IMP::system Namespace Reference

---

Detailed Description

This module provides helper functions for biological systems.

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

Author(s): Daniel Russel

Version: SVN.r14091

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, “Putting the pieces together: integrative structure determination of macromolecular assemblies”, PLoS Biology, 2012. 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.
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.
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

def IMP.system.get_data_input_path

(

name

)

Get the path where the current script should find data files.

def IMP.system.get_input_path

(

name

)

Get the path where the current script should find output of the last 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_output_path

(

name

)

Get the path to where the current script should write output files.

def IMP.system.get_sample_parameters

(

)

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