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Certain functions of MSL require the installation of some open-source external libraries. * '''BOOST''' (portable C++ source libraries) [[http://www.boost.org]] * '''GSL''' (GNU Scientific Library) [[http://www.gnu.org/software/gsl/]] * '''GLPK''' (GNU linear programming kit) [[http://www.gnu.org/software/glpk/]] === How to enable inclusion of the external libraries=== By default MSL will be compiled '''without''' the support of the external libraries and some functionality won't be available. To include the libraries, you need to set some environmental variables. If you use '''bash''', add the following lines to your .bashrc <source lang="bash"> # $MSL_GSL set to "T" if GSL is installed or else to "F" (default) # $MSL_BOOST set to "T" if BOOST is installed or else to "F" (default) # $MSL_GLPK set to "T" if GLPK is installed or else to "F" (default) # $MSL_R set to "T" if R is installed or else to "F" (default) export MSL_GSL=T export MSL_GLPK=T export MSL_BOOST=T export MSL_R=T #export EXTERNAL_LIB_DIR=/usr/lib </source> If you use '''tcsh''', add the following lines to your .cshrc <source lang="text"> # $MSL_GSL set to "T" if GSL is installed or else to "F" (default) # $MSL_BOOST set to "T" if BOOST is installed or else to "F" (default) # $MSL_GLPK set to "T" if GLPK is installed or else to "F" (default) # $MSL_R set to "T" if R is installed or else to "F" (default) setenv MSL_GSL T setenv MSL_GLPK T setenv MSL_BOOST T setenv MSL_R T #setenv EXTERNAL_LIB_DIR /usr/lib </source> The default location of the libraries is '''/usr/lib'''. If you have installed them in a custom location set the $EXTERNAL_LIB_DIR environmental variable to the correct location. === BOOST === The following libraries from the [http://www.boost.org/ Boost C++ Libraries] are used in some MSL objects and programs * Serialization, used for ... in the following objects ** [[MSL_Objects:Atom|Atom]] ** [[MSL_Objects:AtomPointerVector|AtomPointerVector]] ** [[MSL_Objects:CartesianPoint|CartesianPoint]] ** [[MSL_Objects:EnvironmentDatabase|EnvironmentDatabase]] ** [[MSL_Objects:EnvironmentDescriptor|EnvironmentDescriptor]] ** [[MSL_Objects:Frame|Frame]] ** [[MSL_Objects:IcEntry|IcEntry]] ** [[MSL_Objects:InterfaceResidueDescriptor|InterfaceResidueDescriptor]] ** [[MSL_Objects:Line|Line]] ** [[MSL_Objects:Matrix|Matrix]] ** [[MSL_Objects:MoleculeInterfaceDatabase|MoleculeInterfaceDatabase]] ** [[MSL_Objects:PrincipleComponentAnalysis|PrincipleComponentAnalysis]] ** [[MSL_Objects:SphericalPoint|SphericalPoint]] * Archive, used for ... in the following objects ** [[MSL_Objects:Atom|Atom]] ** [[MSL_Objects:AtomPointerVector|AtomPointerVector]] ** [[MSL_Objects:CartesianPoint|CartesianPoint]] ** [[MSL_Objects:EnvironmentDatabase|EnvironmentDatabase]] ** [[MSL_Objects:Frame|Frame]] ** [[MSL_Objects:IcEntry|IcEntry]] ** [[MSL_Objects:InterfaceResidueDescriptor|InterfaceResidueDescriptor]] ** [[MSL_Objects:Line|Line]] ** [[MSL_Objects:Matrix|Matrix]] ** [[MSL_Objects:MoleculeInterfaceDatabase|MoleculeInterfaceDatabase]] ** [[MSL_Objects:PrincipleComponentAnalysis|PrincipleComponentAnalysis]] ** [[MSL_Objects:Selectable|Selectable]] ** [[MSL_Objects:SphericalPoint|SphericalPoint]] * Regex, used for ... in the following objects ** [[MSL_Objects:MslTools|MslTools]] ** [[MSL_Objects:RegEx|RegEx]] * Random, used for ... in the following objects ** [[MSL_Objects:RandomSeqGenerator|RandomSeqGenerator]] Note: if boost is included, version 1.40 (???) or later is required. If '''BOOST''' is enabled, you should see ''-D__BOOST__ -DBOOST_DISABLE_THREADS'' in the compilation command when using make. === GSL === The [[http://www.gnu.org/software/gsl/ GNU Scientific library]] is required by the following objects: * [[MSL_Objects:RandomNumberGenerator | RandomNumberGenerator]] * [[MSL_Objects:GSLMinimizer | GSLMinimizer]] * [[MSL_Objects:MonteCarloOptimization| MonteCarloOptimization]] * [[MSL_Objects:CCD | CCD]] * [[MSL_Objects:BackRub | BackRub]] * [[MSL_Objects:Quench | Quench]] * [[MSL_Objects:SurfaceAreaAndVolume | SurfaceAreaAndVolume]] If '''GSL''' is enabled, you should see ''-D__GSL_'' in the compilation command when using make. === GLPK === The [http://www.gnu.org/software/glpk/ GNU linear programming kit] is required by the [[MSL_Objects:LinearProgrammingOptimization | LinearProgrammingOptimization]] object. If '''GLPK''' is enabled, you should see ''-D__GLPK__'' in the compilation command when using make. === R === The [http://www.r-project.org/ R project] is used by the getDihedrals program. If '''R''' is enabled, you should see ''-D__R__'' in the compilation command when using make. ---- '''[[Tutorial|Back to the tutorial page]]''' [[Category:Tutorial]]

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