IMP  2.1.0
The Integrative Modeling Platform
IMP::restrainer Namespace Reference

See IMP.restrainer for more information.

Classes

class  Display
 A class to display the configuration. More...
 
class  Representation
 Store Representation. More...
 
class  Restraint
 Store Restraint. More...
 
class  SimpleConnectivity
 Simple connectivity restraint. More...
 
class  SimpleDiameter
 Simple diameter restraint. More...
 
class  SimpleDistance
 Simple distance restraint between two particles. More...
 
class  SimpleEMFit
 Simple EM fit restraint. More...
 
class  SimpleExcludedVolume
 Simple excluded volume restraint. More...
 
class  XMLDisplay
 Construct Display from XML file. More...
 
class  XMLRepresentation
 Construct Representation from XML file. More...
 
class  XMLRestraint
 Construct Restraint from XML file. More...
 

Typedefs

typedef IMP::base::Vector
< SimpleConnectivity
SimpleConnectivities
 
typedef IMP::base::Vector
< SimpleDiameter
SimpleDiameters
 
typedef IMP::base::Vector
< SimpleDistance
SimpleDistances
 
typedef IMP::base::Vector
< SimpleEMFit
SimpleEMFits
 
typedef IMP::base::Vector
< SimpleExcludedVolume
SimpleExcludedVolumes
 

Functions

SimpleConnectivity create_simple_connectivity_on_molecules (const atom::Hierarchies &mhs)
 
SimpleConnectivity create_simple_connectivity_on_rigid_bodies (const core::RigidBodies &rbs, Refiner *ref=IMP::core::internal::get_rigid_members_refiner())
 
SimpleDiameter create_simple_diameter (const kernel::Particles &ps, Float diameter)
 
SimpleDistance create_simple_distance (const kernel::Particles &ps)
 
SimpleEMFit create_simple_em_fit (atom::Hierarchies const &mhs, em::DensityMap *dmap)
 
SimpleEMFit create_simple_em_fit (atom::Hierarchy const &mh, em::DensityMap *dmap)
 Creates EM FitRestraint. More...
 
SimpleExcludedVolume create_simple_excluded_volume_on_molecules (const atom::Hierarchies &mhs)
 
SimpleExcludedVolume create_simple_excluded_volume_on_rigid_bodies (const core::RigidBodies &rbs, Refiner *ref=IMP::core::internal::get_rigid_members_refiner())
 
std::string get_data_path (std::string file_name)
 Return the full path to installed data. More...
 
std::string get_example_path (std::string file_name)
 Return the path to installed example data for this module. More...
 
em::DensityMapload_em_density_map (char const *map_fn, float spacing, float resolution)
 
core::RigidBodies set_rigid_bodies (atom::Hierarchies const &mhs)
 

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 ()
 

Typedef Documentation

Pass or store a set of SimpleDiameter .

Definition at line 373 of file simplify_restraint.h.

Pass or store a set of SimpleDistance .

Definition at line 297 of file simplify_restraint.h.

Pass or store a set of SimpleEMFit .

Definition at line 459 of file simplify_restraint.h.

Function Documentation

SimpleConnectivity IMP::restrainer::create_simple_connectivity_on_molecules ( const atom::Hierarchies &  mhs)

Creates ConnectivityRestraint on molecules using LowestRefinedPairScore and LeavesRefiner.

See Also
LowestRefinedPairScore
SphereDistancePairScore
HarmonicUpperBound
LeavesRefiner See SimpleConnectivity
SimpleConnectivity IMP::restrainer::create_simple_connectivity_on_rigid_bodies ( const core::RigidBodies &  rbs,
Refiner *  ref = IMP::core::internal::get_rigid_members_refiner() 
)

Creates ConnectivityRestraint on rigid bodies.

Note
Having the default be RigidMembersRefiner is most likely a bad idea, but it is needed to make things work. The refiner should probably be exposed, otherwise this method cannot be used with the rigid bodies created from molecular hierarchies, which is kind of an unintuitive result. A better solution may be to ensure that everything is an atom.Hierarchy and use the LeavesRefiner implicitly.
SimpleDiameter IMP::restrainer::create_simple_diameter ( const kernel::Particles &  ps,
Float  diameter 
)

Creates DiameterRestraint using HarmonicUpperBound scoring function as default.

Parameters
[in]psPointer to particles in diameter restraint.
[in]diameterDiameter.
See Also
ListSingletonContainer See SimpleDiameter
SimpleDistance IMP::restrainer::create_simple_distance ( const kernel::Particles &  ps)

Creates DistanceRestraint using HarmonicUpperBound scoring function as default.

Parameters
[in]psPointer to two particles in distance restraint. See SimpleDistance
SimpleEMFit IMP::restrainer::create_simple_em_fit ( atom::Hierarchies const &  mhs,
em::DensityMap *  dmap 
)

Creates EM FitRestraint.

See Also
FitRestraint
DensityMap See SimpleEMFit
SimpleEMFit IMP::restrainer::create_simple_em_fit ( atom::Hierarchy const &  mh,
em::DensityMap *  dmap 
)
Parameters
[in]mha molecule to fit in the density
[in]dmapthe density map
See Also
FitRestraint
DensityMap See SimpleEMFit
SimpleExcludedVolume IMP::restrainer::create_simple_excluded_volume_on_molecules ( const atom::Hierarchies &  mhs)

Creates ExcludedVolumeRestraint using RigidMembersRefiner.

See Also
RigidMembersRefiner See SimpleExcludedVolume
SimpleExcludedVolume IMP::restrainer::create_simple_excluded_volume_on_rigid_bodies ( const core::RigidBodies &  rbs,
Refiner *  ref = IMP::core::internal::get_rigid_members_refiner() 
)

Creates ExcludedVolumeRestraint using LeavesRefiner.

See Also
ListSingletonContainer See SimpleExcludedVolume
std::string IMP::restrainer::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.

std::string IMP::restrainer::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.

em::DensityMap* IMP::restrainer::load_em_density_map ( char const *  map_fn,
float  spacing,
float  resolution 
)

Load EM density file (.mrc or .em file).

core::RigidBodies IMP::restrainer::set_rigid_bodies ( atom::Hierarchies const &  mhs)

Set each of the given hierachies to be a rigid body.

Deprecated:
As of IMP release 2.1. See the IMP Deprecation Policy for more information about deprecation in IMP. Use atom::create_rigid_body() instead.