protocols::scoring::methods::saxs::PDDFEnergy Class Reference

#include <PDDFEnergy.hh>

Public Member Functions
	PDDFEnergy ()
	PDDFEnergy (utility::vector1< core::Real > const &, utility::vector1< core::Real > const &)
	c-tors More...
virtual	~PDDFEnergy ()
virtual core::scoring::methods::EnergyMethodOP	clone () const
virtual void	finalize_total_energy (core::pose::Pose &pose, core::scoring::ScoreFunction const &, core::scoring::EnergyMap &totals) const
virtual void	indicate_required_context_graphs (utility::vector1< bool > &) const
core::scoring::methods::EnergyMethodOP	create_energy_method (core::scoring::methods::EnergyMethodOptions const &) const
utility::vector1< core::Real > &	get_pddf ()
utility::vector1< core::Real > &	get_dist_bins ()
utility::vector1< core::Real > &	compute_pddf (const core::pose::Pose &) const
utility::vector1< core::Real > &	compute_pddf_without_ff (const core::pose::Pose &) const
core::Real	compute_chi (utility::vector1< core::Real > const &, utility::vector1< core::Real > const &) const
core::Real	compute_L1 (utility::vector1< core::Real > const &, utility::vector1< core::Real > const &) const
void	create_pddf (core::pose::Pose &, core::Real, core::Real, core::Real)
core::Real	evaluate_pddf_energy (const core::pose::Pose &pose) const

Private Member Functions
void	read_pddf (std::string)
virtual core::Size	version () const

Private Attributes
utility::vector1 < utility::vector1< core::Real > >	factors_
utility::vector1< core::Size >	r_ids_
utility::vector1< core::Size >	a_ids_
utility::vector1 < utility::vector1< core::Real > >	dmatrix_
utility::vector1< bool >	is_glob_
core::Real	norm_
bool	if_fit_area_
utility::vector1< core::Real >	d_
utility::vector1< core::Real >	pose_pddf_
utility::vector1< core::Real >	reference_pddf_
core::scoring::saxs::FormFactorManager *	ff_manager_
core::Real	bin_size_
core::Size	min_bin_
core::Size	max_bin_
bool	if_hydrogens_

Constructor & Destructor Documentation

protocols::scoring::methods::saxs::PDDFEnergy::PDDFEnergy

(

)

References bin_size_, core::chemical::CENTROID, create_pddf(), score::saxs::d_max, score::saxs::d_min, score::saxs::d_step, file, score::saxs::fit_pddf_area, core::chemical::ChemicalManager::get_instance(), if_fit_area_, if_hydrogens_, max_bin_, min_bin_, in::file::native, norm_, basic::options::option, option, core::import_pose::pose_from_pdb(), read_pddf(), score::saxs::ref_pddf, reference_pddf_, in::file::residue_type_set, core::chemical::ChemicalManager::residue_type_set(), core::util::switch_to_residue_type_set(), user, and utility_exit_with_message.

Referenced by clone(), and create_energy_method().

protocols::scoring::methods::saxs::PDDFEnergy::PDDFEnergy	(	utility::vector1< core::Real > const &	reference_d,
		utility::vector1< core::Real > const &	reference_pddf
	)

c-tors

References bin_size_, d_, if_fit_area_, max_bin_, min_bin_, pose_pddf_, and reference_pddf_.

virtual protocols::scoring::methods::saxs::PDDFEnergy::~PDDFEnergy ( )

inlinevirtual

Member Function Documentation

virtual core::scoring::methods::EnergyMethodOP protocols::scoring::methods::saxs::PDDFEnergy::clone ( ) const

inlinevirtual

References PDDFEnergy().

core::Real protocols::scoring::methods::saxs::PDDFEnergy::compute_chi	(	utility::vector1< core::Real > const &	pddf_scored,
		utility::vector1< core::Real > const &	pddf_reference
	)		const

References d_, if_fit_area_, max_bin_, and min_bin_.

Referenced by evaluate_pddf_energy(), and finalize_total_energy().

core::Real protocols::scoring::methods::saxs::PDDFEnergy::compute_L1	(	utility::vector1< core::Real > const &	pddf_scored,
		utility::vector1< core::Real > const &	pddf_reference
	)		const

References sum().

utility::vector1< core::Real > & protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf

(

const core::pose::Pose &

pose

)

const

References a_ids_, core::conformation::Residue::atom_type(), bin_size_, d_, numeric::xyzVector< class >::distance(), dmatrix_, factors_, ff_manager_, core::scoring::saxs::FormFactorManager::get_ff(), if_hydrogens_, is_glob_, core::chemical::AtomType::is_hydrogen(), core::scoring::saxs::FormFactorManager::is_known_atom(), j, core::chemical::AtomType::name(), core::conformation::Residue::natoms(), pose_pddf_, r_ids_, resi, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

utility::vector1< core::Real > & protocols::scoring::methods::saxs::PDDFEnergy::compute_pddf_without_ff

(

const core::pose::Pose &

pose

)

const

References a_ids_, core::conformation::Residue::atom_type(), bin, bin_size_, numeric::xyzVector< class >::distance(), if_hydrogens_, core::chemical::AtomType::is_hydrogen(), j, core::conformation::Residue::natoms(), pose_pddf_, r_ids_, reference_pddf_, resi, core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by create_pddf(), evaluate_pddf_energy(), and finalize_total_energy().

core::scoring::methods::EnergyMethodOP protocols::scoring::methods::saxs::PDDFEnergy::create_energy_method ( core::scoring::methods::EnergyMethodOptions const &  ) const

inline

References PDDFEnergy().

void protocols::scoring::methods::saxs::PDDFEnergy::create_pddf	(	core::pose::Pose &	ref_pose,
		core::Real	d_min,
		core::Real	d_step,
		core::Real	d_max
	)

References bin_size_, compute_pddf_without_ff(), d_, pose_pddf_, and reference_pddf_.

Referenced by PDDFEnergy().

core::Real protocols::scoring::methods::saxs::PDDFEnergy::evaluate_pddf_energy

(

const core::pose::Pose &

pose

)

const

References compute_chi(), compute_pddf_without_ff(), pose_pddf_, and reference_pddf_.

void protocols::scoring::methods::saxs::PDDFEnergy::finalize_total_energy ( core::pose::Pose &  pose, core::scoring::ScoreFunction const &  , core::scoring::EnergyMap &  totals  ) const

virtual

References compute_chi(), compute_pddf_without_ff(), core::scoring::pddf_score, pose_pddf_, PROF_START, PROF_STOP, reference_pddf_, and basic::SAXS.

utility::vector1<core::Real>& protocols::scoring::methods::saxs::PDDFEnergy::get_dist_bins ( )

inline

References d_.

utility::vector1<core::Real>& protocols::scoring::methods::saxs::PDDFEnergy::get_pddf ( )

inline

References pose_pddf_.

virtual void protocols::scoring::methods::saxs::PDDFEnergy::indicate_required_context_graphs ( utility::vector1< bool > &  ) const

inlinevirtual

void protocols::scoring::methods::saxs::PDDFEnergy::read_pddf ( std::string  file_name )

private

References bin_size_, d_, getline(), norm(), pose_pddf_, reference_pddf_, and utility_exit_with_message.

Referenced by PDDFEnergy().

core::Size protocols::scoring::methods::saxs::PDDFEnergy::version ( ) const

privatevirtual

Member Data Documentation

utility::vector1<core::Size> protocols::scoring::methods::saxs::PDDFEnergy::a_ids_

mutableprivate

Referenced by compute_pddf(), and compute_pddf_without_ff().

core::Real protocols::scoring::methods::saxs::PDDFEnergy::bin_size_

private

Referenced by compute_pddf(), compute_pddf_without_ff(), create_pddf(), PDDFEnergy(), and read_pddf().

utility::vector1<core::Real> protocols::scoring::methods::saxs::PDDFEnergy::d_

private

Referenced by compute_chi(), compute_pddf(), create_pddf(), get_dist_bins(), PDDFEnergy(), and read_pddf().

utility::vector1< utility::vector1<core::Real> > protocols::scoring::methods::saxs::PDDFEnergy::dmatrix_

mutableprivate

Referenced by compute_pddf().

utility::vector1< utility::vector1<core::Real> > protocols::scoring::methods::saxs::PDDFEnergy::factors_

mutableprivate

Referenced by compute_pddf().

core::scoring::saxs::FormFactorManager* protocols::scoring::methods::saxs::PDDFEnergy::ff_manager_

private

Referenced by compute_pddf().

bool protocols::scoring::methods::saxs::PDDFEnergy::if_fit_area_

private

Referenced by compute_chi(), and PDDFEnergy().

bool protocols::scoring::methods::saxs::PDDFEnergy::if_hydrogens_

private

Referenced by compute_pddf(), compute_pddf_without_ff(), and PDDFEnergy().

utility::vector1<bool> protocols::scoring::methods::saxs::PDDFEnergy::is_glob_

mutableprivate

Referenced by compute_pddf().

core::Size protocols::scoring::methods::saxs::PDDFEnergy::max_bin_

private

Referenced by compute_chi(), and PDDFEnergy().

core::Size protocols::scoring::methods::saxs::PDDFEnergy::min_bin_

private

Referenced by compute_chi(), and PDDFEnergy().

core::Real protocols::scoring::methods::saxs::PDDFEnergy::norm_

private

Referenced by PDDFEnergy().

utility::vector1<core::Real> protocols::scoring::methods::saxs::PDDFEnergy::pose_pddf_

mutableprivate

Referenced by compute_pddf(), compute_pddf_without_ff(), create_pddf(), evaluate_pddf_energy(), finalize_total_energy(), get_pddf(), PDDFEnergy(), and read_pddf().

utility::vector1<core::Size> protocols::scoring::methods::saxs::PDDFEnergy::r_ids_

mutableprivate

Referenced by compute_pddf(), and compute_pddf_without_ff().

utility::vector1<core::Real> protocols::scoring::methods::saxs::PDDFEnergy::reference_pddf_

private

Referenced by compute_pddf_without_ff(), create_pddf(), evaluate_pddf_energy(), finalize_total_energy(), PDDFEnergy(), and read_pddf().

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

• symlinks/rosetta/src/protocols/scoring/methods/saxs/PDDFEnergy.hh
• symlinks/rosetta/src/protocols/scoring/methods/saxs/PDDFEnergy.cc