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IMP Reference Guide  develop.731656d855,2020/02/16
The Integrative Modeling Platform
IMP::isd::TALOSRestraint Class Reference

phi/psi dihedral restraint between four particles, using data from TALOS. More...

#include <IMP/isd/TALOSRestraint.h>

+ Inheritance diagram for IMP::isd::TALOSRestraint:

Detailed Description

phi/psi dihedral restraint between four particles, using data from TALOS.

The likelihood is

\[ f(\chi_{exp}^1,\cdots,\chi_{exp}^N|\chi(X),\kappa,I) = \frac{1}{2\pi I_0(\kappa)^N} \exp \left(R_0 \kappa \cos (\chi_{exp}-\chi(X)) \right) \]

where the sufficient statistics are \(N\) the number of observations, \(R\) and \(\chi_{exp}\).

See Also
vonMisesSufficient.h for further detail.

Definition at line 32 of file TALOSRestraint.h.

Public Member Functions

 TALOSRestraint (Model *m, Particles p, Floats data, Particle *kappa)
 Create restraint from a list of particles and the data. More...
 
 TALOSRestraint (Model *m, Particle *p1, Particle *p2, Particle *p3, Particle *p4, Floats data, Particle *kappa)
 Create restraint from 4 particles and the data. More...
 
 TALOSRestraint (Model *m, Particles p, unsigned N, double R0, double chiexp, Particle *kappa)
 Create restraint from a list of particles and the sufficient statistics. More...
 
 TALOSRestraint (Model *m, Particle *p1, Particle *p2, Particle *p3, Particle *p4, unsigned N, double R0, double chiexp, Particle *kappa)
 Create restraint from 4 particles and the sufficient statistics. More...
 
virtual IMP::ModelObjectsTemp do_get_inputs () const
 
double get_chiexp () const
 
double get_probability () const
 Call for probability. More...
 
double get_R0 () const
 
virtual std::string get_type_name () const
 
virtual ::IMP::VersionInfo get_version_info () const
 Get information about the module and version of the object. More...
 
virtual double unprotected_evaluate (IMP::DerivativeAccumulator *accum) const
 
- Public Member Functions inherited from IMP::Restraint
 Restraint (Model *m, std::string name)
 
void add_score_and_derivatives (ScoreAccumulator sa) const
 Perform the actual restraint scoring. More...
 
Restraintcreate_current_decomposition () const
 Decompose this restraint into constituent terms for the current conf. More...
 
Restraintcreate_decomposition () const
 Decompose this restraint into constituent terms. More...
 
virtual ScoringFunctioncreate_scoring_function (double weight=1.0, double max=NO_MAX) const
 Create a scoring function with only this restraint. More...
 
virtual RestraintInfoget_dynamic_info () const
 
virtual double get_last_score () const
 
double get_score () const
 
virtual RestraintInfoget_static_info () 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::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...
 
Modelget_model () const
 
ModelObjectsTemp get_outputs () const
 
const ScoreStatesTempget_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
 A restraint should override this to compute the score and derivatives. More...
 
virtual Restraints do_create_current_decomposition () const
 
virtual Restraints do_create_decomposition () const
 
ModelObjectsTemp do_get_outputs () const
 
- 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 ()
 

Constructor & Destructor Documentation

IMP::isd::TALOSRestraint::TALOSRestraint ( Model m,
Particles  p,
Floats  data,
Particle kappa 
)

Create restraint from a list of particles and the data.

Parameters
[in]mthe Model
[in]plist of 4 particles that make the dihedral angle.
[in]datalist of observations for that angle.
[in]kappaPointer to the \(\kappa\) concentration particle.
IMP::isd::TALOSRestraint::TALOSRestraint ( Model m,
Particle p1,
Particle p2,
Particle p3,
Particle p4,
Floats  data,
Particle kappa 
)

Create restraint from 4 particles and the data.

Parameters
[in]mthe Model
[in]p1Pointer to first particle in dihedral restraint.
[in]p2Pointer to second particle in dihedral restraint.
[in]p3Pointer to third particle in dihedral restraint.
[in]p4Pointer to fourth particle in dihedral restraint.
[in]datalist of observations for that angle.
[in]kappaPointer to the \(\kappa\) concentration particle.
IMP::isd::TALOSRestraint::TALOSRestraint ( Model m,
Particles  p,
unsigned  N,
double  R0,
double  chiexp,
Particle kappa 
)

Create restraint from a list of particles and the sufficient statistics.

Parameters
[in]mthe Model
[in]plist of 4 particles that make the dihedral angle.
[in]NNumber of observations
[in]R0component on the x axis
[in]chiexpaverage observed angle.
[in]kappaPointer to the \(\kappa\) concentration particle.
IMP::isd::TALOSRestraint::TALOSRestraint ( Model m,
Particle p1,
Particle p2,
Particle p3,
Particle p4,
unsigned  N,
double  R0,
double  chiexp,
Particle kappa 
)

Create restraint from 4 particles and the sufficient statistics.

Parameters
[in]mthe Model
[in]p1Pointer to first particle in dihedral restraint.
[in]p2Pointer to second particle in dihedral restraint.
[in]p3Pointer to third particle in dihedral restraint.
[in]p4Pointer to fourth particle in dihedral restraint.
[in]NNumber of observations
[in]R0component on the x axis
[in]chiexpaverage observed angle.
[in]kappaPointer to the \(\kappa\) concentration particle.

Member Function Documentation

virtual IMP::ModelObjectsTemp IMP::isd::TALOSRestraint::do_get_inputs ( ) const
virtual

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.

double IMP::isd::TALOSRestraint::get_probability ( ) const

Call for probability.

Definition at line 83 of file TALOSRestraint.h.

virtual ::IMP::VersionInfo IMP::isd::TALOSRestraint::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 92 of file TALOSRestraint.h.


The documentation for this class was generated from the following file: