IMP::restrainer Namespace Reference

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Detailed Description

This module provides a higher level interface for using experimental proteomics data with IMP.

Author:

Elina Tjioe, Keren Lasker, Jeremy Phillips, Ben Webb

Version:

1.0

Overview:

Introduction

Restrainer is an IMP module that provides convenient way of inputting molecule definition and experimental data into IMP. This module will take experimental data in XML format, and translate it into IMP restraints to construct models at a variety of different resolutions or levels.

The XML input data is divided into 3 parts:

1. Representation
   • Each component in the system can have either atomic or geometric shape representation.
2. RestraintSet
   • Restraint can be added for each component, between and among components in the representation.
3. Display
   • Colors for the representation components can be defined and an output file can be generated in chimera format.

The XML schema is provided to check the validation of the input data. The visualization of the XML schema can be seen here.

To check if the XML files are valid use the schema.xsd which can be found as part of the restrainer data.

xmllint --schema schema.xsd --noout *.xml

The process of preparing the input data for restrainer can be best shown using simple examples.

Examples

Examples can be found on the IMP.restrainer 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	Display
	A class to display the configuration. More...
class	Representation
	Store Representation. More...
class	Restraint
	Store Restraint. More...
class	XMLDisplay
	Construct Display from XML file. More...
class	XMLRepresentation
	Construct Representation from XML file. More...
class	XMLRestraint
	Construct Restraint from XML file. More...
Functions
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 ()

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Function Documentation

std::string IMP::restrainer::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::restrainer::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.