IMP::saxs::ProfileFitter< ScoringFunctionT > Class Template Reference

#include <IMP/saxs/ProfileFitter.h>

Inheritance diagram for IMP::saxs::ProfileFitter< ScoringFunctionT >:

Public Member Functions
	ProfileFitter (const Profile *exp_profile)
	Constructor. More...
	ProfileFitter (const Profile *exp_profile, ScoringFunctionT *sf)
Float	compute_offset (const Profile *model_profile) const
	computes offset for fitting for fitting the modeled profile More...
Float	compute_scale_factor (const Profile *model_profile, Float offset=0.0) const
	computes the scaling factor needed for fitting the modeled profile More...
Float	compute_score (const Profile *model_profile, bool use_offset=false, const std::string fit_file_name="") const
	compute fit score
Float	compute_score (const Profile *model_profile, Float min_q, Float max_q) const
	compute fit score in the interval
FitParameters	fit_profile (Profile *partial_profile, float min_c1=0.95, float max_c1=1.05, float min_c2=-2.0, float max_c2=4.0, bool use_offset=false, const std::string fit_file_name="") const
	fit experimental profile through optimization of c1 and c2 parameters More...
void	resample (const Profile *model_profile, Profile *resampled_profile) const
	resampling of the modeled profile is required to fit the q
void	write_SAXS_fit_file (const std::string &file_name, const Profile *model_profile, const Float chi_square, const Float c=1, const Float offset=0) const
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
virtual VersionInfo	get_version_info () const
	Get information about the module and version of the object.
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)
virtual std::string	get_type_name () const

Protected Attributes
base::PointerMember< const Profile >	exp_profile_
ScoringFunctionT *	scoring_function_

Additional Inherited Members
Protected Member Functions inherited from IMP::base::Object
	Object (std::string name)
	Construct an object with the given name. More...
	Object ()

Detailed Description

template<class ScoringFunctionT = ChiScore>
class IMP::saxs::ProfileFitter< ScoringFunctionT >

ProfileFitter is a class for fitting the two profiles with user-defined scoring function that is a template parameter. By default chi score is used. The scoring function template parameter class has to implement three basic functions: compute_score, compute_scale_factor and compute_offset. see ChiScore for example. Currently three scoring functions are implemented: ChiScore, ChiScoreLog and ChiFreeScore.

Definition at line 30 of file ProfileFitter.h.

Constructor & Destructor Documentation

template<class ScoringFunctionT = ChiScore>

IMP::saxs::ProfileFitter< ScoringFunctionT >::ProfileFitter

(

const Profile *

exp_profile

)

Parameters

[in]

exp_profile

Experimental profile we want to fit

Definition at line 36 of file ProfileFitter.h.

Member Function Documentation

template<class ScoringFunctionT = ChiScore>

Float IMP::saxs::ProfileFitter< ScoringFunctionT >::compute_offset

(

const Profile *

model_profile

)

const

resampling of the modeled profile is required prior to calling to this function, in order to match the q values of the exp. profile. this is not done by default to minimize the number of calls to resample.

Definition at line 96 of file ProfileFitter.h.

template<class ScoringFunctionT = ChiScore>

Float IMP::saxs::ProfileFitter< ScoringFunctionT >::compute_scale_factor	(	const Profile *	model_profile,
		Float	offset = 0.0
	)		const

resampling of the modeled profile is required prior to calling to this function, in order to match the q values of the exp. profile. this is not done by default to minimize the number of calls to resample.

Definition at line 84 of file ProfileFitter.h.

template<class ScoringFunctionT >

FitParameters IMP::saxs::ProfileFitter< ScoringFunctionT >::fit_profile	(	Profile *	partial_profile,
		float	min_c1 = 0.95,
		float	max_c1 = 1.05,
		float	min_c2 = -2.0,
		float	max_c2 = 4.0,
		bool	use_offset = false,
		const std::string	fit_file_name = ""
	)		const

c1 - adjusts the excluded volume, valid range [0.95 - 1.05] c2 - adjusts the density of hydration layer, valid range [-2.0 - 4.0]

Parameters

[in]	partial_profile	partial profiles computed
[in]	min_c1	minimal c1 value
[in]	max_c1	maximal c1 value
[in]	min_c2	minimal c2 value
[in]	max_c2	maximal c2 value
[in]	use_offset	use offset in fitting
[in]	fit_file_name	write fit in the given filename, nothing is written if empty

Returns

FitParameters (score, c1, c2)

Definition at line 186 of file ProfileFitter.h.

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

• ProfileFitter.h