IMP Reference Guide
2.14.0
The Integrative Modeling Platform
|
Umbrella-like restraint for rigid bodies. More...
#include <IMP/core/RigidBodyUmbrella.h>
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 \(Q\cdot Q_0^{-1}\)
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... | |
Restraint * | create_current_decomposition () const |
Decompose this restraint into constituent terms for the current conf. More... | |
Restraint * | create_decomposition () const |
Decompose this restraint into constituent terms. More... | |
virtual ScoringFunction * | create_scoring_function (double weight=1.0, double max=NO_MAX) const |
Create a scoring function with only this restraint. More... | |
virtual RestraintInfo * | get_dynamic_info () const |
virtual double | get_last_score () const |
double | get_score () const |
virtual RestraintInfo * | get_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... | |
Model * | get_model () const |
ModelObjectsTemp | get_outputs () const |
const ScoreStatesTemp & | get_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 () |
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.
[in] | m | Model containing the ParticleIndexes. |
[in] | pi | rigid body particle index to restrain |
[in] | ref | rigid 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] | name | restraint 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
\[ x_0 = (1-\lambda) x_1 + \lambda x_2 \]
[in] | m | Model containing the ParticleIndexes. |
[in] | pi | rigid body particle index to restrain |
[in] | ref | rigid 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] | name | restraint name |
|
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 |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 95 of file RigidBodyUmbrella.h.