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IMP Reference Guide  develop.d3e3923077,2019/12/11
The Integrative Modeling Platform
IMP::pmi1 Namespace Reference

Legacy PMI1 module to represent, score, sample and analyze models. More...

Detailed Description

Legacy PMI1 module to represent, score, sample and analyze models.

Build Status codecov

This module contains an older version of the PMI module (PMI1) to support legacy published applications. It is no longer under active development and should not be used for new code - for that, see the current PMI module.

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

Maintainers: Riccardo Pellarin, Charles Greenberg, Daniel Saltzberg

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.
 
 io
 Utility classes and functions for reading and storing PMI files.
 
 macros
 Protocols for sampling structures and analyzing them.
 
 
 mmcif
 Support for the mmCIF file format.
 
 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.
 
 tools
 Miscellaneous utilities.
 
 topology
 Set of python classes to create a multi-state, multi-resolution IMP hierarchy.
 

Classes

class  CompositeRestraint
 A restraint for ambiguous cross-linking MS data and multiple state approach. More...
 
class  InternalCoordinatesConstraint
 An example singleton modifier. More...
 
class  MembraneRestraint
 Membrane Restraint. 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

RestraintSetcreate_elastic_network (const Particles &ps, Float dist_cutoff, Float strength)
 Create an elastic network restraint set. More...
 
Float get_bipartite_minimum_sphere_distance (const IMP::core::XYZRs &m1, const IMP::core::XYZRs &m2)
 
Float get_dihedral_angle (const atom::Atom &p1, const atom::Atom &p2, const atom::Atom &p3, const atom::Atom &p4)
 
Floats get_list_of_bipartite_minimum_sphere_distance (const ParticlesTemps &pss)
 

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 one of this module's data files. More...
 
std::string get_example_path (std::string file_name)
 Return the full path to one of this module's example files. More...
 

Function Documentation

RestraintSet* IMP::pmi1::create_elastic_network ( const Particles &  ps,
Float  dist_cutoff,
Float  strength 
)

Create an elastic network restraint set.

Definition at line 26 of file pmi1/utilities.h.

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std::string IMP::pmi1::get_data_path ( std::string  file_name)

Return the full path to one of this module's data files.

To read the data file "data_library" that was placed in the data directory of this module, do something like

std::ifstream in(IMP::pmi1::get_data_path("data_library"));

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

Note
Each module has its own data directory, so be sure to use this function from the correct module.
std::string IMP::pmi1::get_example_path ( std::string  file_name)

Return the full path to one of this module's example files.

To read the example file "example_protein.pdb" that was placed in the examples directory of this module, do something like

std::ifstream in(IMP::pmi1::get_example_path("example_protein.pdb"));

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

Note
Each module has its own example directory, so be sure to use this function from the correct module.