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IMP Reference Guide  develop.a3ebfe92e8,2023/01/27
The Integrative Modeling Platform
IMP::atom::CHARMMStereochemistryRestraint Class Reference

Enforce CHARMM stereochemistry on the given Hierarchy. More...

#include <IMP/atom/CHARMMStereochemistryRestraint.h>

+ Inheritance diagram for IMP::atom::CHARMMStereochemistryRestraint:

Detailed Description

Enforce CHARMM stereochemistry on the given Hierarchy.

It is assumed that the Hierarchy has already had CHARMM atom types assigned and conforms with the CHARMM topology information (for example, by calling CHARMMTopology::setup_hierarchy() first).

Note
This is a convenient high-level wrapper; the bonds, angles, dihedrals and impropers can also be created manually and evaluated using standard IMP building blocks - for example, angles can be created using CHARMMParameters::create_angles() and then evaluated using an AngleSingletonScore in combination with a container::SingletonsRestraint.

Definition at line 40 of file CHARMMStereochemistryRestraint.h.

Public Member Functions

 CHARMMStereochemistryRestraint (Hierarchy h, CHARMMTopology *topology)
 
 CHARMMStereochemistryRestraint (Hierarchy h, CHARMMTopology *topology, ParticlesTemp limit_to_these_particles)
 Initialize the restraint and limit to a set of particles. More...
 
virtual IMP::ModelObjectsTemp do_get_inputs () const override
 
StereochemistryPairFilterget_full_pair_filter ()
 Get a PairFilter including everything from original topology. More...
 
StereochemistryPairFilterget_pair_filter ()
 Get a PairFilter that excludes all stereochemical pairs. More...
 
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...
 
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
 
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 RestraintInfoget_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...
 
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
 
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_
 

Constructor & Destructor Documentation

IMP::atom::CHARMMStereochemistryRestraint::CHARMMStereochemistryRestraint ( Hierarchy  h,
CHARMMTopology topology,
ParticlesTemp  limit_to_these_particles 
)

Initialize the restraint and limit to a set of particles.

Will only create restraints where every particle in the restraint is in the provided list.

Member Function Documentation

virtual IMP::ModelObjectsTemp IMP::atom::CHARMMStereochemistryRestraint::do_get_inputs ( ) const
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.

StereochemistryPairFilter* IMP::atom::CHARMMStereochemistryRestraint::get_full_pair_filter ( )

Get a PairFilter including everything from original topology.

Returns
a StereochemistryPairFilter that excludes all 1-2 (bond), 1-3 (angle) and 1-4 (dihedral) pairs before limiting to selection.
StereochemistryPairFilter* IMP::atom::CHARMMStereochemistryRestraint::get_pair_filter ( )

Get a PairFilter that excludes all stereochemical pairs.

Returns
a StereochemistryPairFilter that excludes all 1-2 (bond), 1-3 (angle) and 1-4 (dihedral) pairs.
virtual ::IMP::VersionInfo IMP::atom::CHARMMStereochemistryRestraint::get_version_info ( ) const
overridevirtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 75 of file CHARMMStereochemistryRestraint.h.

virtual double IMP::atom::CHARMMStereochemistryRestraint::unprotected_evaluate ( IMP::DerivativeAccumulator da) const
overridevirtual

Return the unweighted score for the restraint.

Reimplemented from IMP::Restraint.


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