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IMP Reference Guide  develop.83df1cabcf,2021/06/15
The Integrative Modeling Platform
IMP::core::RigidBodyUmbrella Class Reference

Umbrella-like restraint for rigid bodies. More...

#include <IMP/core/RigidBodyUmbrella.h>

+ Inheritance diagram for IMP::core::RigidBodyUmbrella:

Detailed Description

Umbrella-like restraint for rigid bodies.

Let \(x\) be the reduced coordinates (ie centroid+rotation) of some rigid body, relative to a reference rigid body. Let \(x_0\) be the center of the umbrella. Then the restraint score is

\[ E(x) = \frac{\alpha}{2} d^2(x,x_0) \]

\(d\) is the distance between x and x_0

\[d^2(x,x_0) = d^2_\text{eucl}(COM,COM_0) + k*d^2_\text{quat}(Q,Q_0)\]

\(d_\text{eucl}\) is the 3D euclidian distance \(d_\text{quat}\) is the geodesic distance between two rotations, i.e. the angle of the rotation \(Q\cdot Q_0^{-1}\)

See Also
RigidBodyTunneler

Definition at line 38 of file RigidBodyUmbrella.h.

Public Member Functions

 RigidBodyUmbrella (Model *m, ParticleIndex pi, ParticleIndex ref, Floats x0, double alpha, double k, std::string name="RigidBodyUmbrella %1%")
 Create the restraint by specifying \(x_0\) directly. More...
 
 RigidBodyUmbrella (Model *m, ParticleIndex pi, ParticleIndex ref, double lambda, Floats x1, Floats x2, double alpha, double k, std::string name="RigidBodyUmbrella %1%")
 Create the restraint by specifying \(x_0\) as a linear interpolation. More...
 
virtual std::string get_type_name () const
 
virtual ::IMP::VersionInfo get_version_info () const
 Get information about the module and version of the object. More...
 
Floats get_x () const
 
Floats get_x0 () const
 
void set_alpha (double alpha)
 
void set_k (double k)
 
void set_x0 (Floats x0)
 
void set_x0 (double lambda, Floats x1, Floats x2)
 
- Public Member Functions inherited from IMP::Restraint
 Restraint (Model *m, std::string name)
 
void add_score_and_derivatives (ScoreAccumulator sa) const
 Perform the actual restraint scoring. More...
 
Restraintcreate_current_decomposition () const
 Decompose this restraint into constituent terms for the current conf. More...
 
Restraintcreate_decomposition () const
 Decompose this restraint into constituent terms. More...
 
virtual ScoringFunctioncreate_scoring_function (double weight=1.0, double max=NO_MAX) const
 Create a scoring function with only this restraint. More...
 
virtual RestraintInfoget_dynamic_info () const
 
virtual double get_last_score () const
 
double get_score () const
 
virtual RestraintInfoget_static_info () const
 
bool get_was_good () const
 
void set_weight (Float weight)
 
Float get_weight () const
 
double get_maximum_score () const
 
void set_maximum_score (double s)
 
- Public Member Functions inherited from IMP::ModelObject
 ModelObject (Model *m, std::string name)
 
bool get_has_dependencies () const
 Return whether this object has dependencies computed. More...
 
bool get_has_required_score_states () const
 Return whether score states are computed. More...
 
ModelObjectsTemp get_inputs () const
 
ModelObjectsTemps get_interactions () const
 Get the interacting sets induced by this ModelObject. More...
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
const ScoreStatesTempget_required_score_states () const
 Get the score states that are ancestors of this in the dependency graph. More...
 
void set_has_dependencies (bool tf)
 Either invalidate the dependencies or ensure they are correct. More...
 
void set_has_required_score_states (bool tf)
 Compute the required score states. More...
 
- Public Member Functions inherited from IMP::Object
virtual void clear_caches ()
 
CheckLevel get_check_level () const
 
LogLevel get_log_level () const
 
void set_check_level (CheckLevel l)
 
void set_log_level (LogLevel l)
 Set the logging level used in this object. More...
 
void set_was_used (bool tf) const
 
void show (std::ostream &out=std::cout) const
 
const std::string & get_name () const
 
void set_name (std::string name)
 

Protected Member Functions

IMP::ModelObjectsTemp do_get_inputs () const
 
double unprotected_evaluate (IMP::DerivativeAccumulator *accum) const
 
- Protected Member Functions inherited from IMP::Restraint
virtual void do_add_score_and_derivatives (ScoreAccumulator sa) const
 A restraint should override this to compute the score and derivatives. More...
 
virtual Restraints do_create_current_decomposition () const
 
virtual Restraints do_create_decomposition () const
 
ModelObjectsTemp do_get_outputs () const
 
- Protected Member Functions inherited from IMP::ModelObject
virtual ModelObjectsTemps do_get_interactions () const
 
virtual void handle_set_has_required_score_states (bool)
 
- Protected Member Functions inherited from IMP::Object
 Object (std::string name)
 Construct an object with the given name. More...
 
virtual void do_destroy ()
 

Constructor & Destructor Documentation

IMP::core::RigidBodyUmbrella::RigidBodyUmbrella ( Model m,
ParticleIndex  pi,
ParticleIndex  ref,
Floats  x0,
double  alpha,
double  k,
std::string  name = "RigidBodyUmbrella %1%" 
)

Create the restraint by specifying \(x_0\) directly.

Parameters
[in]mModel containing the ParticleIndexes.
[in]pirigid body particle index to restrain
[in]refrigid body particle index of reference
[in]x0\(x_0\) the restraint center
[in]alpha\(\alpha\) restraint stiffness
[in]k\(k\) relative weight between centroid and quaternion restraints
[in]namerestraint name
IMP::core::RigidBodyUmbrella::RigidBodyUmbrella ( Model m,
ParticleIndex  pi,
ParticleIndex  ref,
double  lambda,
Floats  x1,
Floats  x2,
double  alpha,
double  k,
std::string  name = "RigidBodyUmbrella %1%" 
)

Create the restraint by specifying \(x_0\) as a linear interpolation.

The restraint input is the triplet \(\lambda,x_1,x_2\) with \(\lambda\in [0,1]\) such that the restraint center is at

\[ x_0 = (1-\lambda) x_1 + \lambda x_2 \]

Parameters
[in]mModel containing the ParticleIndexes.
[in]pirigid body particle index to restrain
[in]refrigid body particle index of reference
[in]lambda\(\lambda\) the restraint center
[in]x1\(x_1\) the restraint center when \(\lambda=0\)
[in]x2\(x_2\) the restraint center when \(\lambda=1\)
[in]alpha\(\alpha\) restraint stiffness
[in]k\(k\) relative weight between centroid and quaternion restraints
[in]namerestraint name

Member Function Documentation

IMP::ModelObjectsTemp IMP::core::RigidBodyUmbrella::do_get_inputs ( ) const
protectedvirtual

Get any Particle, Container or other ModelObjects read by this during evaluation. If you read everything in a container, you can just return that container.

Implements IMP::ModelObject.

virtual ::IMP::VersionInfo IMP::core::RigidBodyUmbrella::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 95 of file RigidBodyUmbrella.h.


The documentation for this class was generated from the following file: