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IMP Reference Guide  develop.97bab1d8fd,2021/09/21
The Integrative Modeling Platform
IMP::saxs::Profile Class Reference

#include <IMP/saxs/Profile.h>

+ Inheritance diagram for IMP::saxs::Profile:

Detailed Description

Basic profile class, can be initialized from the input file (experimental or theoretical) or computed from a set of Model Particles (theoretical)

Definition at line 31 of file Profile.h.

Public Member Functions

 Profile (const std::string &file_name, bool fit_file=false, double max_q=0.0, int units=1)
 init from file More...
 
 Profile (double qmin=0.0, double qmax=0.5, double delta=0.005)
 init for theoretical profile More...
 
void add (const Profile *other_profile, double weight=1.0)
 add another profile - useful for rigid bodies More...
 
void add (const Vector< Profile * > &profiles, const Vector< double > &weights=Vector< double >())
 add other profiles - useful for weighted ensembles More...
 
void add_errors ()
 add simulated error More...
 
void add_noise (double percentage=0.03)
 add simulated noise More...
 
void add_partial_profiles (const Profile *other_profile, double weight=1.0)
 add partial profiles More...
 
void add_partial_profiles (const Vector< Profile * > &profiles, const Vector< double > &weights=Vector< double >())
 add other partial profiles More...
 
void background_adjust (double start_q)
 background adjustment option More...
 
double calculate_I0 (const Particles &particles, FormFactorType ff_type=HEAVY_ATOMS)
 calculate Intensity at zero (= squared number of electrons) More...
 
void calculate_profile (const Particles &particles, FormFactorType ff_type=HEAVY_ATOMS, bool reciprocal=false)
 computes theoretical profile More...
 
void calculate_profile (const Particles &particles1, const Particles &particles2, FormFactorType ff_type=HEAVY_ATOMS)
 
void calculate_profile_constant_form_factor (const Particles &particles, double form_factor=1.0)
 calculate profile for any type of Particles that have coordinates More...
 
void calculate_profile_partial (const Particles &particles, const Vector< double > &surface=Vector< double >(), FormFactorType ff_type=HEAVY_ATOMS)
 compute profile for fitting with hydration layer and excluded volume More...
 
void calculate_profile_partial (const Particles &particles1, const Particles &particles2, const Vector< double > &surface1=Vector< double >(), const Vector< double > &surface2=Vector< double >(), FormFactorType ff_type=HEAVY_ATOMS)
 compute profile for fitting with hydration layer and excluded volume More...
 
void calculate_profile_reciprocal_partial (const Particles &particles, const Vector< double > &surface=Vector< double >(), FormFactorType ff_type=HEAVY_ATOMS)
 
void calculate_profile_symmetric (const Particles &particles, unsigned int n, FormFactorType ff_type=HEAVY_ATOMS)
 
void copy_errors (const Profile *exp_profile)
 
void distribution_2_profile (const RadialDistributionFunction &r_dist)
 convert to reciprocal space I(q) = Sum(P(r)*sin(qr)/qr) More...
 
void downsample (Profile *downsampled_profile, unsigned int point_number) const
 downsample the profile to a given number of points More...
 
double get_average_radius () const
 
double get_delta_q () const
 return sampling resolution More...
 
double get_error (unsigned int i) const
 
const Eigen::VectorXf & get_errors () const
 
unsigned int get_id () const
 
const Eigen::VectorXf & get_intensities () const
 
double get_intensity (unsigned int i) const
 
double get_max_q () const
 return maximal sampling point More...
 
double get_min_q () const
 return minimal sampling point More...
 
std::string get_name () const
 
double get_q (unsigned int i) const
 
const Eigen::VectorXf & get_qs () 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...
 
double get_weight (unsigned int i) const
 
bool is_partial_profile () const
 
bool is_uniform_sampling () const
 checks the sampling of experimental profile More...
 
double mean_intensity () const
 calculate mean intensity More...
 
void offset (double c)
 offset profile by c, I(q) = I(q) - c More...
 
void profile_2_distribution (RadialDistributionFunction &rd, double max_distance) const
 convert to real space P(r) function P(r) = 1/2PI^2 Sum(I(q)*qr*sin(qr)) More...
 
double radius_of_gyration (double end_q_rg=1.3) const
 compute radius of gyration with Guinier approximation More...
 
void read_partial_profiles (const std::string &file_name)
 read a partial profile from file (7 columns) More...
 
void read_SAXS_file (const std::string &file_name, bool fit_file=false, double max_q=0.0, int units=1)
 reads SAXS profile from file More...
 
void resample (const Profile *exp_profile, Profile *resampled_profile) const
 return a profile that is sampled on the q values of the exp_profile More...
 
void scale (double c)
 scale More...
 
void set_average_radius (double r)
 
void set_average_volume (double v)
 
void set_beam_profile (std::string beam_profile_file)
 
void set_errors (const Eigen::VectorXf &e)
 
void set_ff_table (FormFactorTable *ff_table)
 required for reciprocal space calculation More...
 
void set_id (unsigned int id)
 
void set_intensities (const Eigen::VectorXf &i)
 
void set_intensity (unsigned int i, double iq)
 
void set_name (std::string name)
 
void set_qs (const Eigen::VectorXf &q)
 
unsigned int size () const
 return number of entries in SAXS profile More...
 
void sum_partial_profiles (double c1, double c2, bool check_cashed=true)
 computes full profile for given fitting parameters More...
 
void write_partial_profiles (const std::string &file_name) const
 write a partial profile to file More...
 
void write_SAXS_file (const std::string &file_name, double max_q=0.0) const
 print to file 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)
 

Static Public Attributes

static const double modulation_function_parameter_
 

Protected Member Functions

void init (unsigned int size=0, unsigned int partial_profiles_size=0)
 
- Protected Member Functions inherited from IMP::Object
 Object (std::string name)
 Construct an object with the given name. More...
 
virtual void do_destroy ()
 

Protected Attributes

double average_radius_
 
double average_volume_
 
Profilebeam_profile_
 
double c1_
 
double c2_
 
double delta_q_
 
Eigen::VectorXf error_
 
bool experimental_
 
FormFactorTableff_table_
 
unsigned int id_
 
Eigen::VectorXf intensity_
 
double max_q_
 
double min_q_
 
std::string name_
 
std::vector< Eigen::VectorXf > partial_profiles_
 
Eigen::VectorXf q_
 
std::map< double, unsigned int > q_mapping_
 

Constructor & Destructor Documentation

IMP::saxs::Profile::Profile ( const std::string &  file_name,
bool  fit_file = false,
double  max_q = 0.0,
int  units = 1 
)

init from file

Parameters
[in]file_nameprofile file name
[in]fit_fileif true, intensities are read from column 3
[in]max_qread till maximal q value = max_q, or all if max_q<=0
[in]unitsgets 1, 2, or 3 for unknown q units, 1/A, or 1/nm
IMP::saxs::Profile::Profile ( double  qmin = 0.0,
double  qmax = 0.5,
double  delta = 0.005 
)

init for theoretical profile

Member Function Documentation

void IMP::saxs::Profile::add ( const Profile other_profile,
double  weight = 1.0 
)

add another profile - useful for rigid bodies

void IMP::saxs::Profile::add ( const Vector< Profile * > &  profiles,
const Vector< double > &  weights = Vector< double >() 
)

add other profiles - useful for weighted ensembles

void IMP::saxs::Profile::add_errors ( )

add simulated error

void IMP::saxs::Profile::add_noise ( double  percentage = 0.03)

add simulated noise

void IMP::saxs::Profile::add_partial_profiles ( const Profile other_profile,
double  weight = 1.0 
)

add partial profiles

void IMP::saxs::Profile::add_partial_profiles ( const Vector< Profile * > &  profiles,
const Vector< double > &  weights = Vector< double >() 
)

add other partial profiles

void IMP::saxs::Profile::background_adjust ( double  start_q)

background adjustment option

double IMP::saxs::Profile::calculate_I0 ( const Particles particles,
FormFactorType  ff_type = HEAVY_ATOMS 
)

calculate Intensity at zero (= squared number of electrons)

void IMP::saxs::Profile::calculate_profile ( const Particles particles,
FormFactorType  ff_type = HEAVY_ATOMS,
bool  reciprocal = false 
)

computes theoretical profile

Definition at line 50 of file Profile.h.

void IMP::saxs::Profile::calculate_profile ( const Particles particles1,
const Particles particles2,
FormFactorType  ff_type = HEAVY_ATOMS 
)

computes theoretical profile contribution from inter-molecular interactions between the particles

Definition at line 84 of file Profile.h.

void IMP::saxs::Profile::calculate_profile_constant_form_factor ( const Particles particles,
double  form_factor = 1.0 
)

calculate profile for any type of Particles that have coordinates

void IMP::saxs::Profile::calculate_profile_partial ( const Particles particles,
const Vector< double > &  surface = Vector< double >(),
FormFactorType  ff_type = HEAVY_ATOMS 
)

compute profile for fitting with hydration layer and excluded volume

A partial profile is a pre-computed profile, where intensities are split into 6 parts that can be summed up into a regular profile given a pair of c1/c2 values by sum_partial_profiles function. see FoXS paper for details.

void IMP::saxs::Profile::calculate_profile_partial ( const Particles particles1,
const Particles particles2,
const Vector< double > &  surface1 = Vector< double >(),
const Vector< double > &  surface2 = Vector< double >(),
FormFactorType  ff_type = HEAVY_ATOMS 
)

compute profile for fitting with hydration layer and excluded volume

void IMP::saxs::Profile::distribution_2_profile ( const RadialDistributionFunction r_dist)

convert to reciprocal space I(q) = Sum(P(r)*sin(qr)/qr)

void IMP::saxs::Profile::downsample ( Profile downsampled_profile,
unsigned int  point_number 
) const

downsample the profile to a given number of points

double IMP::saxs::Profile::get_delta_q ( ) const

return sampling resolution

Definition at line 155 of file Profile.h.

double IMP::saxs::Profile::get_max_q ( ) const

return maximal sampling point

Definition at line 161 of file Profile.h.

double IMP::saxs::Profile::get_min_q ( ) const

return minimal sampling point

Definition at line 158 of file Profile.h.

virtual ::IMP::VersionInfo IMP::saxs::Profile::get_version_info ( ) const
virtual

Get information about the module and version of the object.

Reimplemented from IMP::Object.

Definition at line 249 of file Profile.h.

bool IMP::saxs::Profile::is_uniform_sampling ( ) const

checks the sampling of experimental profile

double IMP::saxs::Profile::mean_intensity ( ) const

calculate mean intensity

void IMP::saxs::Profile::offset ( double  c)

offset profile by c, I(q) = I(q) - c

void IMP::saxs::Profile::profile_2_distribution ( RadialDistributionFunction rd,
double  max_distance 
) const

convert to real space P(r) function P(r) = 1/2PI^2 Sum(I(q)*qr*sin(qr))

double IMP::saxs::Profile::radius_of_gyration ( double  end_q_rg = 1.3) const

compute radius of gyration with Guinier approximation

ln[I(q)]=ln[I(0)] - (q^2*rg^2)/3

Parameters
[in]end_q_rgdetermines the range of profile used for approximation: i.e. q*rg < end_q_rg. Use 1.3 for globular proteins, 0.8 for elongated
void IMP::saxs::Profile::read_partial_profiles ( const std::string &  file_name)

read a partial profile from file (7 columns)

void IMP::saxs::Profile::read_SAXS_file ( const std::string &  file_name,
bool  fit_file = false,
double  max_q = 0.0,
int  units = 1 
)

reads SAXS profile from file

Parameters
[in]file_nameprofile file name
[in]fit_fileif true, intensities are read from column 3
[in]max_qread till maximal q value = max_q, or all if max_q<=0
[in]unitsgets 1, 2, or 3 for unknown q units, 1/A, or 1/nm
void IMP::saxs::Profile::resample ( const Profile exp_profile,
Profile resampled_profile 
) const

return a profile that is sampled on the q values of the exp_profile

void IMP::saxs::Profile::scale ( double  c)

scale

void IMP::saxs::Profile::set_ff_table ( FormFactorTable ff_table)

required for reciprocal space calculation

Definition at line 197 of file Profile.h.

unsigned int IMP::saxs::Profile::size ( ) const

return number of entries in SAXS profile

Definition at line 178 of file Profile.h.

void IMP::saxs::Profile::sum_partial_profiles ( double  c1,
double  c2,
bool  check_cashed = true 
)

computes full profile for given fitting parameters

void IMP::saxs::Profile::write_partial_profiles ( const std::string &  file_name) const

write a partial profile to file

void IMP::saxs::Profile::write_SAXS_file ( const std::string &  file_name,
double  max_q = 0.0 
) const

print to file

Parameters
[in]file_nameoutput file name
[in]max_qoutput till maximal q value = max_q, or all if max_q<=0

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