IMP  2.3.1
The Integrative Modeling Platform
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:

Namespaces

 analysis
 Tools for clustering and cluster analysis.
 
 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.
 
 samplers
 Sampling of the system.
 
 tools
 Miscellaneous utilities.
 

Classes

class  CompositeRestraint
 
class  Resolution
 Add resolution to a particle. More...
 
class  SigmoidRestraintSphere
 
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

RestraintSetcreate_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

model));

This will ensure that the code works when IMP is installed or used via the setup_environment.sh script.