protocols::mpi_refinement::MultiObjective Class Reference

#include <MultiObjective.hh>

Inheritance diagram for protocols::mpi_refinement::MultiObjective:

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::Real >	obj_dominant_cut_
utility::vector1< core::Real >	obj_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

References core::scoring::constraints::add_constraints_from_cmdline_to_pose(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose(), protocols::mpi_refinement::add_poseinfo_to_ss(), core::chemical::CENTROID, core::import_pose::PDB_file, and core::import_pose::pose_from_file().

void protocols::mpi_refinement::MultiObjective::add_objective_function_info

(

protocols::wum::SilentStructStore &

sstore

)

const

References protocols::wum::SilentStructStore::get_struct(), and protocols::wum::SilentStructStore::size().

void protocols::mpi_refinement::MultiObjective::calculate_pool_diversity

(

protocols::wum::SilentStructStore &

structs

)

const

References protocols::wum::SilentStructStore::get_struct(), and protocols::wum::SilentStructStore::size().

void protocols::mpi_refinement::MultiObjective::calculate_pool_diversity	(	protocols::wum::SilentStructStore &	structs1,
		protocols::wum::SilentStructStore &	structs2
	)		const

References protocols::wum::SilentStructStore::get_struct(), and protocols::wum::SilentStructStore::size().

void protocols::mpi_refinement::MultiObjective::calculate_structure_diversity ( core::io::silent::SilentStructOP  ss1, protocols::wum::SilentStructStore &  structs  ) const

private

References protocols::mpi_refinement::CA_Sscore(), protocols::wum::SilentStructStore::get_struct(), protocols::mpi_refinement::loopstring_to_loopvector(), and protocols::wum::SilentStructStore::size().

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
	)

References protocols::wum::SilentStructStore::begin(), core::kinematics::distance(), protocols::wum::SilentStructStore::end(), core::chemical::element::F, protocols::wum::SilentStructStore::get_struct(), protocols::wum::SilentStructStore::size(), and protocols::mpi_refinement::TR().

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

References core::chemical::element::F, and core::io::silent::SilentStruct::get_energy().

core::Real protocols::mpi_refinement::MultiObjective::get_fobj ( core::io::silent::SilentStruct const &  ss, core::Size  i  ) const

inline

References fobjnames_, and core::io::silent::SilentStruct::get_energy().

core::Real protocols::mpi_refinement::MultiObjective::get_fobj ( core::io::silent::SilentStruct const &  ss, std::string  name  ) const

inline

References core::io::silent::SilentStruct::get_energy().

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

References core::scoring::atom_pair_constraint, core::scoring::coordinate_constraint, core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::goap, and protocols::mpi_refinement::TR().

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
	)

References protocols::wum::SilentStructStore::add(), protocols::wum::SilentStructStore::all_add_energy(), protocols::wum::SilentStructStore::clear(), core::chemical::element::F, protocols::wum::SilentStructStore::get_struct(), core::chemical::rings::q, protocols::wum::SilentStructStore::size(), and protocols::mpi_refinement::TR().

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
	)

References protocols::comparative_modeling::features::A, protocols::wum::SilentStructStore::add(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose(), protocols::mpi_refinement::add_init_dev_penalty(), protocols::wum::SilentStructStore::clear(), core::kinematics::distance(), core::chemical::element::F, protocols::wum::SilentStructStore::get_struct(), core::chemical::element::I, protocols::mean_field::max(), protocols::wum::SilentStructStore::size(), protocols::wum::SilentStructStore::sort_by(), protocols::wum::SilentStructStore::store(), protocols::mpi_refinement::superimpose_all(), and protocols::mpi_refinement::TR().

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

Referenced by iha_penalty_mode(), and set_iha_penalty_mode().

core::Real protocols::mpi_refinement::MultiObjective::iha_penalty_slope_

private

Referenced by iha_penalty_slope(), and set_iha_penalty_slope().

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().

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

• src/protocols/mpi_refinement/MultiObjective.hh
• src/protocols/mpi_refinement/MultiObjective.cc