IMP::test Namespace Reference

Support for running tests of IMP functionality. More...

Detailed Description

Support for running tests of IMP functionality.

Most of this is centered around the Python unittest module.

Info

Author(s): Ben Webb, Daniel Russel

Maintainer: benmwebb

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:

• See main IMP papers list.

Classes
class	ApplicationTestCase
	Super class for simple IMP application test cases. More...
class	DirectorObjectChecker
	Check to make sure the number of director references is as expected. More...
class	RefCountChecker
	Check to make sure the number of C++ object references is as expected. More...
class	RunInTempDir
	Simple RAII-style class to run in a temporary directory. More...
class	TempDir
	Simple RAII-style class to make a temporary directory. More...
class	TestCase
	Super class for IMP test cases. More...

Functions
def	numerical_derivative
	Calculate the derivative of the single-value function func at point val. More...
def	xyz_numerical_derivatives
	Calculate the x,y and z derivatives of model's scoring function on the xyz particle. More...

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 ()
std::string	get_module_name ()
std::string	get_data_path (std::string file_name)
	Return the full path to installed data. More...
std::string	get_example_path (std::string file_name)
	Return the path to installed example data for this module. More...

Function Documentation

std::string IMP::test::get_data_path

(

std::string

file_name

)

Return the full path to installed data.

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 setup_environment.sh script.

std::string IMP::test::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 setup_environment.sh script.

def IMP.test.numerical_derivative	(		func,
			val,
			step
	)

Calculate the derivative of the single-value function func at point val.

The derivative is calculated using simple finite differences starting with the given step; Richardson extrapolation is then used to extrapolate the derivative at step=0.

Definition at line 337 of file test/__init__.py.

def IMP.test.xyz_numerical_derivatives	(		model,
			xyz,
			step
	)

Calculate the x,y and z derivatives of model's scoring function on the xyz particle.

The derivatives are approximated numerically using the numerical_derivatives() function.

Definition at line 373 of file test/__init__.py.