Detailed Description

Restrain atom pairs based on a set of crosslinks.

Definition at line 21 of file AtomicCrossLinkMSRestraint.h.

Public Member Functions
	AtomicCrossLinkMSRestraint (IMP::Model *m, double length, Float slope=0.0, bool i_am_part_of_log_score=false, std::string name="AtomicCrossLinkMSRestraint%1%")
	Constructor. More...

void	add_contribution (const ParticleIndexPair &ppi, const ParticleIndexPair &sigmas, const ParticleIndex &psi)
	Add a contribution to this xlink. More...

virtual IMP::ModelObjectsTemp	do_get_inputs () const

Float	evaluate_for_contributions (Ints c, DerivativeAccumulator *accum) const
	Evaluate the restraint just for a subset of contribution indexes. More...

ParticleIndexPair	get_contribution (int i) const
	Get the particles in a contribution. More...

ParticleIndex	get_contribution_psi (int i) const
	Get the psi nuisance in a contribution. More...

Floats	get_contribution_scores (int index) const
	Returns a description of each contribution (distance, sig1, sig2, psi) More...

ParticleIndexPair	get_contribution_sigmas (int i) const
	Get the sigma nuisances in a contribution. More...

unsigned int	get_number_of_contributions () const
	Get number of contributions added to the restraint. More...

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. More...

void	set_part_of_log_score (bool hey)

void	set_slope (Float slope)

void	show (std::ostream &out) const

virtual double	unprotected_evaluate (IMP::DerivativeAccumulator *accum) const

Public Member Functions inherited from IMP::kernel::Restraint
	Restraint (kernel::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::kernel::ModelObject
	ModelObject (kernel::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::base::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::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...

virtual void	do_destroy ()

Constructor & Destructor Documentation

IMP::isd::AtomicCrossLinkMSRestraint::AtomicCrossLinkMSRestraint	(	IMP::Model *	m,
		double	length,
		Float	slope = `0.0`,
		bool	i_am_part_of_log_score = `false`,
		std::string	name = `"AtomicCrossLinkMSRestraint%1%"`
	)

Constructor.

Parameters

[in]	length	The maximum length of the crosslinker
[in]	slope	Exponential factor added to the score
[in]	i_am_part_of_log_score	Set to True if using LogWrapper
[in]	name	The restraint name

Member Function Documentation

void IMP::isd::AtomicCrossLinkMSRestraint::add_contribution	(	const ParticleIndexPair &	ppi,
		const ParticleIndexPair &	sigmas,
		const ParticleIndex &	psi
	)

Add a contribution to this xlink.

Parameters

[in]	ppi	The particles to which you will apply the restraint
[in]	sigmas	Nuisance parameters (one per residue involved in the XL)
[in]	psi	Nuisance parameter for the data point accuracy (one per pair)

virtual IMP::ModelObjectsTemp IMP::isd::AtomicCrossLinkMSRestraint::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.

Float IMP::isd::AtomicCrossLinkMSRestraint::evaluate_for_contributions	(	Ints	c,
		DerivativeAccumulator *	accum
	)		const

Evaluate the restraint just for a subset of contribution indexes.

ParticleIndexPair IMP::isd::AtomicCrossLinkMSRestraint::get_contribution ( int i ) const

Get the particles in a contribution.

Definition at line 59 of file AtomicCrossLinkMSRestraint.h.

ParticleIndex IMP::isd::AtomicCrossLinkMSRestraint::get_contribution_psi ( int i ) const

Get the psi nuisance in a contribution.

Definition at line 65 of file AtomicCrossLinkMSRestraint.h.

Floats IMP::isd::AtomicCrossLinkMSRestraint::get_contribution_scores ( int index ) const

Returns a description of each contribution (distance, sig1, sig2, psi)

ParticleIndexPair IMP::isd::AtomicCrossLinkMSRestraint::get_contribution_sigmas ( int i ) const

Get the sigma nuisances in a contribution.

Definition at line 62 of file AtomicCrossLinkMSRestraint.h.

unsigned int IMP::isd::AtomicCrossLinkMSRestraint::get_number_of_contributions ( ) const

Get number of contributions added to the restraint.

Definition at line 56 of file AtomicCrossLinkMSRestraint.h.

virtual ::IMP::base::VersionInfo IMP::isd::AtomicCrossLinkMSRestraint::get_version_info ( ) const

virtual

Get information about the module and version of the object.

Reimplemented from IMP::base::Object.

Definition at line 76 of file AtomicCrossLinkMSRestraint.h.

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

AtomicCrossLinkMSRestraint.h

Detailed Description

Public Member Functions

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation