IMP::pmi Namespace Reference

Python classes to represent, score, sample and analyze models. More...

Detailed Description

Python classes to represent, score, sample and analyze models.

The intention of this module is to provide a variety of high-level Python classes to simplify the construction of a modeling protocol in IMP. One recent use of PMI is the modeling of the Nup84 subcomplex of the nuclear pore complex.

This module is still under heavy development, and should be considered experimental.

See also the PMI changelog.

Author(s): Riccardo Pellarin, Peter Cimermancic, Daniel Russel, Charles Greenberg, Ben Webb, Elina Tjioe, Seung Joong Kim, Max Bonomi, Yannick Spill

Maintainer: Riccardo Pellarin

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.

Namespaces
	analysis
	Tools for clustering and cluster analysis.
	dof
	Handling of degrees of freedom.
	io
	Utility classes and functions for reading and storing PMI files.
	macros
	Protocols for sampling structures and analyzing them.
	nonmaintained
	Nonmaintained code.
	output
	Classes for writing output files and processing them.
	representation
	Representation of the system.
	restraints
	Classes to handle different kinds of restraints.
	samplers
	Sampling of the system.
	sampling_tools
	Useful tools for setting up sampling.
	tools
	Miscellaneous utilities.
	topology
	Set up of system representation from topology files.

Classes
class	CompositeRestraint
	A restraint for ambiguous cross-linking MS data and multiple state approach. More...
class	Resolution
	Add resolution to a particle. More...
class	SigmoidRestraintSphere
	Simple sigmoidal score calculated between sphere surfaces. More...
class	Symmetric
	Add symmetric attribute to a particle. More...
class	TransformMover
	Modify the transformation of a rigid body. More...
class	Uncertainty
	Add uncertainty to a particle. More...

Functions
RestraintSet *	create_elastic_network (const Particles &ps, Float dist_cutoff, Float strength)
	Create an elastic network restraint set. 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

RestraintSet* IMP::pmi::create_elastic_network	(	const Particles &	ps,
		Float	dist_cutoff,
		Float	strength
	)

Create an elastic network restraint set.

Definition at line 19 of file utilities.h.

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std::string IMP::pmi::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::pmi::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.