Rosetta Protocols  2014.35
Public Member Functions | Protected Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::normalmode::NormalModeMultifunc Class Reference

Atom tree multifunction class. More...

#include <NormalModeMultiFunc.hh>

Public Member Functions

virtual ~NormalModeMultifunc ()
 Destructor. More...
 
 NormalModeMultifunc (pose::Pose &pose_in, MinimizerMap &min_map_in, 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)
 
virtual Real operator() (Multivec const &vars) const
 
virtual void dfunc (Multivec const &vars, Multivec &dE_dvars) const
 
void set_deriv_check_result (NumericalDerivCheckResultOP deriv_check_result)
 
virtual void dump (Multivec const &vars, Multivec const &vars2) const
 Error state reached – derivative does not match gradient. More...
 
void set_modes (utility::vector1< Size >)
 
Multivec dofs_to_vars (Multivec const &dofs) const
 
Multivec vars_to_dofs (Multivec const &vars) const
 
Size nmodes () const
 
Size nvar () const
 

Protected Member Functions

pose::Posepose () const
 non-const since pose_ is modified by calls to operator() More...
 
MinimizerMap const & min_map () const
 
scoring::ScoreFunction const & score_function () const
 

Private Member Functions

void get_dofs_for_pose0 ()
 
void get_dofs_map ()
 
void set_default_modes ()
 
Real dofs_for_pose0 (Size const i_dof) const
 
Multivec dEddofs_to_dEdvars (Multivec const &dEdtors) const
 
Real get_modescale (Size const modeno) const
 

Private Attributes

pose::Posepose_
 
MinimizerMapmin_map_
 
scoring::ScoreFunction const & score_function_
 
Size nvar_
 
bool use_omega_
 
Real k_dampen_
 
pose::Posepose0_
 
Multivec dofs_for_pose0_
 
protocols::normalmode::NormalMode
const 
NM_
 
utility::vector1< Sizemodes_using_
 
std::map< Size, Sizemap_NM_to_DOF_
 
std::map< Size, Sizemap_DOF_to_NM_
 
std::map< Size, Sizemap_var_to_DOF_
 
std::map< Size, Sizemap_var_to_modeno_
 
utility::vector1< std::stringvar_type_
 
bool deriv_check_
 
bool deriv_check_verbose_
 
NumericalDerivCheckResultOP deriv_check_result_
 

Detailed Description

Atom tree multifunction class.

Constructor & Destructor Documentation

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

Destructor.

protocols::normalmode::NormalModeMultifunc::NormalModeMultifunc ( pose::Pose pose_in,
MinimizerMap min_map_in,
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 ( Multivec const &  dEdtors) const
private
void protocols::normalmode::NormalModeMultifunc::dfunc ( Multivec const &  vars,
Multivec dE_dvars 
) const
virtual
Real protocols::normalmode::NormalModeMultifunc::dofs_for_pose0 ( Size const  i_dof) const
inlineprivate

Referenced by dofs_to_vars().

Multivec protocols::normalmode::NormalModeMultifunc::dofs_to_vars ( Multivec const &  dofs) const
void protocols::normalmode::NormalModeMultifunc::dump ( Multivec const &  vars,
Multivec const &  vars2 
) const
virtual
void protocols::normalmode::NormalModeMultifunc::get_dofs_for_pose0 ( )
private
void protocols::normalmode::NormalModeMultifunc::get_dofs_map ( )
private
Real protocols::normalmode::NormalModeMultifunc::get_modescale ( 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_.

Size protocols::normalmode::NormalModeMultifunc::nmodes ( ) const
inline
Size protocols::normalmode::NormalModeMultifunc::nvar ( ) const
inline
Real protocols::normalmode::NormalModeMultifunc::operator() ( Multivec const &  vars) const
virtual
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 ( NumericalDerivCheckResultOP  deriv_check_result)

References deriv_check_result_.

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

Member Data Documentation

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

Referenced by dump().

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().

Multivec protocols::normalmode::NormalModeMultifunc::dofs_for_pose0_
private

Referenced by get_dofs_for_pose0(), and vars_to_dofs().

Real protocols::normalmode::NormalModeMultifunc::k_dampen_
private
std::map< Size, Size > protocols::normalmode::NormalModeMultifunc::map_DOF_to_NM_
private

Referenced by dofs_to_vars(), and get_dofs_map().

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

Referenced by get_dofs_map().

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

Referenced by get_dofs_for_pose0().

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

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

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: