IMP  2.2.1
The Integrative Modeling Platform
IMP::misc Namespace Reference

See IMP.misc for more information.

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  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::base::Vector
< CustomXYZR
CustomXYZRs
 

Functions

template<class LowerBound , class UpperBound >
core::ClosePairsFindercreate_metric_close_pairs_finder (LowerBound lb, UpperBound ub)
 
std::string get_data_path (std::string file_name)
 Return the full path to installed data. More...
 
double get_distance (CustomXYZR a, CustomXYZR b)
 Compute the distance between a pair of particles. More...
 
std::string get_example_path (std::string file_name)
 Return the path to installed example data for this module. More...
 
const algebra::Sphere3D get_sphere_d_geometry (CustomXYZR d)
 
void set_sphere_d_geometry (CustomXYZR d, const algebra::Sphere3D &v)
 

Standard module methods

All IMP modules have a set of standard methods to help get information about the module and about files associated with the module.

std::string get_module_version ()
 
std::string get_module_name ()
 

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 197 of file MetricClosePairsFinder.h.

std::string IMP::misc::get_data_path ( std::string  file_name)

Each module has its own data directory, so be sure to use the version of this function in the correct module. To read the data file "data_library" that was placed in the data directory of module "mymodule", do something like

std::ifstream in(IMP::mymodule::get_data_path("data_library"));

This will ensure that the code works when IMP is installed or used via the setup_environment.sh script.

double IMP::misc::get_distance ( CustomXYZR  a,
CustomXYZR  b 
)

See XYZR

Definition at line 85 of file CustomXYZR.h.

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std::string IMP::misc::get_example_path ( std::string  file_name)

Each module has its own example directory, so be sure to use the version of this function in the correct module. For example to read the file example_protein.pdb located in the examples directory of the IMP::atom module, do

model));

This will ensure that the code works when IMP is installed or 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.

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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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