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::DensityMap *	load_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

typedef IMP::base::Vector< SimpleConnectivity > IMP::restrainer::SimpleConnectivities

Pass or store a set of SimpleConnectivity .

Definition at line 222 of file simplify_restraint.h.

typedef IMP::base::Vector< SimpleDiameter > IMP::restrainer::SimpleDiameters

Pass or store a set of SimpleDiameter .

Definition at line 373 of file simplify_restraint.h.

typedef IMP::base::Vector< SimpleDistance > IMP::restrainer::SimpleDistances

Pass or store a set of SimpleDistance .

Definition at line 297 of file simplify_restraint.h.

typedef IMP::base::Vector< SimpleEMFit > IMP::restrainer::SimpleEMFits

Pass or store a set of SimpleEMFit .

Definition at line 459 of file simplify_restraint.h.

typedef IMP::base::Vector< SimpleExcludedVolume > IMP::restrainer::SimpleExcludedVolumes

Pass or store a set of SimpleExcludedVolume .

Definition at line 419 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]	ps	Pointer to particles in diameter restraint.
[in]	diameter	Diameter.

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] ps Pointer 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]	mh	a molecule to fit in the density
[in]	dmap	the 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

IMP::atom::read_pdb(IMP::atom::get_example_path("example_protein.pdb",

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.

Classes

Typedefs

Functions

Standard module methods

Typedef Documentation

Function Documentation