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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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#include <IMP/isd/FretRestraint.h>
Inheritance diagram for IMP::isd::FretRestraint:A restraint for using in-vivo ensemble FRET data, see Muller et al. Mol Biol Cell 16, 3341, 2005 for more info.
Definition at line 22 of file FretRestraint.h.
Public Member Functions | |
| FretRestraint (kernel::Particles pd, kernel::Particles pa, kernel::Particle *kda, kernel::Particle *Ida, kernel::Particle *R0, kernel::Particle *sigma0, kernel::Particle *Pbl, double fexp, double m_d=1.0, double m_a=1.0) | |
| Create the restraint. More... | |
| FretRestraint (kernel::Particle *kda, kernel::Particle *Ida, kernel::Particle *sumFi, kernel::Particle *sigma0, kernel::Particle *Pbl, double fexp) | |
| FretRestraint (kernel::Particle *prd, algebra::Vector3D GMMterd, algebra::Vector3Ds GMMctrd, Floats GMMwd, Floats GMMsigd, kernel::Particle *pra, algebra::Vector3D GMMtera, algebra::Vector3Ds GMMctra, Floats GMMwa, Floats GMMsiga, kernel::Particle *kda, kernel::Particle *Ida, kernel::Particle *sigma0, kernel::Particle *Pbl, FretData *data, double fexp) | |
| virtual IMP::kernel::ModelObjectsTemp | do_get_inputs () const |
| double | get_average_sigma (double fmod) const |
| double | get_experimental_value () const |
| double | get_model_fretr () const |
| double | get_probability () const |
| double | get_standard_error () const |
| double | get_sumFi () 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... | |
| void | set_experimental_value (double fexp) |
| 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::FretRestraint::FretRestraint | ( | kernel::Particles | pd, |
| kernel::Particles | pa, | ||
| kernel::Particle * | kda, | ||
| kernel::Particle * | Ida, | ||
| kernel::Particle * | R0, | ||
| kernel::Particle * | sigma0, | ||
| kernel::Particle * | Pbl, | ||
| double | fexp, | ||
| double | m_d = 1.0, |
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| double | m_a = 1.0 |
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| ) |
Create the restraint.
kernel::Restraints should store the particles they are to act on, preferably in a Singleton or PairContainer as appropriate.
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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 102 of file FretRestraint.h.
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This macro declares the basic needed methods: evaluate and show