Detailed Description

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

Examples: profile, profile fit

List of all members.

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_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)
	computes theoretical profile
void	calculate_profile (const Particles &particles1, const Particles &particles2, FormFactorType ff_type=HEAVY_ATOMS)
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)
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_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_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_SAXS_file (const String &file_name) const
	print to file

Static Public Attributes
static const Float	modulation_function_parameter_

Protected Attributes
Float	average_radius_
Float	delta_q_
bool	experimental_
FormFactorTable *	ff_table_
Float	max_q_
Float	min_q_
std::vector< Profile >	partial_profiles_
std::vector< IntensityEntry >	profile_

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

Constructor & Destructor Documentation

IMP::saxs::Profile::Profile ( const String & file_name )

init from file

IMP::saxs::Profile::Profile	(	Float	qmin = `0.0`,
		Float	qmax = `0.5`,
		Float	delta = `0.005`
	)

init for theoretical profile

Member Function Documentation

void IMP::saxs::Profile::add	(	const Profile &	other_profile,
		Float	weight = `1.0`
	)

add another profile - useful for rigid bodies

void IMP::saxs::Profile::add_entry	(	Float	q,
		Float	intensity,
		Float	error = `1.0`
	)

add intensity entry to profile

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

add simulated error

void IMP::saxs::Profile::add_partial_profiles	(	const Profile &	other_profile,
		Float	weight = `1.0`
	)

add partial profiles

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

background adjustment option

Float 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

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

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

void IMP::saxs::Profile::calculate_profile_constant_form_factor	(	const Particles &	particles,
		Float	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 Floats &	surface = `Floats()`,
		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)

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

return sampling resolution

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

return maximal sampling point

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

return minimal sampling point

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

checks the sampling of experimental profile

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

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

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

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

void IMP::saxs::Profile::read_SAXS_file ( const String & file_name )

reads SAXS profile from file

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

scale

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

required for reciprocal space calculation

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

return number of entries in SAXS profile

void IMP::saxs::Profile::sum_partial_profiles	(	Float	c1,
		Float	c2,
		Profile &	out_profile
	)

computes full profile for given fitting parameters

void IMP::saxs::Profile::write_SAXS_file ( const String & file_name ) const

print to file

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

Profile.h

Detailed Description

Public Member Functions

Static Public Attributes

Protected Attributes

Friends

Constructor & Destructor Documentation

Member Function Documentation