protocols::electron_density::BfactorMultifunc Class Reference

Bfactor multifunc. More...

#include <BfactorFittingMover.hh>

Public Member Functions
	BfactorMultifunc (core::pose::Pose &pose_in, core::Real wt_adp, core::Real wt_dens, core::Real rmax, core::Real radius_exp, core::Real scorescale, bool exact, bool verbose, bool deriv_check)
virtual	~BfactorMultifunc ()
virtual core::Real	operator() (core::optimization::Multivec const &vars) const
	B factor optimization multifunc. More...
virtual void	dfunc (core::optimization::Multivec const &vars, core::optimization::Multivec &dE_dvars) const
virtual void	dump (core::optimization::Multivec const &x1, core::optimization::Multivec const &x2) const
void	poseBfacts2multivec (core::pose::Pose &pose, core::optimization::Multivec &y) const
	pose with B factors –> multivec More...
void	multivec2poseBfacts (core::optimization::Multivec const &vars, core::pose::Pose &pose) const
	multivec —> pose B factors More...

Private Attributes
core::pose::Pose &	pose_
core::Real	scorescale_
core::Real	wt_adp_
core::Real	wt_dens_
core::Real	rmax_
core::Real	radius_exp_
bool	exact_
bool	verbose_
bool	deriv_check_
core::id::AtomID_Map< core::Size >	atom_indices_
utility::vector1 < core::id::AtomID >	moving_atoms_
core::Real	B_EPS

Detailed Description

Bfactor multifunc.

Constructor & Destructor Documentation

protocols::electron_density::BfactorMultifunc::BfactorMultifunc	(	core::pose::Pose &	pose_in,
		core::Real	wt_adp,
		core::Real	wt_dens,
		core::Real	rmax,
		core::Real	radius_exp,
		core::Real	scorescale,
		bool	exact,
		bool	verbose,
		bool	deriv_check
	)

References core::chemical::aa_vrt, atom_indices_, B_EPS, core::pose::Pose::conformation(), core::pose::initialize_atomid_map(), core::pose::symmetry::is_symmetric(), moving_atoms_, core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::pose::Pose::total_residue().

virtual protocols::electron_density::BfactorMultifunc::~BfactorMultifunc ( )

inlinevirtual

Member Function Documentation

void protocols::electron_density::BfactorMultifunc::dfunc ( core::optimization::Multivec const &  vars, core::optimization::Multivec &  dE_dvars  ) const

virtual

Implements core::optimization::Multifunc.

References core::chemical::aa_vrt, atom_indices_, core::id::AtomID::atomno(), B_EPS, core::pose::Pose::conformation(), core::graph::Node::const_upper_edge_list_end(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdBs(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), exact_, core::graph::Edge::get_node(), core::scoring::electron_density::getDensityMap(), core::pose::symmetry::is_symmetric(), j, l, length, moving_atoms_, multivec2poseBfacts(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::pdb_info(), pose_, radius_exp_, core::pose::Pose::residue(), rmax_, core::id::AtomID::rsd(), score, scorescale_, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), verbose_, wt_adp_, and wt_dens_.

Referenced by dump().

void protocols::electron_density::BfactorMultifunc::dump ( core::optimization::Multivec const &  x1, core::optimization::Multivec const &  x2  ) const

virtual

Reimplemented from core::optimization::Multifunc.

References deriv_check_, dfunc(), and score.

void protocols::electron_density::BfactorMultifunc::multivec2poseBfacts	(	core::optimization::Multivec const &	vars,
		core::pose::Pose &	pose
	)		const

multivec —> pose B factors

References core::id::AtomID::atomno(), moving_atoms_, core::pose::Pose::pdb_info(), core::id::AtomID::rsd(), and runtime_assert.

Referenced by protocols::electron_density::BfactorFittingMover::apply(), dfunc(), and operator()().

core::Real protocols::electron_density::BfactorMultifunc::operator() ( core::optimization::Multivec const &  vars ) const

virtual

B factor optimization multifunc.

Implements core::optimization::Multifunc.

References core::chemical::aa_vrt, atom_indices_, B_EPS, core::scoring::electron_density::ElectronDensity::calcRhoC(), core::pose::Pose::conformation(), core::graph::Node::const_upper_edge_list_end(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), exact_, core::graph::Edge::get_node(), core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::ElectronDensity::getRSCC(), core::pose::symmetry::is_symmetric(), j, l, length, core::scoring::electron_density::ElectronDensity::matchResFast(), moving_atoms_, multivec2poseBfacts(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::pdb_info(), pose_, radius_exp_, core::pose::Pose::residue(), rmax_, scorescale_, core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), core::pose::Pose::total_residue(), verbose_, wt_adp_, wt_dens_, and core::scoring::electron_density::poseCoord::x_.

void protocols::electron_density::BfactorMultifunc::poseBfacts2multivec	(	core::pose::Pose &	pose,
		core::optimization::Multivec &	y
	)		const

pose with B factors –> multivec

References core::id::AtomID::atomno(), protocols::comparative_modeling::features::B, log(), moving_atoms_, core::pose::Pose::pdb_info(), core::id::AtomID::rsd(), and runtime_assert.

Referenced by protocols::electron_density::BfactorFittingMover::apply().

Member Data Documentation

core::id::AtomID_Map< core::Size > protocols::electron_density::BfactorMultifunc::atom_indices_

private

Referenced by BfactorMultifunc(), dfunc(), and operator()().

core::Real protocols::electron_density::BfactorMultifunc::B_EPS

private

Referenced by BfactorMultifunc(), dfunc(), and operator()().

bool protocols::electron_density::BfactorMultifunc::deriv_check_

private

Referenced by dump().

bool protocols::electron_density::BfactorMultifunc::exact_

private

Referenced by dfunc(), and operator()().

utility::vector1< core::id::AtomID > protocols::electron_density::BfactorMultifunc::moving_atoms_

private

Referenced by BfactorMultifunc(), dfunc(), multivec2poseBfacts(), operator()(), and poseBfacts2multivec().

core::pose::Pose& protocols::electron_density::BfactorMultifunc::pose_

private

Referenced by dfunc(), and operator()().

core::Real protocols::electron_density::BfactorMultifunc::radius_exp_

private

Referenced by dfunc(), and operator()().

core::Real protocols::electron_density::BfactorMultifunc::rmax_

private

Referenced by dfunc(), and operator()().

core::Real protocols::electron_density::BfactorMultifunc::scorescale_

private

Referenced by dfunc(), and operator()().

bool protocols::electron_density::BfactorMultifunc::verbose_

private

Referenced by dfunc(), and operator()().

core::Real protocols::electron_density::BfactorMultifunc::wt_adp_

private

Referenced by dfunc(), and operator()().

core::Real protocols::electron_density::BfactorMultifunc::wt_dens_

private

Referenced by dfunc(), and operator()().

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

• symlinks/rosetta/src/protocols/electron_density/BfactorFittingMover.hh
• symlinks/rosetta/src/protocols/electron_density/BfactorFittingMover.cc