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 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
Ok this way it works... Regards, Evgueni On 30 July 2010 09:52, Greg Landrum wrote: > On Fri, Jul 30, 2010 at 10:50 AM, Evgueni Kolossov > 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
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 wrote: > On Fri, Jul 30, 2010 at 9:55 AM, Evgueni Kolossov > 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
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 wrote: > Hi Evgueni, > > On Thu, Jul 29, 2010 at 9:08 PM, Evgueni Kolossov > 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
Dear Greg, - 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 Regards, Evgueni On 29 July 2010 19:34, Greg Landrum wrote: > Hi Evgueni, > > On Thu, Jul 29, 2010 at 10:14 AM, Evgueni Kolossov > wrote: > > > > > 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) > > Are you sure when you built you included "install" in the bjam command > line? > Here's my command line: > bjam toolset=msvc link=shared --with-python ---with-thread > --with-regex release install > > You should also try looking in c:/boost/lib: > /c/boost/boost_1_43_0 >ls /c/boost/lib/*regex*43* > /c/boost/lib/boost_regex-vc90-mt-1_43.dll > /c/boost/lib/boost_regex-vc90-mt-1_43.lib > /c/boost/lib/libboost_regex-vc90-mt-1_43.lib > > If all three files are there, then I'm really going to start wondering. > > Have you updated the CMakeLists.txt to add 1.43 to the > Boost_ADDITIONAL_VERSIONS line? (This is described on the wiki). Make > sure to delete the cache and rerun configure in cmake after making any > of these changes. > > Best, > -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, Is it possible you have a wrong name for regex - it looking for boost_regex but library actually called libboost_regex Regards, Evgueni On 29 July 2010 09:14, Evgueni Kolossov wrote: > 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 wrote: > >> Dear all, >> >> On Wed, Jul 28, 2010 at 4:04 PM, Evgueni Kolossov >> 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
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 wrote: > Dear all, > > On Wed, Jul 28, 2010 at 4:04 PM, Evgueni Kolossov > 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 $1 Million in cash or HP Products. Visit us here for more details: http://p.sf.net/sfu/dev2dev-palm___ Rdkit-discuss mailing list Rdkit-discuss@lists.sourceforge.net https://lists.sourceforge.net/lists/listinfo/rdkit-discuss
Re: [Rdkit-discuss] Build on Windows
Thanks, I think I will install 1_42 from install package and rebuild all with 1_42 until installation package will be available for 1_43 Regards, Evgueni On 28 July 2010 15:38, Peter Schmidtke wrote: > Ah sorry mea culpa this was for unix based systems. > However, on windows you should use : > > .\bjam.exe --toolset=msvc --with-python --with-regex release install > > > instead I think to build boost. I'm not 100% sure about this as the rkdit > build documentation for windows says something different. > > Try to build boost with this and build rdkit again. > > > On 28/07/2010, at 16:34, Evgueni Kolossov wrote: > > No, what is this for? > > On 28 July 2010 15:31, Peter Schmidtke wrote: > >> Did you ./boostrap boost with regex using : >> >> ./bootstrap.sh --prefix=$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 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 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 wrote: >>>> >>>>> On 28 July 2010 15:04, Evgueni Kolossov 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 >>>>> > >>>>> > -- >>>>> > >>>>> > >
Re: [Rdkit-discuss] Build on Windows
No, what is this for? On 28 July 2010 15:31, Peter Schmidtke 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 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 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 wrote: >>> >>>> On 28 July 2010 15:04, Evgueni Kolossov 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
Yes this is set in environmental variables and I am using CMake 2.8 On 28 July 2010 15:24, Peter Schmidtke 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 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 wrote: >> >>> On 28 July 2010 15:04, Evgueni Kolossov 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 -- 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
There is no binary installer for booat 1_43, so I build it: .\bjam.exe --toolset=msvc --without-python release install and I can see that it have been built at ...\bin.v2\libs\regex\msvc-9.0\release\link-static\threading-multi On 28 July 2010 15:18, Noel O'Boyle wrote: > 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 wrote: > > Tried Run cmake with -DBoost_LIBRARYDIR=whatever > > but it still cannot find regex > > > > On 28 July 2010 15:07, Noel O'Boyle wrote: > >> > >> On 28 July 2010 15:04, Evgueni Kolossov 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 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 wrote: > >> On 28 July 2010 15:04, Evgueni Kolossov 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
Tried Run cmake with -DBoost_LIBRARYDIR=whatever but it still cannot find regex On 28 July 2010 15:07, Noel O'Boyle wrote: > On 28 July 2010 15:04, Evgueni Kolossov 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
[Rdkit-discuss] Build on Windows
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. 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
Re: [Rdkit-discuss] Q2 2010 Release
Thank you very much Regards, Evgueni On 2 July 2010 07:11, Greg Landrum wrote: > Hi Evgueni, > > On Fri, Jul 2, 2010 at 8:06 AM, Evgueni Kolossov > 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, Thank you very much. I understood I need to rebuild again to have all libraries in one place or copy them manually? Regards, Evgueni On 2 July 2010 04:40, Greg Landrum wrote: > Dear Evgueni, > > On Thu, Jul 1, 2010 at 3:18 PM, Evgueni Kolossov > wrote: > > > > Am I right that the libraries names are changed, for example: > > libChemicalFeatures.lib now called just ChemicalFeatures.lib, etc.? > > > > That's what it looks like; cmake has a different approach to this than > bjam I guess. The cmake variant is somehow more windows-like than the > bjam one. > > You also pointed out on the wiki that there is no INSTALL target when > you don't build the python wrappers. This seems to be the case. In > fact, the libraries are built and left in the build directory (this > happens even if the python wrappers are included in the build; the > INSTALL target there just copies the wrappers). This morning I fixed > that: now there's always an INSTALL target and the libraries are > always copied to $RDBASE/lib after being built. > > Best Regards, > -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 wrote: > On 1 July 2010 13:43, Evgueni Kolossov 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 wrote: > >> > >> On Thu, Jul 1, 2010 at 1:38 PM, Evgueni Kolossov > >> 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] 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 wrote: > On Thu, Jul 1, 2010 at 1:38 PM, Evgueni Kolossov > 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
t; > -- > 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 > -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Scientific Software Solutions Ltd. www.scisoftpro.com Tel. +44(0)1628 647 333 Mob. +44(0)7812070446 -- 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
Greg,
Should we now install CMake? if so, you probably need to add this into
installation guide.
Regards,
Evgueni
On 30 June 2010 21:16, Greg Landrum wrote:
> Dear all,
>
> I'm very happy to announce that the next version of the RDKit --
> Q22010_1 -- is released.
>
> The release notes are below.
>
> The source release and windows binaries (python 2.6 only this time,
> please let me know if anyone needs a python 2.5 release) will be on
> the sourceforge downloads page:
> http://sourceforge.net/projects/rdkit/files/rdkit/Q2_2010/
> The files can also be downloaded from the google project page:
> http://code.google.com/p/rdkit/downloads/list
>
> I have also updated the online documentation.
>
> Thanks to the everyone who submitted bug reports and suggestions for
> this release!
>
> Please let me know if you find any problems with the release or have
> suggestions for the next one.
>
> -greg
>
> ** Release_Q22010_1 ***
> (Changes relative to Release_Q12010_1)
>
> !! IMPORTANT !!
> - There are a couple of refactoring changes that affect people using
> the RDKit from C++. Please look in the Other section below for a list.
> - If you are building the RDKit yourself, changes made in this
> release require that you use a reasonably up-to-date version of
> flex to build it. Please look in the Other section below for more
> information.
>
> Acknowledgements:
> - Andrew Dalke, James Davidson, Kirk DeLisle, Thomas Heller, Peter Gedeck,
> Greg Magoon, Noel O'Boyle, Nik Stiefl,
>
> Bug Fixes:
> - The depictor no longer generates NaNs for some molecules on
> windows (issue 2995724)
> - [X] query features work correctly with chiral atoms. (issue
> 3000399)
> - mols will no longer be deleted by python when atoms/bonds returned
> from mol.Get{Atom,Bond}WithIdx() are still active. (issue 3007178)
> - a problem with force-field construction for five-coordinate atoms
> was fixed. (issue 3009337)
> - double bonds to terminal atoms are no longer marked as "any" bonds
> when writing mol blocks. (issue 3009756)
> - a problem with stereochemistry of double bonds linking rings was
> fixed. (issue 3009836)
> - a problem with R/S assignment was fixed. (issue 3009911)
> - error and warning messages are now properly displayed when cmake
> builds are used on windows.
> - a canonicalization problem with double bonds incident onto aromatic
> rings was fixed. (issue 3018558)
> - a problem with embedding fused small ring systems was fixed.
> (issue 3019283)
>
> New Features:
> - RXN files can now be written. (issue 3011399)
> - reaction smarts can now be written.
> - v3000 RXN files can now be read. (issue 3009807)
> - better support for query information in mol blocks is present.
> (issue 2942501)
> - Depictions of reactions can now be generated.
> - Morgan fingerprints can now be calculated as bit vectors (as
> opposed to count vectors.
> - the method GetFeatureDefs() has been added to
> MolChemicalFeatureFactory
> - repeated recursive SMARTS queries in a single SMARTS will now be
> recognized and matched much faster.
> - the SMILES and SMARTS parsers can now be run safely in
> multi-threaded code.
>
> Deprecated modules (to be removed in next release):
> - rdkit/qtGui
> - Projects/SDView
>
> Removed modules:
> - SVD code: External/svdlibc External/svdpackc rdkit/PySVD
> - rdkit/Chem/CDXMLWriter.py
>
> Other:
> - The large scale changes in the handling of stereochemistry were
> made for this release. These should make the code more robust.
> - If you are building the RDKit yourself, changes made in this
> release require that you use a reasonably up-to-date version of
> flex to build it. This is likely to be a problem on Redhat, and
> redhat-derived systems. Specifically: if your version of flex is
> something like 2.5.4 (as opposed to something like 2.5.33, 2.5.34,
> etc.), you will need to get a newer version from
> http://flex.sourceforge.net in order to build the RDKit.
>
> - Changes only affecting C++ programmers:
> - The code for calculating topological-torsion and atom-pair
> fingerprints has been moved from $RDBASE/Code/GraphMol/Descriptors
> to $RDBASE/Code/GraphMol/Fingerprints.
> - The naming convention for methods of ExplicitBitVect and
> SparseBitVect have been changed to make it more consistent with
> the rest of the RDKit.
> - the bjam-based build system should be considered
> deprecated. This is the last release it will be actively
> maintained.
>
>
> --
> 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
Great! Good job Greg!
Will try to build for C++ tomorrow
On 30 June 2010 21:16, Greg Landrum wrote:
> Dear all,
>
> I'm very happy to announce that the next version of the RDKit --
> Q22010_1 -- is released.
>
> The release notes are below.
>
> The source release and windows binaries (python 2.6 only this time,
> please let me know if anyone needs a python 2.5 release) will be on
> the sourceforge downloads page:
> http://sourceforge.net/projects/rdkit/files/rdkit/Q2_2010/
> The files can also be downloaded from the google project page:
> http://code.google.com/p/rdkit/downloads/list
>
> I have also updated the online documentation.
>
> Thanks to the everyone who submitted bug reports and suggestions for
> this release!
>
> Please let me know if you find any problems with the release or have
> suggestions for the next one.
>
> -greg
>
> ** Release_Q22010_1 ***
> (Changes relative to Release_Q12010_1)
>
> !! IMPORTANT !!
> - There are a couple of refactoring changes that affect people using
> the RDKit from C++. Please look in the Other section below for a list.
> - If you are building the RDKit yourself, changes made in this
> release require that you use a reasonably up-to-date version of
> flex to build it. Please look in the Other section below for more
> information.
>
> Acknowledgements:
> - Andrew Dalke, James Davidson, Kirk DeLisle, Thomas Heller, Peter Gedeck,
> Greg Magoon, Noel O'Boyle, Nik Stiefl,
>
> Bug Fixes:
> - The depictor no longer generates NaNs for some molecules on
> windows (issue 2995724)
> - [X] query features work correctly with chiral atoms. (issue
> 3000399)
> - mols will no longer be deleted by python when atoms/bonds returned
> from mol.Get{Atom,Bond}WithIdx() are still active. (issue 3007178)
> - a problem with force-field construction for five-coordinate atoms
> was fixed. (issue 3009337)
> - double bonds to terminal atoms are no longer marked as "any" bonds
> when writing mol blocks. (issue 3009756)
> - a problem with stereochemistry of double bonds linking rings was
> fixed. (issue 3009836)
> - a problem with R/S assignment was fixed. (issue 3009911)
> - error and warning messages are now properly displayed when cmake
> builds are used on windows.
> - a canonicalization problem with double bonds incident onto aromatic
> rings was fixed. (issue 3018558)
> - a problem with embedding fused small ring systems was fixed.
> (issue 3019283)
>
> New Features:
> - RXN files can now be written. (issue 3011399)
> - reaction smarts can now be written.
> - v3000 RXN files can now be read. (issue 3009807)
> - better support for query information in mol blocks is present.
> (issue 2942501)
> - Depictions of reactions can now be generated.
> - Morgan fingerprints can now be calculated as bit vectors (as
> opposed to count vectors.
> - the method GetFeatureDefs() has been added to
> MolChemicalFeatureFactory
> - repeated recursive SMARTS queries in a single SMARTS will now be
> recognized and matched much faster.
> - the SMILES and SMARTS parsers can now be run safely in
> multi-threaded code.
>
> Deprecated modules (to be removed in next release):
> - rdkit/qtGui
> - Projects/SDView
>
> Removed modules:
> - SVD code: External/svdlibc External/svdpackc rdkit/PySVD
> - rdkit/Chem/CDXMLWriter.py
>
> Other:
> - The large scale changes in the handling of stereochemistry were
> made for this release. These should make the code more robust.
> - If you are building the RDKit yourself, changes made in this
> release require that you use a reasonably up-to-date version of
> flex to build it. This is likely to be a problem on Redhat, and
> redhat-derived systems. Specifically: if your version of flex is
> something like 2.5.4 (as opposed to something like 2.5.33, 2.5.34,
> etc.), you will need to get a newer version from
> http://flex.sourceforge.net in order to build the RDKit.
>
> - Changes only affecting C++ programmers:
> - The code for calculating topological-torsion and atom-pair
> fingerprints has been moved from $RDBASE/Code/GraphMol/Descriptors
> to $RDBASE/Code/GraphMol/Fingerprints.
> - The naming convention for methods of ExplicitBitVect and
> SparseBitVect have been changed to make it more consistent with
> the rest of the RDKit.
> - the bjam-based build system should be considered
> deprecated. This is the last release it will be actively
> maintained.
>
>
> --
> This SF.net email is sponsored by Sprint
> What will you do first with EVO
Re: [Rdkit-discuss] Installation on Windows
Dear Greg, Thank you very much Regards, Evgueni On 22 June 2010 08:32, Greg Landrum wrote: > Hi Evgueni, > > On Tue, Jun 22, 2010 at 9:07 AM, Evgueni Kolossov > wrote: > > > > I have decided now to move into latest version and got couple of > questions: > > - What the latest boost version you can recommend? > > It looks like any of the boost versions (up to 1.43 at least) work, so > you might as well use either 1.42 or 1.43. > > > - I believe before it was requirement to install some additional boost > > libraries. Is it still required or not? > > No, now you get everything from boost.org; no additional libraries are > required at this point. > > FYI: I should be doing a new release next week. If you're planning on > moving to a new version, I would recommend waiting for that before > switching. > > Best Regards, > -greg > -- 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
[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 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 wrote: > Dear Evgueni, > > 2010/4/19 Evgueni Kolossov : > > > > 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® 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 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 > 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® 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 wrote: > Hi Evgueni, > > On Wed, Feb 10, 2010 at 11:02 AM, Evgueni Kolossov > 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,
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!!
Regards,
Evgueni
On 6 February 2010 05:21, Greg Landrum wrote:
> Dear Evgueni,
>
> On Fri, Feb 5, 2010 at 11:21 AM, Evgueni Kolossov
> wrote:
> > 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?
>
> The boost smart pointers can be copied without problems, so this
> shouldn't cause any corruption. Building on the small example I was
> doing before, the following 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]);
> m_vF.push_back(ROMOL_SPTR(nm));
>
>RDKit::MOL_SPTR_VECT m_vF2;
>m_vF2.resize(m_vF.size());
>std::copy(m_vF.begin(),m_vF.end(),m_vF2.begin());
>std::cerr<getNumAtoms()< }
>
>
> The original error you saw, from here:
> > T * operator-> () const
> > {
> > BOOST_ASSERT(px != 0);
> > return px;
> > }
> is triggered when you try to dereference a smart pointer that has a
> null pointer as its contents. I'd suggest being sure that your
> original vector doesn't have any empty elements (cases where the
> molecule was a null pointer).
>
> -greg
>
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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 wrote:
> Hi Evgueni,
>
> On Thu, Feb 4, 2010 at 5:25 PM, Evgueni Kolossov
> 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
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[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
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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 > >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 > >> On Tue, Dec 1, 2009 at 12:31 PM, Evgueni Kolossov >> 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
Re: [Rdkit-discuss] SubstructMatch
I cannot agree about default behaviour - at IDBS we have done different way and this why fragment-based models based on IDBS fragment-structure mapping was so good... looking like I will need to write my own mapping... Regards, Evgueni 2009/12/1 Adrian Schreyer > You need to provide a more specific query. * is very generic and hits > everything in the molecule except the sulfur and the imidazole. I am not > sure about 17 hits but I can count at least 15. This is the default > behaviour in every toolkit, by the way. > > You should try the SMARTS tester from Daylight to visualise your > substructure matches > http://www.daylight.com/daycgi_tutorials/depictmatch.cgi > > Adrian > > On Tue, Dec 1, 2009 at 11:39, Evgueni Kolossov wrote: > >> >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 >> >>> On Tue, Dec 1, 2009 at 12:31 PM, Evgueni Kolossov >>> 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 >> >> > -- 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
>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 > On Tue, Dec 1, 2009 at 12:31 PM, Evgueni Kolossov > 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
Re: [Rdkit-discuss] SubstructMatch
I can investigate but even without this cyclic/non-cyclic problem there cannot be 17 matches! Especially with uniquify set to true. So, this function is actually useless. 2009/12/1 Greg Landrum > On Tue, Dec 1, 2009 at 12:01 PM, Evgueni Kolossov > wrote: > > I believe none of them if take in account cyclic and non-cyclic atoms > > That's definitely the case. If you want to include that information in > your query, you have to explicitly do so. In order to do this, you are > going to have to either express your queries as SMARTS or CTABs > (instead of SMILES) or edit the atoms by hand to replace each Atom > with a QueryAtom and expand that QueryAtom's query to include ring > membership (or lack thereof). > > -greg > > > > > 2009/12/1 Greg Landrum > >> > >> Evgueni, > >> > >> Please provide specific maps that don't make sense. > >> > >> -greg > >> > >> > >> On Tue, Dec 1, 2009 at 11:50 AM, Evgueni Kolossov > >> wrote: > >> > Fragment: * > >> > Structure: S=C(CC1C1)N1CCC(c2nc[nH]c2)CC1 > >> > > -- 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] SubstructMatch
I believe none of them if take in account cyclic and non-cyclic atoms
2009/12/1 Greg Landrum
> Evgueni,
>
> Please provide specific maps that don't make sense.
>
> -greg
>
>
> On Tue, Dec 1, 2009 at 11:50 AM, Evgueni Kolossov
> wrote:
> > 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; igetNumAtoms(); 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
> >>
> >> 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
> >> wrote:
> >> > Yes, Greg,
> >> >
> >> > I believe that result 17 matches for this fragment does not make any
> >> > sense
> >> >
> >> > 2009/12/1 Greg Landrum
> >> >>
> >> >> 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
> >> >
> >> >
> >> >
> >> > --
> >
> >
>
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[Rdkit-discuss] Fwd: SubstructMatch
-- Forwarded message --
From: Evgueni Kolossov
Date: 2009/12/1
Subject: Re: [Rdkit-discuss] SubstructMatch
To: Greg Landrum
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; igetNumAtoms(); 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
> 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
> wrote:
> > Yes, Greg,
> >
> > I believe that result 17 matches for this fragment does not make any
> sense
> >
> > 2009/12/1 Greg Landrum
> >>
> >> Dear Evgueni,
> >>
> >> On Tue, Dec 1, 2009 at 10:21 AM, Evgueni Kolossov
> >> 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
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Mob. +44(0)7812070446
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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 > Dear Evgueni, > > On Tue, Dec 1, 2009 at 10:21 AM, Evgueni Kolossov > 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] 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 <><>-- 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
>are you doing the replace dummy for each fragment every time before >you do a search or do you do it just once? I am iterating through all the structures and all the fragments: so for each structure do for each fragment ( and need to replace dummy here) probably can do it another way: for each fragment do for each structure In this case will need to do it only once for each fragment Regards, Evgueni 2009/11/7 Greg Landrum > On Sat, Nov 7, 2009 at 3:44 PM, Evgueni Kolossov > wrote: > > > > I have not done full profiling - this came just from the difference > between > > time with and without Replace Dummmy > > are you doing the replace dummy for each fragment every time before > you do a search or do you do it just once? > > I would guess that replacing the dummy atoms shouldn't take very long > at all, and then doing the searches should also be reasonably quick. > One complication might be that having the query atoms will return a > lot more matches than the non-query dummies; this will naturally take > longer. > > -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, I have not done full profiling - this came just from the difference between time with and without Replace Dummmy Regards, Evgueni 2009/11/7 Greg Landrum > On Sat, Nov 7, 2009 at 12:35 PM, Evgueni Kolossov > wrote: > > > > I have calculated it will slow down on about 30% using this replacement > > which is significant for big datasets. > > Agreed, that's a huge difference. How does it come about? Where is the > time being spent? > > -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
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 > Combining two answers into one: > > On Fri, Nov 6, 2009 at 7:59 AM, Evgueni Kolossov > 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 > 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
> 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
>
> On Wed, Nov 4, 2009 at 7:54 PM, Greg Landrum
>> wrote:
>> >
>> > On Wed, Nov 4, 2009 at 3:26 PM, Evgueni Kolossov
>> 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
>>
>> void replaceDummies(RWMol *frag){
>> QueryAtom *qat = new QueryAtom();
>> qat->setQuery(makeAtomNullQuery());
>> for(unsigned int i=0;igetNumAtoms();++i){
>>if(frag->getAtomWithIdx(i)->getAtomicNum()==0){
>> frag->replaceAtom(i,qat);
>>}
>> }
>> delete qat;
>> }
>> //-
>>
>> I hope this helps,
>> -greg
>>
>
>
>
>
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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
> On Wed, Nov 4, 2009 at 7:54 PM, Greg Landrum
> wrote:
> >
> > On Wed, Nov 4, 2009 at 3:26 PM, Evgueni Kolossov
> 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
>
> void replaceDummies(RWMol *frag){
> QueryAtom *qat = new QueryAtom();
> qat->setQuery(makeAtomNullQuery());
> for(unsigned int i=0;igetNumAtoms();++i){
>if(frag->getAtomWithIdx(i)->getAtomicNum()==0){
> frag->replaceAtom(i,qat);
>}
> }
> delete qat;
> }
> //-
>
> I hope this helps,
> -greg
>
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Re: [Rdkit-discuss] Substructure search
Hi Greg, I found that SubstructMatch would not work if query is a fragment (with * atoms). Can you suggest solution for this problem? Regards, Evgueni 2009/10/21 Greg Landrum > Dear Evgueni, > > On Wed, Oct 21, 2009 at 3:25 PM, Evgueni Kolossov > wrote: > > > > I do not quite understand how SubstructMatch function works - what will > be > > in vector matchVect which is vector? is it Atomic matches? > > It's a vector with information about the match: > atom id in query : atom id in matched molecule > > > What is the simplest way to find substructures/superstructures/exact > match > > of query structure in the set of molecules? > > substructure: use SubstructMatch(mol,query,...) > superstructure: use SubstructMatch(query,mol,...) > exact match: use canonical SMILES > > -greg > > > > -greg > -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446 -- 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] Substructure search
Dear Greg, I do not quite understand how SubstructMatch function works - what will be in vector matchVect which is vector? is it Atomic matches? What is the simplest way to find substructures/superstructures/exact match of query structure in the set of molecules? 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
Hi Greg, Just try to copy any aromatic ring the way I described it and at the end do: fragMol->updatePropertyCache(); MolOps::sanitizeMol(fragMol); I believe aromaticity suppose to be set in sanitize and I do not need to call MolOps::setAromaticity Regards, Evgueni 2009/10/20 Greg Landrum > Dear Evgueni, > > On Mon, Oct 19, 2009 at 9:11 PM, Evgueni Kolossov > wrote: > > 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); > > hmm, I'm afraid I don't really see anything here that would lead to a > molecule that has aromatic rings where all bonds are double. Do you > have a specific example you can show (preferably including the output > of debugMol) that demonstrate the problem? > > -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] 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 > On Mon, Oct 19, 2009 at 12:06 PM, Evgueni Kolossov > 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
[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] beta of Q3 2009 release up
Dear Greg, I want to have a fragment where atom (*) can be set to aromatic Regards, Evgueni 2009/10/12 Greg Landrum > Dear Evgueni, > > On Mon, Oct 12, 2009 at 9:03 AM, Evgueni Kolossov > wrote: > > > > You have fixed the problem with the chain aromatic atom but is it > possible > > to add an exclusion for special atom types (like (*), A, etc.) to allow > the > > difference between fragments connected to the aromatic and non-aromatic > > atoms? > > I'm not sure I understand the question. Can you give an example of > what you'd like to be able to do? > > -greg > -- 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] beta of Q3 2009 release up
Dear Greg, You have fixed the problem with the chain aromatic atom but is it possible to add an exclusion for special atom types (like (*), A, etc.) to allow the difference between fragments connected to the aromatic and non-aromatic atoms? Regards, Evgueni 2009/10/10 Greg Landrum > Dear all, > > I have tagged a beta of the Q3 2009 release in svn: > https://rdkit.svn.sourceforge.net/svnroot/rdkit/tags/Release_Q32009_1beta1 > and uploaded a source distribution to the google code page for those > who don't want to deal with svn: > http://code.google.com/p/rdkit/downloads > Release notes are here: > > http://rdkit.svn.sourceforge.net/viewvc/rdkit/tags/Release_Q32009_1beta1/ReleaseNotes.txt?revision=1255&view=markup > > If there's demand for a windows (or mac) binary, I can build those as well. > > As usual: if no problems come up in the next week I will go ahead and > do the actual release. > > Best regards, > -greg > > > -- > 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 > -- 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 > 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 > <>
Re: [Rdkit-discuss] Fragmentation
Bug found and fixed. 2009/8/13 Evgueni Kolossov > Sorry - forgot to fix one more things. > Now it's final. > > > Regards, > Evgueni > > 2009/8/13 Evgueni Kolossov > >> Sorry - forgot that anion in nitro group and perchlorate can be affected - >> fixed now. >> >> Regards, >> Evgueni >> >> 2009/8/13 Evgueni Kolossov >> >> 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::vector & 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 >>> >>> On Wed, Aug 12, 2009 at 11:54 AM, Evgueni Kolossov >>>> wrote: >>>> > Greg, >>>> > >>>> > Am I right that the function >>>> > std::vector> 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 >>>> >>> >>> >>> >>> > <>
Re: [Rdkit-discuss] Fragmentation
Sorry - forgot to fix one more things. Now it's final. Regards, Evgueni 2009/8/13 Evgueni Kolossov > Sorry - forgot that anion in nitro group and perchlorate can be affected - > fixed now. > > Regards, > Evgueni > > 2009/8/13 Evgueni Kolossov > > 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::vector & 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 >> >> On Wed, Aug 12, 2009 at 11:54 AM, Evgueni Kolossov >>> wrote: >>> > Greg, >>> > >>> > Am I right that the function >>> > std::vector> 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 >>> >> >> >> >> <>
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 > 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::vector & 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 > > On Wed, Aug 12, 2009 at 11:54 AM, Evgueni Kolossov >> wrote: >> > Greg, >> > >> > Am I right that the function >> > std::vector> 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 >> > > > > <>
Re: [Rdkit-discuss] Fragmentation
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::vector & 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 > On Wed, Aug 12, 2009 at 11:54 AM, Evgueni Kolossov > wrote: > > Greg, > > > > Am I right that the function > > std::vector> 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
Thanks - this actually doing what we need at once Regards, Evgueni 2009/8/12 Greg Landrum > On Wed, Aug 12, 2009 at 11:54 AM, Evgueni Kolossov > wrote: > > Greg, > > > > Am I right that the function > > std::vector> 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, Am I right that the function std::vector> getMolFrags(const ROMol & mol, bool sanitizeFrags=true, INT_VECT *frags=0) will return the vector of fragments as ROMol's? Regards, Evgueni 2009/7/21 Greg Landrum > On Tue, Jul 21, 2009 at 8:09 AM, Evgueni Kolossov > wrote: > > > > One more question - is there function to get how many structures is in > mol? > > MolOps::getMolFrags() > -- 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 > On Mon, Aug 10, 2009 at 12:43 PM, Evgueni Kolossov > 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 > Hi Evgueni > > On Mon, Jul 20, 2009 at 7:05 PM, Evgueni Kolossov > 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 > On Tue, Jul 21, 2009 at 8:09 AM, Evgueni Kolossov > wrote: > > > > One more question - is there function to get how many structures is in > mol? > > MolOps::getMolFrags() >
Re: [Rdkit-discuss] Fragmentation
Greg, One more question - is there function to get how many structures is in mol? Regards, Evgueni 2009/7/20 Evgueni Kolossov > Thanks Greg, > > Let's go this way... > > Regards, > Evgueni > > 2009/7/20 Greg Landrum > >> Evgueni, >> >> >> >> On Mon, Jul 20, 2009 at 9:02 PM, Evgueni Kolossov >> wrote: >> > >> > This is the best (on my opinion) way to do salt stripping - to have a >> > library of salts... >> >> agreed. It would be a very useful addition to the open-source version >> of the rdkit too. >> >> > Another question - is there function to map fragment to structure (to >> get >> > how many times this fragment appeared in structure)? >> >> Yeah, the substructure matching code does this >> (Substruct/SubstructMatch.h) >> >> -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
Re: [Rdkit-discuss] Fragmentation
Thanks Greg, Let's go this way... Regards, Evgueni 2009/7/20 Greg Landrum > Evgueni, > > > On Mon, Jul 20, 2009 at 9:02 PM, Evgueni Kolossov > wrote: > > > > This is the best (on my opinion) way to do salt stripping - to have a > > library of salts... > > agreed. It would be a very useful addition to the open-source version > of the rdkit too. > > > Another question - is there function to map fragment to structure (to get > > how many times this fragment appeared in structure)? > > Yeah, the substructure matching code does this (Substruct/SubstructMatch.h) > > -greg > -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
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 > Hi Evgueni > > On Mon, Jul 20, 2009 at 7:05 PM, Evgueni Kolossov > 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
Thanks Greg,
What about fingerprints to use for this?
Regards,
Evgueni
2009/7/16 Greg Landrum
> HI Evgueni,
>
> On Thu, Jul 16, 2009 at 11:23 AM, Evgueni Kolossov
> wrote:
> > 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?
>
> The easy answer would be to use the canonical smiles for the fragment.
> This *might* work, and it would be easy, but I'm not sure I'd trust
> it.
> Here's a simple example where it did work:
> [6] >>> m1 = Chem.MolFromSmiles('O',False)
>
> [7] >>> m2 = Chem.MolFromSmiles('O',False)
>
> [8] >>> m1.UpdatePropertyCache()
>
> [9] >>> m2.UpdatePropertyCache()
>
> [10] >>> Chem.MolToSmiles(m1)
> Out[10]: 'O'
>
> [11] >>> Chem.MolToSmiles(m2)
> Out[11]: 'O'
>
> An answer that's more likely to be correct, but perhaps more difficult
> to implement, is the use of subgraph invariants. This is what the
> existing RDKit fragment catalog code does. Take a look at the
> getDiscrims() method of FragCatalogEntry
> ($RDBASE/Code/GraphMol/FragCatalog/FragCatalogEntry.cpp); it shows an
> approach that I have more confidence in than the "canonical smiles for
> pieces of molecules" method.
>
> -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::vector 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] Fragmentation
Dear Greg,
Now I have found that Compute2DCoords(m) failing in Atom::getNumImplicitHs()
on
PRECONDITION(d_implicitValence>-1, "getNumImplicitHs() called without
preceding call to calcImplicitValence()")
mol it trying to process: [*]NC(=N)N[*]
>To have a chance at getting something reasonable for
>fragments, you probably ought to generate 2D coordinates for the full
>molecule, then manually set the positions of the atoms in the
>fragment's conformer.
And how I can do that?
Regards,
Evgueni
2009/7/6 Greg Landrum
> Dear Evgueni,
>
>
> On Mon, Jul 6, 2009 at 8:03 PM, Evgueni Kolossov
> wrote:
> >
> > To display structure I need to put string MDLMol into the control.
> >
> > If I call compute2DCoords - it raised an exception but if do not - all
> >
> > atoms in one dot and you cannot see it at all The same is if I try to
> >
> > read call sanitizeMol.
> >
> > Looking like problem in Kekilizer because some of my fragments can
> >
> > contain atoms and bonds taken from the aromatic ring (and it must be so).
> >
> > Simple fragments like chain fragments displayed Ok because they are
> >
> > not causing exception in compute2Dcoords.
>
> RDKit::MolToMolBlock (or MolToMolFile) each take an optional kekulize
> argument (the last one). If you set this to false, the mol file writer
> will not attempt to kekulize aromatic bonds. Here's an example of
> doing this from python:
>
> [72]>>> m = Chem.MolFromSmiles('',sanitize=False)
> [73]>>> AllChem.Compute2DCoords(m)
> Out[73] 0
> [74]>>> print Chem.MolToMolBlock(m,kekulize=False)
>
> RDKit 2D
>
> 4 3 0 0 0 0 0 0 0 0999 V2000
>0.0.0. C 0 0 0 0 0 0 0 0 0 0 0 0
> -0. -1.50000. C 0 0 0 0 0 0 0 0 0 0 0 0
> -0. -3.0. C 0 0 0 0 0 0 0 0 0 0 0 0
> -0. -4.50000. C 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 4 0
> 2 3 4 0
> 3 4 4 0
> M END
>
>
> A note: as this example shows the coordinates generated by the
> depictor for unsanitized molecules are likely to be less than
> pleasing. To have a chance at getting something reasonable for
> fragments, you probably ought to generate 2D coordinates for the full
> molecule, then manually set the positions of the atoms in the
> fragment's conformer.
>
> Best Regards,
> -greg
>
[Rdkit-discuss] Fragmentation
Hi Greg, Thanks - it works with smart pointers but I got another problem: To display structure I need to put string MDLMol into the control. If I call compute2DCoords - it raised an exception but if do not - all atoms in one dot and you cannot see it at all The same is if I try to read call sanitizeMol. Looking like problem in Kekilizer because some of my fragments can contain atoms and bonds taken from the aromatic ring (and it must be so). Simple fragments like chain fragments displayed Ok because they are not causing exception in compute2Dcoords. What can you suggest? 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::vector 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 > 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?
Thank you very much - this is what I been expecting...
2009/5/26 Greg Landrum
> On Tue, May 26, 2009 at 9:51 AM, Evgueni Kolossov
> wrote:
> >
> > 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)?
>
> There's no difference between the results, the sanitization step done
> by MolToSmiles() or by reading molecules in from a mol block "fixes"
> the system by generating the zwitterionic form:
>
> [2]>>> m = Chem.MolFromSmiles('CN(=O)(=O)')
>
> [3]>>> print Chem.MolToMolBlock(m)
>
> RDKit
>
> 4 3 0 0 0 0 0 0 0 0999 V2000
>0.0.0. C 0 0 0 0 0 0 0 0 0 0 0 0
>0.0.0. N 0 0 0 0 0 0 0 0 0 0 0 0
>0.0.0. O 0 0 0 0 0 0 0 0 0 0 0 0
>0.0.0. O 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> 2 3 1 0
> 2 4 2 0
> M CHG 2 2 1 3 -1
> M END
>
>
> [4]>>> m2 = Chem.MolFromSmiles('C[N+](=O)([O-])')
>
> [5]>>> print Chem.MolToMolBlock(m)
>
> RDKit
>
> 4 3 0 0 0 0 0 0 0 0999 V2000
>0.0.0. C 0 0 0 0 0 0 0 0 0 0 0 0
>0.0.0. N 0 0 0 0 0 0 0 0 0 0 0 0
>0.0.0. O 0 0 0 0 0 0 0 0 0 0 0 0
>0.0.0. O 0 0 0 0 0 0 0 0 0 0 0 0
> 1 2 1 0
> 2 3 1 0
> 2 4 2 0
> M CHG 2 2 1 3 -1
> M END
>
>
>
> -greg
>
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
> Dear Tao-wei,
>
> On Fri, May 22, 2009 at 2:59 AM, Tao-wei Huang 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 "", line 1, in
> > 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.
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>
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 > On Fri, May 1, 2009 at 8:06 AM, Evgueni Kolossov > 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
[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 : > 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 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 : >>> Yes, the database containing the 214K molecules is 167MB >>> >>> >>> On Thu, Apr 30, 2009 at 7:55 PM, Evgueni Kolossov >>> 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 : >>>>> [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] Question
Ok , so the average size 781 byte. What's the max size of one molecule can be in theory? 2009/4/30 Greg Landrum : > Yes, the database containing the 214K molecules is 167MB > > > On Thu, Apr 30, 2009 at 7:55 PM, Evgueni Kolossov 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 : >>> [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
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 : > [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 > wrote: >> and what's the length of Pickles? >> >> 2009/4/30 Evgueni Kolossov : >>> Greg, >>> >>> In this case you probably storing Pickles into database together with >>> fingerprints. Am I right? >>> >>> Regards, >>> Evgueni >>> >>> 2009/4/30 Greg Landrum : >>>> nope... the transformation is a lossy one >>>> >>>> On Thu, Apr 30, 2009 at 9:56 AM, Evgueni Kolossov >>>> 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] Fingerprints writing
Thanks Greg,
Looking like everything is OK - I just converted this string back to vector:
ExplicitBitVect vRtn(strSSS)
and got exactly the same vector.
Only one thing still confusing:
This string ("àÿÿÿ") id the same for all of this:
RDKit::RDKFingerprintMol(*mol)
RDKit::RDKFingerprintMol(*mol, 1, 7, 2048,4, true, 0.3)
RDKit::LayeredFingerprintMol(*mol)
but all of them convering back to a DIFFERENT vectors!!!
And are you sure I should write to database this "àÿÿÿ"?
Regards,
Evgueni
2009/4/7 Greg Landrum
> Dear Evgueni,
>
> On Tue, Apr 7, 2009 at 10:37 AM, Evgueni Kolossov
> wrote:
> >
> > looking like ToString() method producing some strange result or I am
> doing
> > something wrong.
> > This is the code:
> > strSM is equal to "CNC(=NC#N)NCCSCc1nc[nH]c1C"
> > RWMol *mol = SmilesToMol(strSM) //not null, contained atoms, bonds, so
> > looking like OK
> > ExplicitBitVect *fpSSS = RDKit::RDKFingerprintMol(*mol); //looking like
> OK -
> > see details in enclosed file
> > std::string strSSS = fpSSS->ToString(); //result is very strange: "àÿÿÿ"
> >
> > Can you help, please?
>
> It's hard to be sure. The output from fpSSS->ToString() is a binary
> string that is really only useful as an input to one of the
> constructors of ExplicitBitVect (or SparseBitVect). It's not intended
> to be printed, so it's not particularly readable.
>
> If you want a string of zeroes and ones (probably less efficient for
> your database, but more human readable), you can get one using
> BitVectToText():
>
> http://www.rdkit.org/C++_Docs/BitOps_8h.html#36835d36d5bd537c22d48f61c15bb9d7
> And convert that back into a BitVector using FromBitString():
>
> http://www.rdkit.org/C++_Docs/BitVectUtils_8h.html#2a9c53ad7c640781d6547cc6b47e75f9
> (These should really be declared in the same header file; that's
> something for the next release)
>
> here's some untested sample code:
>std::string bits = BitVectToText(fp1);
>ExplicitBitVect fp2(bits.length());
>FromBitString(fp2,bits);
>
> Best Regards,
> -greg
>
--
Dr. Evgueni Kolossov (PhD)
ekolos...@gmail.com
Tel. +44(0)1628 627168
Mob. +44(0)7812070446
Re: [Rdkit-discuss] Fingerprints writing
Dear Greg,
looking like ToString() method producing some strange result or I am doing
something wrong.
This is the code:
strSM is equal to "CNC(=NC#N)NCCSCc1nc[nH]c1C"
RWMol *mol = SmilesToMol(strSM) //not null, contained atoms, bonds, so
looking like OK
ExplicitBitVect *fpSSS = RDKit::RDKFingerprintMol(*mol); //looking like OK -
see details in enclosed file
std::string strSSS = fpSSS->ToString(); //result is very strange: "àÿÿÿ"
Can you help, please?
Regards,
Evgueni
2009/4/6 Greg Landrum
> Dear Evgueni,
>
> On Mon, Apr 6, 2009 at 1:48 PM, Evgueni Kolossov
> wrote:
> >
> > Thank you very much but in this case to compare we need somehow to covert
> it
> > back when extracting from the database.
> > How to do this?
>
> If you mean convert it back into a bit vector, that's the second part
> of my message below:
> >> The various bit vector classes have constructors that accept these
> >> strings:
> >> ExplicitBitVect bv2(pkl);
>
> Alternatively, if you already have a bit vector and you want to
> re-initialize it, you can use bv2.InitializeFromText
>
> -greg
>
> >
> > 2009/4/6 Greg Landrum
> >>
> >> Dear Evgueni,
> >>
> >> Fingerprints can be converted into a binary string using their
> >> ToString() method:
> >> std::string pkl=bv.ToString();
> >> The various bit vector classes have constructors that accept these
> >> strings:
> >> ExplicitBitVect bv2(pkl);
> >>
> >> The strings from ToString() are suitable for storing in databases
> >> (there's a lot of this in the python-based RDKit DbCLI code).
> >> -greg
> >>
> >> On Mon, Apr 6, 2009 at 10:17 AM, Evgueni Kolossov
> >> wrote:
> >> > Dear Greg,
> >> >
> >> > Can you suggest the way to write fingerprints into database? Say, we
> can
> >> > have ExplicitBitVect *ev = RDKFingerprintMol(...). Now I need
> write
> >> > it
> >> > into database (BLOB). So, do I need to convert ExplicitBitVect to
> binary
> >> > stream or something?
> >> >
> >> > Regards,
> >> > Evgueni
> >> >
> >> >
> >> >
> >
> >
> >
> >
> >
> --
> >
> > ___
> > 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
strSM "CNC(=NC#N)NCCSCc1nc[nH]c1C"
ExplicitBitVect *fpSSS = RDKit::RDKFingerprintMol(*mol);
/
RESULT:
fpSSS 0x0328acf0 {dp_bits=0x0326b698 d_size=2048 d_numOnBits=571 }
m_bits
[64](2194145288,204086784,3305505812,1076527680,141855249,4489216,13650245,1508262172,2216853584,1075839192,2483093773,2723710868,49283083,3291571264,2047877188,398594176,88101157,136134210,117489736,5538960,3779863106,3224374340,271069743,2149076038,349176018,453706853,570428930,622855949,676726273,111542794,1076565827,69501072,2771506209,10191425,813795378,276931585,127959592,214908,19719,...,...)
std::vector >
[0] 2194145288 unsigned long
[1] 204086784 unsigned long
[2] 3305505812 unsigned long
[3] 1076527680 unsigned long
[4] 141855249 unsigned long
[5] 4489216 unsigned long
[6] 13650245unsigned long
[7] 1508262172 unsigned long
[8] 2216853584 unsigned long
[9] 1075839192 unsigned long
[10]2483093773 unsigned long
[11]2723710868 unsigned long
[12]49283083unsigned long
[13]3291571264 unsigned long
[14]2047877188 unsigned long
[15]398594176 unsigned long
[16]88101157unsigned long
[17]136134210 unsigned long
[18]117489736 unsigned long
[19]5538960 unsigned long
[20]3779863106 unsigned long
[21]3224374340 unsigned long
[22]271069743 unsigned long
[23]2149076038 unsigned long
[24]349176018 unsigned long
[25]453706853 unsigned long
[26]570428930 unsigned long
[27]622855949 unsigned long
[28]676726273 unsigned long
[29]111542794 unsigned long
[30]1076565827 unsigned long
[31]69501072unsigned long
[32]2771506209 unsigned long
[33]10191425unsigned long
[34]813795378 unsigned long
[35]276931585 unsigned long
[36]127959592 unsigned long
[37]2149
Re: [Rdkit-discuss] Fingerprints writing
Thanks Greg - I just missed that Regards, Evgueni 2009/4/6 Greg Landrum > Dear Evgueni, > > On Mon, Apr 6, 2009 at 1:48 PM, Evgueni Kolossov > wrote: > > > > Thank you very much but in this case to compare we need somehow to covert > it > > back when extracting from the database. > > How to do this? > > If you mean convert it back into a bit vector, that's the second part > of my message below: > >> The various bit vector classes have constructors that accept these > >> strings: > >> ExplicitBitVect bv2(pkl); > > Alternatively, if you already have a bit vector and you want to > re-initialize it, you can use bv2.InitializeFromText > > -greg > > > > > 2009/4/6 Greg Landrum > >> > >> Dear Evgueni, > >> > >> Fingerprints can be converted into a binary string using their > >> ToString() method: > >> std::string pkl=bv.ToString(); > >> The various bit vector classes have constructors that accept these > >> strings: > >> ExplicitBitVect bv2(pkl); > >> > >> The strings from ToString() are suitable for storing in databases > >> (there's a lot of this in the python-based RDKit DbCLI code). > >> -greg > >> > >> On Mon, Apr 6, 2009 at 10:17 AM, Evgueni Kolossov > >> wrote: > >> > Dear Greg, > >> > > >> > Can you suggest the way to write fingerprints into database? Say, we > can > >> > have ExplicitBitVect *ev = RDKFingerprintMol(...). Now I need > write > >> > it > >> > into database (BLOB). So, do I need to convert ExplicitBitVect to > binary > >> > stream or something? > >> > > >> > Regards, > >> > Evgueni > >> > > >> > > >> > > > > > > > > > > > > -- > > > > ___ > > Rdkit-discuss mailing list > > Rdkit-discuss@lists.sourceforge.net > > https://lists.sourceforge.net/lists/listinfo/rdkit-discuss > > > > >
Re: [Rdkit-discuss] Fingerprints writing
Dear Greg, Thank you very much but in this case to compare we need somehow to covert it back when extracting from the database. How to do this? Regards, Evgueni 2009/4/6 Greg Landrum > Dear Evgueni, > > Fingerprints can be converted into a binary string using their > ToString() method: > std::string pkl=bv.ToString(); > The various bit vector classes have constructors that accept these strings: > ExplicitBitVect bv2(pkl); > > The strings from ToString() are suitable for storing in databases > (there's a lot of this in the python-based RDKit DbCLI code). > -greg > > On Mon, Apr 6, 2009 at 10:17 AM, Evgueni Kolossov > wrote: > > Dear Greg, > > > > Can you suggest the way to write fingerprints into database? Say, we can > > have ExplicitBitVect *ev = RDKFingerprintMol(...). Now I need write > it > > into database (BLOB). So, do I need to convert ExplicitBitVect to binary > > stream or something? > > > > Regards, > > Evgueni > > > > > > >
[Rdkit-discuss] Fingerprints writing
Dear Greg, Can you suggest the way to write fingerprints into database? Say, we can have ExplicitBitVect *ev = RDKFingerprintMol(...). Now I need write it into database (BLOB). So, do I need to convert ExplicitBitVect to binary stream or something? Regards, Evgueni
Re: [Rdkit-discuss] Fingerprints length
Dear Greg, I understood that default it set to 2048 and default density set to 0.0 with minimum size set default to 128, minPath to 1, maxPath to 7, and nBitsPerHash to 4. Can you please justify this selection for better understanding the principles? Do you have any comparison data? I believe it can be useful not only for myself. Regards, Evgueni 2009/3/26 Greg Landrum > Dear Evgueni, > > On Thu, Mar 26, 2009 at 4:27 PM, Evgueni Kolossov > wrote: > > What is the maximum length of RDKFingerprintMol? > > hmm... good question. I guess the theoretical limit is somewhere > around 2^31, but it wouldn't be practical to do fingerprints that size > since the densities would be amazingly low. > > I don't think I've done anything larger than 4096, but that's mainly > because it hasn't seemed useful to go larger. > > -greg >
[Rdkit-discuss] Fingerprints length
Greg, What is the maximum length of RDKFingerprintMol? Regards, Evgueni
Re: [Rdkit-discuss] Beta of next release up.
OK, I sort it out. Should be:
ATOM_SPTR at2=(*mol)[*atBegin];
Regards,
Evgueni
2009/3/26 Evgueni Kolossov
> Greg,
>
> In your example:
> ATOM_SPTR at2=mol[*atBegin];
> is not working: 'initializing' cannot convert from RDKit::ROMol to
> boost::shared_ptr
>
> Regards,
> Evgueni
>
> 2009/3/25 Greg Landrum
>
>> [Redirected to the list because the question is of general interest]
>>
>>
>> Hi Evgueni,
>>
>> On Wed, Mar 25, 2009 at 10:56 AM, Evgueni Kolossov
>> 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] Beta of next release up.
Greg,
In your example:
ATOM_SPTR at2=mol[*atBegin];
is not working: 'initializing' cannot convert from RDKit::ROMol to
boost::shared_ptr
Regards,
Evgueni
2009/3/25 Greg Landrum
> [Redirected to the list because the question is of general interest]
>
> Hi Evgueni,
>
> On Wed, Mar 25, 2009 at 10:56 AM, Evgueni Kolossov
> 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] Beta of next release up.
Thank you very much!
Regards,
Evgueni
2009/3/25 Greg Landrum
> [Redirected to the list because the question is of general interest]
>
> Hi Evgueni,
>
> On Wed, Mar 25, 2009 at 10:56 AM, Evgueni Kolossov
> 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
Greg, I have noticed a new version of bjam as well (3.1.17). have you tryed it? Regards, Evgueni 2009/2/12 Evgueni Kolossov > Thank you very much > > 2009/2/12 Greg Landrum > > Dear Evgueni, >> >> On Thu, Feb 12, 2009 at 10:22 AM, Evgueni Kolossov >> 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
Thank you very much 2009/2/12 Greg Landrum > Dear Evgueni, > > On Thu, Feb 12, 2009 at 10:22 AM, Evgueni Kolossov > 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
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 > Thanks - will try to rebuild with msvc-9 option > > Regards, > Evgueni > > 2009/2/11 Greg Landrum > >> 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 >> 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 >> >> >> >> Did the RDKit build (with bjam) use the VS2008 compiler? >> >> >> >> On Wed, Feb 11, 2009 at 5:39 PM, Evgueni Kolossov > > >> >> wrote: >> >> > Greg, >> >> > >> >> > All RDKit staff build with jam not with VS >> >> > >> >> > 2009/2/11 Greg Landrum >> >> >> >> >> >> 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 >> >> >> >> >> >> >> >> Dear Evgueni, >> >> >> >> >> >> >> >> On Wed, Feb 11, 2009 at 4:38 PM, Evgueni Kolossov >> >> >> >> >> >> >> >> 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
Thanks - will try to rebuild with msvc-9 option Regards, Evgueni 2009/2/11 Greg Landrum > 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 > 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 > >> > >> Did the RDKit build (with bjam) use the VS2008 compiler? > >> > >> On Wed, Feb 11, 2009 at 5:39 PM, Evgueni Kolossov > >> wrote: > >> > Greg, > >> > > >> > All RDKit staff build with jam not with VS > >> > > >> > 2009/2/11 Greg Landrum > >> >> > >> >> 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 > >> >> >> > >> >> >> Dear Evgueni, > >> >> >> > >> >> >> On Wed, Feb 11, 2009 at 4:38 PM, Evgueni Kolossov > >> >> >> > >> >> >> 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
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 > Dear Evgueni, > > On Wed, Feb 11, 2009 at 4:38 PM, Evgueni Kolossov > 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
Re: [Rdkit-discuss] Compiling for VS 2008
Hi Greg, I have attached errors file. I have mentioned new boost version because they stated it will work with VS 2008 Regards, Evgueni 2009/2/11 Greg Landrum > Hi Evgueni, > > On Tue, Feb 10, 2009 at 9:48 PM, Evgueni Kolossov > wrote: > > > > I am moving into Visual Studio 2008 and updated project giving me a lot > of > > unresolved externals in RDKit libs. > > Should I just recompile RDKit (but cannot see what difference it will > make) > > or I need for example update boost to 1.38 or need to do something else? > > Any suggestions? > > Since I don't use the visual studio environment to build the RDKit, > this is a hard one to diagnose without a lot more information (like > what unresolved externals you are seeing). > > One thing that's sure: you don't need a recent version of boost. The > RDKit should work for 1.35+ > > -greg > Error 5 error LNK2001: unresolved external symbol "__declspec(dllimport) public: void __thiscall std::_Container_base::_Orphan_all(void)const " (__imp_?_orphan_...@_container_base@std@@QBEXXZ)libGraphMol.lib Prometheus Error 6 error LNK2001: unresolved external symbol "__declspec(dllimport) public: void __thiscall std::_Container_base::_Orphan_all(void)const " (__imp_?_orphan_...@_container_base@std@@QBEXXZ)libSmilesParse.lib Prometheus Error 7 error LNK2001: unresolved external symbol "__declspec(dllimport) public: void __thiscall std::_Container_base::_Orphan_all(void)const " (__imp_?_orphan_...@_container_base@std@@QBEXXZ)libSmilesParse.lib Prometheus Error 8 error LNK2019: unresolved external symbol "__declspec(dllimport) public: void __thiscall std::_Container_base::_Orphan_all(void)const " (__imp_?_orphan_...@_container_base@std@@QBEXXZ) referenced in function "protected: static class std::basic_string,class std::allocator > const & __cdecl std::_Tree,class std::allocator > const ,class boost::any,struct std::less,class std::allocator > const >,class std::allocator,class std::allocator > const ,class boost::any> >,0> >::_Key(struct std::_Tree_nod,class std::allocator > const ,class boost::any,struct std::less,class std::allocator > const >,class std::allocator,class std::allocator > const ,class boost::any> >,0> >::_Node *)" (?_...@?$_tree@v?$_tmap_tra...@$$cbv?$basic_string@du?$char_tra...@d@std@@v?$alloca...@d@2@@std@@v...@boost@@u?$l...@$$cbv?$basic_string@du?$char_tra...@d@std@@v?$alloca...@d@2@@std@@@2...@v?$allocator@u?$p...@$$cbv?$basic_string@du?$char_tra...@d@std@@v?$alloca...@d@2@@std@@v...@boost@@@std@@@2...@$0a@@std@@@std@@kaabv?$basic_str...@du?$char_traits@d...@std@@v?$alloca...@d@2@@2...@pau_node@?$_tree_...@v?$_tmap_traits@$$cbv?$basic_str...@du?$char_traits@d...@std@@v?$alloca...@d@2@@std@@v...@boost@@u?$l...@$$cbv?$basic_string@du?$char_tra...@d@std@@v?$alloca...@d@2@@std@@@2...@v?$allocator@u?$p...@$$cbv?$basic_string@du?$char_tra...@d@std@@v?$alloca...@d@2@@std@@v...@boost@@@std@@@2...@$0a@@std@@@2@@Z) libSmilesParse.lib Prometheus Error 9 error LNK2001: unresolved external symbol "__declspec(dllimport) public: void __thiscall std::_Container_base::_Orphan_all(void)const " (__imp_?_orphan_...@_container_base@std@@QBEXXZ)libSmilesParse.lib Prometheus Error 10 error LNK2001: unresolved external symbol "__declspec(dllimport) public: void __thiscall std::_Container_base::_Orphan_all(void)const " (__imp_?_orphan_...@_container_base@std@@QBEXXZ)libRDGeneral.lib Prometheus Error 11 error LNK2001: unresolved external symbol "__declspec(dllimport) public: void __thiscall std::_Container_base::_Orphan_all(void)const " (__imp_?_orphan_...@_container_base@std@@QBEXXZ)libSmilesParse.lib Prometheus Error 12 error LNK2001: unresolved external symbol "__declspec(dllimport) public: void __thiscall std::_Container_base::_Orphan_all(void)const " (__imp_?_orphan_...@_container_base@std@@QBEXXZ)libSmilesParse.lib Prometheus Error 13 error LNK2001: unresolved external symbol "__declspec(dllimport) public: void __thiscall std::_Container_base::_Orphan_all(void)const " (__imp_?_orphan_...@_container_base@std@@QBEXXZ)libSmilesParse.lib Prometheus Error 14 error LNK2001: unresolved external symbol "__declspec(dllimport) public: void __thiscall std::_Container_base::_Orphan_all(void)const " (__imp_?_orphan_...@_container_base@std@@QBEXXZ)libGraphMol.lib Prometheus Error 15 error LNK2001: unresolved external symbol "__declspec(dllimport) public: void __thiscall std::_Container_base::_Orphan_all(void)const " (__imp_?_orphan_...@_container_base@std@@QBEXXZ)
[Rdkit-discuss] Compiling for VS 2008
Hi Greg, I am moving into Visual Studio 2008 and updated project giving me a lot of unresolved externals in RDKit libs. Should I just recompile RDKit (but cannot see what difference it will make) or I need for example update boost to 1.38 or need to do something else? Any suggestions? Regards, Evgueni
[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::tuple __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] Some problems including aromaticity
Thanks Greg, I can accept explanation for aromaticity but for structure 11 it will be good to have ability to read it with warning for example. All structure editors can read it! Regards, Evgueni 2008/9/2 Greg Landrum > Dear Evgueni, > > > > I have enclosed SDF file with some structures and file with problems. > > The main things is that SDMolSupplier cannot read structure #11 which any > > other tool will read without any problems and in some structures some > cycles > > ROMol will consider wrong as aromatic (see structures 3,4,5 for example) > - > > see Problems.doc for details. > > > > Any suggestions? > > I have not looked at all the structures with problems, but I don't see > anything here that's overly alarming. > > The aromaticity cases you refer to as "wrong" match the RDKit > definition of aromaticity : the ring c1nc(=O)cc[nH]1 is conjugated and > has 6 pi electrons (0 from the C with the extracyclic double bond to > O, 2 from the NH, 1 from the other atoms), so it's considered > aromatic. > > Structure 11 contains the substructure CN1=C[NH]N=C1, which contains a > 4-coordinate neutral nitrogen in a non-aromatic ring. This is not > considered a valid valence state for the N, so the RDKit won't process > the molecule. > > Best Regards, > -greg > -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
[Rdkit-discuss] Some problems including aromaticity
Hi Greg, I have enclosed SDF file with some structures and file with problems. The main things is that SDMolSupplier cannot read structure #11 which any other tool will read without any problems and in some structures some cycles ROMol will consider wrong as aromatic (see structures 3,4,5 for example) - see Problems.doc for details. Any suggestions? Regards, Evgueni Problems.doc Description: MS-Word document Zhang.sdf Description: Binary data
Re: [Rdkit-discuss] Rings
So, RingInfo::numRings return the number of smallest rings? 2008/8/20 Greg Landrum > Dear Evgueni, > > On Wed, Aug 20, 2008 at 11:46 AM, Evgueni Kolossov > 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
[Rdkit-discuss] Rings
Hi Greg, Is there any way to get separately total number of Rings and number of SMALLEST rings? Regards, Evgueni
Re: [Rdkit-discuss] Calculation of atomic descriptors, Code snippet
Thanks Greg, Will this give the SHORTEST distance? Regards, Evgueni 2008/8/18 Greg Landrum > On Mon, Aug 18, 2008 at 12:42 PM, Evgueni Kolossov > 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] Fwd: Calculation of atomic descriptors, Code snippet
Ok, I understood - there is no function to get the number of non-terminal rotatable bonds... Another question - is there function to calculate the longest chain of non-hydrogen atoms? Regards, Evgueni 2008/8/18 Greg Landrum > On Mon, Aug 18, 2008 at 2:55 PM, Evgueni Kolossov > wrote: > > > > Another question: getAllRotatableBonds(RDKit::ROMol &mol) - will this > take > > in account hydrogens or not? > > I think you're talking about the function that's in : > .../Code/GraphMol/Depictor/DepictUtils.h > That looks for bonds that are rotatable as far as the depictor is > concerned, which probably isn't interesting to you. > > I would otherwise define rotatable bonds using a SMARTS pattern. This > is the one used in the python descriptor calculator: > > [!$(*#*)&!D1]-&!...@[!$(*#*)&!D1] > > (heh, taken out of context SMARTS really can look like line noise!) > > There's already sample code connected with this in the Getting Started cpp. > > -greg > -- Dr. Evgueni Kolossov (PhD) ekolos...@gmail.com Tel. +44(0)1628 627168 Mob. +44(0)7812070446
[Rdkit-discuss] Fwd: Calculation of atomic descriptors, Code snippet
-- Forwarded message --
From: Evgueni Kolossov
Date: 2008/8/18
Subject: Re: [Rdkit-discuss] Calculation of atomic descriptors, Code snippet
To: Greg Landrum
Greg,
Another question: getAllRotatableBonds(RDKit::ROMol &mol) - will this take
in account hydrogens or not?
> Regards,
> Evgueni
>
> 2008/8/17 Greg Landrum
>
> Dear Evgueni,
>>
>> > 2008/8/17 Evgueni Kolossov
>> >>
>> >> 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.
>>
>> It's a vector of ring atom indices. You can use these to get the
>> corresponding atoms from the molecule.
>>
>> >> 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; i> >> {
>> >> RDKit::Atom * pAtom = mol.getAtomWithIdx(ringIt[i]) ;
>> >> ..
>> >> }
>> >> but this is not working.
>>
>> Here's a sample that is actually tested. It's now part of the getting
>> started in C++ sample code. We loop over all atom rings, then grab
>> each atom in the 5-rings and test to see if it's aromatic.
>> I think this, combined with the earlier stuff I posted, should get you
>> started:
>>
>> ---
>> mol=SmilesToMol("C1CC2=C(C1)C1=C(NC3=C1C=CC=C3)C=C2");
>> ringInfo = mol->getRingInfo();
>> atomRings=ringInfo->atomRings();
>>
>> unsigned int nMatchingAtoms=0;
>> for(VECT_INT_VECT_CI ringIt=atomRings.begin();
>> ringIt!=atomRings.end();++ringIt){
>>if(ringIt->size()!=5){
>> continue;
>>}
>>bool isAromatic=true;
>>for(INT_VECT_CI atomIt=ringIt->begin();
>>atomIt!=ringIt->end();++atomIt){
>> if(!mol->getAtomWithIdx(*atomIt)->getIsAromatic()){
>>isAromatic=false;
>>break;
>> }
>>}
>>if(isAromatic){
>> nMatchingAtoms+=5;
>>}
>> }
>> TEST_ASSERT(nMatchingAtoms==5);
>> ---
>>
>> Best Regards,
>> -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
