Main.Build History

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March 16, 2009, at 06:13 PM by 148.187.130.153 -
Changed lines 1-2 from:

(:title Build Instructions:)

to:

(:title Build:)

Changed line 87 from:

III Test

to:

III Run

March 16, 2009, at 05:48 PM by 148.187.130.153 -
Changed lines 26-29 from:
  1. Install CMake (http://www.cmake.org)
  2. Install the Open Source verion of Qt (http://www.trolltech.com/products/qt); Qt has to be installed before VTK because VTK needs some Qt libraries.
  3. Install VTK 5.x (http://www.vtk.org)
    • if you build from source make sure the following parameters are set to ON
to:
  1. Install Qt (http://www.trolltech.com/products/qt); Qt has to be installed before VTK because VTK needs some Qt libraries.
  2. Install VTK 5.x (http://www.vtk.org)
    • build VTK from source and make sure the following parameters are set to ON
Changed lines 33-43 from:
  1. Install OpenBabel 2.x libraries (http://openbabel.sourceforge.net)
    • If you are building on Windows with MinGW check out the OpenBabel OS specific issues below.
  2. Install OpenInventor and Molecular Inventor
  • Any implementation of OpenInventor 2.x will work; you can get an open source version here (Coin3D): http://www.coin3d.org
    • Note that in case you want to build OpenMOIV (or any program requiring coin) you also have to have in the PATH the directory where coin-config resides. In case Coin3D is installed as a framework on Mac OS this is not required.
  • An open source implementation of Molecular Inventor(OpenMOIV) can be downloaded here: http://www.tecn.upf.es/openMOIV
  • When building OpenMOIV on Linux/MinGW/VC++ make sure you set the OIV_DIR environment variable to the installation dir of Coin3D (where the include and lib dirs are) e.g. export OIV_DIR=/usr/local You do not need to do this on Mac OS X if you installed Coin3D as a framework (which is the default).
  • Make sure you read the build information for OpenMOIV to undestand how to deal with fonts on different platform.

On MinGW you need to make sure that the gettimeofday function is available (check in include/sys/time.h); in case it's not then download the latest mingw-runtime environment or have a look at the OpenBabel build page.

to:
  1. Install OpenBabel 2.x libraries (http://openbabel.sourceforge.net)
    • If you are building on Windows with MinGW check out the OpenBabel OS specific issues below.
  2. Install OpenInventor and Molecular Inventor
  • Any implementation of OpenInventor 2.x will work; you can get an open source version here (Coin3D): http://www.coin3d.org
    • Note that in case you want to build OpenMOIV (or any program requiring Coin3D) you also have to have in the PATH the directory where the coin-config file resides. In case Coin3D is installed as a framework on Mac OS this is not required.
  • An open source implementation of Molecular Inventor (OpenMOIV) can be downloaded here: http://www.tecn.upf.es/openMOIV
  • When building OpenMOIV on Linux/MinGW/VC++ make sure you set the OIV_DIR environment variable to the installation directory of Coin3D (where the include and lib dirs are) e.g. export OIV_DIR=/usr/local You do not need to do this on Mac OS X if you installed Coin3D as a framework (which is the default).
  • Make sure you read the build information for OpenMOIV to undestand how to deal with fonts on different platforms.

When building with MinGW you need to make sure that the gettimeofday function is available (check in include/sys/time.h); in case it is not then download the latest mingw-runtime environment or have a look at the OpenBabel build page.

Changed lines 46-48 from:
  1. Uncompress the molekel source archive, cd to the top level distribution dir and create a cmakebuild folder:
to:

These build instruction are useful only if you want to run CMake yourself instead of using one of the scripts available in the build directory.

  1. Uncompress the Molekel source archive, cd to the top level distribution dir and create a cmakebuild folder:
Changed lines 50-51 from:
  • cd to cmakebuild folder
  1. Modify the PATH variable so that the correct binary Qt dir is found: Cmake finds Qt looking for the qmake executable so you need to have the right qmake executable as the first one in the path.
to:
  • cd to the cmakebuild folder
  1. Modify the PATH variable so that the correct binary Qt dir is found: CMake finds Qt looking for the qmake executable so you need to have the right qmake executable as the first one in the path.
Changed line 60 from:
  1. Run ccmake (Linux, Mac OS) or CMakeSetup(Windows) and make sure that all the parameters are correct.
to:
  1. Run ccmake (Linux, Mac OS) or CMakeSetup.exe (Windows) and make sure that all the parameters are correct.
Changed lines 62-71 from:
  • IV_DYNAMIC and MOIV_DYNAMIC should be set to ON in case dynamic libraries are used; to OFF otherwise. Note that this only seems to be required on MINGW.
  • The following parameters need to be set (make sure you also read the OS specific section) from within ccmake(Linux, Mac) or CMakeSetup(Windows):
    • OPENBABEL_INCLUDE_DIR: OpenBabel include dir; where the openbabel include dir is e.g. /usr/local/include/openbabel-2.0
    • OPENBABEL_LINK_DIR: OpenBabel library dir; where the libopenbabel file is.
    • IV_INCLUDE_DIR: OpenInventor(Coin3D) include dir; where the Inventor include dir resides. Not required on Mac if Coin installed as a framework.
    • IV_LINK_DIR: OpenInventor(Coin3D) lib dir. Not required on Mac if Coin installed as a framework.
    • MOIV_INCLUDE_DIR: Molecular Inventor include dir; where the ChemKit2 include directory is.
    • MOIV_LINK_DIR: Molecular Inventor lib dir;
    • VTK_DIR: VTK dir e.g. /usr/local/lib/vtk-5.0
  1. Generate the makefiles with ccmake or ''CMakeSetup (configure then generate):
to:
  • IV_DYNAMIC and MOIV_DYNAMIC should be set to ON in case dynamic libraries are used; to OFF otherwise. Note that this only seems to be required on MinGW.
  • The following parameters need to be set (make sure you also read the OS specific section) from within ccmake (Linux, Mac) or CMakeSetup.exe (Windows):
    • OPENBABEL_INCLUDE_DIR: OpenBabel include dir; where the openbabel include dir is e.g. /usr/local/include/openbabel-2.0
    • OPENBABEL_LINK_DIR: OpenBabel library dir; where the libopenbabel.<dll|so> file is.
    • IV_INCLUDE_DIR: OpenInventor (Coin3D) include dir; where the Inventor include dir resides. Not required on Mac if Coin is installed as a framework.
    • IV_LINK_DIR: OpenInventor (Coin3D) lib dir. Not required on Mac if Coin is installed as a framework.
    • MOIV_INCLUDE_DIR: Molecular Inventor include dir; where the ChemKit2 include directory is.
    • MOIV_LINK_DIR: Molecular Inventor lib dir;
    • VTK_DIR: VTK dir e.g. /usr/local/lib/vtk-5.0
  1. Generate the makefiles with ccmake or CMakeSetup.exe (configure then generate):
Changed lines 74-77 from:
  • Whenever you change one or more parameter values in ccmake or CMakeSetup you'll have to configure before you can generate.
  1. Run make.

The build process will generate the following tree in the build dir:

to:
  • Whenever you change one or more parameter values in ccmake or CMakeSetup you'll have to configure before you can generate.
  1. Run make or nmake.

The build process will generate the following tree in the build directory:

Changed lines 87-90 from:

III Run

In order to launch Molekel you need to make sure that all the required dynamic libraries are accessible from the executable.

to:

III Test

In order to launch Molekel you need to make sure that all the required dynamic libraries are accessible from the executable.

Changed lines 92-93 from:
All the required dlls must be in directories listed in the PATH environment variable or in the same directory as the executable.
to:
All the required dlls must be in directories listed in the PATH environment variable or in the same directory as the executable.
Changed line 95 from:
You can make all the required shared objects accessible by adding the directories where the libraries reside to the LD_LIBRARY_PATH environment variable. To find the list of used dlls run: ldd dist/bin/Molekel from the build directory.
to:
You can make all the required shared objects accessible by adding the directories where the libraries reside to the LD_LIBRARY_PATH environment variable. To find the list of used dlls run: ldd dist/bin/Molekel from within the build directory.
March 16, 2009, at 05:32 PM by 148.187.130.153 -
Changed lines 3-7 from:

In order to build Molekel from source you need the following tools

  • Subversion client - to get the code from the repository, optional if you download the source code archive
  • CMake ( http://www.cmake.org ) - makefile generation tool
  • A C++ compiler such as gcc (MacOS X, Unix), MinGW (Windows) or Visual C++ (Windows, recommended, free version available at http://www.microsoft.com/express/vc)
  • wget (optional but useful to automate the build process as done in the Molekel build scripts)
to:

In order to build Molekel from source you need the following tools

  • Subversion client - to get the code from the repository, optional if you download the source code archive
  • CMake ( http://www.cmake.org ) - makefile generation tool
  • A C++ compiler such as gcc (MacOS X, Unix), MinGW (Windows) or Visual C++ (Windows, recommended, free version available at http://www.microsoft.com/express/vc)
  • wget (optional but useful to automate the build process as done in the Molekel build scripts)
Changed lines 10-16 from:
  • Qt: http://www.trolltech.com/products/qt
  • Qwt: http://qwt.sourceforge.net
  • VTK 5.x: http://www.vtk.org
  • Coin3D: http://www.coin3d.org
  • OpenMOIV: http://www.tecn.upf.es/openMOIV
  • OpenBabel: http://openbabel.sourceforge.net
to:
  • Qt: http://www.trolltech.com/products/qt
  • Qwt: http://qwt.sourceforge.net
  • VTK 5.x: http://www.vtk.org
  • Coin3D: http://www.coin3d.org
  • OpenMOIV: http://www.tecn.upf.es/openMOIV
  • OpenBabel: http://openbabel.sourceforge.net
Changed line 18 from:
  • (RECOMMENDED) get one of the run_<environment>_cmake.sh/bat files from the build directory of the source distribution and change the paths to suit your environment then execute the script OR
to:
  • (RECOMMENDED) get one of the run_<environment>_cmake.sh/bat files from the build directory of the source distribution and change the paths to suit your environment then execute the script OR
Changed line 23 from:

Steps

to:

Detailed instructions

March 16, 2009, at 05:27 PM by 148.187.130.153 -
Deleted lines 2-5:

This section describes the procedure to follow when building Molekel on Linux, Windows and Mac OS X.

Molekel is built with CMake and make/nmake and some libraries need to be installed before you can build the executable from source.

Changed line 5 from:
  • CMake
to:
  • CMake ( http://www.cmake.org ) - makefile generation tool
Changed lines 17-21 from:

The best way of building Molekel is to look at the shell scripts found in the build and install directories which are used to automate the build process and perform tasks such as check out the required components from the source code repository and invoke CMake with the proper configuration parameters.

to:

After all the dependencies are installed and you have downloaded the source code you need to generate the makefiles with CMake; three options available:

  • (RECOMMENDED) get one of the run_<environment>_cmake.sh/bat files from the build directory of the source distribution and change the paths to suit your environment then execute the script OR
  • run ccmake (Unix/Mac OS X) or CMakeSetup.exe (Windows) and specify the include and library path through an interactive interface then execute make/nmake OR
  • run cmake on the command line specifying the path to the CMakeLists.txt configuration file and the include/library paths on the command line then execute make/nmake
March 16, 2009, at 02:03 PM by 148.187.130.153 -
Changed lines 27-28 from:
  1. Install the Open Source verion of Qt

(http://www.trolltech.com/products/qt); Qt has to be installed before VTK because VTK needs some Qt libraries.

to:
  1. Install the Open Source verion of Qt (http://www.trolltech.com/products/qt); Qt has to be installed before VTK because VTK needs some Qt libraries.
March 16, 2009, at 02:02 PM by 148.187.130.153 -
Deleted lines 21-22:

Building the above lbraries (when needed) on Mac OS, and Linux is straightforward, it takes some time but you should not encounter any issues; building everything except OpenBabel with MinGW is fairly easy too.

March 16, 2009, at 02:01 PM by 148.187.130.153 -
Changed line 3 from:

This setcion describes the procedure to follow when building Molekel on Linux, Windows and Mac OS X.

to:

This section describes the procedure to follow when building Molekel on Linux, Windows and Mac OS X.

March 13, 2009, at 04:01 PM by 148.187.130.153 -
Changed line 1 from:

Build Instructions

to:

(:title Build Instructions:)

March 13, 2009, at 04:01 PM by 148.187.130.153 -
Changed line 11 from:
  • wget (optional but useful to automate the build process as done in the Molekel build scripts)
to:
  • wget (optional but useful to automate the build process as done in the Molekel build scripts)
March 13, 2009, at 04:00 PM by 148.187.130.153 -
Changed line 8 from:
  • Subversion client
to:
  • Subversion client - to get the code from the repository, optional if you download the source code archive
March 13, 2009, at 03:51 PM by 148.187.130.153 -
Changed lines 7-13 from:

Some shell scripts found in the build and install directories are available to automate the build process, these are useful to build redistributable archives but can also be used to e.g. check out the required components from the source code repository and invoke CMake with the proper configuration parameters.

Molekel now (December 2008) builds with Microsft Visual C++ (free version available at http://www.microsoft.com/express/vc). The easiest way of building Molekel on If you need to build Molekel on Windows you might want to check out the mingw scripts since they will take care of checking out the code, downloading all the dependencies except Qt and build everything, provided you have the following tools/toolkits already installed:

  • MinGW
  • MSYS
  • SVN
to:

In order to build Molekel from source you need the following tools

  • Subversion client
Changed lines 10-13 from:
  • wget (used only to get the dependency archive through ftp; can be done manually)
  • unix2dos (optional - used to convert all text files in the distribution to win format)

It is recommended that you get the libraries from the following sites:

to:
  • A C++ compiler such as gcc (MacOS X, Unix), MinGW (Windows) or Visual C++ (Windows, recommended, free version available at http://www.microsoft.com/express/vc)
  • wget (optional but useful to automate the build process as done in the Molekel build scripts)
  • unix2dos and dos2unix (both optional) to convert EOL separators

and libraries:

Changed lines 19-20 from:
  • OpenBabel: http://openbabel.sourceforge.net
to:
  • OpenBabel: http://openbabel.sourceforge.net

The best way of building Molekel is to look at the shell scripts found in the build and install directories which are used to automate the build process and perform tasks such as check out the required components from the source code repository and invoke CMake with the proper configuration parameters.

Deleted lines 24-26:

We do have pre-built and source distributions of the above libraries on our ftp site at this address: ftp://ftp.cscs.ch/out/molekel/molekel_5.3/dep.

Added lines 29-30:
  1. Install the Open Source verion of Qt

(http://www.trolltech.com/products/qt); Qt has to be installed before VTK because VTK needs some Qt libraries.

Deleted line 36:
  1. Install the Open Source verion of Qt 4.2 (http://www.trolltech.com/products/qt)
Changed line 43 from:
  • When building OpenMOIV on Linux/MinGW make sure you set the OIV_DIR environment variable to the installation dir of Coin3D (where the include and lib dirs are) e.g. export OIV_DIR=/usr/local You do not need to do this on Mac OS X if you installe Coin3D as a framework (which is the default).
to:
  • When building OpenMOIV on Linux/MinGW/VC++ make sure you set the OIV_DIR environment variable to the installation dir of Coin3D (where the include and lib dirs are) e.g. export OIV_DIR=/usr/local You do not need to do this on Mac OS X if you installed Coin3D as a framework (which is the default).
Changed lines 115-116 from:

To enable printing on standard output on Mac you'll have to invoke the actual executable in the Molekel.app folder i.e. Molekel.app/Contents/MacOS/Molekel.

to:

To enable printing on standard output on Mac you'll have to invoke the actual executable in the Molekel.app folder i.e. Molekel.app/Contents/MacOS/Molekel.

March 13, 2009, at 03:14 PM by 148.187.130.153 -
Changed lines 3-6 from:

This setcion describes the procedure to follow when building Molekel on Linux (gcc), Windows (MinGW) and Mac OS X (gcc).

Molekel is built with CMake and Make and some libraries need to be installed before you can build the executable.

to:

This setcion describes the procedure to follow when building Molekel on Linux, Windows and Mac OS X.

Molekel is built with CMake and make/nmake and some libraries need to be installed before you can build the executable from source.

Changed line 9 from:

Molekel now (December 2008) builds with Microsft Visual C++ (free version available at http://www.microsoft.com/express/vc).

to:

Molekel now (December 2008) builds with Microsft Visual C++ (free version available at http://www.microsoft.com/express/vc). The easiest way of building Molekel on

Deleted lines 17-19:

Note:

it is possible to build everything with MS VC++ compiler 7.1 or better, but this requires the use of the commercial version of Qt or the unsupported Qt distribution you can find through this page: http://psi-im.org/wiki/Compiling_Qt4_on_Windows. It might be however a problem to build OpenBabel libraries with VC++ since as of OpenBabel 2.0.2 the provided Visual Studio (6 and 8) project files can be used to build the executable only, not the libraries.
Changed lines 19-20 from:
  • Qt 4.2: http://www.trolltech.com/products/qt
to:
  • Qt: http://www.trolltech.com/products/qt
  • Qwt: http://qwt.sourceforge.net
March 13, 2009, at 02:57 PM by 148.187.130.153 -
Added lines 8-9:

Molekel now (December 2008) builds with Microsft Visual C++ (free version available at http://www.microsoft.com/express/vc).

March 13, 2009, at 02:50 PM by 148.187.130.153 -
Changed line 60 from:

[@

to:
[@
March 13, 2009, at 02:49 PM by 148.187.130.153 -
Added lines 16-18:

Note:

it is possible to build everything with MS VC++ compiler 7.1 or better, but this requires the use of the commercial version of Qt or the unsupported Qt distribution you can find through this page: http://psi-im.org/wiki/Compiling_Qt4_on_Windows. It might be however a problem to build OpenBabel libraries with VC++ since as of OpenBabel 2.0.2 the provided Visual Studio (6 and 8) project files can be used to build the executable only, not the libraries.
Added lines 26-27:

Building the above lbraries (when needed) on Mac OS, and Linux is straightforward, it takes some time but you should not encounter any issues; building everything except OpenBabel with MinGW is fairly easy too.

Changed lines 30-32 from:

Building the above lbraries (when needed) on Mac OS, and Linux is straightforward, it takes some time but you should not encounter any issues; building everything except OpenBabel with MinGW is fairly easy too.

to:
Added line 60:

[@

Added line 66:

@]

March 13, 2009, at 02:49 PM by 148.187.130.153 -
Changed lines 57-61 from:

SET( MOLEKEL_VERSION_MAJOR 5 ) SET( MOLEKEL_VERSION_MINOR 0 ) SET( MOLEKEL_VERSION_PATCH 0 ) SET( MOLEKEL_VERSION_BUILD 0 ) SET( MOLEKEL_VERSION_TYPE "development" )

to:

SET( MOLEKEL_VERSION_MAJOR 5 ) SET( MOLEKEL_VERSION_MINOR 0 ) SET( MOLEKEL_VERSION_PATCH 0 ) SET( MOLEKEL_VERSION_BUILD 0 ) SET( MOLEKEL_VERSION_TYPE "development" )

March 13, 2009, at 02:48 PM by 148.187.130.153 -
Changed lines 57-63 from:

SET( MOLEKEL_VERSION_MAJOR 5 ) SET( MOLEKEL_VERSION_MINOR 0 ) SET( MOLEKEL_VERSION_PATCH 0 ) SET( MOLEKEL_VERSION_BUILD 0 ) SET( MOLEKEL_VERSION_TYPE "development" )

to:

SET( MOLEKEL_VERSION_MAJOR 5 ) SET( MOLEKEL_VERSION_MINOR 0 ) SET( MOLEKEL_VERSION_PATCH 0 ) SET( MOLEKEL_VERSION_BUILD 0 ) SET( MOLEKEL_VERSION_TYPE "development" )

March 13, 2009, at 02:47 PM by 148.187.130.153 -
Changed line 57 from:

@@

to:

[=

Changed line 63 from:

@@

to:

=]

March 13, 2009, at 02:46 PM by 148.187.130.153 -
Changed line 57 from:

[@

to:

@@

Changed line 63 from:

@]

to:

@@

February 14, 2008, at 02:43 PM by 148.187.130.131 -
Deleted lines 15-17:

Note:

it is possible to build everything with MS VC++ compiler 7.1 or better, but this requires the use of the commercial version of Qt or the unsupported Qt distribution you can find through this page: http://psi-im.org/wiki/Compiling_Qt4_on_Windows. It might be however a problem to build OpenBabel libraries with VC++ since as of OpenBabel 2.0.2 the provided Visual Studio (6 and 8) project files can be used to build the executable only, not the libraries.
Added lines 23-24:

We do have pre-built and source distributions of the above libraries on our ftp site at this address: ftp://ftp.cscs.ch/out/molekel/molekel_5.3/dep.

Changed lines 27-29 from:

We do have pre-built and source distributions of the above libraries on our ftp site at this address: ftp://ftp.cscs.ch/out/molekel/molekel_5.3/dep.

to:
February 14, 2008, at 02:43 PM by 148.187.130.131 -
Changed lines 28-30 from:

We do have pre-built and source distribution of the above libraries on our ftp site at this address: ftp://ftp.cscs.ch/out/molekel/molekel_5.3/dep.

to:

We do have pre-built and source distributions of the above libraries on our ftp site at this address: ftp://ftp.cscs.ch/out/molekel/molekel_5.3/dep.

February 14, 2008, at 02:15 PM by 148.187.130.131 -
Changed lines 26-28 from:

Building the above lbraries (when needed) on Mac OS, and Linux is straightforward, it takes some time but you should not encounter any issues; building everything except OpenBabel with MinGW is fairly easy too, if however you prefer to use precompiled versions of the libraries you can find prebuilt versions for MinGW and other platform on this site under the Support Files section which is currently password protected; contact us through the Contact form if you need to download precompiled versions of the above libraries.

to:

Building the above lbraries (when needed) on Mac OS, and Linux is straightforward, it takes some time but you should not encounter any issues; building everything except OpenBabel with MinGW is fairly easy too.

We do have pre-built and source distribution of the above libraries on our ftp site at this address: ftp://ftp.cscs.ch/out/molekel/molekel_5.3/dep.

February 14, 2008, at 01:43 PM by 148.187.130.131 -
Changed lines 108-110 from:

In case you have rendering problems, get messages about errors in Coin or the program crashes when loading files without reporting any error, you can set the value of two environment variables as follows:

to:

Molekel versions 5.3 or above use some advanced multi-pass rendering techniques to enhance visual quality; these techniques may generate visual artifacts on transparent surfaces on some specific graphic cards. We have experienced problems on SuSE 10.3 x86-32/NVIDIA 8800 Ultra and Windows XP 32bit/NVIDIA 8800 Ultra system; on Windows problems can be fixed by selecting Let the 3D application decide (which should be the default) in the Image Settings page of the NVIDIA Control Panel.

In general, in case you have rendering problems, get messages about errors in Coin or the program crashes when loading files without reporting any error, you can set the value of two environment variables as follows:

Added lines 115-116:

To set the environment variables permanently on Windows XP right-click on My Computer then select the Advanced tab and click on the Environment Variables button.

June 27, 2007, at 05:23 PM by 148.187.130.131 -
Changed lines 5-6 from:

Molekel is built with CMake and Make and some libraries need to be installed before you can build the executable.

to:

Molekel is built with CMake and Make and some libraries need to be installed before you can build the executable.

Some shell scripts found in the build and install directories are available to automate the build process, these are useful to build redistributable archives but can also be used to e.g. check out the required components from the source code repository and invoke CMake with the proper configuration parameters. If you need to build Molekel on Windows you might want to check out the mingw scripts since they will take care of checking out the code, downloading all the dependencies except Qt and build everything, provided you have the following tools/toolkits already installed:

  • MinGW
  • MSYS
  • SVN
  • CMake
  • wget (used only to get the dependency archive through ftp; can be done manually)
  • unix2dos (optional - used to convert all text files in the distribution to win format)
June 27, 2007, at 05:10 PM by 148.187.130.131 -
Changed lines 3-4 from:

This setcion describes the procedure to follow when building Molekel on Linux (gcc), Windows (MinGW) and Mac OS X (gcc). The information on this section is a subset of the information containted in the doc/developer/build.txt file found in the source code repository.

to:

This setcion describes the procedure to follow when building Molekel on Linux (gcc), Windows (MinGW) and Mac OS X (gcc).

Changed lines 17-19 from:

Building the above lbraries (when needed) on Mac OS, and Linux is straightforward, it takes some time but you should not encounter any issues; building everything except OpenBabel with MinGW is fairly easy too, if however you prefer to use precompiled versions of the libraries you can find prebuilt versions for MinGW and other platform on this site under the Support Files section which is currently password protected; contact me through the Contact form if you need to download precompiled versions of the above libraries.

to:

Building the above lbraries (when needed) on Mac OS, and Linux is straightforward, it takes some time but you should not encounter any issues; building everything except OpenBabel with MinGW is fairly easy too, if however you prefer to use precompiled versions of the libraries you can find prebuilt versions for MinGW and other platform on this site under the Support Files section which is currently password protected; contact us through the Contact form if you need to download precompiled versions of the above libraries.

Added lines 40-41:

On MinGW you need to make sure that the gettimeofday function is available (check in include/sys/time.h); in case it's not then download the latest mingw-runtime environment or have a look at the OpenBabel build page.

January 08, 2007, at 10:26 AM by Ugo Varetto -
Added lines 95-96:

Rendering issues

January 08, 2007, at 10:25 AM by Ugo Varetto -
Changed line 95 from:

In case you have rendering problems (or get messages about errors in Coin) you can set the value of two environment variables as follows:

to:

In case you have rendering problems, get messages about errors in Coin or the program crashes when loading files without reporting any error, you can set the value of two environment variables as follows:

Changed lines 98-99 from:
to:

before launching Molekel to disable the use of advanced OpenGL features.

January 05, 2007, at 10:03 AM by Ugo Varetto -
Changed lines 86-87 from:
all the required dlls must be in directories listed in the PATH environment variable or in the same directory as the executable.
to:
All the required dlls must be in directories listed in the PATH environment variable or in the same directory as the executable.
Changed lines 89-90 from:
you can make all the required shared objects accessible by adding the directories where the libraries reside to the LD_LIBRARY_PATH environment variable. To find the list of used dlls run: ldd dist/bin/Molekel from the build directory.
to:
You can make all the required shared objects accessible by adding the directories where the libraries reside to the LD_LIBRARY_PATH environment variable. To find the list of used dlls run: ldd dist/bin/Molekel from the build directory.
Changed lines 92-93 from:
you should not have to do anything to run the program; if for whatever reason the program cannot find some dynamic libraries you can add the directories where the dynamic libraries reside to the DYLD_LIBRARY_PATH environment variable. To find the list of dynamic libraries and frameworks used run otool -L dist/bundle/Molekel.app/Contents/MacOS/Molekel from the build directory.
to:
You should not have to do anything to run the program; if for whatever reason the program cannot find some dynamic libraries you can add the directories where the dynamic libraries reside to the DYLD_LIBRARY_PATH environment variable. To find the list of dynamic libraries and frameworks used run otool -L dist/bundle/Molekel.app/Contents/MacOS/Molekel from the build directory.
All the resources in the resource directory (including the toolbar dir) must be copied into Molekel.app/Contents/Resources.
December 22, 2006, at 05:52 PM by Ugo Varetto -
Changed line 46 from:
  1. Create a text file version_info.cmake in the build directory; this file is included by the main CMakeLists.txt file to set version information. Open version_info.cmake and add somthing like (use whatever version numbers you want).
to:
  1. Create a text file version_info.cmake in the build directory; this file is included by the main CMakeLists.txt file to set version information. Open version_info.cmake and add something like (use whatever version numbers you want).
December 22, 2006, at 05:51 PM by Ugo Varetto -
Added lines 46-53:
  1. Create a text file version_info.cmake in the build directory; this file is included by the main CMakeLists.txt file to set version information. Open version_info.cmake and add somthing like (use whatever version numbers you want).
SET( MOLEKEL_VERSION_MAJOR 5 )
SET( MOLEKEL_VERSION_MINOR 0 )
SET( MOLEKEL_VERSION_PATCH 0 )
SET( MOLEKEL_VERSION_BUILD 0 )
SET( MOLEKEL_VERSION_TYPE "development" )
December 21, 2006, at 04:59 PM by Ugo Varetto -
Changed lines 11-19 from:
  • Qt 4.2
  • VTK 5.x
  • Coin3D
  • OpenMOIV
  • OpenBabel

Building the above lbraries (when needed) on Mac OS, and Linux is straightforward, it takes some time but you should not encounter any issues; building everything except OpenBabel on MinGW is fairly easy too, if however you prefer to use precompiled versions of the libraries you can find prebuilt versions for MinGW and other platform on this site under the Support Files section which is currently password protected, contact me through the Contact form if you need to download precompiled versions of the above libraries.

to:
  • Qt 4.2: http://www.trolltech.com/products/qt
  • VTK 5.x: http://www.vtk.org
  • Coin3D: http://www.coin3d.org
  • OpenMOIV: http://www.tecn.upf.es/openMOIV
  • OpenBabel: http://openbabel.sourceforge.net

Building the above lbraries (when needed) on Mac OS, and Linux is straightforward, it takes some time but you should not encounter any issues; building everything except OpenBabel with MinGW is fairly easy too, if however you prefer to use precompiled versions of the libraries you can find prebuilt versions for MinGW and other platform on this site under the Support Files section which is currently password protected; contact me through the Contact form if you need to download precompiled versions of the above libraries.

December 21, 2006, at 04:56 PM by Ugo Varetto -
Changed line 11 from:
  • Qt 4.2
to:
  • Qt 4.2
Changed lines 17-19 from:

Building the above lbraries (when needed) on Mac OS, and Linux is straightforward, it takes some time but you should not encounter any issues; building everything except OpenBabel on MinGW is fairly easy too, if however you prefer to use precompiled versions of the libraries you can find prebuilt versions for MinGW and other platform on this site under the Support Files section which is currently password protected, contact me through the Contact form if you need to get access to the Support Files section.

to:

Building the above lbraries (when needed) on Mac OS, and Linux is straightforward, it takes some time but you should not encounter any issues; building everything except OpenBabel on MinGW is fairly easy too, if however you prefer to use precompiled versions of the libraries you can find prebuilt versions for MinGW and other platform on this site under the Support Files section which is currently password protected, contact me through the Contact form if you need to download precompiled versions of the above libraries.

December 21, 2006, at 04:52 PM by Ugo Varetto -
Deleted lines 0-1:

Update in progress

Added lines 10-19:

It is recommended that you get the libraries from the following sites:

  • Qt 4.2
  • VTK 5.x
  • Coin3D
  • OpenMOIV
  • OpenBabel

Building the above lbraries (when needed) on Mac OS, and Linux is straightforward, it takes some time but you should not encounter any issues; building everything except OpenBabel on MinGW is fairly easy too, if however you prefer to use precompiled versions of the libraries you can find prebuilt versions for MinGW and other platform on this site under the Support Files section which is currently password protected, contact me through the Contact form if you need to get access to the Support Files section.

December 21, 2006, at 03:39 PM by Ugo Varetto -
Changed lines 10-11 from:
it should be possible to build everything with MS VC++ compiler 7.1 or better, but this requires the use of the commercial version of Qt or the unsupported Qt distribution you can find through this page: http://psi-im.org/wiki/Compiling_Qt4_on_Windows.
to:
it is possible to build everything with MS VC++ compiler 7.1 or better, but this requires the use of the commercial version of Qt or the unsupported Qt distribution you can find through this page: http://psi-im.org/wiki/Compiling_Qt4_on_Windows. It might be however a problem to build OpenBabel libraries with VC++ since as of OpenBabel 2.0.2 the provided Visual Studio (6 and 8) project files can be used to build the executable only, not the libraries.
Changed lines 72-96 from:

Linux: you can make all the required shared objects accessible

       by adding the directories where the libraries reside
       to the LD_LIBRARY_PATH environment variable.
       To find the list of used dlls run: ldd dist/bin/Molekel
       from the build directory.

MacOS: add the directories where the dynamic libraries reside

       to the DYLD_LIBRARY_PATH environment variable.
       To find the list of dynamic libraries  and frameworks
       used run:
       otool -L dist/bundle/Molekel.app/Contents/MacOS/Molekel
       from the build directory.

In case you have rendering problems (or get messages about errors in Coin) you can set the value of two environment variables as follows:

COIN_FULL_INDIRECT_RENDERING = 0 COIN_FORCE_GL1_0_ONLY = 1

You can also set the COIN_DEBUG_GLGLUE environment variable to 1 before starting Molekel in a console window to print OpenGL debug information. To enable printing on standard output on Mac you'll have to invoke the actual executable in the Molekel.app folder i.e. Molekel.app/Contents/MacOS/Molekel.

to:

Linux

you can make all the required shared objects accessible by adding the directories where the libraries reside to the LD_LIBRARY_PATH environment variable. To find the list of used dlls run: ldd dist/bin/Molekel from the build directory.

MacOS

you should not have to do anything to run the program; if for whatever reason the program cannot find some dynamic libraries you can add the directories where the dynamic libraries reside to the DYLD_LIBRARY_PATH environment variable. To find the list of dynamic libraries and frameworks used run otool -L dist/bundle/Molekel.app/Contents/MacOS/Molekel from the build directory.

In case you have rendering problems (or get messages about errors in Coin) you can set the value of two environment variables as follows:

  • COIN_FULL_INDIRECT_RENDERING=0
  • COIN_FORCE_GL1_0_ONLY=1

You can also set the COIN_DEBUG_GLGLUE environment variable to 1 before starting Molekel in a console window to print OpenGL debug information. To enable printing on standard output on Mac you'll have to invoke the actual executable in the Molekel.app folder i.e. Molekel.app/Contents/MacOS/Molekel.

December 21, 2006, at 03:31 PM by Ugo Varetto -
Changed lines 10-14 from:
it should be possible to build everything with MS VC++ compiler
7.1 or better, but this requires the use of the commercial version
of Qt or the unsupported Qt distribution you can find through this page:
http://psi-im.org/wiki/Compiling_Qt4_on_Windows.
to:
it should be possible to build everything with MS VC++ compiler 7.1 or better, but this requires the use of the commercial version of Qt or the unsupported Qt distribution you can find through this page: http://psi-im.org/wiki/Compiling_Qt4_on_Windows.
December 21, 2006, at 03:28 PM by Ugo Varetto -
Added lines 66-99:

III Run

In order to launch Molekel you need to make sure that all the required dynamic libraries are accessible from the executable.

Windows

all the required dlls must be in directories listed in the PATH environment variable or in the same directory as the executable.

Linux: you can make all the required shared objects accessible

       by adding the directories where the libraries reside
       to the LD_LIBRARY_PATH environment variable.
       To find the list of used dlls run: ldd dist/bin/Molekel
       from the build directory.

MacOS: add the directories where the dynamic libraries reside

       to the DYLD_LIBRARY_PATH environment variable.
       To find the list of dynamic libraries  and frameworks
       used run:
       otool -L dist/bundle/Molekel.app/Contents/MacOS/Molekel
       from the build directory.

In case you have rendering problems (or get messages about errors in Coin) you can set the value of two environment variables as follows:

COIN_FULL_INDIRECT_RENDERING = 0 COIN_FORCE_GL1_0_ONLY = 1

You can also set the COIN_DEBUG_GLGLUE environment variable to 1 before starting Molekel in a console window to print OpenGL debug information. To enable printing on standard output on Mac you'll have to invoke the actual executable in the Molekel.app folder i.e. Molekel.app/Contents/MacOS/Molekel.

December 21, 2006, at 03:23 PM by Ugo Varetto -
Changed lines 38-39 from:
  • mkdir cmakebuild
  • cd to cmakebuild folder
to:
  • mkdir cmakebuild
  • cd to cmakebuild folder
Changed lines 42-51 from:
  • ccmake ../src
  • IV_DYNAMIC and MOIV_DYNAMIC should be set to ON in case dynamic libraries are used; to OFF otherwise. Note that this only seems to be required on MINGW.
  • The following parameters need to be set (make sure you also read the OS specific section) from within ccmake(Linux, Mac) or CMakeSetup(Windows):
    • OPENBABEL_INCLUDE_DIR: OpenBabel include dir; where the openbabel include dir is e.g. /usr/local/include/openbabel-2.0
    • OPENBABEL_LINK_DIR: OpenBabel library dir; where the libopenbabel file is.
    • IV_INCLUDE_DIR: OpenInventor(Coin3D) include dir; where the Inventor include dir resides. Not required on Mac if Coin installed as a framework.
    • IV_LINK_DIR: OpenInventor(Coin3D) lib dir. Not required on Mac if Coin installed as a framework.
    • MOIV_INCLUDE_DIR: Molecular Inventor include dir; where the ChemKit2 include directory is.
    • MOIV_LINK_DIR: Molecular Inventor lib dir;
    • VTK_DIR: VTK dir e.g. /usr/local/lib/vtk-5.0
to:
  • ccmake ../src
  • IV_DYNAMIC and MOIV_DYNAMIC should be set to ON in case dynamic libraries are used; to OFF otherwise. Note that this only seems to be required on MINGW.
  • The following parameters need to be set (make sure you also read the OS specific section) from within ccmake(Linux, Mac) or CMakeSetup(Windows):
    • OPENBABEL_INCLUDE_DIR: OpenBabel include dir; where the openbabel include dir is e.g. /usr/local/include/openbabel-2.0
    • OPENBABEL_LINK_DIR: OpenBabel library dir; where the libopenbabel file is.
    • IV_INCLUDE_DIR: OpenInventor(Coin3D) include dir; where the Inventor include dir resides. Not required on Mac if Coin installed as a framework.
    • IV_LINK_DIR: OpenInventor(Coin3D) lib dir. Not required on Mac if Coin installed as a framework.
    • MOIV_INCLUDE_DIR: Molecular Inventor include dir; where the ChemKit2 include directory is.
    • MOIV_LINK_DIR: Molecular Inventor lib dir;
    • VTK_DIR: VTK dir e.g. /usr/local/lib/vtk-5.0
Changed line 65 from:

Note: with MinGW 3.4.5 compilation of MolekelData.cpp can be very slow; to speed up build time during development #define MOLEKEL_USE_COMMON_FILE_FORMATS

to:

Note: with MinGW 3.4.5 compilation of MolekelData.cpp can be very slow; to speed up build time during development #define MOLEKEL_USE_COMMON_FILE_FORMATS

December 21, 2006, at 03:18 PM by Ugo Varetto -
Changed lines 3-6 from:

Build

This setcion describes the procedure to follow when building Molekel on Linux (gcc), Windows (MinGW) and Mac OS X (gcc).

to:

Build Instructions

This setcion describes the procedure to follow when building Molekel on Linux (gcc), Windows (MinGW) and Mac OS X (gcc). The information on this section is a subset of the information containted in the doc/developer/build.txt file found in the source code repository.

Changed lines 33-65 from:
  • Make sure you read the build information for OpenMOIV to undestand how to deal with fonts on different platform.
to:
  • Make sure you read the build information for OpenMOIV to undestand how to deal with fonts on different platform.

II Build

  1. Uncompress the molekel source archive, cd to the top level distribution dir and create a cmakebuild folder:
  • mkdir cmakebuild
  • cd to cmakebuild folder
  1. Modify the PATH variable so that the correct binary Qt dir is found: Cmake finds Qt looking for the qmake executable so you need to have the right qmake executable as the first one in the path.
  2. Run ccmake (Linux, Mac OS) or CMakeSetup(Windows) and make sure that all the parameters are correct.
  • ccmake ../src
  • IV_DYNAMIC and MOIV_DYNAMIC should be set to ON in case dynamic libraries are used; to OFF otherwise. Note that this only seems to be required on MINGW.
  • The following parameters need to be set (make sure you also read the OS specific section) from within ccmake(Linux, Mac) or CMakeSetup(Windows):
    • OPENBABEL_INCLUDE_DIR: OpenBabel include dir; where the openbabel include dir is e.g. /usr/local/include/openbabel-2.0
    • OPENBABEL_LINK_DIR: OpenBabel library dir; where the libopenbabel file is.
    • IV_INCLUDE_DIR: OpenInventor(Coin3D) include dir; where the Inventor include dir resides. Not required on Mac if Coin installed as a framework.
    • IV_LINK_DIR: OpenInventor(Coin3D) lib dir. Not required on Mac if Coin installed as a framework.
    • MOIV_INCLUDE_DIR: Molecular Inventor include dir; where the ChemKit2 include directory is.
    • MOIV_LINK_DIR: Molecular Inventor lib dir;
    • VTK_DIR: VTK dir e.g. /usr/local/lib/vtk-5.0
  1. Generate the makefiles with ccmake or ''CMakeSetup (configure then generate):
    1. Check that all the parameters are set to the proper values.
    2. Press [c](Mac, Linux) or Configure(Windows) to configure then [g](Mac, Linux) or Ok(Windows) to generate the makefiles.
    • Whenever you change one or more parameter values in ccmake or CMakeSetup you'll have to configure before you can generate.
  2. Run make.

The build process will generate the following tree in the build dir:

  • dist - release notes, license, readme
    • bin OR bundle - binary or Mac bundle
    • resources - images, configuration files...
      • toolbar - toolbar icons
    • doc - user documentation

Note: with MinGW 3.4.5 compilation of MolekelData.cpp can be very slow; to speed up build time during development #define MOLEKEL_USE_COMMON_FILE_FORMATS

December 21, 2006, at 02:56 PM by Ugo Varetto -
Added lines 29-30:
  • Any implementation of OpenInventor 2.x will work; you can get an open source version here (Coin3D): http://www.coin3d.org
    • Note that in case you want to build OpenMOIV (or any program requiring coin) you also have to have in the PATH the directory where coin-config resides. In case Coin3D is installed as a framework on Mac OS this is not required.
Changed lines 33-35 from:
  • Make sure you read the build information for OpenMOIV to undestand how to deal with fonts on different platform.
  • Any implementation of OpenInventor 2.x will work; you can get an open source version here (Coin3D): http://www.coin3d.org
    • Note that in case you want to build OpenMOIV (or any program requiring coin) you also have to have in the PATH the directory where coin-config resides. Again, in case Coin3D is installed as a framework on Mac OS this is not required.
to:
  • Make sure you read the build information for OpenMOIV to undestand how to deal with fonts on different platform.
December 21, 2006, at 02:54 PM by Ugo Varetto -
Changed line 25 from:
  • Install the Open Source verion of Qt 4.2 (http://www.trolltech.com/products/qt)
to:
  1. Install the Open Source verion of Qt 4.2 (http://www.trolltech.com/products/qt)
December 21, 2006, at 02:54 PM by Ugo Varetto -
Changed lines 26-55 from:

4) Install OpenBabel 2.x libraries

   http://openbabel.sourceforge.net
   If you are building on Windows with MinGW check out the OS specific issues below.

5) Install OpenInventor and Molecular Inventor

   An open source implementation of Molecular Inventor(OpenMOIV) can be
   downloaded here:

   http://www.tecn.upf.es/openMOIV

   When building OpenMOIV on Linux/MinGW make sure you set the OIV_DIR
   environment variable to the installation dir of Coin3D (where the
   include and lib dirs are) e.g.
   export OIV_DIR=/usr/local
   You do not need to do this on Mac OS X if you installe Coin3D as a
   framework (which is the default).

   Make sure you read the build information for OpenMOIV to undestand
   how to deal with fonts.

   Any implementation of OpenInventor 2.x will work; you can get an
   open source version here (Coin3D):

   http://www.coin3d.org

   Note that in case you want to build OpenMOIV (or any program requiring coin)
   you also have to have in the PATH the directory where coin-config resides.
   Again, in case Coin3D is installed as a framework on Mac OS this is not required.
to:
  1. Install OpenBabel 2.x libraries (http://openbabel.sourceforge.net)
    • If you are building on Windows with MinGW check out the OpenBabel OS specific issues below.
  2. Install OpenInventor and Molecular Inventor
  • An open source implementation of Molecular Inventor(OpenMOIV) can be downloaded here: http://www.tecn.upf.es/openMOIV
  • When building OpenMOIV on Linux/MinGW make sure you set the OIV_DIR environment variable to the installation dir of Coin3D (where the include and lib dirs are) e.g. export OIV_DIR=/usr/local You do not need to do this on Mac OS X if you installe Coin3D as a framework (which is the default).
  • Make sure you read the build information for OpenMOIV to undestand how to deal with fonts on different platform.
  • Any implementation of OpenInventor 2.x will work; you can get an open source version here (Coin3D): http://www.coin3d.org
    • Note that in case you want to build OpenMOIV (or any program requiring coin) you also have to have in the PATH the directory where coin-config resides. Again, in case Coin3D is installed as a framework on Mac OS this is not required.
December 21, 2006, at 02:47 PM by Ugo Varetto -
Added lines 1-2:

Update in progress

December 21, 2006, at 02:46 PM by Ugo Varetto -
Changed lines 22-26 from:
  • Check out OS specific information below.

3) Install the Open Source verion of Qt 4.x

   http://www.trolltech.com/products/qt
to:
  • Check out OS specific information below.
  • Install the Open Source verion of Qt 4.2 (http://www.trolltech.com/products/qt)
December 21, 2006, at 02:41 PM by Ugo Varetto -
Changed lines 5-6 from:

Molekel is built with CMake and Make and a number of libraries need to be installed before you can build the executable.

to:

Molekel is built with CMake and Make and some libraries need to be installed before you can build the executable.

Changed lines 11-55 from:
http://psi-im.org/wiki/Compiling_Qt4_on_Windows.
to:
http://psi-im.org/wiki/Compiling_Qt4_on_Windows.

Steps

I Dependencies

  1. Install CMake (http://www.cmake.org)
  2. Install VTK 5.x (http://www.vtk.org)
    • if you build from source make sure the following parameters are set to ON
      • VTK_USE_GUISUPPORT
      • VTK_USE_QVTK
      • VTK_USE_GL2PS
      • Check out OS specific information below.

3) Install the Open Source verion of Qt 4.x

   http://www.trolltech.com/products/qt

4) Install OpenBabel 2.x libraries

   http://openbabel.sourceforge.net
   If you are building on Windows with MinGW check out the OS specific issues below.

5) Install OpenInventor and Molecular Inventor

   An open source implementation of Molecular Inventor(OpenMOIV) can be
   downloaded here:

   http://www.tecn.upf.es/openMOIV

   When building OpenMOIV on Linux/MinGW make sure you set the OIV_DIR
   environment variable to the installation dir of Coin3D (where the
   include and lib dirs are) e.g.
   export OIV_DIR=/usr/local
   You do not need to do this on Mac OS X if you installe Coin3D as a
   framework (which is the default).

   Make sure you read the build information for OpenMOIV to undestand
   how to deal with fonts.

   Any implementation of OpenInventor 2.x will work; you can get an
   open source version here (Coin3D):

   http://www.coin3d.org

   Note that in case you want to build OpenMOIV (or any program requiring coin)
   you also have to have in the PATH the directory where coin-config resides.
   Again, in case Coin3D is installed as a framework on Mac OS this is not required.
December 21, 2006, at 02:39 PM by Ugo Varetto -
Added lines 1-11:

Build

This setcion describes the procedure to follow when building Molekel on Linux (gcc), Windows (MinGW) and Mac OS X (gcc).

Molekel is built with CMake and Make and a number of libraries need to be installed before you can build the executable.

Note:

it should be possible to build everything with MS VC++ compiler
7.1 or better, but this requires the use of the commercial version
of Qt or the unsupported Qt distribution you can find through this page:
http://psi-im.org/wiki/Compiling_Qt4_on_Windows.