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IMP Reference Guide
2.22.0
The Integrative Modeling Platform
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Restraints designed for modeling the Nuclear Pore Complex (NPC) More...
Restraints designed for modeling the Nuclear Pore Complex (NPC)
This modules provides special-purpose restraints for modeling the Nuclear Pore Complex (NPC). They may also be useful for other modeling applications.
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... | |
Standard module functions | |
All | |
| 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 IMP::Vector<IMP::Pointer< SlabWithSphericalIndentMBMScore > > IMP::npc::SlabWithSphericalIndentMBMScores |
A vector of reference-counting object pointers.
Definition at line 53 of file SlabWithSphericalIndentMBMScore.h.
| typedef IMP::Vector<IMP::WeakPointer< SlabWithSphericalIndentMBMScore > > IMP::npc::SlabWithSphericalIndentMBMScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 53 of file SlabWithSphericalIndentMBMScore.h.
| typedef IMP::Vector<IMP::Pointer< SlabWithToroidalPoreGoPairScore > > IMP::npc::SlabWithToroidalPoreGoPairScores |
A vector of reference-counting object pointers.
Definition at line 53 of file SlabWithToroidalPoreGoPairScore.h.
| typedef IMP::Vector<IMP::WeakPointer< SlabWithToroidalPoreGoPairScore > > IMP::npc::SlabWithToroidalPoreGoPairScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 53 of file SlabWithToroidalPoreGoPairScore.h.
| typedef IMP::Vector<IMP::Pointer< SlabWithToroidalPoreMBMScore > > IMP::npc::SlabWithToroidalPoreMBMScores |
A vector of reference-counting object pointers.
Definition at line 53 of file SlabWithToroidalPoreMBMScore.h.
| typedef IMP::Vector<IMP::WeakPointer< SlabWithToroidalPoreMBMScore > > IMP::npc::SlabWithToroidalPoreMBMScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 53 of file SlabWithToroidalPoreMBMScore.h.
| typedef IMP::Vector<IMP::Pointer< SphericalIndentSurfaceDepthPairScore > > IMP::npc::SphericalIndentSurfaceDepthPairScores |
A vector of reference-counting object pointers.
Definition at line 53 of file SphericalIndentSurfaceDepthPairScore.h.
| typedef IMP::Vector<IMP::WeakPointer< SphericalIndentSurfaceDepthPairScore > > IMP::npc::SphericalIndentSurfaceDepthPairScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 53 of file SphericalIndentSurfaceDepthPairScore.h.
| typedef IMP::Vector<IMP::Pointer< ToroidalPoreSurfaceDepthPairScore > > IMP::npc::ToroidalPoreSurfaceDepthPairScores |
A vector of reference-counting object pointers.
Definition at line 53 of file ToroidalPoreSurfaceDepthPairScore.h.
| typedef IMP::Vector<IMP::WeakPointer< ToroidalPoreSurfaceDepthPairScore > > IMP::npc::ToroidalPoreSurfaceDepthPairScoresTemp |
A vector of weak (non reference-counting) pointers to specified objects.
Definition at line 53 of file ToroidalPoreSurfaceDepthPairScore.h.
| 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
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.
| 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
This will ensure that the code works both when IMP is installed or if used via the setup_environment.sh script.
| std::string IMP::npc::get_module_version | ( | ) |
Return the version of this module, as a string.
Definition at line 5 of file EMageFit/__init__.py.