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protocols::normalmode::NormalModeMultifunc Class Reference

Atom tree multifunction class. More...

#include <NormalModeMultiFunc.hh>

Inheritance diagram for protocols::normalmode::NormalModeMultifunc:
Inheritance graph
[legend]

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::Posepose () 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...
 
Multifuncoperator= (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::Posepose_
 
core::optimization::MinimizerMapmin_map_
 
core::scoring::ScoreFunction
const & 
score_function_
 
core::Size nvar_
 
bool use_omega_
 
core::Real k_dampen_
 
core::pose::Posepose0_
 
core::optimization::Multivec dofs_for_pose0_
 
protocols::normalmode::NormalMode
const 
NM_
 
utility::vector1< core::Sizemodes_using_
 
std::map< core::Size, core::Sizemap_NM_to_DOF_
 
std::map< core::Size, core::Sizemap_DOF_to_NM_
 
std::map< core::Size, core::Sizemap_var_to_DOF_
 
std::map< core::Size, core::Sizemap_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

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

Destructor.

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 
)

Member Function Documentation

Multivec protocols::normalmode::NormalModeMultifunc::dEddofs_to_dEdvars ( core::optimization::Multivec const &  dEdtors) const
private
void protocols::normalmode::NormalModeMultifunc::dfunc ( core::optimization::Multivec const &  vars,
core::optimization::Multivec dE_dvars 
) const
overridevirtual
core::Real protocols::normalmode::NormalModeMultifunc::dofs_for_pose0 ( core::Size const  i_dof) const
inlineprivate

References dofs_for_pose0_.

Referenced by dofs_to_vars().

Multivec protocols::normalmode::NormalModeMultifunc::dofs_to_vars ( core::optimization::Multivec const &  dofs) const
void protocols::normalmode::NormalModeMultifunc::dump ( core::optimization::Multivec const &  vars,
core::optimization::Multivec const &  vars2 
) const
overridevirtual
void protocols::normalmode::NormalModeMultifunc::get_dofs_for_pose0 ( )
private
void protocols::normalmode::NormalModeMultifunc::get_dofs_map ( )
private
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().

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

References min_map_.

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

References modes_using_.

core::Size protocols::normalmode::NormalModeMultifunc::nvar ( ) const
inline
Real protocols::normalmode::NormalModeMultifunc::operator() ( core::optimization::Multivec const &  vars) const
overridevirtual
core::pose::Pose & protocols::normalmode::NormalModeMultifunc::pose ( ) const
protected

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

References pose_.

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

References score_function_.

void protocols::normalmode::NormalModeMultifunc::set_default_modes ( )
private
void protocols::normalmode::NormalModeMultifunc::set_deriv_check_result ( core::optimization::NumericalDerivCheckResultOP  deriv_check_result)

References deriv_check_result_.

void protocols::normalmode::NormalModeMultifunc::set_modes ( utility::vector1< core::Size modes_using_in)
Multivec protocols::normalmode::NormalModeMultifunc::vars_to_dofs ( core::optimization::Multivec const &  vars) const

Member Data Documentation

bool protocols::normalmode::NormalModeMultifunc::deriv_check_
private

Referenced by dump().

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

Referenced by set_deriv_check_result().

bool protocols::normalmode::NormalModeMultifunc::deriv_check_verbose_
private

Referenced by dump().

core::optimization::Multivec protocols::normalmode::NormalModeMultifunc::dofs_for_pose0_
private
core::Real protocols::normalmode::NormalModeMultifunc::k_dampen_
private
std::map< core::Size, core::Size > protocols::normalmode::NormalModeMultifunc::map_DOF_to_NM_
private

Referenced by dofs_to_vars(), and get_dofs_map().

std::map< core::Size, core::Size > protocols::normalmode::NormalModeMultifunc::map_NM_to_DOF_
private
std::map< core::Size, core::Size > protocols::normalmode::NormalModeMultifunc::map_var_to_DOF_
private
std::map< core::Size, core::Size > protocols::normalmode::NormalModeMultifunc::map_var_to_modeno_
private
core::optimization::MinimizerMap& protocols::normalmode::NormalModeMultifunc::min_map_
private
utility::vector1< core::Size > protocols::normalmode::NormalModeMultifunc::modes_using_
private
protocols::normalmode::NormalMode const protocols::normalmode::NormalModeMultifunc::NM_
private
core::Size protocols::normalmode::NormalModeMultifunc::nvar_
private

Referenced by get_dofs_map(), and nvar().

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

Referenced by get_dofs_for_pose0().

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

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

core::scoring::ScoreFunction const& protocols::normalmode::NormalModeMultifunc::score_function_
private
bool protocols::normalmode::NormalModeMultifunc::use_omega_
private

Referenced by get_dofs_map().

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

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