#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

◆ MultiObjective()

protocols::mpi_refinement::MultiObjective::MultiObjective ( )

◆ ~MultiObjective()

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

overridedefault

Member Function Documentation

◆ add_objective_function_info() [1/2]

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().

◆ add_objective_function_info() [2/2]

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().

◆ calculate_pool_diversity() [1/2]

void protocols::mpi_refinement::MultiObjective::calculate_pool_diversity ( protocols::wum::SilentStructStore & structs ) const

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

◆ calculate_pool_diversity() [2/2]

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().

◆ calculate_structure_diversity()

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().

◆ filter_similar()

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::add(), 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().

◆ fobjnames()

std::string protocols::mpi_refinement::MultiObjective::fobjnames ( core::Size i ) const

inline

References fobjnames_.

◆ formatted_objs_names()

std::string protocols::mpi_refinement::MultiObjective::formatted_objs_names ( ) const

◆ formatted_objs_values()

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().

◆ get_fobj() [1/3]

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().

◆ get_fobj() [2/3]

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().

◆ get_fobj() [3/3]

core::Real protocols::mpi_refinement::MultiObjective::get_fobj	(	core::io::silent::SilentStructCOP	pss,
		core::Size	i
	)		const

inline

References fobjnames_.

◆ get_scorefxn()

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

inline

References objsfxnOPs_.

◆ has_score()

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

inline

References fobjnames_.

◆ iha_cut()

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

inline

References iha_cut_.

◆ iha_penalty_mode()

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

inline

References iha_penalty_mode_.

◆ iha_penalty_slope()

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

inline

References iha_penalty_slope_.

◆ init_pose()

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

inline

References init_pose_.

◆ is_dominant()

bool protocols::mpi_refinement::MultiObjective::is_dominant	(	core::io::silent::SilentStructCOP	ss1,
		core::io::silent::SilentStructCOP	ss2
	)

private

◆ nobjs()

core::Size protocols::mpi_refinement::MultiObjective::nobjs ( ) const

inline

References fobjnames_.

◆ nremain_reset()

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

inline

References nremain_reset_.

◆ set_defaults()

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().

◆ set_iha_cut()

void protocols::mpi_refinement::MultiObjective::set_iha_cut ( core::Real value )

inline

References iha_cut_.

◆ set_iha_penalty_mode()

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

inline

References iha_penalty_mode_.

◆ set_iha_penalty_slope()

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

inline

References iha_penalty_slope_.

◆ set_init_pose()

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

inline

References init_pose_.

◆ set_nremain_reset()

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

inline

References nremain_reset_.

◆ succeed_substitute_info()

void protocols::mpi_refinement::MultiObjective::succeed_substitute_info	(	core::io::silent::SilentStructOP	ss_sub,
		core::io::silent::SilentStructCOP	ss_ref,
		bool const	reset
	)		const

◆ update_library_NSGAII()

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(), protocols::wum::SilentStructStore::sort_by(), and protocols::mpi_refinement::TR().

◆ update_library_seeds()

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

◆ fobjnames_

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

private

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

◆ iha_cut_

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

private

Referenced by iha_cut(), and set_iha_cut().

◆ iha_penalty_mode_

std::string protocols::mpi_refinement::MultiObjective::iha_penalty_mode_

private

Referenced by iha_penalty_mode(), and set_iha_penalty_mode().

◆ iha_penalty_slope_

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

private

Referenced by iha_penalty_slope(), and set_iha_penalty_slope().

◆ init_pose_

core::pose::Pose protocols::mpi_refinement::MultiObjective::init_pose_

private

Referenced by init_pose(), and set_init_pose().

◆ nremain_reset_

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

private

Referenced by nremain_reset(), and set_nremain_reset().

◆ obj_cut_increment_

utility::vector1< core::Real > protocols::mpi_refinement::MultiObjective::obj_cut_increment_

private

◆ obj_dominant_cut_

utility::vector1< core::Real > protocols::mpi_refinement::MultiObjective::obj_dominant_cut_

private

◆ objsfxnOPs_

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:

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

Public Member Functions

Private Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ MultiObjective()

◆ ~MultiObjective()

Member Function Documentation

◆ add_objective_function_info() [1/2]

◆ add_objective_function_info() [2/2]

◆ calculate_pool_diversity() [1/2]

◆ calculate_pool_diversity() [2/2]

◆ calculate_structure_diversity()

◆ filter_similar()

◆ fobjnames()

◆ formatted_objs_names()

◆ formatted_objs_values()

◆ get_fobj() [1/3]

◆ get_fobj() [2/3]

◆ get_fobj() [3/3]

◆ get_scorefxn()

◆ has_score()

◆ iha_cut()

◆ iha_penalty_mode()

◆ iha_penalty_slope()

◆ init_pose()

◆ is_dominant()

◆ nobjs()

◆ nremain_reset()

◆ set_defaults()

◆ set_iha_cut()

◆ set_iha_penalty_mode()

◆ set_iha_penalty_slope()

◆ set_init_pose()

◆ set_nremain_reset()

◆ succeed_substitute_info()

◆ update_library_NSGAII()

◆ update_library_seeds()

Member Data Documentation

◆ fobjnames_

◆ iha_cut_

◆ iha_penalty_mode_

◆ iha_penalty_slope_

◆ init_pose_

◆ nremain_reset_

◆ obj_cut_increment_

◆ obj_dominant_cut_

◆ objsfxnOPs_