Detailed Description

This module provides helper functions for biological systems.

See the ef systems_index "biological systems page" for a more complete description of what an IMP protocol should look like.

Author(s)

Daniel Russel

Version

SVN 8931

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 Velázquez-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.

Functions
def	get_data_input_path
	Get the path where the current script should find data files.
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.
def	get_input_path
	Get the path where the current script should find output of the last script.
def	get_is_test
	Return whether this run is called with --test.
std::string	get_module_name ()
const VersionInfo &	get_module_version_info ()
def	get_output_path
	Get the path to where the current script should write output files.
def	get_sample_parameters
	Return the index and the number of parts to divide the job in to.

Function Documentation

std::string IMP::system::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::system::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.

def IMP::system::get_is_test ( )

Return whether this run is called with --test.

Scripts that use this can't don't expect -j and -n and so an error will be thrown if they are passed.

def IMP::system::get_sample_parameters ( )

Return the index and the number of parts to divide the job in to.