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.

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:

• See main IMP papers list.

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.
	metadata
	Classes for attaching metadata to PMI objects.
	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
RestraintSet *	create_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 ()
	Return the version of this module, as a string. More...
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.

std::string IMP::pmi1::get_module_version

(

)

Return the version of this module, as a string.

Note

This function is only available in Python.

Definition at line 5 of file EMageFit/__init__.py.