#include <IMP/saxs/Profile.h>

Public Member Functions
	Profile (const String &file_name)
	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_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	background_adjust (double start_q)
	background adjustment option

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

void	calculate_profile (const Particles &particles, FormFactorType ff_type=HEAVY_ATOMS, bool reciprocal=false, bool variance=false, double variance_tau=0.1)
	computes theoretical profile

void	calculate_profile (const Particles &particles1, const Particles &particles2, FormFactorType ff_type=HEAVY_ATOMS, bool variance=false, double variance_tau=0.1)

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

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

void	calculate_profile_partial (const Particles &particles1, const 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 Particles &particles, const Floats &surface=Floats(), FormFactorType ff_type=HEAVY_ATOMS)

void	calculate_profile_symmetric (const Particles &particles, unsigned int n, FormFactorType ff_type=HEAVY_ATOMS)

void	distribution_2_profile (const RadialDistributionFunction &r_dist)
	convert to reciprocal space I(q) = Sum(P(r)*sin(qr)/qr)

Float	get_average_radius () const

Float	get_delta_q () const
	return sampling resolution

Float	get_error (unsigned int i) 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

Float	get_q (unsigned int i) const

Float	get_variance (unsigned int i, unsigned int j) const

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

void	read_SAXS_file (const String &file_name)
	reads SAXS profile from file

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_intensity (unsigned int i, Float iq)

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

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

void	write_partial_profiles (const String &file_name) const

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

Static Public Attributes
static const Float	modulation_function_parameter_

Protected Attributes
Float	average_radius_

Float	average_volume_

Float	delta_q_

bool	experimental_

FormFactorTable *	ff_table_

Float	max_q_

Float	min_q_

std::vector< Profile >	partial_profiles_

std::vector< IntensityEntry >	profile_

std::vector< std::vector < double > >	variances_

Friends
std::ostream &	operator<< (std::ostream &q, const IntensityEntry &e)

std::istream &	operator>> (std::istream &q, IntensityEntry &e)

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 28 of file Profile.h.

Member Function Documentation

void IMP::saxs::Profile::calculate_profile	(	const Particles &	particles1,
		const Particles &	particles2,
		FormFactorType	ff_type = `HEAVY_ATOMS`,
		bool	variance = `false`,
		double	variance_tau = `0.1`
	)

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

Definition at line 86 of file Profile.h.

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 Attributes

Friends

Detailed Description

Member Function Documentation