IMP Reference Guide
2.20.2
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>
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 \(\chi_{exp}\).
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 override |
double | get_chiexp () const |
double | get_probability () const |
Call for probability. More... | |
double | get_R0 () const |
virtual std::string | get_type_name () const override |
virtual ::IMP::VersionInfo | get_version_info () const override |
Get information about the module and version of the object. More... | |
virtual double | unprotected_evaluate (IMP::DerivativeAccumulator *accum) const override |
Return the unweighted score for the restraint. More... | |
Public Member Functions inherited from IMP::Restraint | |
Restraint (Model *m, std::string name) | |
Create a restraint and register it with the model. More... | |
Restraint () | |
Default constructor. 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 RestraintInfo * | get_dynamic_info () const |
bool | get_is_aggregate () const |
Return whether this restraint wraps a number of other restraints. More... | |
double | get_last_last_score () const |
Get the unweighted score from the last-but-one time it was evaluated. More... | |
virtual double | get_last_score () const |
double | get_score () const |
virtual RestraintInfo * | get_static_info () const |
bool | get_was_good () const |
double | evaluate (bool calc_derivs) const |
double | evaluate_moved (bool calc_derivs, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const |
double | evaluate_moved_if_below (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const |
double | evaluate_moved_if_good (bool calc_derivatives, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const |
double | evaluate_if_good (bool calc_derivatives) const |
double | evaluate_if_below (bool calc_derivatives, double max) const |
virtual double | unprotected_evaluate_moved (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const |
Return the unweighted score, taking moving particles into account. More... | |
virtual double | unprotected_evaluate_if_good (DerivativeAccumulator *da, double max) const |
virtual double | unprotected_evaluate_if_below (DerivativeAccumulator *da, double max) const |
The function calling this will treat any score >= max as bad. More... | |
virtual double | unprotected_evaluate_moved_if_below (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) const |
virtual double | unprotected_evaluate_moved_if_good (DerivativeAccumulator *da, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis, double max) 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... | |
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::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 |
virtual void | do_add_score_and_derivatives_moved (ScoreAccumulator sa, const ParticleIndexes &moved_pis, const ParticleIndexes &reset_pis) const |
virtual Restraints | do_create_current_decomposition () const |
virtual Restraints | do_create_decomposition () const |
ModelObjectsTemp | do_get_outputs () const override |
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 () |
Protected Attributes inherited from IMP::Restraint | |
bool | is_aggregate_ |
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.
[in] | m | the Model |
[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 | ( | Model * | m, |
Particles | p, | ||
unsigned | N, | ||
double | R0, | ||
double | chiexp, | ||
Particle * | kappa | ||
) |
Create restraint from a list of particles and the sufficient statistics.
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.
[in] | m | the Model |
[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. |
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overridevirtual |
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.
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overridevirtual |
Get information about the module and version of the object.
Reimplemented from IMP::Object.
Definition at line 92 of file TALOSRestraint.h.
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overridevirtual |
Return the unweighted score for the restraint.
Reimplemented from IMP::Restraint.