IMP Reference Guide
2.8.0
The Integrative Modeling Platform
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Miscellaneous functionality that is not expected to be used by many IMP users. More...
Miscellaneous functionality that is not expected to be used by many IMP users.
As a result, the code contained in this module may be poorly tested, liable to change or experimental in nature.
In particular, other modules should not depend on IMP.misc (e.g. don't create a class in another module that derives from one in IMP.misc. If you find yourself relying on such functionality, discuss moving it to a specialized module or something like IMP.core or IMP.atom).
Author(s): Daniel Russel
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 | CommonEndpointPairFilter |
Return true for any pair of bonds sharing an endpoint. More... | |
class | CustomXYZR |
A decorator for a particle with x,y,z coordinates and a radius. More... | |
class | DecayPairContainerOptimizerState |
Maintain a pair container with a decaying list of pairs. More... | |
class | FreelyJointedChain |
Score on end-to-end distance of freely jointed chain. More... | |
class | LogPairScore |
Track the pairs of particles passed. More... | |
class | LowestRefinedPairScore |
Refine both particles with the refiner and score on the lowest pair. More... | |
class | MetricClosePairsFinder |
class | SoftCylinderPairScore |
Apply a function to the distance between the cylinders defined by two bonds. More... | |
class | StateAdaptor |
Allow OptimizerStates to be used as ScoreStates. More... | |
class | WormLikeChain |
Worm-like-chain energy for polymer chains. More... | |
Typedefs | |
typedef IMP::Vector< CustomXYZR > | CustomXYZRs |
Functions | |
template<class LowerBound , class UpperBound > | |
core::ClosePairsFinder * | create_metric_close_pairs_finder (LowerBound lb, UpperBound ub) |
double | get_distance (CustomXYZR a, CustomXYZR b) |
Compute the distance between a pair of particles. More... | |
const algebra::Sphere3D | get_sphere_d_geometry (CustomXYZR d) |
void | set_sphere_d_geometry (CustomXYZR d, const algebra::Sphere3D &v) |
Standard module functions | |
All | |
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... | |
core::ClosePairsFinder* IMP::misc::create_metric_close_pairs_finder | ( | LowerBound | lb, |
UpperBound | ub | ||
) |
Create a new MetricClosePairsFinder, handling types.
Definition at line 189 of file MetricClosePairsFinder.h.
std::string IMP::misc::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.
double IMP::misc::get_distance | ( | CustomXYZR | a, |
CustomXYZR | b | ||
) |
Compute the distance between a pair of particles.
Definition at line 85 of file CustomXYZR.h.
std::string IMP::misc::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.
const algebra::Sphere3D IMP::misc::get_sphere_d_geometry | ( | CustomXYZR | d | ) |
See generic geometry for more information.
Definition at line 90 of file CustomXYZR.h.
void IMP::misc::set_sphere_d_geometry | ( | CustomXYZR | d, |
const algebra::Sphere3D & | v | ||
) |
See generic geometry for more information.
Definition at line 95 of file CustomXYZR.h.