IMP  2.1.1
The Integrative Modeling Platform
Public Member Functions | Public Attributes | List of all members
IMP::multifit::ComplementarityRestraint Class Reference

Compute the complementarity between two molecules. More...

#include <IMP/multifit/ComplementarityRestraint.h>

+ Inheritance diagram for IMP::multifit::ComplementarityRestraint:

Public Member Functions

 ComplementarityRestraint (const kernel::ParticlesTemp &a, const kernel::ParticlesTemp &b, std::string name="ComplementarityRestraint %1%")
 
virtual
IMP::kernel::ModelObjectsTemp 		do_get_inputs () 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.
 
float get_voxel_size () const
 
void set_boundary_coefficient (double bc)
 
void set_complementarity_coefficient (double cc)
 
void set_complementarity_thickness (double th)
 
void set_complementarity_value (double th)
 
void set_interior_layer_thickness (double th)
 
void set_maximum_penetration (double d)
 
void set_maximum_penetration_score (double s)
 
void set_maximum_separation (double s)
 
void set_penetration_coefficient (double pc)
 
- Public Member Functions inherited from IMP::kernel::Restraint
 Restraint (kernel::Model *m, std::string name)
 
 Restraint (std::string name="Restraint %1%")
 
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 (kernel::Model *m, std::string name)
 
 ModelObject (std::string name)
 
virtual void do_set_model (kernel::Model *)
 
bool get_has_dependencies () const
 Return whether this object has dependencies computed.
 
bool get_has_required_score_states () const
 
ModelObjectsTemp get_inputs () const
 
ModelObjectsTemps get_interactions () const
 
bool get_is_part_of_model () const
 
Model * get_model () const
 
ModelObjectsTemp get_outputs () const
 
const ScoreStatesTemp & get_required_score_states () const
 
void set_has_dependencies (bool tf)
 
void set_has_required_score_states (bool tf)
 
virtual void set_model (kernel::Model *m)
 
- Public Member Functions inherited from IMP::base::Object
virtual void clear_caches ()
 
virtual void do_destroy ()
 
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)
 

Public Attributes

virtual double const
 

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...
 
 Object ()
 

Detailed Description

The score returned is infinity if the two molecules overlap by more than the value set for set_maximum_penetration_score() or if the two molecules are separated by more than set_maximum_separation().

Otherwise, the integral of the set_complementarity_value() value over a layer of thickness set_complementarity_thickness() around the molecule is returned.

Note
currently each of the particle lists must belong to exactly one rigid body. And, currently, each rigid body can only be associated with one list of particles (that is, there cannot be multiple restraints with different lists of particles that all belong to the same rigid body).
The restraint does not support derivatives.
The restraint pretty much only makes sense for use with Domino as it returns infinity for many cases. Monte Carlo might make sense with certain parameters.

Definition at line 40 of file ComplementarityRestraint.h.

Member Function Documentation

virtual IMP::kernel::ModelObjectsTemp IMP::multifit::ComplementarityRestraint::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::kernel::ModelObject.

void IMP::multifit::ComplementarityRestraint::set_complementarity_thickness ( double  th)

Set the thickness to use for the external complementarity layer.

Definition at line 64 of file ComplementarityRestraint.h.

void IMP::multifit::ComplementarityRestraint::set_complementarity_value ( double  th)

Set the value to use for external complementarity voxels.

Definition at line 70 of file ComplementarityRestraint.h.

void IMP::multifit::ComplementarityRestraint::set_interior_layer_thickness ( double  th)

Set the thickness of the interior layers.

Definition at line 74 of file ComplementarityRestraint.h.

void IMP::multifit::ComplementarityRestraint::set_maximum_penetration ( double  d)

Alternatively, you can bound the maximum allowed penetration.

Definition at line 54 of file ComplementarityRestraint.h.

void IMP::multifit::ComplementarityRestraint::set_maximum_penetration_score ( double  s)

If the two molecules have a penetration score of more than this, infinity is returned as the score. This score is roughly the number of cubic angstroms that the two molecules overlap (assuming only one internal layer).

Definition at line 49 of file ComplementarityRestraint.h.

void IMP::multifit::ComplementarityRestraint::set_maximum_separation ( double  s)

If the two molecules' bounding sphere surfaces are separated by more than this distance, infinity is returned.

Definition at line 60 of file ComplementarityRestraint.h.

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