IMP
2.3.1
The Integrative Modeling Platform
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Python classes to represent, score, sample and analyze models. More...
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 | |
RestraintSet * | create_elastic_network (const Particles &ps, Float dist_cutoff, Float strength) |
Create an elastic network restraint set. More... | |
Standard module functions | |
All | |
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... | |
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.
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
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
This will ensure that the code works when IMP
is installed or used via the setup_environment.sh
script.