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IMP Reference Guide
develop.d97d4ead1f,2024/11/21
The Integrative Modeling Platform
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#include <IMP/saxs/FormFactorTable.h>
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 50 of file FormFactorTable.h.
Public Member Functions | |
| FormFactorTable () | |
| default constructor More... | |
| FormFactorTable (const std::string &table_name, double min_q, double max_q, double delta_q) | |
| constructor with form factor table file (required for full form factors) More... | |
| double | get_dummy_form_factor (Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const |
| f(0) for solvent More... | |
| const Vector< double > & | get_dummy_form_factors (Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const |
| for reciprocal space profile calculation More... | |
| double | get_dummy_water_form_factor () const |
| f(0) for water (solvent) More... | |
| double | get_form_factor (Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const |
| get f(0), ie q=0 for real space profile calculation More... | |
| const Vector< double > & | get_form_factors (Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const |
| full form factor for reciprocal space profile calculation More... | |
| double | get_radius (Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const |
| radius More... | |
| double | get_vacuum_form_factor (Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const |
| f(0) in vacuum More... | |
| const Vector< double > & | get_vacuum_form_factors (Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const |
| for reciprocal space profile calculation More... | |
| double | get_vacuum_water_form_factor () const |
| f(0) for water in vacuum More... | |
| double | get_volume (Particle *p, FormFactorType ff_type=HEAVY_ATOMS) const |
| volume More... | |
| const Vector< double > & | get_water_dummy_form_factors () const |
| full water dummy form factor More... | |
| double | get_water_form_factor () const |
| f(0) for water More... | |
| const Vector< double > & | get_water_form_factors () const |
| full water form factor More... | |
| const Vector< double > & | get_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 double | rho_ |
| IMP::saxs::FormFactorTable::FormFactorTable | ( | ) |
default constructor
| IMP::saxs::FormFactorTable::FormFactorTable | ( | const std::string & | table_name, |
| double | min_q, | ||
| double | max_q, | ||
| double | delta_q | ||
| ) |
constructor with form factor table file (required for full form factors)
| double IMP::saxs::FormFactorTable::get_dummy_form_factor | ( | Particle * | p, |
| FormFactorType | ff_type = HEAVY_ATOMS |
||
| ) | const |
f(0) for solvent
| const Vector<double>& IMP::saxs::FormFactorTable::get_dummy_form_factors | ( | Particle * | p, |
| FormFactorType | ff_type = HEAVY_ATOMS |
||
| ) | const |
for reciprocal space profile calculation
| double IMP::saxs::FormFactorTable::get_dummy_water_form_factor | ( | ) | const |
f(0) for water (solvent)
Definition at line 82 of file FormFactorTable.h.
| double IMP::saxs::FormFactorTable::get_form_factor | ( | Particle * | p, |
| FormFactorType | ff_type = HEAVY_ATOMS |
||
| ) | const |
get f(0), ie q=0 for real space profile calculation
| const Vector<double>& IMP::saxs::FormFactorTable::get_form_factors | ( | Particle * | p, |
| FormFactorType | ff_type = HEAVY_ATOMS |
||
| ) | const |
full form factor for reciprocal space profile calculation
| double IMP::saxs::FormFactorTable::get_radius | ( | Particle * | p, |
| FormFactorType | ff_type = HEAVY_ATOMS |
||
| ) | const |
radius
| double IMP::saxs::FormFactorTable::get_vacuum_form_factor | ( | Particle * | p, |
| FormFactorType | ff_type = HEAVY_ATOMS |
||
| ) | const |
f(0) in vacuum
| const Vector<double>& IMP::saxs::FormFactorTable::get_vacuum_form_factors | ( | Particle * | p, |
| FormFactorType | ff_type = HEAVY_ATOMS |
||
| ) | const |
for reciprocal space profile calculation
| double IMP::saxs::FormFactorTable::get_vacuum_water_form_factor | ( | ) | const |
f(0) for water in vacuum
Definition at line 77 of file FormFactorTable.h.
| double IMP::saxs::FormFactorTable::get_volume | ( | Particle * | p, |
| FormFactorType | ff_type = HEAVY_ATOMS |
||
| ) | const |
volume
| const Vector<double>& IMP::saxs::FormFactorTable::get_water_dummy_form_factors | ( | ) | const |
full water dummy form factor
Definition at line 111 of file FormFactorTable.h.
| double IMP::saxs::FormFactorTable::get_water_form_factor | ( | ) | const |
f(0) for water
Definition at line 74 of file FormFactorTable.h.
| const Vector<double>& IMP::saxs::FormFactorTable::get_water_form_factors | ( | ) | const |
full water form factor
Definition at line 101 of file FormFactorTable.h.
| const Vector<double>& IMP::saxs::FormFactorTable::get_water_vacuum_form_factors | ( | ) | const |
full water vacuum form factor
Definition at line 106 of file FormFactorTable.h.
| void IMP::saxs::FormFactorTable::show | ( | std::ostream & | out = std::cout, |
| std::string | prefix = "" |
||
| ) | const |
print tables