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IMP Reference Guide  develop.cd20b1e321,2019/12/14
The Integrative Modeling Platform
IMP::foxs Namespace Reference

Determine small angle X-ray (SAXS) profiles. More...

Detailed Description

Determine small angle X-ray (SAXS) profiles.

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:

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 one of this module's data files. More...
 
std::string get_example_path (std::string file_name)
 Return the full path to one of this module's example files. More...
 

Function Documentation

std::string IMP::foxs::get_data_path ( std::string  file_name)

Return the full path to one of this module's data files.

To read the data file "data_library" that was placed in the data directory of this module, do something like

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

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

Note
Each module has its own data directory, so be sure to use this function from the correct module.
std::string IMP::foxs::get_example_path ( std::string  file_name)

Return the full path to one of this module's example files.

To read the example file "example_protein.pdb" that was placed in the examples directory of this module, do something like

std::ifstream in(IMP::foxs::get_example_path("example_protein.pdb"));

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

Note
Each module has its own example directory, so be sure to use this function from the correct module.