Detailed Description

Compute the complementarity between two molecules.

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.

Public Member Functions
	ComplementarityRestraint (const ParticlesTemp &a, const ParticlesTemp &b, std::string name="ComplementarityRestraint %1%")

virtual IMP::ModelObjectsTemp	do_get_inputs () 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...

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)

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...

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 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::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
	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 ()

Member Function Documentation

virtual IMP::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::ModelObject.

virtual ::IMP::VersionInfo IMP::multifit::ComplementarityRestraint::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 84 of file ComplementarityRestraint.h.

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

Set the thickness to use for the external complementarity layer.

Definition at line 60 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 66 of file ComplementarityRestraint.h.

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

Set the thickness of the interior layers.

Definition at line 68 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 58 of file ComplementarityRestraint.h.

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

ComplementarityRestraint.h

Detailed Description

Public Member Functions

Additional Inherited Members

Member Function Documentation