protocols::normalmode::NormalModeMultifunc Class Reference

Atom tree multifunction class. More...

#include <NormalModeMultiFunc.hh>

Inheritance diagram for protocols::normalmode::NormalModeMultifunc:

Public Member Functions
	~NormalModeMultifunc () override
	Destructor. More...
	NormalModeMultifunc (core::pose::Pose &pose_in, core::optimization::MinimizerMap &min_map_in, core::scoring::ScoreFunction const &scorefxn_in, protocols::normalmode::NormalMode const &normalmode_in, bool const use_omega=true, bool const deriv_check_in=false, bool const deriv_check_verbose_in=false)
core::Real	operator() (core::optimization::Multivec const &vars) const override
void	dfunc (core::optimization::Multivec const &vars, core::optimization::Multivec &dE_dvars) const override
void	set_deriv_check_result (core::optimization::NumericalDerivCheckResultOP deriv_check_result)
void	dump (core::optimization::Multivec const &vars, core::optimization::Multivec const &vars2) const override
	Error state reached – derivative does not match gradient. More...
void	set_modes (utility::vector1< core::Size >)
core::optimization::Multivec	dofs_to_vars (core::optimization::Multivec const &dofs) const
core::optimization::Multivec	vars_to_dofs (core::optimization::Multivec const &vars) const
core::Size	nmodes () const
core::Size	nvar () const
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...

Protected Member Functions
core::pose::Pose &	pose () const
	non-const since pose_ is modified by calls to operator() More...
core::optimization::MinimizerMap const &	min_map () const
core::scoring::ScoreFunction const &	score_function () const
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...

Private Member Functions
void	get_dofs_for_pose0 ()
void	get_dofs_map ()
void	set_default_modes ()
core::Real	dofs_for_pose0 (core::Size const i_dof) const
core::optimization::Multivec	dEddofs_to_dEdvars (core::optimization::Multivec const &dEdtors) const
core::Real	get_modescale (core::Size const modeno) const

Private Attributes
core::pose::Pose &	pose_
core::optimization::MinimizerMap &	min_map_
core::scoring::ScoreFunction const &	score_function_
core::Size	nvar_
bool	use_omega_
core::Real	k_dampen_
core::pose::Pose &	pose0_
core::optimization::Multivec	dofs_for_pose0_
protocols::normalmode::NormalMode const	NM_
utility::vector1< core::Size >	modes_using_
std::map< core::Size, core::Size >	map_NM_to_DOF_
std::map< core::Size, core::Size >	map_DOF_to_NM_
std::map< core::Size, core::Size >	map_var_to_DOF_
std::map< core::Size, core::Size >	map_var_to_modeno_
utility::vector1< std::string >	var_type_
bool	deriv_check_
bool	deriv_check_verbose_
core::optimization::NumericalDerivCheckResultOP	deriv_check_result_

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

Detailed Description

Atom tree multifunction class.

Constructor & Destructor Documentation

~NormalModeMultifunc()

protocols::normalmode::NormalModeMultifunc::~NormalModeMultifunc ( )

overridedefault

Destructor.

NormalModeMultifunc()

protocols::normalmode::NormalModeMultifunc::NormalModeMultifunc	(	core::pose::Pose &	pose_in,
		core::optimization::MinimizerMap &	min_map_in,
		core::scoring::ScoreFunction const &	scorefxn_in,
		protocols::normalmode::NormalMode const &	normalmode_in,
		bool const	use_omega = true,
		bool const	deriv_check_in = false,
		bool const	deriv_check_verbose_in = false
	)

References get_dofs_for_pose0(), get_dofs_map(), k_dampen_, NM_, protocols::normalmode::NormalMode::ntor(), set_default_modes(), protocols::normalmode::NormalMode::torsion(), and protocols::TR().

Member Function Documentation

dEddofs_to_dEdvars()

Multivec protocols::normalmode::NormalModeMultifunc::dEddofs_to_dEdvars ( core::optimization::Multivec const &  dEdtors ) const

private

References protocols::normalmode::NormalMode::get_eigvec_tor(), get_modescale(), map_NM_to_DOF_, map_var_to_DOF_, map_var_to_modeno_, NM_, nvar(), and var_type_.

Referenced by dfunc().

dfunc()

void protocols::normalmode::NormalModeMultifunc::dfunc ( core::optimization::Multivec const &  vars, core::optimization::Multivec &  dE_dvars  ) const

overridevirtual

Implements core::optimization::Multifunc.

References core::optimization::atom_tree_dfunc(), dEddofs_to_dEdvars(), min_map_, pose_, score_function_, and vars_to_dofs().

Referenced by protocols::normalmode::NormalModeMinimizer::deriv_check_local(), and dump().

dofs_for_pose0()

core::Real protocols::normalmode::NormalModeMultifunc::dofs_for_pose0 ( core::Size const  i_dof ) const

inlineprivate

References dofs_for_pose0_.

Referenced by dofs_to_vars().

dofs_to_vars()

Multivec protocols::normalmode::NormalModeMultifunc::dofs_to_vars

(

core::optimization::Multivec const &

dofs

)

const

References dofs_for_pose0(), protocols::normalmode::NormalMode::get_eigvec_tor(), get_modescale(), map_DOF_to_NM_, map_var_to_DOF_, map_var_to_modeno_, NM_, protocols::normalmode::NormalMode::ntor(), nvar(), and var_type_.

Referenced by protocols::normalmode::NormalModeMinimizer::apply().

dump()

void protocols::normalmode::NormalModeMultifunc::dump ( core::optimization::Multivec const &  vars, core::optimization::Multivec const &  vars2  ) const

overridevirtual

Error state reached – derivative does not match gradient.

Useful debugging code that can be re-enabled by changing the boolean variables at the top of this function.

Reimplemented from core::optimization::Multifunc.

References core::scoring::hbonds::HBond::acc_atm(), core::scoring::hbonds::HBond::acc_res(), core::scoring::hbonds::HBondSet::allow_hbond(), core::optimization::symmetry::check_hbonds, core::optimization::symmetry::check_rama, core::optimization::symmetry::check_score_components, core::optimization::symmetry::check_score_components_verbose, core::optimization::MinimizerMap::copy_dofs_to_pose(), core::optimization::symmetry::debug_inaccurateG, deriv_check_, deriv_check_verbose_, dfunc(), core::scoring::hbonds::HBond::don_hatm(), core::scoring::hbonds::HBond::don_res(), core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), core::scoring::hbonds::HBond::energy(), core::scoring::hbonds::fill_hbond_set(), core::scoring::hbonds::HBondSet::hbond(), min_map_, core::scoring::n_score_types, core::scoring::hbonds::HBondSet::nhbonds(), pose_, score_function_, core::scoring::EMapVector::show_weighted(), core::id::to_string(), core::scoring::Energies::total_energies(), core::scoring::hbonds::HBond::weight(), and core::scoring::ScoreFunction::weights().

get_dofs_for_pose0()

void protocols::normalmode::NormalModeMultifunc::get_dofs_for_pose0 ( )

private

References core::optimization::MinimizerMap::copy_dofs_from_pose(), core::optimization::MinimizerMap::dof_nodes(), dofs_for_pose0_, min_map_, and pose0_.

Referenced by NormalModeMultifunc(), and set_modes().

get_dofs_map()

void protocols::normalmode::NormalModeMultifunc::get_dofs_map ( )

private

References core::optimization::MinimizerMap::dof_nodes(), protocols::normalmode::NormalMode::get_torID(), map_DOF_to_NM_, map_NM_to_DOF_, map_var_to_DOF_, map_var_to_modeno_, min_map_, modes_using_, NM_, nvar_, core::id::omega_torsion(), core::id::RB1, core::id::RB2, core::id::RB3, core::id::RB4, core::id::RB5, core::id::RB6, core::id::TorsionID::rsd(), core::id::TorsionID::torsion(), protocols::TR(), use_omega_, and var_type_.

Referenced by NormalModeMultifunc(), and set_modes().

get_modescale()

Real protocols::normalmode::NormalModeMultifunc::get_modescale ( core::Size const  modeno ) const

private

References k_dampen_.

Referenced by dEddofs_to_dEdvars(), dofs_to_vars(), and vars_to_dofs().

min_map()

MinimizerMap const & protocols::normalmode::NormalModeMultifunc::min_map ( ) const

protected

References min_map_.

nmodes()

core::Size protocols::normalmode::NormalModeMultifunc::nmodes ( ) const

inline

References modes_using_.

nvar()

core::Size protocols::normalmode::NormalModeMultifunc::nvar ( ) const

inline

References nvar_.

Referenced by dEddofs_to_dEdvars(), protocols::normalmode::NormalModeMinimizer::deriv_check_local(), and dofs_to_vars().

operator()()

Real protocols::normalmode::NormalModeMultifunc::operator() ( core::optimization::Multivec const &  vars ) const

overridevirtual

Implements core::optimization::Multifunc.

References core::optimization::MinimizerMap::copy_dofs_to_pose(), min_map_, pose_, protocols::hybridization::score, score_function_, and vars_to_dofs().

pose()

core::pose::Pose & protocols::normalmode::NormalModeMultifunc::pose ( ) const

protected

non-const since pose_ is modified by calls to operator()

References pose_.

score_function()

core::scoring::ScoreFunction const & protocols::normalmode::NormalModeMultifunc::score_function ( ) const

protected

References score_function_.

set_default_modes()

void protocols::normalmode::NormalModeMultifunc::set_default_modes ( )

private

References protocols::mean_field::min(), modes_using_, NM_, and protocols::normalmode::NormalMode::ntor().

Referenced by NormalModeMultifunc().

set_deriv_check_result()

void protocols::normalmode::NormalModeMultifunc::set_deriv_check_result

(

core::optimization::NumericalDerivCheckResultOP

deriv_check_result

)

References deriv_check_result_.

set_modes()

void protocols::normalmode::NormalModeMultifunc::set_modes

(

utility::vector1< core::Size >

modes_using_in

)

References get_dofs_for_pose0(), get_dofs_map(), modes_using_, and protocols::TR().

Referenced by protocols::normalmode::NormalModeMinimizer::apply().

vars_to_dofs()

Multivec protocols::normalmode::NormalModeMultifunc::vars_to_dofs

(

core::optimization::Multivec const &

vars

)

const

References core::optimization::MinimizerMap::dof_nodes(), dofs_for_pose0_, protocols::normalmode::NormalMode::get_eigvec_tor(), get_modescale(), protocols::normalmode::NormalMode::get_torID(), map_NM_to_DOF_, map_var_to_DOF_, map_var_to_modeno_, min_map_, NM_, and var_type_.

Referenced by protocols::normalmode::NormalModeMinimizer::apply(), dfunc(), and operator()().

Member Data Documentation

deriv_check_

bool protocols::normalmode::NormalModeMultifunc::deriv_check_

private

Referenced by dump().

deriv_check_result_

core::optimization::NumericalDerivCheckResultOP protocols::normalmode::NormalModeMultifunc::deriv_check_result_

private

Referenced by set_deriv_check_result().

deriv_check_verbose_

bool protocols::normalmode::NormalModeMultifunc::deriv_check_verbose_

private

Referenced by dump().

dofs_for_pose0_

core::optimization::Multivec protocols::normalmode::NormalModeMultifunc::dofs_for_pose0_

private

Referenced by dofs_for_pose0(), get_dofs_for_pose0(), and vars_to_dofs().

k_dampen_

core::Real protocols::normalmode::NormalModeMultifunc::k_dampen_

private

Referenced by get_modescale(), and NormalModeMultifunc().

map_DOF_to_NM_

std::map< core::Size, core::Size > protocols::normalmode::NormalModeMultifunc::map_DOF_to_NM_

private

Referenced by dofs_to_vars(), and get_dofs_map().

map_NM_to_DOF_

std::map< core::Size, core::Size > protocols::normalmode::NormalModeMultifunc::map_NM_to_DOF_

private

Referenced by dEddofs_to_dEdvars(), get_dofs_map(), and vars_to_dofs().

map_var_to_DOF_

std::map< core::Size, core::Size > protocols::normalmode::NormalModeMultifunc::map_var_to_DOF_

private

Referenced by dEddofs_to_dEdvars(), dofs_to_vars(), get_dofs_map(), and vars_to_dofs().

map_var_to_modeno_

std::map< core::Size, core::Size > protocols::normalmode::NormalModeMultifunc::map_var_to_modeno_

private

Referenced by dEddofs_to_dEdvars(), dofs_to_vars(), get_dofs_map(), and vars_to_dofs().

min_map_

core::optimization::MinimizerMap& protocols::normalmode::NormalModeMultifunc::min_map_

private

Referenced by dfunc(), dump(), get_dofs_for_pose0(), get_dofs_map(), min_map(), operator()(), and vars_to_dofs().

modes_using_

utility::vector1< core::Size > protocols::normalmode::NormalModeMultifunc::modes_using_

private

Referenced by get_dofs_map(), nmodes(), set_default_modes(), and set_modes().

NM_

protocols::normalmode::NormalMode const protocols::normalmode::NormalModeMultifunc::NM_

private

Referenced by dEddofs_to_dEdvars(), dofs_to_vars(), get_dofs_map(), NormalModeMultifunc(), set_default_modes(), and vars_to_dofs().

nvar_

core::Size protocols::normalmode::NormalModeMultifunc::nvar_

private

Referenced by get_dofs_map(), and nvar().

pose0_

core::pose::Pose& protocols::normalmode::NormalModeMultifunc::pose0_

private

Referenced by get_dofs_for_pose0().

pose_

core::pose::Pose& protocols::normalmode::NormalModeMultifunc::pose_

private

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

score_function_

core::scoring::ScoreFunction const& protocols::normalmode::NormalModeMultifunc::score_function_

private

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

use_omega_

bool protocols::normalmode::NormalModeMultifunc::use_omega_

private

Referenced by get_dofs_map().

var_type_

utility::vector1< std::string > protocols::normalmode::NormalModeMultifunc::var_type_

private

Referenced by dEddofs_to_dEdvars(), dofs_to_vars(), get_dofs_map(), and vars_to_dofs().

---

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

• src/protocols/normalmode/NormalModeMultiFunc.hh
• src/protocols/normalmode/NormalModeMultiFunc.cc