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IMP
2.3.1
The Integrative Modeling Platform
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IMP
2.3.1
The Integrative Modeling Platform
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#include <IMP/saxs/WeightedProfileFitter.h>
Inheritance diagram for IMP::saxs::WeightedProfileFitter:Fitting of multiple profiles to the experimental one. The weights of the profiles are computed analytically using non-negative least squares fitting (NNLS).
Definition at line 27 of file WeightedProfileFitter.h.
Public Member Functions | |
| WeightedProfileFitter (const Profile *exp_profile) | |
| Constructor. More... | |
| Float | compute_score (const ProfilesTemp &profiles, std::vector< double > &weights, bool NNLS=true) const |
| compute a weighted score that minimizes chi More... | |
| WeightedFitParameters | fit_profile (ProfilesTemp partial_profiles, float min_c1=0.95, float max_c1=1.05, float min_c2=-2.0, float max_c2=4.0) const |
| fit profiles by optimization of c1/c2 and weights More... | |
| void | write_fit_file (ProfilesTemp partial_profiles, const WeightedFitParameters &fp, const std::string fit_file_name) const |
| write a fit file More... | |
| Public Member Functions inherited from IMP::saxs::ProfileFitter< ChiScore > | |
| ProfileFitter (const Profile *exp_profile) | |
| Constructor. More... | |
| ProfileFitter (const Profile *exp_profile, ChiScore *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 More... | |
| Float | compute_score (const Profile *model_profile, Float min_q, Float max_q) const |
| compute fit score in the interval More... | |
| 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 More... | |
| 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 () |
| 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. More... | |
| 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 |
Additional Inherited Members | |
| Protected Member Functions inherited from IMP::base::Object | |
| Object (std::string name) | |
| Construct an object with the given name. More... | |
| virtual void | do_destroy () |
| Protected Attributes inherited from IMP::saxs::ProfileFitter< ChiScore > | |
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base::PointerMember< const Profile > | exp_profile_ |
| ChiScore * | scoring_function_ |
| IMP::saxs::WeightedProfileFitter::WeightedProfileFitter | ( | const Profile * | exp_profile | ) |
Constructor.
| [in] | exp_profile | Experimental profile we want to fit |
| Float IMP::saxs::WeightedProfileFitter::compute_score | ( | const ProfilesTemp & | profiles, |
| std::vector< double > & | weights, | ||
| bool | NNLS = true |
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| ) | const |
compute a weighted score that minimizes chi
it is assumed that the q values of the profiles are the same as the q values of the experimental profile. Use Profile::resample to resample if(NNLS = true, solve non-negative least squares, otherwise solve just least squares, that may return negative weights to be discarded later
| WeightedFitParameters IMP::saxs::WeightedProfileFitter::fit_profile | ( | ProfilesTemp | partial_profiles, |
| float | min_c1 = 0.95, |
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| float | max_c1 = 1.05, |
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| float | min_c2 = -2.0, |
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| float | max_c2 = 4.0 |
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| ) | const |
fit profiles by optimization of c1/c2 and weights
it is assumed that the q values of the profiles are the same as the q values of the experimental profile. Use Profile::resample to resample
| void IMP::saxs::WeightedProfileFitter::write_fit_file | ( | ProfilesTemp | partial_profiles, |
| const WeightedFitParameters & | fp, | ||
| const std::string | fit_file_name | ||
| ) | const |
write a fit file