentation, but if no substantial problems are found, I will do the release towards the end of the month. Release notes (more complete than usual) are below. -greg ** Release_Q22009_1 *** (Changes relative to Release_Q12009_2) Acknowledgements - Uwe Hoffmann, Marshall Levesque, Armin Widmer Bug Fixes - handling of crossed bonds in mol files fixed (issue 2804599) - serialization bug fixed (issue 2788233) - pi systems with 2 electrons now flagged as aromatic (issue 2787221) - Chirality swap on AddHs (issue 2762917) - core leak in UFFOptimizeMolecule fixed (issue 2757824) New Features - cairo support in the mol drawing code (from Uwe Hoffmann) (issue 2720611) - Tversky and Tanimoto similarities now supported for SparseIntVects - AllProbeBitsMatch supported for BitVect-BitVect comparisons - ChemicalReactions support serialization (pickling) (issue 2799770) - GetAtomPairFingerprint() supports minLength and maxLength arguments - GetHashedTopologicalTorsionFingerprint() added - preliminary support added for v3K mol files - ForwardSDMolSupplier added - CompressedSDMolSupplier added (not supported on windows) - UFFHasAllMoleculeParams() added - substructure searching code now uses an RDKit implementation of the vf2 algorithm. It's much faster. - Atom.GetPropNames() and Bond.GetPropNames() now available from python - BRICS code now supports FindBRICSBonds() and BreakBRICSBonds() - atom labels Q, A, and * in CTABs are more correctly supported (issue 2797708) - rdkit.Chem.PropertyMol added (issue 2742959) - support has been added for enabling and disabling logs (issue 2738020) Other - A demo has been added for using MPI with the RDKit ($RDBASE/Code/Demos/RDKit/MPI). - Embedding code is now better at handling chiral structures and should produce results for molecules with atoms that don't have UFF parameters. - the UFF code is more robust w.r.t. missing parameters - GetHashedAtomPairFingerprint() returns SparseIntVect instead of ExplicitBitVect - the CTAB parser (used for mol files and SD files) is faster - extensive changes to the layered fingerprinting code; fingerprinting queries is now possible - molecule discriminator code moved into $RDBASE/Code/GraphMol/Subgraphs - the SDView4 prototype has been expanded - $RDBASE/Regress has been added to contain regression and benchmarking data and scripts. - support for sqlalchemy has been added to $RDBASE/rdkit/Chem/MolDb - the BRICS code has been refactored -- Are you an open source citizen? Join us for the Open Source Bridge conference! Portland, OR, June 17-19. Two days of sessions, one day of unconference: $250. Need another reason to go? 24-hour hacker lounge. Register today! http://ad.doubleclick.net/clk;215844324;13503038;v?http://opensourcebridge.org ___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Cannot read compounds containing nitro group?
Hi Greg,
One additional question about this subject:
If we have molecules in both tautomeric forms:'C[N+](=O)([O-])' and
CN(=O)(=O)'
than what we will have after SmilesToMol() and MolToSmiles() (which will
sanitise molecule)?
Regards,
Evgueni
2009/5/25 Greg Landrum greg.land...@gmail.com
Dear Tao-wei,
On Fri, May 22, 2009 at 2:59 AM, Tao-wei Huang yelve...@gmail.com wrote:
Dear All,
I encountered problems while reading compounds containing Nitro group
(-NO2)
or building molecules containing smarts like [N+][O-]. It seems that
rdkit
only allows the maximum valence of N to be 3 in these processes. One
example
is as followings (the sdf file is attached):
spl=cm.SDMolSupplier('pyrazoloacridine.sdf')
print spl[0]
None
mm=cm.MolFromMolFile('pyrazoloacridine.sdf')
Traceback (most recent call last):
File pyshell#20, line 1, in module
mm=cm.MolFromMolFile('pyrazoloacridine.sdf')
ValueError: Sanitization error: Explicit valence for atom # 13 N greater
than permitted
Could anyone provide some solution for this problem? I did't notice this
problem when I started building model. But now I cannot run through the
whole dataset probably because of this problem. Thanks in advance.
The RDKit is, by design, very picky about valence and only tries to
repair bad valences in very limited situations. Nitro groups are, in
fact, one case where the system will clean things up. For example,
both of these work:
[2] m = Chem.MolFromSmiles('C[N+](=O)([O-])')
[3] m = Chem.MolFromSmiles('CN(=O)(=O)')
But here an error is raised:
[4] m = Chem.MolFromSmiles('CN(=O)(O)')
[06:11:51] Explicit valence for atom # 1 N greater than permitted
Your input file contains an N like the one in [4] above: neutral and
four coordinate. The fix is to either change the single N-O bond (the
bond between atoms 14 and 19) to a double or to set the appropriate
charges on atoms 14 and 19 in your SD file. [Note: just in case it
causes confusion, the RDKit numbers the atoms starting at zero, but in
the SD file they are numbered starting at 1, so when the RDKit
complains about atom #13, it's numbered 14 in the SD file.]
Best Regards,
-greg
--
Register Now for Creativity and Technology (CaT), June 3rd, NYC. CaT
is a gathering of tech-side developers brand creativity professionals.
Meet
the minds behind Google Creative Lab, Visual Complexity, Processing,
iPhoneDevCamp asthey present alongside digital heavyweights like Barbarian
Group, R/GA, Big Spaceship. http://www.creativitycat.com
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
[Rdkit-discuss] Fwd: Question
Thank you very much Greg, Couple of more things to clarify: - in documentation you have mentioned pickle files. Can you please give an example read/write for this kind of files; - in SDF the records separated by quite definite sequence which allow us to create an index file and have direct access to particular record number. Is it possible with pickle files? Regards, Evgueni 2009/4/30 Greg Landrum greg.land...@gmail.com: There really isn't a maximum. It depends on the number of atoms, number of bonds, and number of conformers. On Thu, Apr 30, 2009 at 9:09 PM, Evgueni Kolossov ekolos...@gmail.com wrote: Ok , so the average size 781 byte. What's the max size of one molecule can be in theory? 2009/4/30 Greg Landrum greg.land...@gmail.com: Yes, the database containing the 214K molecules is 167MB On Thu, Apr 30, 2009 at 7:55 PM, Evgueni Kolossov ekolos...@gmail.com wrote: Thanks Greg, Unfortunately I do not quite got it - you mean the size of your example is 167240704 bytes? Regards, Evgueni 2009/4/30 Greg Landrum greg.land...@gmail.com: [redirecting to list since this may be of general interest] Yes, I generally store molecules in databases in blob columns containing the pickles. The primary reason for this is that one can then skip all the work of parsing the molecule, perceiving the chemistry, etc. I don't have a good general answer for how long pickles are. It really depends on the molecules. One example I have handy is a sqlite database containing the pubchem screening deck. The molecules are stores as follows: sqlite .schema CREATE TABLE molecules (compound_id varchar not null unique,molpkl blob); sqlite select count(*) from molecules; 214178 % ls -l Compounds.sqlt -rw-r--r-- 1 landrgr1 staff 167240704 Nov 22 07:28 Compounds.sqlt There is, no doubt, some overhead associated with the sqlite data, but this gives a rough estimate. -greg -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446 -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446 -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
Re: [Rdkit-discuss] Fwd: Question
Ok Greg, What if we will try to define the format and start with the record separator - may be use the same as SDF? Index file can be created during the writing. Regards, Evgueni 2009/5/1 Greg Landrum greg.land...@gmail.com On Fri, May 1, 2009 at 8:06 AM, Evgueni Kolossov ekolos...@gmail.com wrote: Thank you very much Greg, Couple of more things to clarify: - in documentation you have mentioned pickle files. Can you please give an example read/write for this kind of files; The documentation is primarily focused on python. Python has it's own method for serializing (pickling) objects. From C++ I never really did too much with writing to/reading from binary files. I guess one could just write the binary data directly to the stream and read it back the same way, but this doesn't answer your next question: - in SDF the records separated by quite definite sequence which allow us to create an index file and have direct access to particular record number. Is it possible with pickle files? If you create your own convention for how you write the files, sure. Otherwise you have to just build files and then write out the result of an fget after each read is finished. On reading you can seek to the relevant position and then start reading. It probably would be useful to have a standardized binary format for reading from C++ (or python), but I have never had the pressing need; so it hasn't happened. -greg -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
Re: [Rdkit-discuss] Question
Thanks Greg, Unfortunately I do not quite got it - you mean the size of your example is 167240704 bytes? Regards, Evgueni 2009/4/30 Greg Landrum greg.land...@gmail.com: [redirecting to list since this may be of general interest] Yes, I generally store molecules in databases in blob columns containing the pickles. The primary reason for this is that one can then skip all the work of parsing the molecule, perceiving the chemistry, etc. I don't have a good general answer for how long pickles are. It really depends on the molecules. One example I have handy is a sqlite database containing the pubchem screening deck. The molecules are stores as follows: sqlite .schema CREATE TABLE molecules (compound_id varchar not null unique,molpkl blob); sqlite select count(*) from molecules; 214178 % ls -l Compounds.sqlt -rw-r--r-- 1 landrgr1 staff 167240704 Nov 22 07:28 Compounds.sqlt There is, no doubt, some overhead associated with the sqlite data, but this gives a rough estimate. -greg On Thu, Apr 30, 2009 at 10:55 AM, Evgueni Kolossov ekolos...@gmail.com wrote: and what's the length of Pickles? 2009/4/30 Evgueni Kolossov ekolos...@gmail.com: Greg, In this case you probably storing Pickles into database together with fingerprints. Am I right? Regards, Evgueni 2009/4/30 Greg Landrum greg.land...@gmail.com: nope... the transformation is a lossy one On Thu, Apr 30, 2009 at 9:56 AM, Evgueni Kolossov ekolos...@gmail.com wrote: Hi Greg, Another probably stupid question - is it possible to re-create ROMol from fingerprints? Regards, Evgueni --
[Rdkit-discuss] IronPython
Dear Greg, Do you know about IronPython ( http://www.codeplex.com/Wiki/View.aspx?ProjectName=IronPython)? It actually combining Visual Studio and Python. It can be very interesting solution for RDKit. What you think? Regards, Evgueni
Re: [Rdkit-discuss] Beta of next release up.
Thank you very much!
Regards,
Evgueni
2009/3/25 Greg Landrum greg.land...@gmail.com
[Redirected to the list because the question is of general interest]
Hi Evgueni,
On Wed, Mar 25, 2009 at 10:56 AM, Evgueni Kolossov
ekolos...@btinternet.com wrote:
Got some problems with looping over an atom's bonds when I need to
compare
(see below):
double CRDKitDescriptor::GetEdgeDegree(RDKit::Bond * Bond_in, bool
bWeighted) const
{
double dRtn = 0.0;
RDKit::ROMol::OEDGE_ITER beg,end;
RDKit::ROMol mol = Bond_in-getOwningMol();
//OLD CODE//RDKit::ROMol::GRAPH_MOL_BOND_PMAP::type pMap =
mol.getBondPMap();
// Take two atoms involved in this bond.
RDKit::Atom *pAtom[2] = { Bond_in-getBeginAtom(),
Bond_in-getEndAtom() };
for (int i=0; i 2; i++)
{
// Add degrees of other bonds (not connected to H) on this
atom.
boost::tie(beg,end) = mol.getAtomBonds(pAtom[i]);
while(beg!=end)
{
//OLD CODE//RDKit::Bond *pCurrentBond =
pMap[*beg];
//NEW CODE//RDKit::BOND_SPTR pCurrentBond =
(mol)[*beg];
//NOW I have RDKit::Bond pointer and RDKit::BOND_SPTR instead of 2
RDKit::Bond pointers
//and how I am going to compare them?
if (pCurrentBond != Bond_in
pCurrentBond-getOtherAtom(pAtom[i])-getAtomicNum() != 1)//not 'H' and
not
the same bond
{
// Bond contributes its weight, or 1 if
we're not considering weights.
dRtn += bWeighted ? GetBondWeight(pCurrentBond) : 1.0;
}
++beg;
}
}
return dRtn;
}
Can you help please!!!
Indeed, I can.
A BOND_SPTR is a boost shared pointer that contains a Bond *. To get
the Bond * itself, you call the shared pointer's get() method.
Something like this:
if (pCurrentBond.get() != Bond_in)
Best Regards,
-greg
--
___
Rdkit-discuss mailing list
Rdkit-discuss@lists.sourceforge.net
https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Compiling for VS 2008
Hi Greg, Thank you very much - it all works now. Another question - I still have boost 1.35 and I have noticed you are using 1.36. I want to pick up the latest dev. from svn and according to your message about C++ API changes do the fixes I need to implement in my code. The problem is - from boost site I can only get 1.38 (the latest) but not 1.36. What you will suggest? Regards, Evgueni 2009/2/11 Evgueni Kolossov ekolos...@gmail.com Thanks - will try to rebuild with msvc-9 option Regards, Evgueni 2009/2/11 Greg Landrum greg.land...@gmail.com You can specify the version of msvc at the command line. Take a look at the boost build documentation: http://www.boost.org/doc/libs/1_38_0/more/getting_started/windows.html (note: that mentions 1.38, but the instructions work for earlier versions of boost as well. You will need to rebuild the boost.python and boost.thread libraris as well, following the usual recipe in the rdkit build instructions). -greg On Wed, Feb 11, 2009 at 6:00 PM, Evgueni Kolossov ekolos...@gmail.com wrote: No, and how I can tell bjam which compiler to use (I have both VS2005 and 2008 on this machine)? 2009/2/11 Greg Landrum greg.land...@gmail.com Did the RDKit build (with bjam) use the VS2008 compiler? On Wed, Feb 11, 2009 at 5:39 PM, Evgueni Kolossov ekolos...@gmail.com wrote: Greg, All RDKit staff build with jam not with VS 2009/2/11 Greg Landrum greg.land...@gmail.com I'm afraid I'm not understanding. It looks like you are, in your VS2008 project, trying to link against libraries built using VS2005. You apparently can't do this. You need to rebuild all the libraries (including the relevant boost libraries) using VS2008. -greg On Wed, Feb 11, 2009 at 4:52 PM, Evgueni Kolossov ekolos...@gmail.com wrote: Yes, This is why I am talking about new boost version... It refer to libraries of RDKit built with the old version. Regards, Evgueni 2009/2/11 Greg Landrum greg.land...@gmail.com Dear Evgueni, On Wed, Feb 11, 2009 at 4:38 PM, Evgueni Kolossov ekolos...@gmail.com wrote: I have attached errors file. Google seems to indicate that these errors occur when you link against a library built using an older version of visual studio. -greg -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446 -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446 -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446 -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446 -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
Re: [Rdkit-discuss] Compiling for VS 2008
Thank you very much 2009/2/12 Greg Landrum greg.land...@gmail.com Dear Evgueni, On Thu, Feb 12, 2009 at 10:22 AM, Evgueni Kolossov ekolos...@gmail.com wrote: Thank you very much - it all works now. Glad to hear it. Another question - I still have boost 1.35 and I have noticed you are using 1.36. I want to pick up the latest dev. from svn and according to your message about C++ API changes do the fixes I need to implement in my code. The problem is - from boost site I can only get 1.38 (the latest) but not 1.36. What you will suggest? I haven't tested yet with 1.38, so I can't answer for sure about that. I don't imagine it would be a problem, but I'm not sure. If you want older versions of boost (I've tested with up to v1.37), you can get them here: http://www.boost.org/users/history/ -greg
Re: [Rdkit-discuss] Compiling for VS 2008
Yes, This is why I am talking about new boost version... It refer to libraries of RDKit built with the old version. Regards, Evgueni 2009/2/11 Greg Landrum greg.land...@gmail.com Dear Evgueni, On Wed, Feb 11, 2009 at 4:38 PM, Evgueni Kolossov ekolos...@gmail.com wrote: I have attached errors file. Google seems to indicate that these errors occur when you link against a library built using an older version of visual studio. -greg -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
[Rdkit-discuss] Fragmentation
Hi Greg, Can you please describe (or forward me to description) what rules you applied for fragmentation process. Can they be modified, etc. Regards, Evgueni
[Rdkit-discuss] computeBalabanJ
Hi Greg, I am trying to use your function to calculate Balaban index J: doubel dResult = RDKit::MolOps::computeBalabanJ(*mol, true, true, 0, false) and getting linker problems (see enclosed file). Probably need to #include some files? Can you help please? Regards, Evgueni Error 7 error LNK2019: unresolved external symbol void __cdecl LaEigSolve(class LaSymmMatDouble const ,class LaVectorDouble ) (?LaEigSolve@@YAXABVLaSymmMatDouble@@AAVLaVectorDouble@@@Z) referenced in function class boost::tuples::tupledouble,double,double,struct boost::tuples::null_type,struct boost::tuples::null_type,struct boost::tuples::null_type,struct boost::tuples::null_type,struct boost::tuples::null_type,struct boost::tuples::null_type,struct boost::tuples::null_type __cdecl RDKit::MolOps::computeDiscriminators(double *,int,int) (?computediscriminat...@molops@RDKit@@ya?av?$tu...@nnnunull_type@tup...@boost@@u...@u123@u...@u123@u...@u123@@tup...@boost@@pa...@z) libGraphMol.lib Error 8 error LNK2001: unresolved external symbol private: static int * LaLowerTriangMatDouble::info_ (?in...@lalowertriangmatdouble@@0PAHA) libGraphMol.lib Error 9 error LNK2019: unresolved external symbol public: __thiscall LaGenMatDouble::LaGenMatDouble(double *,int,int) (??0LaGenMatDouble@@q...@panhh@Z) referenced in function public: __thiscall LaLowerTriangMatDouble::LaLowerTriangMatDouble(double *,int,int) (??0LaLowerTriangMatDouble@@q...@panhh@Z)libGraphMol.lib Error 10 error LNK2019: unresolved external symbol public: virtual __thiscall LaGenMatDouble::~LaGenMatDouble(void) (??1LaGenMatDouble@@u...@xz) referenced in function public: __thiscall LaLowerTriangMatDouble::~LaLowerTriangMatDouble(void) (??1LaLowerTriangMatDouble@@q...@xz)libGraphMol.lib Error 11 error LNK2019: unresolved external symbol public: __thiscall LaGenMatDouble::LaGenMatDouble(int,int) (??0LaGenMatDouble@@q...@hh@Z) referenced in function public: __thiscall LaVectorDouble::LaVectorDouble(int) (??0LaVectorDouble@@q...@h@Z) libGraphMol.lib
Re: [Rdkit-discuss] Rings
So, RingInfo::numRings return the number of smallest rings? 2008/8/20 Greg Landrum greg.land...@gmail.com Dear Evgueni, On Wed, Aug 20, 2008 at 11:46 AM, Evgueni Kolossov ekolos...@gmail.com wrote: Is there any way to get separately total number of Rings and number of SMALLEST rings? The number of smallest rings is directly accessible through the SSSR functions, the total number of rings is not. For the total number of rings you'd need to do a breadth-first search and accumulate the rings you encounter. -greg -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
Re: [Rdkit-discuss] Calculation of atomic descriptors, Code snippet
Thanks Greg, Will this give the SHORTEST distance? Regards, Evgueni 2008/8/18 Greg Landrum greg.land...@gmail.com On Mon, Aug 18, 2008 at 12:42 PM, Evgueni Kolossov ekolos...@gmail.com wrote: Thanks Greg - this is works. Another question: Can you please provide an example of use MolOps::getDistanceMat with the samples how to extract distance data from this matrix I'm not clear what you're looking for. double *dm = MolOps::getDistanceMat(mol); // distance between atom 3 and 7: dm[3*mol.getNumAtoms()+7]; -greg -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
Re: [Rdkit-discuss] Calculation of atomic descriptors, Code snippet
2008/8/17 Evgueni Kolossov ekolos...@gmail.com
Thanks Greg,
But this is not enough:
unsigned int minRingSize=ringInfo-
minAtomRingSize(atomIdx);
for(VECT_INT_VECT_CI ringIt=ringInfo-atomRings().begin();
ringIt!=ringInfo-atomRings().end();++ringIt){
if(ringIt-size()==minRingSize){
if(std::find(ringIt-begin(),ringIt-end(),atomIdx)!=ringIt-end()){
// our atom is in this ring; do something
}
}
}
}
In this case we got an iterator (ringIt) which is itself a vector (if I am
right) of Ring atoms.
So to do something with atoms inside this ring we need somehow iterate
through the atoms...
Can you show how to do this?
I have tried to do it this way:
for (unsighed int i=0; iminRingSize; i++)
{
RDKit::Atom * pAtom = mol.getAtomWithIdx(ringIt[i]) ;
..
}
but this is not working.
Regards,
Evgueni
2008/8/15 Greg Landrum greg.land...@gmail.com
Dear Evgueni,
this is a general interest answer, so I'm directing it to the mailing
list.
On Fri, Aug 15, 2008 at 11:56 AM, Evgueni Kolossov
ekolos...@btinternet.com wrote:
I need to understand a little bit more about RingInfo.
For a given atom I got:
- the number of rings atom involved (pRingInfo-numAtomRings(Atom_Idx))
- the size of the smallest ring atom involved
(pRingInfo-minAtomRingSize(Atom_Idx))
correct.
Now I need to iterate through the atoms in the smallest ring with my
atom. I
can get atoms using pRingInfo-atomRings() but how I know this will give
me
the list of atoms in the smallest ring and in the ring where is my atom?
sample code, not actually tested, should give the idea:
unsigned int minRingSize=ringInfo-minAtomRingSize(atomIdx);
for(VECT_INT_VECT_CI ringIt=ringInfo-atomRings().begin();
ringIt!=ringInfo-atomRings().end();++ringIt){
if(ringIt-size()==minRingSize){
if(std::find(ringIt-begin(),ringIt-end(),atomIdx)!=ringIt-end()){
// our atom is in this ring; do something
}
}
}
}
What if my atom is a member of more than one ring?
The above code should work in that case as well.
-greg
-
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
--
Dr. Evgueni Kolossov (PhD)
ekolos...@gmail.com
Tel. +44(0)1628 627168
Mob. +44(0)7812070446
--
Dr. Evgueni Kolossov (PhD)
ekolos...@gmail.com
Tel. +44(0)1628 627168
Mob. +44(0)7812070446
Re: [Rdkit-discuss] Mol property
Thanks Greg, All works properly Regards, Evgueni 2008/8/12 Greg Landrum greg.land...@gmail.com Dear Evgueni, I checked in some changes this morning that added two optional arguments to ROMol.getPropList() includePrivate and includeComputed. These behave the same in C++ as they do in Python. The default behavior is the same as before: to show all properties. -greg On Mon, Aug 11, 2008 at 2:24 PM, Evgueni Kolossov ekolos...@gmail.com wrote: Hi Greg, ROMol::getPropList() will return not only properties from the SDFile but also some default properties. Is there way(param) to get only properties loaded from the file? Regards, Evgueni - 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 -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
Re: [Rdkit-discuss] SD File output
Dear Greg, Can you please show how to extract text from stringstream (which in your case actually ostream) into string? ROMol *mol; mol = SmilesToMol(strSmile); ostream *ss = new stringstream(); SDWriter *writer = new SDWriter(ss, false); writer-write(*mol); string strMolStructure; //Now we want to put MDLMol into the string. For stringstream ss-str() will do the job but ss is ostream) Regards, Evgueni -Original Message- From: rdkit-discuss-boun...@lists.sourceforge.net [mailto: rdkit-discuss-boun...@lists.sourceforge.net] On Behalf Of Greg Landrum Sent: 05 August 2008 19:07 To: Igor Filippov [Contr] Cc: rdkit-discuss@lists.sourceforge.net Subject: Re: [Rdkit-discuss] SD File output Dear Igor, This is a good one for the mailing list, so I'm cross-posting my reply. On Tue, Aug 5, 2008 at 6:47 PM, Igor Filippov [Contr] ig...@helix.nih.gov wrote: Is there any way to convert a mol object into an SD file (i.e. CTAB plus user-defined properties) and have the result in a string? MolToMolBlock() only outputs CTAB portion without the properties. Indeed there is. You can construct an SDWriter (defined in $RDBASE/GraphMol/FileParsers/MolWriters.h) using a pointer to a stringstream, then use the SDWriter's write() method. It's probably safest to call the flush() method before reading your text out of the stringstream. An example for using this with a SmilesWriter is in the function testSmilesWriter2() in testMolWriter.cpp. Using an SDWriter is exactly equivalent. -greg - 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
[Rdkit-discuss] VS2005 solution
Hi, If anybody interested, I have made single RDKit.sln as well as separate solutions for each dll in RDKit for Visual Studio 2005. All builds OK. Regards, Evgueni
