IMP::helper Namespace Reference

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Detailed Description

This module provides high level functionality to assist in setting up and manipulating models.

Author:

Daniel Russel, Elina Tjioe, Keren Lasker, Ben Webb

Version:

1.0

Overview:

This module contains a variety of functionality which encapsulate pieces of standard protocols involving a variety of other modules.

Examples

Examples can be found on the IMP.helper 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	SimpleConnectivity
	Simple connectivity restraint. More...
class	SimpleDiameter
	Simple diameter restraint. More...
class	SimpleDistance
	Simple distance restraint between two particles. More...
class	SimpleEMFit
	Simple EM fit restraint. More...
class	SimpleExcludedVolume
	Simple excluded volume restraint. More...
Functions
SimpleConnectivity	create_simple_connectivity_on_rigid_bodies (const core::RigidBodies &rbs, Refiner *ref=IMP::core::internal::get_rigid_members_refiner())
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 ()
em::DensityMap *	load_em_density_map (char const *map_fn, float spacing, float resolution)
core::RigidBodies	set_rigid_bodies (atom::Hierarchies const &mhs)

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Function Documentation

std::string IMP::helper::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::helper::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.

em::DensityMap* IMP::helper::load_em_density_map	(	char const *	map_fn,
		float	spacing,
		float	resolution
	)

Load EM density file (.mrc or .em file).