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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 an NOE distance restraint between two particles. More...
#include <IMP/isd/MarginalNOERestraint.h>
Inheritance diagram for IMP::isd::MarginalNOERestraint:Apply an NOE distance restraint between two particles.
Marginal of the NOE lognormal model. Since restraint is complicated, pass individual particles to add_contribution() command. Supports ambiguous NOEs and derivatives.
\[p(D|X,I) = SS^{-\frac{N-1}{2}} \quad SS = \sum_{i=1}^N \log^2\left(\frac{V_i^{exp}}{d_i^{-6}(X) \hat{\gamma}}\right) \quad \hat{\gamma} = \left(\prod_{i=1}^N \frac{V_i^{exp}}{d_i^{-6}}\right)^{1/N} \]
Definition at line 30 of file MarginalNOERestraint.h.
Public Member Functions | |
| MarginalNOERestraint (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_log_gammahat () const |
| unsigned | get_number_of_contributions () const |
| double | get_probability () const |
| double | get_SS () 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::MarginalNOERestraint::MarginalNOERestraint | ( | 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 43 of file MarginalNOERestraint.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 69 of file MarginalNOERestraint.h.
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This macro declares the basic needed methods: evaluate and show