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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/ProfileFitter.h>
Inheritance diagram for 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.
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 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 |
Protected Attributes | |
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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... | |
| virtual void | do_destroy () |
| IMP::saxs::ProfileFitter< ScoringFunctionT >::ProfileFitter | ( | const Profile * | exp_profile | ) |
Constructor.
| [in] | exp_profile | Experimental profile we want to fit |
Definition at line 36 of file ProfileFitter.h.
| Float IMP::saxs::ProfileFitter< ScoringFunctionT >::compute_offset | ( | const Profile * | model_profile | ) | const |
computes offset for fitting for fitting the modeled profile
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 93 of file ProfileFitter.h.
| Float IMP::saxs::ProfileFitter< ScoringFunctionT >::compute_scale_factor | ( | const Profile * | model_profile, |
| Float | offset = 0.0 |
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| ) | const |
computes the scaling factor needed for fitting the modeled profile
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 81 of file ProfileFitter.h.
| Float IMP::saxs::ProfileFitter< ScoringFunctionT >::compute_score | ( | const Profile * | model_profile, |
| bool | use_offset = false, |
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| const std::string | fit_file_name = "" |
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| ) | const |
compute fit score
Definition at line 222 of file ProfileFitter.h.
Here is the call graph for this function:| Float IMP::saxs::ProfileFitter< ScoringFunctionT >::compute_score | ( | const Profile * | model_profile, |
| Float | min_q, | ||
| Float | max_q | ||
| ) | const |
compute fit score in the interval
Definition at line 209 of file ProfileFitter.h.
Here is the call graph for this function:| FitParameters IMP::saxs::ProfileFitter< ScoringFunctionT >::fit_profile | ( | Profile * | partial_profile, |
| 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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| bool | use_offset = false, |
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| const std::string | fit_file_name = "" |
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| ) | const |
fit experimental profile through optimization of c1 and c2 parameters
c1 - adjusts the excluded volume, valid range [0.95 - 1.05] c2 - adjusts the density of hydration layer, valid range [-2.0 - 4.0]
| [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 |
Definition at line 183 of file ProfileFitter.h.
Here is the call graph for this function:| void IMP::saxs::ProfileFitter< ScoringFunctionT >::resample | ( | const Profile * | model_profile, |
| Profile * | resampled_profile | ||
| ) | const |
resampling of the modeled profile is required to fit the q
Definition at line 121 of file ProfileFitter.h.
Here is the call graph for this function: