IMP  2.4.0
The Integrative Modeling Platform
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IMP::saxs::FormFactorTable Class Reference

#include <IMP/saxs/FormFactorTable.h>

Detailed Description

class that deals with form factor computation two form factors are supported: (i) zero form factors for faster approximated calculations (ii) full form factors for slower accurate calculations

Each form factor can be divided into two parts: vacuum and dummy. dummy is an approximated excluded volume (solvent) form factor. The approximation is done using Fraser, MacRae and Suzuki (1978) model.

Definition at line 48 of file FormFactorTable.h.

Public Member Functions

 FormFactorTable ()
 default constructor More...
 
 FormFactorTable (const String &table_name, Float min_q, Float max_q, Float delta_q)
 constructor with form factor table file (required for full form factors) More...
 
Float get_dummy_form_factor (kernel::Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
 f(0) for solvent More...
 
const Floatsget_dummy_form_factors (kernel::Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
 for reciprocal space profile calculation More...
 
Float get_dummy_water_form_factor () const
 f(0) for water (solvent) More...
 
Float get_form_factor (kernel::Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
 get f(0), ie q=0 for real space profile calculation More...
 
const Floatsget_form_factors (kernel::Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
 full form factor for reciprocal space profile calculation More...
 
Float get_radius (kernel::Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
 radius More...
 
Float get_vacuum_form_factor (kernel::Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
 f(0) in vacuum More...
 
const Floatsget_vacuum_form_factors (kernel::Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
 for reciprocal space profile calculation More...
 
Float get_vacuum_water_form_factor () const
 f(0) for water in vacuum More...
 
Float get_volume (kernel::Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const
 volume More...
 
const Floatsget_water_dummy_form_factors () const
 full water dummy form factor More...
 
Float get_water_form_factor () const
 f(0) for water More...
 
const Floatsget_water_form_factors () const
 full water form factor More...
 
const Floatsget_water_vacuum_form_factors () const
 full water vacuum form factor More...
 
void show (std::ostream &out=std::cout, std::string prefix="") const
 print tables More...
 

Static Public Attributes

static Float rho_
 

Friends

std::ostream & operator<< (std::ostream &s, const AtomFactorCoefficients &atom_factor_coefficients)
 
std::istream & operator>> (std::istream &s, AtomFactorCoefficients &atom_factor_coefficients)
 

Constructor & Destructor Documentation

IMP::saxs::FormFactorTable::FormFactorTable ( )

default constructor

IMP::saxs::FormFactorTable::FormFactorTable ( const String table_name,
Float  min_q,
Float  max_q,
Float  delta_q 
)

constructor with form factor table file (required for full form factors)

Member Function Documentation

Float IMP::saxs::FormFactorTable::get_dummy_form_factor ( kernel::Particle p,
FormFactorType  ff_type = HEAVY_ATOMS 
) const

f(0) for solvent

const Floats& IMP::saxs::FormFactorTable::get_dummy_form_factors ( kernel::Particle p,
FormFactorType  ff_type = HEAVY_ATOMS 
) const

for reciprocal space profile calculation

Float IMP::saxs::FormFactorTable::get_dummy_water_form_factor ( ) const

f(0) for water (solvent)

Definition at line 80 of file FormFactorTable.h.

Float IMP::saxs::FormFactorTable::get_form_factor ( kernel::Particle p,
FormFactorType  ff_type = HEAVY_ATOMS 
) const

get f(0), ie q=0 for real space profile calculation

const Floats& IMP::saxs::FormFactorTable::get_form_factors ( kernel::Particle p,
FormFactorType  ff_type = HEAVY_ATOMS 
) const

full form factor for reciprocal space profile calculation

Float IMP::saxs::FormFactorTable::get_radius ( kernel::Particle p,
FormFactorType  ff_type = HEAVY_ATOMS 
) const

radius

Float IMP::saxs::FormFactorTable::get_vacuum_form_factor ( kernel::Particle p,
FormFactorType  ff_type = HEAVY_ATOMS 
) const

f(0) in vacuum

const Floats& IMP::saxs::FormFactorTable::get_vacuum_form_factors ( kernel::Particle p,
FormFactorType  ff_type = HEAVY_ATOMS 
) const

for reciprocal space profile calculation

Float IMP::saxs::FormFactorTable::get_vacuum_water_form_factor ( ) const

f(0) for water in vacuum

Definition at line 75 of file FormFactorTable.h.

Float IMP::saxs::FormFactorTable::get_volume ( kernel::Particle p,
FormFactorType  ff_type = HEAVY_ATOMS 
) const

volume

const Floats& IMP::saxs::FormFactorTable::get_water_dummy_form_factors ( ) const

full water dummy form factor

Definition at line 109 of file FormFactorTable.h.

Float IMP::saxs::FormFactorTable::get_water_form_factor ( ) const

f(0) for water

Definition at line 72 of file FormFactorTable.h.

const Floats& IMP::saxs::FormFactorTable::get_water_form_factors ( ) const

full water form factor

Definition at line 101 of file FormFactorTable.h.

const Floats& IMP::saxs::FormFactorTable::get_water_vacuum_form_factors ( ) const

full water vacuum form factor

Definition at line 104 of file FormFactorTable.h.

void IMP::saxs::FormFactorTable::show ( std::ostream &  out = std::cout,
std::string  prefix = "" 
) const

print tables


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