IMP::gsl Namespace Reference

Several general purpose optimizers from the GNU Scientific Library (GSL). More...

Detailed Description

Several general purpose optimizers from the GNU Scientific Library (GSL).

The most useful is probably the IMP::gsl::Simplex optimizer. Note that GSL is licensed under the GPLv3, which requires that all other software linked with it also be licensed under a GPL-compatible license.

GSL

The IMP.gsl module requires GSL. It is available as a prebuilt package on all supported platforms. Note that GSL is distributed under the GPL and so cannot be used in C++ applications with certain other dependencies such as CGAL.

Info

Author(s): Daniel Russel

Maintainer: benmwebb

License: GPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU General Public License as published by the Free Software Foundation; either version 3 of the License, or (at your option) any later version.

Publications:

• See main IMP papers list.

Classes
class	ConjugateGradients
	A conjugate gradients optimizer taken from GSL. More...
class	GSLOptimizer
	A base class for GSL-based optimizers. More...
class	QuasiNewton
	A quasi-Newton optimizer taken from GSL. More...
class	Simplex
	A simplex optimizer taken from GSL. More...

Typedefs
typedef IMP::base::Vector < IMP::base::Pointer < GSLOptimizer > >	GSLOptimizers
typedef IMP::base::Vector < IMP::base::WeakPointer < GSLOptimizer > >	GSLOptimizersTemp

Standard module functions
All IMP modules have a set of standard functions to help get information about the module and about files associated with the module.
std::string	get_module_version ()
std::string	get_module_name ()
std::string	get_data_path (std::string file_name)
	Return the full path to installed data. More...
std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module. More...

Typedef Documentation

typedef IMP::base::Vector<IMP::base::Pointer< GSLOptimizer > > IMP::gsl::GSLOptimizers

Store a set of objects.

Definition at line 56 of file GSLOptimizer.h.

typedef IMP::base::Vector<IMP::base::WeakPointer< GSLOptimizer > > IMP::gsl::GSLOptimizersTemp

Pass a set of objects.

See Also

GSLOptimizer

Definition at line 56 of file GSLOptimizer.h.

Function Documentation

std::string IMP::gsl::get_data_path

(

std::string

file_name

)

Return the full path to installed data.

Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data directory of module "mymodule", do something like

std::ifstream in(IMP::mymodule::get_data_path("data_library"));

This will ensure that the code works when IMP is installed or used via the setup_environment.sh script.

std::string IMP::gsl::get_example_path

(

std::string

file_name

)

Return the path to installed example data for this module.

Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb located in the examples directory of the IMP::atom module, do

 IMP::atom::read_pdb(IMP::atom::get_example_path("example_protein.pdb",
model));

This will ensure that the code works when IMP is installed or used via the setup_environment.sh script.