core::scoring::saxs Namespace Reference

Classes
class	DistanceHistogram
class	FastSAXSEnergy
class	FastSAXSEnergyCreator
class	FormFactor
class	FormFactorManager
	selects a given number of fragments using a quota scheme More...
class	SAXSEnergy
class	SAXSEnergyCEN
class	SAXSEnergyCreator
class	SAXSEnergyCreatorCEN
class	SAXSEnergyCreatorFA
class	SAXSEnergyFA
class	SinXOverX

Typedefs
typedef utility::pointer::owning_ptr < DistanceHistogram >	DistanceHistogramOP
typedef utility::pointer::owning_ptr < DistanceHistogram const >	DistanceHistogramCOP
typedef utility::pointer::owning_ptr < FormFactor >	FormFactorOP
typedef utility::pointer::owning_ptr < FormFactor const >	FormFactorCOP
typedef utility::pointer::owning_ptr < FormFactorManager >	FormFactorManagerOP
typedef utility::pointer::owning_ptr < FormFactorManager const >	FormFactorManagerCOP

Functions
static basic::Tracer	TR ("core.scoring.saxs.FastSAXSEnergy")
core::Size	aa2idx (core::chemical::AA aa)
void	load_fastsax_spectrum (core::Size &nq, utility::vector1< core::Real >::iterator &q, utility::vector1< core::Real >::iterator &i_obs, utility::vector1< core::Real >::iterator &i_sig)
void	load_form_factors (core::Size nq, utility::vector1< core::Real >::iterator &q_in, utility::vector1< utility::vector1< core::Real > >::iterator &spectrum)
static basic::Tracer	trFormFactor ("core.scoring.saxs.FormFactor")
static basic::Tracer	trFormFactorManager ("core.scoring.saxs.FormFactorManager")
static basic::Tracer	trSAXSEnergy ("core.scoring.saxs.SAXSEnergy")

Variables
core::Real	ref_spectrum [][21]

Typedef Documentation

typedef utility::pointer::owning_ptr<DistanceHistogram const> core::scoring::saxs::DistanceHistogramCOP

Definition at line 30 of file DistanceHistogram.fwd.hh.

typedef utility::pointer::owning_ptr<DistanceHistogram> core::scoring::saxs::DistanceHistogramOP

Definition at line 25 of file DistanceHistogram.fwd.hh.

typedef utility::pointer::owning_ptr<FormFactor const> core::scoring::saxs::FormFactorCOP

Definition at line 30 of file FormFactor.fwd.hh.

typedef utility::pointer::owning_ptr<FormFactorManager const> core::scoring::saxs::FormFactorManagerCOP

Definition at line 30 of file FormFactorManager.fwd.hh.

typedef utility::pointer::owning_ptr<FormFactorManager> core::scoring::saxs::FormFactorManagerOP

Definition at line 25 of file FormFactorManager.fwd.hh.

typedef utility::pointer::owning_ptr<FormFactor> core::scoring::saxs::FormFactorOP

Definition at line 25 of file FormFactor.fwd.hh.

Function Documentation

core::Size core::scoring::saxs::aa2idx

(

core::chemical::AA

aa)

Definition at line 489 of file FastSAXSEnergy.cc.

References core::chemical::aa_ala, core::chemical::aa_arg, core::chemical::aa_asn, core::chemical::aa_asp, core::chemical::aa_cys, core::chemical::aa_gln, core::chemical::aa_glu, core::chemical::aa_gly, core::chemical::aa_his, core::chemical::aa_ile, core::chemical::aa_leu, core::chemical::aa_lys, core::chemical::aa_met, core::chemical::aa_phe, core::chemical::aa_pro, core::chemical::aa_ser, core::chemical::aa_thr, core::chemical::aa_trp, core::chemical::aa_tyr, and core::chemical::aa_val.

Referenced by core::scoring::saxs::FastSAXSEnergy::setup_for_derivatives(), and core::scoring::saxs::FastSAXSEnergy::setup_for_scoring().

void core::scoring::saxs::load_fastsax_spectrum	(	core::Size &	nq,
		utility::vector1< core::Real >::iterator &	q,
		utility::vector1< core::Real >::iterator &	i_obs,
		utility::vector1< core::Real >::iterator &	i_sig
	)

Definition at line 529 of file FastSAXSEnergy.cc.

References ref_spectrum, and TR().

Referenced by core::scoring::saxs::FastSAXSEnergy::setup_for_derivatives(), and core::scoring::saxs::FastSAXSEnergy::setup_for_scoring().

void core::scoring::saxs::load_form_factors	(	core::Size	nq,
		utility::vector1< core::Real >::iterator &	q_in,
		utility::vector1< utility::vector1< core::Real > >::iterator &	spectrum
	)

Definition at line 571 of file FastSAXSEnergy.cc.

References ref_spectrum, and TR().

Referenced by core::scoring::saxs::FastSAXSEnergy::setup_for_derivatives(), and core::scoring::saxs::FastSAXSEnergy::setup_for_scoring().

static basic::Tracer core::scoring::saxs::TR ( "core.scoring.saxs.FastSAXSEnergy"  )

static

Referenced by load_fastsax_spectrum(), load_form_factors(), and core::scoring::saxs::FastSAXSEnergy::setup_for_scoring().

static basic::Tracer core::scoring::saxs::trFormFactor ( "core.scoring.saxs.FormFactor"  )

static

Referenced by core::scoring::saxs::FormFactor::FormFactor().

static basic::Tracer core::scoring::saxs::trFormFactorManager ( "core.scoring.saxs.FormFactorManager"  )

static

Referenced by core::scoring::saxs::FormFactorManager::get_ff(), core::scoring::saxs::FormFactorManager::load_ff(), and core::scoring::saxs::FormFactorManager::load_ff_from_db().

static basic::Tracer core::scoring::saxs::trSAXSEnergy ( "core.scoring.saxs.SAXSEnergy"  )

static

Referenced by core::scoring::saxs::SAXSEnergy::compute_chi(), core::scoring::saxs::SAXSEnergy::compute_chi_with_fit(), core::scoring::saxs::SAXSEnergy::compute_L1(), core::scoring::saxs::SAXSEnergy::init_ff(), core::scoring::saxs::SAXSEnergy::read_spectrum(), core::scoring::saxs::SAXSEnergy::rehash_form_factors(), core::scoring::saxs::SAXSEnergy::SAXSEnergy(), and core::scoring::saxs::SAXSEnergy::set_up_q().

Variable Documentation

core::Real core::scoring::saxs::ref_spectrum[][21]

Definition at line 78 of file FastSAXSEnergy.cc.

Referenced by protocols::abinitio::AbrelaxApplication::check_filters(), protocols::symmetric_docking::SymDockProtocol::docking_lowres_filter(), load_fastsax_spectrum(), load_form_factors(), and core::scoring::saxs::SAXSEnergy::SAXSEnergy().