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IMP Reference Guide  develop.e1fe35f,2019/09/16
The Integrative Modeling Platform
IMP::misc Namespace Reference

Miscellaneous functionality that is not expected to be used by many IMP users. More...

Detailed Description

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).

Info

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< CustomXYZRCustomXYZRs
 

Functions

template<class LowerBound , class UpperBound >
core::ClosePairsFindercreate_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 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

template<class LowerBound , class UpperBound >
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

std::ifstream in(IMP::misc::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.
double IMP::misc::get_distance ( CustomXYZR  a,
CustomXYZR  b 
)

Compute the distance between a pair of particles.

See Also
XYZR

Definition at line 85 of file CustomXYZR.h.

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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

std::ifstream in(IMP::misc::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.
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.

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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.

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