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IMP Reference Guide
develop.d97d4ead1f,2024/11/21
The Integrative Modeling Platform
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gaussian process restraint More...
#include <IMP/isd/GaussianProcessInterpolationRestraint.h>
Inheritance diagram for IMP::isd::GaussianProcessInterpolationRestraint:gaussian process restraint
Definition at line 31 of file GaussianProcessInterpolationRestraint.h.
Public Member Functions | |
| GaussianProcessInterpolationRestraint (Model *m, GaussianProcessInterpolation *gpi) | |
| IMP::ModelObjectsTemp | do_get_inputs () const override |
| Eigen::MatrixXd | get_hessian () const |
| Get hessian of the minus log likelihood. More... | |
| FloatsList | get_hessian (bool unused) const |
| call this one from Python More... | |
| double | get_logdet_hessian () const |
| Get log determinant of hessian. More... | |
| double | get_minus_exponent () const |
| double | get_minus_log_normalization () const |
| Get minus log normalization and minus exponent separately. More... | |
| double | get_probability () const |
| 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... | |
| void | set_use_cg (bool use, double tol) |
| Use conjugate gradients when possible (default false) More... | |
| double | unprotected_evaluate (IMP::DerivativeAccumulator *accum) const override |
| Return the unweighted score for the restraint. More... | |
| 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) |
Additional Inherited Members | |
| 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 () |
| Protected Attributes inherited from IMP::Restraint | |
| bool | is_aggregate_ |
| IMP::isd::GaussianProcessInterpolationRestraint::GaussianProcessInterpolationRestraint | ( | Model * | m, |
| GaussianProcessInterpolation * | gpi | ||
| ) |
This is a restraint on other restraints. It first constructs the necessary vectors from GaussianProcessInterpolation, then creates a multivariate normal distribution around it. Upon evaluation, it checks if parameters have changed, reconstructs the matrix if necessary, changes the DA weight and passes it to the functions.
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overridevirtual |
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.
| Eigen::MatrixXd IMP::isd::GaussianProcessInterpolationRestraint::get_hessian | ( | ) | const |
Get hessian of the minus log likelihood.
| FloatsList IMP::isd::GaussianProcessInterpolationRestraint::get_hessian | ( | bool | unused | ) | const |
call this one from Python
| double IMP::isd::GaussianProcessInterpolationRestraint::get_logdet_hessian | ( | ) | const |
Get log determinant of hessian.
| double IMP::isd::GaussianProcessInterpolationRestraint::get_minus_log_normalization | ( | ) | const |
Get minus log normalization and minus exponent separately.
| double IMP::isd::GaussianProcessInterpolationRestraint::get_probability | ( | ) | const |
To call this, you need to update the scorestate before. calling model.evaluate(False) is enough.
Definition at line 55 of file GaussianProcessInterpolationRestraint.h.
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 77 of file GaussianProcessInterpolationRestraint.h.
| void IMP::isd::GaussianProcessInterpolationRestraint::set_use_cg | ( | bool | use, |
| double | tol | ||
| ) |
Use conjugate gradients when possible (default false)
Definition at line 58 of file GaussianProcessInterpolationRestraint.h.
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overridevirtual |
Return the unweighted score for the restraint.
Reimplemented from IMP::Restraint.