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From: Jerome P. <j.p...@pa...> - 2015-01-25 23:08:29
|
Hi, I did not send any news since a long time ago. First of all, I wish you a very happy new Year! I have moved the Mychem code to GitHub. If you want to retrieve the last version of the source code: git clone https://github.com/mychem/mychem-code.git If you want to contribute, you should first fork the project in your GitHub repository and then propose any modification via Pull Request. I will add you also to the GitHub project. The website remains hosted at SourceForge, as the official source packages. The last official version of Mychem is 0.9.2: https://sourceforge.net/projects/mychem/files/mychem/0.9.2/ This release contains a fix for bug #15 (https://sourceforge.net/p/mychem/bugs/15/) Cheers, Jerome |
From: Fredrik W. <fr...@wa...> - 2013-09-18 08:18:32
|
Hi again, I would say that the script in Appendix C is just as reference for python programmers, and it's not overly commented. But if you look at line 55 it will insert the mol file to a table named as the variable table but with a suffix of _mol, so if you specified the table name to be mychem.compounds on line 15 then it will use the table mychem.compounds_mol and you will have to create it beforehand the same way you probably already created mychem.compounds. If you don't use python regularly, I would again advice to use the mychemdb-manager.py script from appendix D which is much more complete. Kind regards, Fredrik 18 sep 2013 kl. 10:11 skrev acanada <ac...@cn...>: > Hi, > > Thanks for your answer. That's exactly what I did. I created the tables in MySQL and then, when using the python script to parse the SDF, I get that error. > >>> _mysql_exceptions.ProgrammingError: (1146, "Table 'mychem.compounds_mol' doesn't exist") > > > It seems that the _mol table should be created beforehand but there's no specifications of how this table should be created... > > > Kind regards, > Andrés > > > El Sep 18, 2013, a las 9:47 AM, Fredrik Wallner escribió: > >> Hi, >> >> That script will only parse an SDfile and put the names in one table and the structure (connection table) in another (named with a _mol suffix). You will have to create the tables and the database beforehand in MySQL, either in the command line or through a user interface like phpmyadmin or Sequel Pro (http://www.sequelpro.com) or something similar. This will also not use any of the mychem features itself, it will just load a bunch of mol files that can be used in subsequent queries. Another option would be to use mychemdb-manager.py as described in http://mychem.sourceforge.net/doc/apds02.html. >> >> Kind regards, >> Fredrik >> >> 17 sep 2013 kl. 12:46 skrev acanada <ac...@cn...>: >> >>> Hello, >>> >>> I have installed mychem (thanks to Fredrik and Jerome :-) >>> I'm not chemist, so maybe this questions are not well formed or have no sense at all. Sorry for this. >>> I'm following the mychem documentation and I'd like to insert some data to the tables created. In order to do this I'm using the python script of the Appendix C (http://mychem.sourceforge.net/doc/apc.html) >>> I have download from internet sources some sdf files (there are not database.sdf testing files from mychem project, are there?) >>> >>> For example, I have downloaded http://www.drugbank.ca/system/downloads/current/structures/all.sdf.zip >>> Then, when I try to load the data I get the following error: >>> >>> _mysql_exceptions.ProgrammingError: (1146, "Table 'mychem.compounds_mol' doesn't exist") >>> >>> How should I create this table? >>> Is there any testing database.sdf file? >>> >>> Kind regards, >>> Andrés >>> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. >>> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. >>> >>> >>> ------------------------------------------------------------------------------ >>> LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! >>> 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint >>> 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes >>> Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. >>> http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk >>> _______________________________________________ >>> Mychem-devel mailing list >>> Myc...@li... >>> https://lists.sourceforge.net/lists/listinfo/mychem-devel >> > > > > **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. > > **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. > > |
From: Fredrik W. <fr...@wa...> - 2013-09-18 07:47:38
|
Hi, That script will only parse an SDfile and put the names in one table and the structure (connection table) in another (named with a _mol suffix). You will have to create the tables and the database beforehand in MySQL, either in the command line or through a user interface like phpmyadmin or Sequel Pro (http://www.sequelpro.com) or something similar. This will also not use any of the mychem features itself, it will just load a bunch of mol files that can be used in subsequent queries. Another option would be to use mychemdb-manager.py as described in http://mychem.sourceforge.net/doc/apds02.html. Kind regards, Fredrik 17 sep 2013 kl. 12:46 skrev acanada <ac...@cn...>: > Hello, > > I have installed mychem (thanks to Fredrik and Jerome :-) > I'm not chemist, so maybe this questions are not well formed or have no sense at all. Sorry for this. > I'm following the mychem documentation and I'd like to insert some data to the tables created. In order to do this I'm using the python script of the Appendix C (http://mychem.sourceforge.net/doc/apc.html) > I have download from internet sources some sdf files (there are not database.sdf testing files from mychem project, are there?) > > For example, I have downloaded http://www.drugbank.ca/system/downloads/current/structures/all.sdf.zip > Then, when I try to load the data I get the following error: > > _mysql_exceptions.ProgrammingError: (1146, "Table 'mychem.compounds_mol' doesn't exist") > > How should I create this table? > Is there any testing database.sdf file? > > Kind regards, > Andrés > **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. > **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. > > > ------------------------------------------------------------------------------ > LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! > 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint > 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes > Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. > http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk > _______________________________________________ > Mychem-devel mailing list > Myc...@li... > https://lists.sourceforge.net/lists/listinfo/mychem-devel |
From: acanada <ac...@cn...> - 2013-09-17 10:46:42
|
Hello, I have installed mychem (thanks to Fredrik and Jerome :-) I'm not chemist, so maybe this questions are not well formed or have no sense at all. Sorry for this. I'm following the mychem documentation and I'd like to insert some data to the tables created. In order to do this I'm using the python script of the Appendix C (http://mychem.sourceforge.net/doc/apc.html) I have download from internet sources some sdf files (there are not database.sdf testing files from mychem project, are there?) For example, I have downloaded http://www.drugbank.ca/system/downloads/current/structures/all.sdf.zip Then, when I try to load the data I get the following error: _mysql_exceptions.ProgrammingError: (1146, "Table 'mychem.compounds_mol' doesn't exist") How should I create this table? Is there any testing database.sdf file? Kind regards, Andrés **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. |
From: acanada <ac...@cn...> - 2013-09-17 08:17:49
|
Hi, It worked with Fredrik's solution so I didn't have to try with the tutorial. Thankyou very much! Andrés El Sep 16, 2013, a las 11:21 PM, Fredrik Wallner escribió: > Hi, > > In your second cmake command, you are lacking two D:s. To set a cmake variable from the command line you use the option -Dvar=value so try with >> cmake .. -DOPENBABEL2_INCLUDE_DIR=/usr/local/include/openbabel-2.0 -DOPENBABEL2_LIBRARIES=/usr/local/lib/libopenbabel.dylib > I would also recommend ccmake .. as an alternative. Then you will be able to see the variablenames that are used in the script. > > Kind regards, > Fredrik > > Skickat från min iPhone > > 16 sep 2013 kl. 18:59 skrev "acanada" <ac...@cn...>: > >> Hello, >> >> I'm trying to install mychem in a mac os x (10.7.5) >> >> laptop:mychem-0.9.1 $ mkdir build >> laptop:mychem-0.9.1 $ cd build/ >> laptop:build $ cmake .. >> -- The C compiler identification is GNU 4.2.1 >> -- The CXX compiler identification is GNU 4.2.1 >> -- Checking whether C compiler has -isysroot >> -- Checking whether C compiler has -isysroot - yes >> -- Checking whether C compiler supports OSX deployment target flag >> -- Checking whether C compiler supports OSX deployment target flag - yes >> -- Check for working C compiler: /usr/bin/cc >> -- Check for working C compiler: /usr/bin/cc -- works >> -- Detecting C compiler ABI info >> -- Detecting C compiler ABI info - done >> -- Checking whether CXX compiler has -isysroot >> -- Checking whether CXX compiler has -isysroot - yes >> -- Checking whether CXX compiler supports OSX deployment target flag >> -- Checking whether CXX compiler supports OSX deployment target flag - yes >> -- Check for working CXX compiler: /usr/bin/c++ >> -- Check for working CXX compiler: /usr/bin/c++ -- works >> -- Detecting CXX compiler ABI info >> -- Detecting CXX compiler ABI info - done >> -- The build type is RelWithDebInfo >> -- Test module disabled >> -- Found PkgConfig: /sw/bin/pkg-config (found version "0.21") >> -- WARNING: you are using the obsolete 'PKGCONFIG' macro, use FindPkgConfig >> -- PKGCONFIG() indicates that openbabel-2.0 is not installed (install the package which contains openbabel-2.0.pc if you want to support this feature) >> -- OPENBABEL_MINI_FOUND <> >> -- Open Babel Exe: /usr/local/bin/babel >> -- Using mysql-config: /usr/local/mysql/bin/mysql_config >> -- MySQL Plugin Dir: >> -- Found MySQL 5.6.13: /usr/local/mysql/include, /usr/local/mysql/lib/libmysqlclient.dylib >> -- Mychem installation directory: /usr/local/lib >> -- Looking for stdlib.h >> -- Looking for stdlib.h - found >> -- Looking for stdio.h >> -- Looking for stdio.h - found >> -- Looking for string.h >> -- Looking for string.h - found >> -- Looking for C++ include sstream >> -- Looking for C++ include sstream - found >> -- Defining dlhandler source files >> 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: >> OPENBABEL2_INCLUDE_DIR (ADVANCED) >> used as include directory in directory /Users//Downloads/mychem-0.9.1/src >> used as include directory in directory /Users//Downloads/mychem-0.9.1/tests >> used as include directory in directory /Users//Downloads/mychem-0.9.1/tests >> used as include directory in directory /Users//Downloads/mychem-0.9.1/tests >> used as include directory in directory /Users//Downloads/mychem-0.9.1/tests >> used as include directory in directory /Users//Downloads/mychem-0.9.1/tests >> >> -- Configuring incomplete, errors occurred! >> ****************************************************************************************** >> >> So I type: >> ****************************************************************************************** >> laptop:build $ cmake .. -OPENBABEL2_INCLUDE_DIR=/usr/local/include/openbabel-2.0 -OPENBABEL2_LIBRARIES=/usr/local/lib/libopenbabel.dylib >> -- The build type is RelWithDebInfo >> -- Test module disabled >> -- WARNING: you are using the obsolete 'PKGCONFIG' macro, use FindPkgConfig >> -- PKGCONFIG() indicates that openbabel-2.0 is not installed (install the package which contains openbabel-2.0.pc if you want to support this feature) >> -- OPENBABEL_MINI_FOUND <> >> -- Using mysql-config: /usr/local/mysql/bin/mysql_config >> -- MySQL Plugin Dir: >> -- Found MySQL 5.6.13: /usr/local/mysql/include, /usr/local/mysql/lib/libmysqlclient.dylib >> -- Mychem installation directory: /usr/local/lib >> -- Defining dlhandler source files >> 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: >> OPENBABEL2_INCLUDE_DIR (ADVANCED) >> used as include directory in directory /Users//Downloads/mychem-0.9.1/src >> used as include directory in directory /Users//Downloads/mychem-0.9.1/tests >> used as include directory in directory /Users//Downloads/mychem-0.9.1/tests >> used as include directory in directory /Users//Downloads/mychem-0.9.1/tests >> used as include directory in directory /Users//Downloads/mychem-0.9.1/tests >> used as include directory in directory /Users//Downloads/mychem-0.9.1/tests >> >> -- Configuring incomplete, errors occurred! >> laptop:build $ >> ****************************************************************************************** >> >> Those are good paths for these variables... Is there anything that I'm missing? Could you please help me? >> Thankyou very much! >> >> Andrés. >> >> >> >> **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. >> **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. >> >> >> ------------------------------------------------------------------------------ >> LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! >> 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint >> 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes >> Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. >> http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk >> _______________________________________________ >> Mychem-devel mailing list >> Myc...@li... >> https://lists.sourceforge.net/lists/listinfo/mychem-devel **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. |
From: Jerome P. <j.p...@pa...> - 2013-09-17 00:43:20
|
Dear Andrés, A colleague has written a tutorial for the Mac OS X installation: http://www.silicos-it.com/cookbook/configuring_osx_for_chemoinformatics/configuring_osx_for_chemoinformatics.html#mychem-cartridge-for-openbabel It should be working. Can you test it? Cheers, Jerome ps: I am in Madrid from Wednesday until Friday. Le lundi 16 septembre 2013 à 18:59 +0200, acanada a écrit : > Hello, > > I'm trying to install mychem in a mac os x (10.7.5) > > laptop:mychem-0.9.1 $ mkdir build > laptop:mychem-0.9.1 $ cd build/ > laptop:build $ cmake .. > -- The C compiler identification is GNU 4.2.1 > -- The CXX compiler identification is GNU 4.2.1 > -- Checking whether C compiler has -isysroot > -- Checking whether C compiler has -isysroot - yes > -- Checking whether C compiler supports OSX deployment target flag > -- Checking whether C compiler supports OSX deployment target flag - yes > -- Check for working C compiler: /usr/bin/cc > -- Check for working C compiler: /usr/bin/cc -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Checking whether CXX compiler has -isysroot > -- Checking whether CXX compiler has -isysroot - yes > -- Checking whether CXX compiler supports OSX deployment target flag > -- Checking whether CXX compiler supports OSX deployment target flag - yes > -- Check for working CXX compiler: /usr/bin/c++ > -- Check for working CXX compiler: /usr/bin/c++ -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- The build type is RelWithDebInfo > -- Test module disabled > -- Found PkgConfig: /sw/bin/pkg-config (found version "0.21") > -- WARNING: you are using the obsolete 'PKGCONFIG' macro, use FindPkgConfig > -- PKGCONFIG() indicates that openbabel-2.0 is not installed (install the package which contains openbabel-2.0.pc if you want to support this feature) > -- OPENBABEL_MINI_FOUND <> > -- Open Babel Exe: /usr/local/bin/babel > -- Using mysql-config: /usr/local/mysql/bin/mysql_config > -- MySQL Plugin Dir: > -- Found MySQL 5.6.13: /usr/local/mysql/include, /usr/local/mysql/lib/libmysqlclient.dylib > -- Mychem installation directory: /usr/local/lib > -- Looking for stdlib.h > -- Looking for stdlib.h - found > -- Looking for stdio.h > -- Looking for stdio.h - found > -- Looking for string.h > -- Looking for string.h - found > -- Looking for C++ include sstream > -- Looking for C++ include sstream - found > -- Defining dlhandler source files > 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: > OPENBABEL2_INCLUDE_DIR (ADVANCED) > used as include directory in directory /Users//Downloads/mychem-0.9.1/src > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > > -- Configuring incomplete, errors occurred! > ****************************************************************************************** > > So I type: > ****************************************************************************************** > laptop:build $ cmake .. -OPENBABEL2_INCLUDE_DIR=/usr/local/include/openbabel-2.0 -OPENBABEL2_LIBRARIES=/usr/local/lib/libopenbabel.dylib > -- The build type is RelWithDebInfo > -- Test module disabled > -- WARNING: you are using the obsolete 'PKGCONFIG' macro, use FindPkgConfig > -- PKGCONFIG() indicates that openbabel-2.0 is not installed (install the package which contains openbabel-2.0.pc if you want to support this feature) > -- OPENBABEL_MINI_FOUND <> > -- Using mysql-config: /usr/local/mysql/bin/mysql_config > -- MySQL Plugin Dir: > -- Found MySQL 5.6.13: /usr/local/mysql/include, /usr/local/mysql/lib/libmysqlclient.dylib > -- Mychem installation directory: /usr/local/lib > -- Defining dlhandler source files > 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: > OPENBABEL2_INCLUDE_DIR (ADVANCED) > used as include directory in directory /Users//Downloads/mychem-0.9.1/src > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > > -- Configuring incomplete, errors occurred! > laptop:build $ > ****************************************************************************************** > > Those are good paths for these variables... Is there anything that I'm missing? Could you please help me? > Thankyou very much! > > Andrés. > > > > **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. > **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. > > > ------------------------------------------------------------------------------ > LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! > 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint > 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes > Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. > http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk > _______________________________________________ > Mychem-devel mailing list > Myc...@li... > https://lists.sourceforge.net/lists/listinfo/mychem-devel |
From: Fredrik W. <fr...@wa...> - 2013-09-16 21:21:58
|
Hi, In your second cmake command, you are lacking two D:s. To set a cmake variable from the command line you use the option -Dvar=value so try with > cmake .. -DOPENBABEL2_INCLUDE_DIR=/usr/local/include/openbabel-2.0 -DOPENBABEL2_LIBRARIES=/usr/local/lib/libopenbabel.dylib I would also recommend ccmake .. as an alternative. Then you will be able to see the variablenames that are used in the script. Kind regards, Fredrik Skickat från min iPhone 16 sep 2013 kl. 18:59 skrev "acanada" <ac...@cn...>: > Hello, > > I'm trying to install mychem in a mac os x (10.7.5) > > laptop:mychem-0.9.1 $ mkdir build > laptop:mychem-0.9.1 $ cd build/ > laptop:build $ cmake .. > -- The C compiler identification is GNU 4.2.1 > -- The CXX compiler identification is GNU 4.2.1 > -- Checking whether C compiler has -isysroot > -- Checking whether C compiler has -isysroot - yes > -- Checking whether C compiler supports OSX deployment target flag > -- Checking whether C compiler supports OSX deployment target flag - yes > -- Check for working C compiler: /usr/bin/cc > -- Check for working C compiler: /usr/bin/cc -- works > -- Detecting C compiler ABI info > -- Detecting C compiler ABI info - done > -- Checking whether CXX compiler has -isysroot > -- Checking whether CXX compiler has -isysroot - yes > -- Checking whether CXX compiler supports OSX deployment target flag > -- Checking whether CXX compiler supports OSX deployment target flag - yes > -- Check for working CXX compiler: /usr/bin/c++ > -- Check for working CXX compiler: /usr/bin/c++ -- works > -- Detecting CXX compiler ABI info > -- Detecting CXX compiler ABI info - done > -- The build type is RelWithDebInfo > -- Test module disabled > -- Found PkgConfig: /sw/bin/pkg-config (found version "0.21") > -- WARNING: you are using the obsolete 'PKGCONFIG' macro, use FindPkgConfig > -- PKGCONFIG() indicates that openbabel-2.0 is not installed (install the package which contains openbabel-2.0.pc if you want to support this feature) > -- OPENBABEL_MINI_FOUND <> > -- Open Babel Exe: /usr/local/bin/babel > -- Using mysql-config: /usr/local/mysql/bin/mysql_config > -- MySQL Plugin Dir: > -- Found MySQL 5.6.13: /usr/local/mysql/include, /usr/local/mysql/lib/libmysqlclient.dylib > -- Mychem installation directory: /usr/local/lib > -- Looking for stdlib.h > -- Looking for stdlib.h - found > -- Looking for stdio.h > -- Looking for stdio.h - found > -- Looking for string.h > -- Looking for string.h - found > -- Looking for C++ include sstream > -- Looking for C++ include sstream - found > -- Defining dlhandler source files > 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: > OPENBABEL2_INCLUDE_DIR (ADVANCED) > used as include directory in directory /Users//Downloads/mychem-0.9.1/src > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > > -- Configuring incomplete, errors occurred! > ****************************************************************************************** > > So I type: > ****************************************************************************************** > laptop:build $ cmake .. -OPENBABEL2_INCLUDE_DIR=/usr/local/include/openbabel-2.0 -OPENBABEL2_LIBRARIES=/usr/local/lib/libopenbabel.dylib > -- The build type is RelWithDebInfo > -- Test module disabled > -- WARNING: you are using the obsolete 'PKGCONFIG' macro, use FindPkgConfig > -- PKGCONFIG() indicates that openbabel-2.0 is not installed (install the package which contains openbabel-2.0.pc if you want to support this feature) > -- OPENBABEL_MINI_FOUND <> > -- Using mysql-config: /usr/local/mysql/bin/mysql_config > -- MySQL Plugin Dir: > -- Found MySQL 5.6.13: /usr/local/mysql/include, /usr/local/mysql/lib/libmysqlclient.dylib > -- Mychem installation directory: /usr/local/lib > -- Defining dlhandler source files > 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: > OPENBABEL2_INCLUDE_DIR (ADVANCED) > used as include directory in directory /Users//Downloads/mychem-0.9.1/src > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > used as include directory in directory /Users//Downloads/mychem-0.9.1/tests > > -- Configuring incomplete, errors occurred! > laptop:build $ > ****************************************************************************************** > > Those are good paths for these variables... Is there anything that I'm missing? Could you please help me? > Thankyou very much! > > Andrés. > > > > **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. > **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. > > > ------------------------------------------------------------------------------ > LIMITED TIME SALE - Full Year of Microsoft Training For Just $49.99! > 1,500+ hours of tutorials including VisualStudio 2012, Windows 8, SharePoint > 2013, SQL 2012, MVC 4, more. BEST VALUE: New Multi-Library Power Pack includes > Mobile, Cloud, Java, and UX Design. Lowest price ever! Ends 9/20/13. > http://pubads.g.doubleclick.net/gampad/clk?id=58041151&iu=/4140/ostg.clktrk > _______________________________________________ > Mychem-devel mailing list > Myc...@li... > https://lists.sourceforge.net/lists/listinfo/mychem-devel |
From: acanada <ac...@cn...> - 2013-09-16 17:07:46
|
Hello, I'm trying to install mychem in a mac os x (10.7.5) laptop:mychem-0.9.1 $ mkdir build laptop:mychem-0.9.1 $ cd build/ laptop:build $ cmake .. -- The C compiler identification is GNU 4.2.1 -- The CXX compiler identification is GNU 4.2.1 -- Checking whether C compiler has -isysroot -- Checking whether C compiler has -isysroot - yes -- Checking whether C compiler supports OSX deployment target flag -- Checking whether C compiler supports OSX deployment target flag - yes -- Check for working C compiler: /usr/bin/cc -- Check for working C compiler: /usr/bin/cc -- works -- Detecting C compiler ABI info -- Detecting C compiler ABI info - done -- Checking whether CXX compiler has -isysroot -- Checking whether CXX compiler has -isysroot - yes -- Checking whether CXX compiler supports OSX deployment target flag -- Checking whether CXX compiler supports OSX deployment target flag - yes -- Check for working CXX compiler: /usr/bin/c++ -- Check for working CXX compiler: /usr/bin/c++ -- works -- Detecting CXX compiler ABI info -- Detecting CXX compiler ABI info - done -- The build type is RelWithDebInfo -- Test module disabled -- Found PkgConfig: /sw/bin/pkg-config (found version "0.21") -- WARNING: you are using the obsolete 'PKGCONFIG' macro, use FindPkgConfig -- PKGCONFIG() indicates that openbabel-2.0 is not installed (install the package which contains openbabel-2.0.pc if you want to support this feature) -- OPENBABEL_MINI_FOUND <> -- Open Babel Exe: /usr/local/bin/babel -- Using mysql-config: /usr/local/mysql/bin/mysql_config -- MySQL Plugin Dir: -- Found MySQL 5.6.13: /usr/local/mysql/include, /usr/local/mysql/lib/libmysqlclient.dylib -- Mychem installation directory: /usr/local/lib -- Looking for stdlib.h -- Looking for stdlib.h - found -- Looking for stdio.h -- Looking for stdio.h - found -- Looking for string.h -- Looking for string.h - found -- Looking for C++ include sstream -- Looking for C++ include sstream - found -- Defining dlhandler source files 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: OPENBABEL2_INCLUDE_DIR (ADVANCED) used as include directory in directory /Users//Downloads/mychem-0.9.1/src used as include directory in directory /Users//Downloads/mychem-0.9.1/tests used as include directory in directory /Users//Downloads/mychem-0.9.1/tests used as include directory in directory /Users//Downloads/mychem-0.9.1/tests used as include directory in directory /Users//Downloads/mychem-0.9.1/tests used as include directory in directory /Users//Downloads/mychem-0.9.1/tests -- Configuring incomplete, errors occurred! ****************************************************************************************** So I type: ****************************************************************************************** laptop:build $ cmake .. -OPENBABEL2_INCLUDE_DIR=/usr/local/include/openbabel-2.0 -OPENBABEL2_LIBRARIES=/usr/local/lib/libopenbabel.dylib -- The build type is RelWithDebInfo -- Test module disabled -- WARNING: you are using the obsolete 'PKGCONFIG' macro, use FindPkgConfig -- PKGCONFIG() indicates that openbabel-2.0 is not installed (install the package which contains openbabel-2.0.pc if you want to support this feature) -- OPENBABEL_MINI_FOUND <> -- Using mysql-config: /usr/local/mysql/bin/mysql_config -- MySQL Plugin Dir: -- Found MySQL 5.6.13: /usr/local/mysql/include, /usr/local/mysql/lib/libmysqlclient.dylib -- Mychem installation directory: /usr/local/lib -- Defining dlhandler source files 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: OPENBABEL2_INCLUDE_DIR (ADVANCED) used as include directory in directory /Users//Downloads/mychem-0.9.1/src used as include directory in directory /Users//Downloads/mychem-0.9.1/tests used as include directory in directory /Users//Downloads/mychem-0.9.1/tests used as include directory in directory /Users//Downloads/mychem-0.9.1/tests used as include directory in directory /Users//Downloads/mychem-0.9.1/tests used as include directory in directory /Users//Downloads/mychem-0.9.1/tests -- Configuring incomplete, errors occurred! laptop:build $ ****************************************************************************************** Those are good paths for these variables... Is there anything that I'm missing? Could you please help me? Thankyou very much! Andrés. **NOTA DE CONFIDENCIALIDAD** Este correo electrónico, y en su caso los ficheros adjuntos, pueden contener información protegida para el uso exclusivo de su destinatario. Se prohíbe la distribución, reproducción o cualquier otro tipo de transmisión por parte de otra persona que no sea el destinatario. Si usted recibe por error este correo, se ruega comunicarlo al remitente y borrar el mensaje recibido. **CONFIDENTIALITY NOTICE** This email communication and any attachments may contain confidential and privileged information for the sole use of the designated recipient named above. Distribution, reproduction or any other use of this transmission by any party other than the intended recipient is prohibited. If you are not the intended recipient please contact the sender and delete all copies. |
From: Jerome P. <jer...@ip...> - 2010-06-10 09:02:21
|
Hi Adrian, Could you test several type of SMARTS query without atom numbering ? Thanks, Jerome PS: I've uploaded code on the SVN for official MySQL 5.1 support. Le jeudi 21 janvier 2010 12:28:59, Adrian Schreyer a écrit : > Hi Jerome, > > I stumbled upon a weird behaviour of the match_substruct function. > Basically, the result set is not stable and will vary upon query > execution. For the following query, I get between every number between > 55 and 60 hits (10652 PDB chemical components). There is no error in > mysql.log either so it is hard to figure out if the problem is in the > query, the ChemOBMol table, MySQL or Open Babel. With OEChem I get 58 > hits. > > SELECT * > FROM ChemOBMol > WHERE MATCH_SUBSTRUCT('[#7;D2]1[#6][#6;x3][#6;x3][#7;D2]1', obmol) = > 1 DROP TABLE IF EXISTS ChemOBMol; > > This is how I created the table: > > CREATE TABLE `ChemOBMol` ( > `het_id` VARCHAR(15) NOT NULL, > `obmol` BLOB, > PRIMARY KEY (`het_id`) > ) ENGINE=MYISAM DEFAULT CHARSET=utf8; > INSERT INTO ChemOBMol > SELECT het_id, MOLECULE_TO_SERIALIZEDOBMOL(REMOVE_HYDROGENS(sdf)) > FROM ChemSDF; > > Adrian > > --------------------------------------------------------------------------- > --- Throughout its 18-year history, RSA Conference consistently attracts > the world's best and brightest in the field, creating opportunities for > Conference attendees to learn about information security's most important > issues through interactions with peers, luminaries and emerging and > established companies. http://p.sf.net/sfu/rsaconf-dev2dev > _______________________________________________ > Mychem-devel mailing list > Myc...@li... > https://lists.sourceforge.net/lists/listinfo/mychem-devel -- Jerome Pansanel IPHC 23, rue du Loess BP 28 F-67037 STRASBOURG CEDEX 2 Tel: +33 (0)3 88 10 66 24 Fax: +33 (0)3 88 10 62 34 |
From: Jérôme P. <j.p...@pa...> - 2010-01-24 22:04:44
|
Hi Adrian, Could you tell me which configuration of Mychem are you using, with which version of MySQL and your OS. I will test also your query on my personnal database. Thanks for the bug report, Best regard, Jerome Pansanel Le jeudi 21 janvier 2010 12:28:59, Adrian Schreyer a écrit : > Hi Jerome, > > I stumbled upon a weird behaviour of the match_substruct function. > Basically, the result set is not stable and will vary upon query > execution. For the following query, I get between every number between > 55 and 60 hits (10652 PDB chemical components). There is no error in > mysql.log either so it is hard to figure out if the problem is in the > query, the ChemOBMol table, MySQL or Open Babel. With OEChem I get 58 > hits. > > SELECT * > FROM ChemOBMol > WHERE MATCH_SUBSTRUCT('[#7;D2]1[#6][#6;x3][#6;x3][#7;D2]1', obmol) = > 1 DROP TABLE IF EXISTS ChemOBMol; > > This is how I created the table: > > CREATE TABLE `ChemOBMol` ( > `het_id` VARCHAR(15) NOT NULL, > `obmol` BLOB, > PRIMARY KEY (`het_id`) > ) ENGINE=MYISAM DEFAULT CHARSET=utf8; > INSERT INTO ChemOBMol > SELECT het_id, MOLECULE_TO_SERIALIZEDOBMOL(REMOVE_HYDROGENS(sdf)) > FROM ChemSDF; > > Adrian > > --------------------------------------------------------------------------- > --- Throughout its 18-year history, RSA Conference consistently attracts > the world's best and brightest in the field, creating opportunities for > Conference attendees to learn about information security's most important > issues through interactions with peers, luminaries and emerging and > established companies. http://p.sf.net/sfu/rsaconf-dev2dev > _______________________________________________ > Mychem-devel mailing list > Myc...@li... > https://lists.sourceforge.net/lists/listinfo/mychem-devel > |
From: Adrian S. <ma...@ad...> - 2010-01-21 12:00:17
|
Hi Jerome, I stumbled upon a weird behaviour of the match_substruct function. Basically, the result set is not stable and will vary upon query execution. For the following query, I get between every number between 55 and 60 hits (10652 PDB chemical components). There is no error in mysql.log either so it is hard to figure out if the problem is in the query, the ChemOBMol table, MySQL or Open Babel. With OEChem I get 58 hits. SELECT * FROM ChemOBMol WHERE MATCH_SUBSTRUCT('[#7;D2]1[#6][#6;x3][#6;x3][#7;D2]1', obmol) = 1 DROP TABLE IF EXISTS ChemOBMol; This is how I created the table: CREATE TABLE `ChemOBMol` ( `het_id` VARCHAR(15) NOT NULL, `obmol` BLOB, PRIMARY KEY (`het_id`) ) ENGINE=MYISAM DEFAULT CHARSET=utf8; INSERT INTO ChemOBMol SELECT het_id, MOLECULE_TO_SERIALIZEDOBMOL(REMOVE_HYDROGENS(sdf)) FROM ChemSDF; Adrian |
From: Jerome P. <j.p...@pa...> - 2009-11-24 09:37:58
|
Hi Miguel, Thanks for reporting this error. Could you try to remove "-fno-exceptions" on line 150 in the CMakeLists.txt file (at the root of the project directory) ? Cheers, Jerome Le lundi 23 novembre 2009 16:41:23, Miguel Rojas Cherto a écrit : > Hi > > I try to compile mychem and I stock in some of the steps. I tried a > lot of different versions but any of them works correctly for me. I > attached the output > > >svn co https://mychem.svn.sourceforge.net/svnroot/mychem/mychem3 mychem3 > >cd mychem3 > >cmake > > -DOPENBABEL2_INCLUDE_DIR=/home/mrc/development/sourceforge/openbabelDir/o > >penbabel-2.2.3/include/ -DOPENBABEL2_LIBRARIES=/usr/lib/openbabel/2.2.3 > > -DMYSQL_INCLUDE_DIR=/usr/include/mysql -DMYSQL_LIBRARIES=/usr/share/mysql > > make 2>&1 | tee make.out > > Scanning dependencies of target mychem-lib > [ 3%] Building C object src/CMakeFiles/mychem-lib.dir/conversion.c.o > In file included from > /home/mrc/development/sourceforge/mychemDir/mychem3/src/conversion.h:45, > from > /home/mrc/development/sourceforge/mychemDir/mychem3/src/conversion.c:31: > /usr/include/mysql/my_global.h:240:1: warning: "inline1" is not defined > [ 7%] Building CXX object > src/CMakeFiles/mychem-lib.dir/conversion_wrapper.cpp.o > In file included from > /home/mrc/development/sourceforge/mychemDir/mychem3/src/conversion_wrapper. > cpp:38: > /home/mrc/development/sourceforge/openbabelDir/openbabel-2.2.3/include/ope > nbabel/fingerprint.h:73: warning: unused parameter ‘fp’ > /home/mrc/development/sourceforge/openbabelDir/openbabel-2.2.3/include/open > babel/fingerprint.h:73: warning: unused parameter ‘bSet’ > /home/mrc/development/sourceforge/mychemDir/mychem3/src/conversion_wrapper. > cpp: In function ‘char* conversion(const char*, const char*, const char*)’: > /home/mrc/development/sourceforge/mychemDir/mychem3/src/conversion_wrapper > .cpp:80: error: exception handling disabled, use -fexceptions to enable > make[2]: *** [src/CMakeFiles/mychem-lib.dir/conversion_wrapper.cpp.o] Error > 1 make[1]: *** [src/CMakeFiles/mychem-lib.dir/all] Error 2 > make: *** [all] Error 2 > > Could you help me please? Maybe It is some think that I am missing > > -- > Miguel Rojas Cherto > Netherlands Metabolomics Centre > Analytical Biosciences > Leiden University > Einsteinweg 55 > NL-2333 CC Leiden > tel : +31 715276326 > fax: +31 715274277 > > --------------------------------------------------------------------------- > --- 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 > _______________________________________________ > Mychem-devel mailing list > Myc...@li... > https://lists.sourceforge.net/lists/listinfo/mychem-devel > |
From: Miguel R. C. <mig...@go...> - 2009-11-23 15:41:56
|
Hi I try to compile mychem and I stock in some of the steps. I tried a lot of different versions but any of them works correctly for me. I attached the output >svn co https://mychem.svn.sourceforge.net/svnroot/mychem/mychem3 mychem3 >cd mychem3 >cmake -DOPENBABEL2_INCLUDE_DIR=/home/mrc/development/sourceforge/openbabelDir/openbabel-2.2.3/include/ -DOPENBABEL2_LIBRARIES=/usr/lib/openbabel/2.2.3 -DMYSQL_INCLUDE_DIR=/usr/include/mysql -DMYSQL_LIBRARIES=/usr/share/mysql > make 2>&1 | tee make.out Scanning dependencies of target mychem-lib [ 3%] Building C object src/CMakeFiles/mychem-lib.dir/conversion.c.o In file included from /home/mrc/development/sourceforge/mychemDir/mychem3/src/conversion.h:45, from /home/mrc/development/sourceforge/mychemDir/mychem3/src/conversion.c:31: /usr/include/mysql/my_global.h:240:1: warning: "inline1" is not defined [ 7%] Building CXX object src/CMakeFiles/mychem-lib.dir/conversion_wrapper.cpp.o In file included from /home/mrc/development/sourceforge/mychemDir/mychem3/src/conversion_wrapper.cpp:38: /home/mrc/development/sourceforge/openbabelDir/openbabel-2.2.3/include/openbabel/fingerprint.h:73: warning: unused parameter ‘fp’ /home/mrc/development/sourceforge/openbabelDir/openbabel-2.2.3/include/openbabel/fingerprint.h:73: warning: unused parameter ‘bSet’ /home/mrc/development/sourceforge/mychemDir/mychem3/src/conversion_wrapper.cpp: In function ‘char* conversion(const char*, const char*, const char*)’: /home/mrc/development/sourceforge/mychemDir/mychem3/src/conversion_wrapper.cpp:80: error: exception handling disabled, use -fexceptions to enable make[2]: *** [src/CMakeFiles/mychem-lib.dir/conversion_wrapper.cpp.o] Error 1 make[1]: *** [src/CMakeFiles/mychem-lib.dir/all] Error 2 make: *** [all] Error 2 Could you help me please? Maybe It is some think that I am missing -- Miguel Rojas Cherto Netherlands Metabolomics Centre Analytical Biosciences Leiden University Einsteinweg 55 NL-2333 CC Leiden tel : +31 715276326 fax: +31 715274277 |