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_
Profile *	beam_profile_
double	c1_
double	c2_
double	delta_q_
Eigen::VectorXf	error_
bool	experimental_
FormFactorTable *	ff_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_name	profile file name
[in]	fit_file	if true, intensities are read from column 3
[in]	max_q	read till maximal q value = max_q, or all if max_q<=0
[in]	units	gets 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_rg

determines 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_name	profile file name
[in]	fit_file	if true, intensities are read from column 3
[in]	max_q	read till maximal q value = max_q, or all if max_q<=0
[in]	units	gets 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_name	output file name
[in]	max_q	output till maximal q value = max_q, or all if max_q<=0

---

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

• Profile.h