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IMP Reference Guide  develop.031dafb4d2,2024/05/21
The Integrative Modeling Platform
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:

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  OverallPositionRestraint
 Restrain particle to a specific position. 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  SlabWithPore
 
class  SlabWithSphericalIndent
 A decorator for a particle that represents a slab containing a spherical cap indent. More...
 
class  SlabWithSphericalIndentGeometry
 
class  SlabWithSphericalIndentMBMScore
 
class  SlabWithToroidalPore
 
class  SlabWithToroidalPoreGoPairScore
 apply a harmonic to the distance between a particle and the normal to toroidal membrane More...
 
class  SlabWithToroidalPoreMBMScore
 apply harmonic walls to the distance between a particle and the normal to toroidal membrane More...
 
class  SlabWithToroidalPoreWireGeometry
 A decorator for a particle that represents a toroidal pore. More...
 
class  SphericalIndentSurfaceDepthPairScore
 
class  ToroidalPoreSurfaceDepthPairScore
 apply repulsive force to the distance between a particle and the normal to toroidal membrane More...
 
class  XAxialPositionLowerRestraint
 Restrain particles by their x coordinate. More...
 
class  XAxialPositionRestraint
 Restrain particles by their x coordinate. More...
 
class  XAxialPositionUpperRestraint
 Restrain particles by their x coordinate. 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...
 

Typedefs

typedef IMP::Vector< SlabWithPoreSlabsWithPores
 
typedef IMP::Vector
< SlabWithToroidalPore
SlabsWithToroidalPores
 
typedef IMP::Vector
< IMP::Pointer
< SlabWithSphericalIndentMBMScore > > 
SlabWithSphericalIndentMBMScores
 
typedef IMP::Vector
< IMP::WeakPointer
< SlabWithSphericalIndentMBMScore > > 
SlabWithSphericalIndentMBMScoresTemp
 
typedef IMP::Vector
< SlabWithSphericalIndent
SlabWithSphericalIndents
 
typedef IMP::Vector
< IMP::Pointer
< SlabWithToroidalPoreGoPairScore > > 
SlabWithToroidalPoreGoPairScores
 
typedef IMP::Vector
< IMP::WeakPointer
< SlabWithToroidalPoreGoPairScore > > 
SlabWithToroidalPoreGoPairScoresTemp
 
typedef IMP::Vector
< IMP::Pointer
< SlabWithToroidalPoreMBMScore > > 
SlabWithToroidalPoreMBMScores
 
typedef IMP::Vector
< IMP::WeakPointer
< SlabWithToroidalPoreMBMScore > > 
SlabWithToroidalPoreMBMScoresTemp
 
typedef IMP::Vector
< IMP::Pointer
< SphericalIndentSurfaceDepthPairScore > > 
SphericalIndentSurfaceDepthPairScores
 
typedef IMP::Vector
< IMP::WeakPointer
< SphericalIndentSurfaceDepthPairScore > > 
SphericalIndentSurfaceDepthPairScoresTemp
 
typedef IMP::Vector
< IMP::Pointer
< ToroidalPoreSurfaceDepthPairScore > > 
ToroidalPoreSurfaceDepthPairScores
 
typedef IMP::Vector
< IMP::WeakPointer
< ToroidalPoreSurfaceDepthPairScore > > 
ToroidalPoreSurfaceDepthPairScoresTemp
 

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...
 

Typedef Documentation

A vector of reference-counting object pointers.

Definition at line 53 of file SlabWithSphericalIndentMBMScore.h.

A vector of weak (non reference-counting) pointers to specified objects.

See Also
SlabWithSphericalIndentMBMScore

Definition at line 53 of file SlabWithSphericalIndentMBMScore.h.

A vector of reference-counting object pointers.

Definition at line 53 of file SlabWithToroidalPoreGoPairScore.h.

A vector of weak (non reference-counting) pointers to specified objects.

See Also
SlabWithToroidalPoreGoPairScore

Definition at line 53 of file SlabWithToroidalPoreGoPairScore.h.

A vector of reference-counting object pointers.

Definition at line 53 of file SlabWithToroidalPoreMBMScore.h.

A vector of weak (non reference-counting) pointers to specified objects.

See Also
SlabWithToroidalPoreMBMScore

Definition at line 53 of file SlabWithToroidalPoreMBMScore.h.

A vector of weak (non reference-counting) pointers to specified objects.

See Also
SphericalIndentSurfaceDepthPairScore

Definition at line 53 of file SphericalIndentSurfaceDepthPairScore.h.

A vector of reference-counting object pointers.

Definition at line 53 of file ToroidalPoreSurfaceDepthPairScore.h.

A vector of weak (non reference-counting) pointers to specified objects.

See Also
ToroidalPoreSurfaceDepthPairScore

Definition at line 53 of file ToroidalPoreSurfaceDepthPairScore.h.

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