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IMP Reference Guide
develop.d97d4ead1f,2024/11/21
The Integrative Modeling Platform
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Umbrella-like restraint for rigid bodies. More...
#include <IMP/core/RigidBodyUmbrella.h>
Inheritance diagram for IMP::core::RigidBodyUmbrella: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 euclidean 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 override |
| virtual ::IMP::VersionInfo | get_version_info () const override |
| 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) | |
| Create a restraint and register it with the model. More... | |
| Restraint () | |
| Default constructor. 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 |
| bool | get_is_aggregate () const |
| Return whether this restraint wraps a number of other restraints. More... | |
| double | get_last_last_score () const |
| Get the unweighted score from the last-but-one time it was evaluated. More... | |
| virtual double | get_last_score () const |
| double | get_score () const |
| virtual RestraintInfo * | get_static_info () const |
| bool | get_was_good () const |
| double | evaluate (bool calc_derivs) const |
| double | evaluate_moved (bool calc_derivs, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const |
| double | evaluate_moved_if_below (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const |
| double | evaluate_moved_if_good (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const |
| double | evaluate_if_good (bool calc_derivatives) const |
| double | evaluate_if_below (bool calc_derivatives, double max) const |
| virtual double | unprotected_evaluate_moved (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const |
| Return the unweighted score, taking moving particles into account. More... | |
| virtual double | unprotected_evaluate_if_good (DerivativeAccumulator *da, double max) const |
| virtual double | unprotected_evaluate_if_below (DerivativeAccumulator *da, double max) const |
| The function calling this will treat any score >= max as bad. More... | |
| virtual double | unprotected_evaluate_moved_if_below (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const |
| virtual double | unprotected_evaluate_moved_if_good (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) 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 override |
| double | unprotected_evaluate (IMP::DerivativeAccumulator *accum) const override |
| Return the unweighted score for the restraint. More... | |
| Protected Member Functions inherited from IMP::Restraint | |
| virtual void | do_add_score_and_derivatives (ScoreAccumulator sa) const |
| virtual void | do_add_score_and_derivatives_moved (ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const |
| virtual Restraints | do_create_current_decomposition () const |
| virtual Restraints | do_create_decomposition () const |
| ModelObjectsTemp | do_get_outputs () const override |
| 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 () |
Additional Inherited Members | |
| Protected Attributes inherited from IMP::Restraint | |
| bool | is_aggregate_ |
| IMP::core::RigidBodyUmbrella::RigidBodyUmbrella | ( | Model * | m, |
| ParticleIndex | pi, | ||
| ParticleIndex | ref, | ||
| Floats | x0, | ||
| double | alpha, | ||
| double | k, | ||
| std::string | name = "RigidBodyUmbrella %1%" |
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| ) |
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%" |
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| ) |
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 |
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overrideprotectedvirtual |
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.
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 96 of file RigidBodyUmbrella.h.
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overrideprotectedvirtual |
Return the unweighted score for the restraint.
Reimplemented from IMP::Restraint.