IMP
2.0.1
The Integrative Modeling Platform
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phi/psi dihedral restraint between four particles, using data from TALOS. More...
#include <IMP/isd/TALOSRestraint.h>
Public Member Functions | |
TALOSRestraint (Particles p, Floats data, Particle *kappa) | |
Create restraint from a list of particles and the data. More... | |
TALOSRestraint (Particle *p1, Particle *p2, Particle *p3, Particle *p4, Floats data, Particle *kappa) | |
Create restraint from 4 particles and the data. More... | |
TALOSRestraint (Particles p, unsigned N, double R0, double chiexp, Particle *kappa) | |
Create restraint from a list of particles and the sufficient statistics. More... | |
TALOSRestraint (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 void | do_show (std::ostream &out) const |
double | get_chiexp () const |
double | get_probability () const |
Call for probability. | |
double | get_R0 () const |
Public Member Functions inherited from IMP::kernel::Restraint | |
Restraint (Model *m, std::string name) | |
void | add_score_and_derivatives (ScoreAccumulator sa) const |
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 |
ContainersTemp | get_input_containers () const |
ParticlesTemp | get_input_particles () const |
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 (Model *m, std::string name) | |
ModelObjectsTemp | get_inputs () const |
ModelObjectsTemps | get_interactions () const |
Model * | get_model () const |
ModelObjectsTemp | get_outputs () const |
Public Member Functions inherited from IMP::base::Object | |
virtual void | clear_caches () |
virtual IMP::base::VersionInfo | get_version_info () const =0 |
Get information about the module and version of the object. | |
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 |
virtual void | do_update_dependencies () |
Related Functions inherited from IMP::kernel::Restraint | |
typedef IMP::base::Vector < IMP::base::WeakPointer < Restraint > > | RestraintsTemp |
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 \(\chi_{exp}\).
Definition at line 32 of file TALOSRestraint.h.
[in] | p | list of 4 particles that make the dihedral angle. |
[in] | data | list of observations for that angle. |
[in] | kappa | Pointer to the \(\kappa\) concentration particle. |
IMP::isd::TALOSRestraint::TALOSRestraint | ( | Particle * | p1, |
Particle * | p2, | ||
Particle * | p3, | ||
Particle * | p4, | ||
Floats | data, | ||
Particle * | kappa | ||
) |
[in] | p1 | Pointer to first particle in dihedral restraint. |
[in] | p2 | Pointer to second particle in dihedral restraint. |
[in] | p3 | Pointer to third particle in dihedral restraint. |
[in] | p4 | Pointer to fourth particle in dihedral restraint. |
[in] | data | list of observations for that angle. |
[in] | kappa | Pointer to the \(\kappa\) concentration particle. |
IMP::isd::TALOSRestraint::TALOSRestraint | ( | Particles | p, |
unsigned | N, | ||
double | R0, | ||
double | chiexp, | ||
Particle * | kappa | ||
) |
[in] | p | list of 4 particles that make the dihedral angle. |
[in] | N | Number of observations |
[in] | R0 | component on the x axis |
[in] | chiexp | average observed angle. |
[in] | kappa | Pointer to the \(\kappa\) concentration particle. |
IMP::isd::TALOSRestraint::TALOSRestraint | ( | Particle * | p1, |
Particle * | p2, | ||
Particle * | p3, | ||
Particle * | p4, | ||
unsigned | N, | ||
double | R0, | ||
double | chiexp, | ||
Particle * | kappa | ||
) |
[in] | p1 | Pointer to first particle in dihedral restraint. |
[in] | p2 | Pointer to second particle in dihedral restraint. |
[in] | p3 | Pointer to third particle in dihedral restraint. |
[in] | p4 | Pointer to fourth particle in dihedral restraint. |
[in] | N | Number of observations |
[in] | R0 | component on the x axis |
[in] | chiexp | average observed angle. |
[in] | kappa | Pointer to the \(\kappa\) concentration particle. |