IMP::npc Namespace Reference

Restraints designed for modeling the Nuclear Pore Complex (NPC) More...

Detailed Description

Restraints designed for modeling the Nuclear Pore Complex (NPC)

NPC complex

This modules provides special-purpose restraints for modeling the Nuclear Pore Complex (NPC). They may also be useful for other modeling applications.

Information

Author(s): Elina Tjioe, Frank Alber, Seung Joong Kim, Ben Webb

Maintainer: benmwebb

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:

• Frank Alber*, Svetlana Dokudovskaya*, et al, The Molecular Architecture of the Nuclear Pore Complex, Nature 450, 695-701, 2007.
• See main IMP papers list.

Classes
class	AssemblySymmetryByDihedralRestraint
	Restrain two interparticle dihedrals to be the same. More...
class	AssemblySymmetryByDistanceRestraint
	Restrain two interparticle distances to be the same. More...
class	CompositeRestraint
	Score a set of particles that form a composite. More...
class	MembraneExclusionRestraint
	Try to keep particles away from a membrane. More...
class	MembraneSurfaceLocationConditionalRestraint
	Try to keep one set of particles localized on a membrane surface. More...
class	MembraneSurfaceLocationRestraint
	Try to keep particles localized on a membrane surface. More...
class	MinimumSphereDistancePairScore
	Apply a UnaryFunction to the minimum transformed sphere-sphere distance. More...
class	PerinuclearVolumeLocationRestraint
	Try to keep particles on the perinuclear side of a membrane. More...
class	PoreSideVolumeLocationRestraint
	Try to keep particles on the pore side of a membrane. More...
class	ProteinChainRestraint
	Try to keep particle surfaces in contact in a chain. More...
class	ProteinContactRestraint
	Try to keep all particle surfaces in contact. More...
class	ProteinProximityRestraint
	Restrain a set of particles to be proximate to each other. More...
class	XYRadialPositionLowerRestraint
	Restrain particles by their distance from the z axis in the xy plane. More...
class	XYRadialPositionRestraint
	Restrain particles by their distance from the z axis in the xy plane. More...
class	XYRadialPositionUpperRestraint
	Restrain particles by their distance from the z axis in the xy plane. More...
class	YAxialPositionLowerRestraint
	Restrain particles by their y coordinate. More...
class	YAxialPositionRestraint
	Restrain particles by their y coordinate. More...
class	YAxialPositionUpperRestraint
	Restrain particles by their y coordinate. More...
class	ZAxialPositionLowerRestraint
	Restrain particles by their z coordinate. More...
class	ZAxialPositionRestraint
	Restrain particles by their z coordinate. More...
class	ZAxialPositionUpperRestraint
	Restrain particles by their z coordinate. 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 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

std::string IMP::npc::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::npc::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::npc::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::npc::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.