IMP::saxs Namespace Reference

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Detailed Description

This module adds small angle x-ray scatter support to IMP.

Author:

Dina Schneidman, Seung Joong Kim

Version:

1.0

Examples

Examples can be found on the IMP.saxs examples page.

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:

• Daniel Russel, Keren Lasker, Ben Webb, Dina Schneidman, Javier Velazquez-Muriel, Andrej Sali, “Integrative assembly modeling using IMP”, submitted, 2010. This paper provides an overview of the key concepts in IMP and how to apply them to biological problems.
• Frank Alber, Friedrich Foerster, Dmitry Korkin, Maya Topf, Andrej Sali, “Integrating diverse data for structure determination of macromolecular assemblies”, Annual Review of Biochemistry, 2008. This paper provides a review of the integrative structure determination methodology and various data sources that can be used.

Data Structures
class	DeltaDistributionFunction
class	Distribution
class	FormFactorTable
class	Profile
class	RadialDistributionFunction
class	Restraint
	Calculate score based on fit to SAXS profile. More...
class	Score
class	SolventAccessibleSurface
Functions
Float	compute_max_distance (const Particles &particles1, const Particles &particles2)
Float	compute_max_distance (const Particles &particles)
	compute max distance
void	copy_coordinates (const Particles &particles, std::vector< algebra::VectorD< 3 > > &coordinates)
void	copy_data (const Particles &particles, FormFactorTable *ff_table, std::vector< algebra::VectorD< 3 > > &coordinates, Floats &form_factors)
FormFactorTable *	default_form_factor_table ()
std::string	get_data_path (std::string file_name)
	Return the path to installed data for this module.
std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module.
std::string	get_module_name ()
const VersionInfo &	get_module_version_info ()
Float	radius_of_gyration (const Particles &particles)
	compute radius_of_gyration
Float	sinc (Float value)

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Function Documentation

Float IMP::saxs::compute_max_distance	(	const Particles &	particles1,
		const Particles &	particles2
	)

compute max distance between pairs of particles one from particles1 and the other from particles2

std::string IMP::saxs::get_data_path

(

std::string

file_name

)

Return the path to installed data for this module.

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 tools/imppy.sh script.

std::string IMP::saxs::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 tools/imppy.sh script.