Bfactor multifunc. More...

#include <BfactorFittingMover.hh>

Inheritance diagram for protocols::electron_density::BfactorMultifunc:

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)

	~BfactorMultifunc () override=default

core::Real	operator() (core::optimization::Multivec const &vars) const override
	B factor optimization multifunc. More...

void	dfunc (core::optimization::Multivec const &vars, core::optimization::Multivec &dE_dvars) const override

void	dump (core::optimization::Multivec const &x1, core::optimization::Multivec const &x2) const override
	Error state reached – derivative does not match gradient Derived classes have the oportunity to now output and or analyze the two vars assignments vars, vars+delta where the derivatives are incorrect. More...

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...

Public Member Functions inherited from core::optimization::Multifunc
	~Multifunc () override=default
	Destructor. More...

virtual bool	abort_min (Multivec const &) const
	Christophe added the following to allow premature end of minimization If you want to abort the minimizer under specific circonstances overload this function and return true if you want to stop, false if you want to continue. FOR THE MOMENT, ONLY IN DFPMIN! 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_

ObjexxFCL::FArray3D< core::Real >	rhoC_

ObjexxFCL::FArray3D< core::Real >	rhoMask_

core::Real	B_EPS

Additional Inherited Members
Public Types inherited from core::optimization::Multifunc
typedef utility::VirtualBase	parent

Protected Member Functions inherited from core::optimization::Multifunc
	Multifunc ()
	Default constructor. More...

	Multifunc (Multifunc const &)
	Copy constructor. More...

Multifunc &	operator= (Multifunc const &)
	Copy assignment. More...

Detailed Description

Bfactor multifunc.

Constructor & Destructor Documentation

◆ BfactorMultifunc()

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::conformation::Residue::aa(), core::chemical::aa_vrt, atom_indices_, core::conformation::Residue::atom_type(), B_EPS, core::pose::Pose::conformation(), core::pose::initialize_atomid_map(), core::pose::symmetry::is_symmetric(), core::chemical::AtomType::is_virtual(), moving_atoms_, core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), and core::pose::Pose::size().

◆ ~BfactorMultifunc()

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

overridedefault

Member Function Documentation

◆ dfunc()

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

overridevirtual

Implements core::optimization::Multifunc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), atom_indices_, core::id::AtomID::atomno(), B_EPS, core::pose::Pose::conformation(), core::scoring::electron_density::ElectronDensity::dCCdB_fastRes(), core::scoring::electron_density::ElectronDensity::dCCdBs(), core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), exact_, core::scoring::electron_density::getDensityMap(), core::pose::symmetry::is_symmetric(), moving_atoms_, multivec2poseBfacts(), core::conformation::Residue::nheavyatoms(), core::pose::Pose::pdb_info(), pose_, radius_exp_, core::pose::Pose::residue(), rhoMask_, rmax_, core::id::AtomID::rsd(), protocols::hybridization::score, scorescale_, core::pose::Pose::size(), verbose_, wt_adp_, wt_dens_, and core::conformation::Atom::xyz().

Referenced by dump().

◆ dump()

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

overridevirtual

Error state reached – derivative does not match gradient Derived classes have the oportunity to now output and or analyze the two vars assignments vars, vars+delta where the derivatives are incorrect.

Reimplemented from core::optimization::Multifunc.

References B_EPS, deriv_check_, dfunc(), and protocols::hybridization::score.

◆ multivec2poseBfacts()

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(), protocols::mean_field::max(), protocols::mean_field::min(), moving_atoms_, core::pose::Pose::pdb_info(), and core::id::AtomID::rsd().

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

◆ operator()()

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

overridevirtual

B factor optimization multifunc.

Implements core::optimization::Multifunc.

References core::conformation::Residue::aa(), core::chemical::aa_vrt, core::conformation::Residue::atom(), atom_indices_, core::conformation::Residue::atom_type(), core::conformation::Residue::atom_type_index(), core::conformation::Residue::atom_type_set(), core::scoring::electron_density::poseCoord::B_, B_EPS, core::scoring::electron_density::ElectronDensity::calcRhoC(), core::pose::Pose::conformation(), core::scoring::electron_density::poseCoord::elt_, core::pose::Pose::energies(), core::scoring::Energies::energy_graph(), exact_, core::scoring::electron_density::getDensityMap(), core::scoring::electron_density::ElectronDensity::getRSCC(), core::pose::symmetry::is_symmetric(), core::chemical::AtomType::is_virtual(), 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(), rhoC_, rhoMask_, rmax_, scorescale_, core::pose::Pose::size(), verbose_, wt_adp_, wt_dens_, core::scoring::electron_density::poseCoord::x_, core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

◆ poseBfacts2multivec()

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(), core::chemical::element::B, moving_atoms_, core::pose::Pose::pdb_info(), and core::id::AtomID::rsd().

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

Member Data Documentation

◆ atom_indices_

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

private

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

◆ B_EPS

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

private

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

◆ deriv_check_

bool protocols::electron_density::BfactorMultifunc::deriv_check_

private

Referenced by dump().

◆ exact_

bool protocols::electron_density::BfactorMultifunc::exact_

private

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

◆ moving_atoms_

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

private

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

◆ pose_

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

private

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

◆ radius_exp_

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

private

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

◆ rhoC_

ObjexxFCL::FArray3D< core::Real > protocols::electron_density::BfactorMultifunc::rhoC_

mutableprivate

Referenced by operator()().

◆ rhoMask_

ObjexxFCL::FArray3D< core::Real > protocols::electron_density::BfactorMultifunc::rhoMask_

private

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

◆ rmax_

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

private

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

◆ scorescale_

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

private

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

◆ verbose_

bool protocols::electron_density::BfactorMultifunc::verbose_

private

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

◆ wt_adp_

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

private

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

◆ wt_dens_

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

private

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

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

src/protocols/electron_density/BfactorFittingMover.hh
src/protocols/electron_density/BfactorFittingMover.cc

Public Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ BfactorMultifunc()

◆ ~BfactorMultifunc()

Member Function Documentation

◆ dfunc()

◆ dump()

◆ multivec2poseBfacts()

◆ operator()()

◆ poseBfacts2multivec()

Member Data Documentation

◆ atom_indices_

◆ B_EPS

◆ deriv_check_

◆ exact_

◆ moving_atoms_

◆ pose_

◆ radius_exp_

◆ rhoC_

◆ rhoMask_

◆ rmax_

◆ scorescale_

◆ verbose_

◆ wt_adp_

◆ wt_dens_