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::Pose & pose () 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::Pose & pose_
 
MinimizerMap & min_map_
 
scoring::ScoreFunction const & score_function_
 
Size nvar_
 
bool use_omega_
 
Real k_dampen_
 
pose::Pose & pose0_
 
Multivec dofs_for_pose0_
 
protocols::normalmode::NormalMode
const 		NM_
 
utility::vector1< Size > modes_using_
 
std::map< Size, Size > map_NM_to_DOF_
 
std::map< Size, Size > map_DOF_to_NM_
 
std::map< Size, Size > map_var_to_DOF_
 
std::map< Size, Size > map_var_to_modeno_
 
utility::vector1< std::string > var_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 
)

References get_dofs_for_pose0(), get_dofs_map(), k_dampen_, NM_, protocols::normalmode::NormalMode::ntor(), basic::options::option, basic::options::OptionKeys::optimization::scale_normalmode_dampen, set_default_modes(), protocols::normalmode::NormalMode::torsion(), and protocols::TR.

Member Function Documentation

Multivec protocols::normalmode::NormalModeMultifunc::dEddofs_to_dEdvars ( Multivec const &  dEdtors) const
private

References protocols::fldsgn::topology::compare(), 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().

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

Implements core::optimization::Multifunc.

References atom_tree_dfunc(), dEddofs_to_dEdvars(), basic::DFUNC, min_map_, pose_, PROF_START, PROF_STOP, score_function_, and vars_to_dofs().

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

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

References protocols::fldsgn::topology::compare(), 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(), var_type_, and vars.

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

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(), check_hbonds, check_rama, check_score_components, check_score_components_verbose, core::optimization::MinimizerMap::copy_dofs_to_pose(), 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(), fill_hbond_set(), core::scoring::hbonds::HBondSet::hbond(), min_map_, core::scoring::hbonds::HBondSet::nhbonds(), pose_, score_function_, scoring, core::scoring::EMapVector::show_weighted(), utility::to_string(), core::scoring::Energies::total_energies(), and core::scoring::hbonds::HBond::weight().

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().

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_, protocols::TR, type, use_omega_, and var_type_.

Referenced by NormalModeMultifunc(), and set_modes().

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

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

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

Implements core::optimization::Multifunc.

References core::optimization::MinimizerMap::copy_dofs_to_pose(), basic::FUNC, min_map_, pose_, PROF_START, PROF_STOP, score, score_function_, and vars_to_dofs().

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

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

Referenced by NormalModeMultifunc().

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)

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

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

Multivec protocols::normalmode::NormalModeMultifunc::vars_to_dofs ( Multivec const &  vars) const

References protocols::fldsgn::topology::compare(), 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 dfunc(), and operator()().

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

Referenced by get_modescale(), and NormalModeMultifunc().

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

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

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

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

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

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

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().

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

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

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().

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

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

bool protocols::normalmode::NormalModeMultifunc::use_omega_
private

Referenced by get_dofs_map().

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:
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