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IMP
2.3.1
The Integrative Modeling Platform
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IMP
2.3.1
The Integrative Modeling Platform
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Apply a lognormal distance restraint between two particles. More...
#include <IMP/isd/MarginalHBondRestraint.h>
Inheritance diagram for IMP::isd::MarginalHBondRestraint:Apply a lognormal distance restraint between two particles.
Marginal of the lognormal model for NOEs where only \(\sigma\) was marginalized, and \(\gamma\) was set to 1. Since the restraint is complicated, pass individual particles to add_contribution() command.
\[p(D|X,I) = \left(\sum_{i=1}^N \log^2\left(\frac{V_i^{exp}} {d_i^{-6}(X)}\right)\right)^{-\frac{N}{2}} \]
Definition at line 30 of file MarginalHBondRestraint.h.
Public Member Functions | |
| MarginalHBondRestraint (kernel::Model *m) | |
| Create the restraint. More... | |
| void | add_contribution (kernel::Particle *p1, kernel::Particle *p2, double Iexp) |
| void | add_contribution (PairContainer *pc, double Iexp) |
| virtual IMP::kernel::ModelObjectsTemp | do_get_inputs () const |
| double | get_logsquares () const |
| unsigned | get_number_of_contributions () const |
| double | get_probability () const |
| virtual std::string | get_type_name () const |
| virtual ::IMP::base::VersionInfo | get_version_info () const |
| Get information about the module and version of the object. More... | |
| virtual double | unprotected_evaluate (IMP::kernel::DerivativeAccumulator *accum) const |
| Public Member Functions inherited from IMP::kernel::Restraint | |
| Restraint (kernel::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 double | get_last_score () const |
| double | get_score () 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::kernel::ModelObject | |
| ModelObject (kernel::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::base::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::kernel::Restraint | |
| virtual void | do_add_score_and_derivatives (ScoreAccumulator sa) const |
| virtual Restraints | do_create_current_decomposition () const |
| virtual Restraints | do_create_decomposition () const |
| ModelObjectsTemp | do_get_outputs () const |
| Protected Member Functions inherited from IMP::kernel::ModelObject | |
| virtual ModelObjectsTemps | do_get_interactions () const |
| virtual void | handle_set_has_required_score_states (bool) |
| Protected Member Functions inherited from IMP::base::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| virtual void | do_destroy () |
| IMP::isd::MarginalHBondRestraint::MarginalHBondRestraint | ( | kernel::Model * | m | ) |
Create the restraint.
kernel::Restraints should store the particles they are to act on, preferably in a Singleton or PairContainer as appropriate.
Definition at line 41 of file MarginalHBondRestraint.h.
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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::kernel::ModelObject.
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Get information about the module and version of the object.
Reimplemented from IMP::base::Object.
Definition at line 64 of file MarginalHBondRestraint.h.
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This macro declares the basic needed methods: evaluate and show