#include <IMP/saxs/Profile.h>

Inheritance diagram for IMP::saxs::Profile:

Public Member Functions
	Profile (const String &file_name, bool fit_file=false)
	init from file

	Profile (Float qmin=0.0, Float qmax=0.5, Float delta=0.005)
	init for theoretical profile

void	add (const Profile *other_profile, Float weight=1.0)
	add another profile - useful for rigid bodies

void	add (const std::vector< Profile * > &profiles, const std::vector< Float > &weights=std::vector< Float >())
	add other profiles - useful for weighted ensembles

void	add_entry (Float q, Float intensity, Float error=1.0)
	add intensity entry to profile

void	add_errors ()
	add simulated error

void	add_noise (Float percentage=0.03)
	add simulated noise

void	add_partial_profiles (const Profile *other_profile, Float weight=1.0)
	add partial profiles

void	add_partial_profiles (const std::vector< Profile * > &profiles, const std::vector< Float > &weights=std::vector< Float >())
	add other partial profiles

void	background_adjust (double start_q)
	background adjustment option

Float	calculate_I0 (const kernel::Particles &particles, FormFactorType ff_type=HEAVY_ATOMS)
	calculate Intensity at zero (= squared number of electrons)

void	calculate_profile (const kernel::Particles &particles, FormFactorType ff_type=HEAVY_ATOMS, bool reciprocal=false)
	computes theoretical profile

void	calculate_profile (const kernel::Particles &particles1, const kernel::Particles &particles2, FormFactorType ff_type=HEAVY_ATOMS)

void	calculate_profile_constant_form_factor (const kernel::Particles &particles, Float form_factor=1.0)
	calculate profile for any type of kernel::Particles that have coordinates

void	calculate_profile_partial (const kernel::Particles &particles, const Floats &surface=Floats(), FormFactorType ff_type=HEAVY_ATOMS)
	compute profile for fitting with hydration layer and excluded volume More...

void	calculate_profile_partial (const kernel::Particles &particles1, const kernel::Particles &particles2, const Floats &surface1=Floats(), const Floats &surface2=Floats(), FormFactorType ff_type=HEAVY_ATOMS)
	compute profile for fitting with hydration layer and excluded volume

void	calculate_profile_reciprocal_partial (const kernel::Particles &particles, const Floats &surface=Floats(), FormFactorType ff_type=HEAVY_ATOMS)

void	calculate_profile_symmetric (const kernel::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)

void	downsample (Profile *downsampled_profile, unsigned int point_number) const
	downsample the profile to a given number of points

Float	get_average_radius () const

Float	get_delta_q () const
	return sampling resolution

Float	get_error (unsigned int i) const

unsigned int	get_id () const

Float	get_intensity (unsigned int i) const

Float	get_max_q () const
	return maximal sampling point

Float	get_min_q () const
	return minimal sampling point

std::string	get_name () const

Float	get_q (unsigned int i) const

virtual std::string	get_type_name () const

virtual ::IMP::base::VersionInfo	get_version_info () const
	Get information about the module and version of the object.

Float	get_weight (unsigned int i) const

bool	is_uniform_sampling () const
	checks the sampling of experimental profile

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

void	profile_2_distribution (RadialDistributionFunction &rd, Float max_distance) const
	convert to real space P(r) function P(r) = 1/2PI^2 Sum(I(q)qrsin(qr))

double	radius_of_gyration (double end_q_rg=1.3) const
	compute radius of gyration with Guinier approximation More...

void	read_partial_profiles (const String &file_name)
	read a partial profile from file (7 columns)

void	read_SAXS_file (const String &file_name, bool fit_file=false)
	reads SAXS profile from file More...

void	resample (const Profile exp_profile, Profile resampled_profile, bool partial_profiles=false) const
	return a profile that is sampled on the q values of the exp_profile

void	scale (Float c)
	scale

void	set_average_radius (Float r)

void	set_average_volume (Float v)

void	set_ff_table (FormFactorTable *ff_table)
	required for reciprocal space calculation

void	set_id (unsigned int id)

void	set_intensity (unsigned int i, Float iq)

void	set_name (std::string name)

unsigned int	size () const
	return number of entries in SAXS profile

void	sum_partial_profiles (Float c1, Float c2)
	computes full profile for given fitting parameters

void	write_partial_profiles (const String &file_name) const
	write a partial profile to file

void	write_SAXS_file (const String &file_name, Float max_q=0.0) const
	print to file More...

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

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 Float	modulation_function_parameter_

Protected Member Functions
void	init ()

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

Protected Attributes
Float	average_radius_

Float	average_volume_

Float	delta_q_

std::vector< double >	error_

bool	experimental_

FormFactorTable *	ff_table_

unsigned int	id_

std::vector< double >	intensity_

Float	max_q_

Float	min_q_

std::string	name_

std::vector< std::vector < double > >	partial_profiles_

std::vector< double >	q_

std::map< float, unsigned int >	q_mapping_

Detailed Description

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

Definition at line 31 of file Profile.h.

Member Function Documentation

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

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

Definition at line 78 of file Profile.h.

void IMP::saxs::Profile::calculate_profile_partial	(	const kernel::Particles &	particles,
		const Floats &	surface = `Floats()`,
		FormFactorType	ff_type = `HEAVY_ATOMS`
	)

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.

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

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_SAXS_file	(	const String &	file_name,
		bool	fit_file = `false`
	)

Parameters

[in]	file_name	profile file name
[in]	fit_file	if true, intensities are read from column 3

void IMP::saxs::Profile::write_SAXS_file	(	const String &	file_name,
		Float	max_q = `0.0`
	)		const

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

Public Member Functions

Static Public Attributes

Protected Member Functions

Protected Attributes

Detailed Description

Member Function Documentation