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protocols::ncbb::SecStructMinimizeMultiFunc Class Reference

class for fitting a length of secondary structure keeping the same dihedrals More...

#include <SecStructMinimizeMultiFunc.hh>

Inheritance diagram for protocols::ncbb::SecStructMinimizeMultiFunc:
Inheritance graph
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Public Member Functions

 ~SecStructMinimizeMultiFunc () override
 Destructor. More...
 
 SecStructMinimizeMultiFunc (core::pose::Pose &pose, core::scoring::ScoreFunction &scorefxn_in, core::optimization::MinimizerMap &min_map, std::string const alpha_beta_pattern, std::string const dihedral_pattern)
 Constructor. More...
 
core::Real operator() (core::optimization::Multivec const &vars) const override
 Calculate function value (rms squared) More...
 
void dfunc (core::optimization::Multivec const &vars, core::optimization::Multivec &dE_dvars) const override
 Calculate function value derivatives. More...
 
core::optimization::Multivec dofs_to_vars (core::optimization::Multivec const &dofs) const
 give short set of torsions from full dofs More...
 
core::optimization::Multivec vars_to_dofs (core::optimization::Multivec const &vars) const
 give full dofs from short set of torsions More...
 
void dump (core::optimization::Multivec const &vars, core::optimization::Multivec const &vars2) const override
 Error state reached – derivative does not match gradient. 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 Member Functions

void get_dofs_for_pose0 ()
 
void get_dofs_map ()
 
core::Real dofs_for_pose0 (core::Size const i_dof) const
 
core::optimization::Multivec dEddofs_to_dEdvars (core::optimization::Multivec const &dEdtors) const
 
void setup_minimization_graph (core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, core::optimization::MinimizerMap const &min_map) const
 
bool uniq_refers_to_beta (char const uniq) const
 

Private Attributes

std::map< core::Size,
utility::vector1< core::Size > > 
map_BB_to_DOF_
 
std::map< core::Size, core::Sizemap_DOF_to_BB_
 
core::pose::Posepose_
 
core::scoring::ScoreFunctionscorefxn_
 
core::optimization::MinimizerMapmin_map_
 
core::pose::Posepose0_
 
core::optimization::Multivec dofs_for_pose0_
 
std::string alpha_beta_pattern_
 
std::string dihedral_pattern_
 The pattern at which dihedrals are applied. More...
 
std::map< core::Size,
utility::vector1
< core::id::TorsionID > > 
vars_index_to_torsion_id_
 
core::Size nvar_
 

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

Detailed Description

class for fitting a length of secondary structure keeping the same dihedrals

Constructor & Destructor Documentation

protocols::ncbb::SecStructMinimizeMultiFunc::~SecStructMinimizeMultiFunc ( )
overridedefault

Destructor.

protocols::ncbb::SecStructMinimizeMultiFunc::SecStructMinimizeMultiFunc ( core::pose::Pose pose,
core::scoring::ScoreFunction scorefxn_in,
core::optimization::MinimizerMap min_map,
std::string const  alpha_beta_pattern,
std::string const  dihedral_pattern 
)

Member Function Documentation

Multivec protocols::ncbb::SecStructMinimizeMultiFunc::dEddofs_to_dEdvars ( core::optimization::Multivec const &  dEdtors) const
private

References map_BB_to_DOF_, and nvar_.

Referenced by dfunc().

void protocols::ncbb::SecStructMinimizeMultiFunc::dfunc ( core::optimization::Multivec const &  vars,
core::optimization::Multivec dE_dvars 
) const
overridevirtual
core::Real protocols::ncbb::SecStructMinimizeMultiFunc::dofs_for_pose0 ( core::Size const  i_dof) const
inlineprivate

References dofs_for_pose0_.

Multivec protocols::ncbb::SecStructMinimizeMultiFunc::dofs_to_vars ( core::optimization::Multivec const &  dofs) const

give short set of torsions from full dofs

References map_BB_to_DOF_, and nvar_.

void protocols::ncbb::SecStructMinimizeMultiFunc::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.

void protocols::ncbb::SecStructMinimizeMultiFunc::get_dofs_for_pose0 ( )
private
void protocols::ncbb::SecStructMinimizeMultiFunc::get_dofs_map ( )
private
Real protocols::ncbb::SecStructMinimizeMultiFunc::operator() ( core::optimization::Multivec const &  vars) const
overridevirtual
void protocols::ncbb::SecStructMinimizeMultiFunc::setup_minimization_graph ( core::pose::Pose pose,
core::scoring::ScoreFunction const &  sfxn,
core::optimization::MinimizerMap const &  min_map 
) const
private
bool protocols::ncbb::SecStructMinimizeMultiFunc::uniq_refers_to_beta ( char const  uniq) const
private
Multivec protocols::ncbb::SecStructMinimizeMultiFunc::vars_to_dofs ( core::optimization::Multivec const &  vars) const

give full dofs from short set of torsions

References dofs_for_pose0_, and map_BB_to_DOF_.

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

Member Data Documentation

std::string protocols::ncbb::SecStructMinimizeMultiFunc::alpha_beta_pattern_
private
std::string protocols::ncbb::SecStructMinimizeMultiFunc::dihedral_pattern_
private

The pattern at which dihedrals are applied.

Referenced by SecStructMinimizeMultiFunc().

core::optimization::Multivec protocols::ncbb::SecStructMinimizeMultiFunc::dofs_for_pose0_
private
std::map< core::Size, utility::vector1< core::Size > > protocols::ncbb::SecStructMinimizeMultiFunc::map_BB_to_DOF_
private
std::map< core::Size, core::Size > protocols::ncbb::SecStructMinimizeMultiFunc::map_DOF_to_BB_
private

Referenced by get_dofs_map().

core::optimization::MinimizerMap& protocols::ncbb::SecStructMinimizeMultiFunc::min_map_
private
core::Size protocols::ncbb::SecStructMinimizeMultiFunc::nvar_
private
core::pose::Pose& protocols::ncbb::SecStructMinimizeMultiFunc::pose0_
private

Referenced by get_dofs_for_pose0().

core::pose::Pose& protocols::ncbb::SecStructMinimizeMultiFunc::pose_
private
core::scoring::ScoreFunction& protocols::ncbb::SecStructMinimizeMultiFunc::scorefxn_
private
std::map< core::Size, utility::vector1< core::id::TorsionID > > protocols::ncbb::SecStructMinimizeMultiFunc::vars_index_to_torsion_id_
private

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