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protocols::mpi_refinement::MultiObjective Class Reference

#include <MultiObjective.hh>

Inheritance diagram for protocols::mpi_refinement::MultiObjective:
Inheritance graph
[legend]

Public Member Functions

 MultiObjective ()
 
 ~MultiObjective () override
 
bool update_library_seeds (protocols::wum::SilentStructStore &structs, protocols::wum::SilentStructStore &new_structs, core::Real const dcut, utility::vector1< core::Size > const seeds, std::string const prefix_in, std::string const objname="", core::Size const maxreplace=100000)
 
bool update_library_NSGAII (protocols::wum::SilentStructStore &structs, protocols::wum::SilentStructStore &new_structs, core::Size const nmax, bool const update_obj_cut=false)
 
void succeed_substitute_info (core::io::silent::SilentStructOP ss_sub, core::io::silent::SilentStructCOP ss_ref, bool const reset) const
 
void filter_similar (protocols::wum::SilentStructStore &structs, std::string const measure, core::Real const criteria, std::string const score_for_priority, core::Size const nmax=0)
 
void add_objective_function_info (core::io::silent::SilentStructOP ss, protocols::wum::SilentStructStore &sstore) const
 
void add_objective_function_info (protocols::wum::SilentStructStore &sstore) const
 
std::string formatted_objs_values (core::io::silent::SilentStruct const &ss) const
 
std::string formatted_objs_names () const
 
core::Size nobjs () const
 
std::string fobjnames (core::Size i) const
 
bool has_score (std::string value) const
 
core::Real get_fobj (core::io::silent::SilentStruct const &ss, core::Size i) const
 
core::Real get_fobj (core::io::silent::SilentStruct const &ss, std::string name) const
 
core::Real get_fobj (core::io::silent::SilentStructCOP pss, core::Size i) const
 
void set_init_pose (core::pose::Pose inpose)
 
core::pose::Pose init_pose () const
 
void set_iha_cut (core::Real value)
 
core::Real iha_cut () const
 
void set_iha_penalty_slope (core::Real value)
 
core::Real iha_penalty_slope () const
 
void set_iha_penalty_mode (std::string value)
 
std::string iha_penalty_mode () const
 
void set_nremain_reset (core::Size value)
 
core::Size nremain_reset () const
 
void calculate_pool_diversity (protocols::wum::SilentStructStore &structs) const
 
void calculate_pool_diversity (protocols::wum::SilentStructStore &structs1, protocols::wum::SilentStructStore &structs2) const
 
core::scoring::ScoreFunctionOP get_scorefxn (core::Size const i) const
 

Private Member Functions

void set_defaults ()
 
bool is_dominant (core::io::silent::SilentStructCOP ss1, core::io::silent::SilentStructCOP ss2)
 
void calculate_structure_diversity (core::io::silent::SilentStructOP ss1, protocols::wum::SilentStructStore &structs) const
 

Private Attributes

utility::vector1< core::Realobj_dominant_cut_
 
utility::vector1< core::Realobj_cut_increment_
 
utility::vector1< std::string > fobjnames_
 
utility::vector1
< core::scoring::ScoreFunctionCOP
objsfxnOPs_
 
core::pose::Pose init_pose_
 
core::Real iha_cut_
 
core::Real iha_penalty_slope_
 
std::string iha_penalty_mode_
 
core::Size nremain_reset_
 

Constructor & Destructor Documentation

protocols::mpi_refinement::MultiObjective::MultiObjective ( )
protocols::mpi_refinement::MultiObjective::~MultiObjective ( )
overridedefault

Member Function Documentation

void protocols::mpi_refinement::MultiObjective::add_objective_function_info ( core::io::silent::SilentStructOP  ss,
protocols::wum::SilentStructStore sstore 
) const
void protocols::mpi_refinement::MultiObjective::add_objective_function_info ( protocols::wum::SilentStructStore sstore) const
void protocols::mpi_refinement::MultiObjective::calculate_pool_diversity ( protocols::wum::SilentStructStore structs) const
void protocols::mpi_refinement::MultiObjective::calculate_pool_diversity ( protocols::wum::SilentStructStore structs1,
protocols::wum::SilentStructStore structs2 
) const
void protocols::mpi_refinement::MultiObjective::calculate_structure_diversity ( core::io::silent::SilentStructOP  ss1,
protocols::wum::SilentStructStore structs 
) const
private
void protocols::mpi_refinement::MultiObjective::filter_similar ( protocols::wum::SilentStructStore structs,
std::string const  measure,
core::Real const  criteria,
std::string const  score_for_priority,
core::Size const  nmax = 0 
)
std::string protocols::mpi_refinement::MultiObjective::fobjnames ( core::Size  i) const
inline

References fobjnames_.

std::string protocols::mpi_refinement::MultiObjective::formatted_objs_names ( ) const
std::string protocols::mpi_refinement::MultiObjective::formatted_objs_values ( core::io::silent::SilentStruct const &  ss) const
core::Real protocols::mpi_refinement::MultiObjective::get_fobj ( core::io::silent::SilentStruct const &  ss,
core::Size  i 
) const
inline
core::Real protocols::mpi_refinement::MultiObjective::get_fobj ( core::io::silent::SilentStruct const &  ss,
std::string  name 
) const
inline
core::Real protocols::mpi_refinement::MultiObjective::get_fobj ( core::io::silent::SilentStructCOP  pss,
core::Size  i 
) const
inline

References fobjnames_.

core::scoring::ScoreFunctionOP protocols::mpi_refinement::MultiObjective::get_scorefxn ( core::Size const  i) const
inline

References objsfxnOPs_.

bool protocols::mpi_refinement::MultiObjective::has_score ( std::string  value) const
inline

References fobjnames_.

core::Real protocols::mpi_refinement::MultiObjective::iha_cut ( ) const
inline

References iha_cut_.

std::string protocols::mpi_refinement::MultiObjective::iha_penalty_mode ( ) const
inline

References iha_penalty_mode_.

core::Real protocols::mpi_refinement::MultiObjective::iha_penalty_slope ( ) const
inline

References iha_penalty_slope_.

core::pose::Pose protocols::mpi_refinement::MultiObjective::init_pose ( ) const
inline

References init_pose_.

bool protocols::mpi_refinement::MultiObjective::is_dominant ( core::io::silent::SilentStructCOP  ss1,
core::io::silent::SilentStructCOP  ss2 
)
private
core::Size protocols::mpi_refinement::MultiObjective::nobjs ( ) const
inline

References fobjnames_.

core::Size protocols::mpi_refinement::MultiObjective::nremain_reset ( ) const
inline

References nremain_reset_.

void protocols::mpi_refinement::MultiObjective::set_defaults ( )
private
void protocols::mpi_refinement::MultiObjective::set_iha_cut ( core::Real  value)
inline

References iha_cut_.

void protocols::mpi_refinement::MultiObjective::set_iha_penalty_mode ( std::string  value)
inline

References iha_penalty_mode_.

void protocols::mpi_refinement::MultiObjective::set_iha_penalty_slope ( core::Real  value)
inline

References iha_penalty_slope_.

void protocols::mpi_refinement::MultiObjective::set_init_pose ( core::pose::Pose  inpose)
inline

References init_pose_.

void protocols::mpi_refinement::MultiObjective::set_nremain_reset ( core::Size  value)
inline

References nremain_reset_.

void protocols::mpi_refinement::MultiObjective::succeed_substitute_info ( core::io::silent::SilentStructOP  ss_sub,
core::io::silent::SilentStructCOP  ss_ref,
bool const  reset 
) const
bool protocols::mpi_refinement::MultiObjective::update_library_NSGAII ( protocols::wum::SilentStructStore structs,
protocols::wum::SilentStructStore new_structs,
core::Size const  nmax,
bool const  update_obj_cut = false 
)
bool protocols::mpi_refinement::MultiObjective::update_library_seeds ( protocols::wum::SilentStructStore structs,
protocols::wum::SilentStructStore new_structs,
core::Real const  dcut,
utility::vector1< core::Size > const  seeds,
std::string const  prefix_in,
std::string const  objname = "",
core::Size const  maxreplace = 100000 
)

Member Data Documentation

utility::vector1< std::string > protocols::mpi_refinement::MultiObjective::fobjnames_
private

Referenced by fobjnames(), get_fobj(), has_score(), and nobjs().

core::Real protocols::mpi_refinement::MultiObjective::iha_cut_
private

Referenced by iha_cut(), and set_iha_cut().

std::string protocols::mpi_refinement::MultiObjective::iha_penalty_mode_
private
core::Real protocols::mpi_refinement::MultiObjective::iha_penalty_slope_
private
core::pose::Pose protocols::mpi_refinement::MultiObjective::init_pose_
private

Referenced by init_pose(), and set_init_pose().

core::Size protocols::mpi_refinement::MultiObjective::nremain_reset_
private

Referenced by nremain_reset(), and set_nremain_reset().

utility::vector1< core::Real > protocols::mpi_refinement::MultiObjective::obj_cut_increment_
private
utility::vector1< core::Real > protocols::mpi_refinement::MultiObjective::obj_dominant_cut_
private
utility::vector1< core::scoring::ScoreFunctionCOP > protocols::mpi_refinement::MultiObjective::objsfxnOPs_
private

Referenced by get_scorefxn().


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