IMP::multi_state Namespace Reference

Functionality for handling multi-state models. More...

Detailed Description

Functionality for handling multi-state models.

These are used in IMP to model systems that are found simultaneously in multiple states. For example, a hinge protein may be found in both 'open' and 'closed' forms, and so some experiments conducted on a sample of the protein will return data from both forms. Building a single model that tries to be consistent with all the data will therefore fail - two models need to be constructed.

multi_foxs

Command line tool to enumerate multi-state models with SAXS profiles. See also IMP::foxs for the similar FoXS command line tool.

multi_foxs_combination

Command line tool to enumerate additions (such as glycans or ions) to a model with SAXS profiles. See also IMP::foxs for the similar FoXS command line tool.

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, John A. Tainer, Andrej Sali, “Accurate SAXS profile computation and its assessment by contrast variation experiments”, Biophysical Journal , 2013.

Classes
class	CompareMultiStateModels
	Utility class to help sort MultiStateModel objects. More...
class	EnsembleGenerator
	Enumeration of an ensemble of good scoring MultiStateModels. More...
class	MultiStateModel
	Keep track of multiple states. More...
class	MultiStateModelScore
	Base class for MultiStateModel scoring classes. More...
class	SAXSMultiCombinationScore
class	SAXSMultiStateModelScore

Typedefs
typedef Vector< MultiStateModel >	Ensemble

Functions
double	get_average (const std::vector< double > &v)
std::pair< double, double >	get_average_and_stdev (const std::vector< double > &v)

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 ()
	Return the version of this module, as a string. More...
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::multi_state::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::multi_state::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::multi_state::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::multi_state::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.

std::string IMP::multi_state::get_module_version

(

)

Return the version of this module, as a string.

Note

This function is only available in Python.

Definition at line 5 of file EMageFit/__init__.py.