IMP::foxs Namespace Reference

Detailed Description

foxs

Determine small angle X-ray (SAXS) profiles. The IMP.saxs module contains functions that, given an atomic protein structure, can calculate its SAXS profile using the Debye formula, and then fit this profile against the experimentally determined one. FoXS is a simple command line interface to this functionality which takes as input a number of PDB files and/or SAXS profiles. There is also a web server available.

Examples:

• Determination of a Nup133 structure

Info

Author(s): Dina Schneidman

Maintainer: duhovka

License: LGPL This library is free software; you can redistribute it and/or modify it under the terms of the GNU Lesser General Public License as published by the Free Software Foundation; either version 2 of the License, or (at your option) any later version.

Publications:

• Dina Schneidman-Duhovny, Michael Hammel, Andrej Sali, “FoXS: A Web server for Rapid Computation and Fitting of SAXS Profiles”, Nucleic Acids Research, 2010.
• Dina Schneidman-Duhovny, Michael Hammel, John A. Tainer, Andrej Sali, “Accurate SAXS profile computation and its assessment by contrast variation experiments”, Biophysical Journal , 2013.

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...

Function Documentation

std::string IMP::foxs::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::foxs::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.