#include <MPIHPool_ConvergenceCheck.hh>

Inheritance diagram for protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD:

Collaboration diagram for protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD:

Public Types
typedef utility::vector1 < core::Size >	Address

Public Member Functions
	MPIHPool_RMSD (std::string const &silent_file, core::Size levels)

core::Size	evaluate_and_add (core::pose::Pose const &pose, std::string &best_decoy, core::Real &best_rmsd)

void	set_discovered_out (std::string const &newout)

std::string const &	get_discovered_out ()

void	set_transition_threshold (core::Real threshold)

void	set_nresidues (core::Size nres)

core::Size	get_nresidues ()

void	max_cache_size (core::Size max_cache)

void	finalize ()

bool	is_in_neighborhood (Address &q_address, Address &ref_address)

core::Real	resolved_level_best_rmsd (Address &addr, utility::vector1< core::Real > &rmsd)

bool	is_new_structure (Address &address, utility::vector1< core::Real > &radii, utility::vector1< core::Real > &rmsds)

bool	is_new_structure (Address &address, utility::vector1< core::Real > &radii, core::Real &rmsds)

core::Size	find_address (Address &query_addr, utility::vector1< Address > &address_database)

void	print_address (Address &addr)

Public Member Functions inherited from protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
	Pool_RMSD (std::string silent_file)

	Pool_RMSD ()

virtual	~Pool_RMSD ()

core::Size	evaluate (core::pose::Pose const &, std::string &best_decoy, core::Real &best_rmsd) const
	return position in pool for the best_decoy More...

core::Size	evaluate (core::io::silent::SilentStruct const &, std::string &best_decoy, core::Real &best_rmsd) const

virtual core::Size	evaluate_and_add (core::pose::Pose const &pose, std::string &cluster_center, core::Real &best_rmsd, core::Real transition_threshold)

core::Size	size () const

void	add (core::io::silent::SilentStruct const &, std::string new_tag="keep_silent_tag")

void	add (core::pose::Pose const &, std::string new_tag)

void	get (core::Size index, ObjexxFCL::FArray2D_double &result)

std::string &	get_tag (core::Size index)

void	pop_back ()

void	clear ()

void	set_reserve_size (int max_size)

core::Size	evaluate_and_add (ObjexxFCL::FArray2D_double &coords, std::string &best_decoy, core::Real &best_rmsd, core::Real transition_threshold)

core::Size	evaluate (ObjexxFCL::FArray2D_double &, std::string &best_decoy, core::Real &best_rmsd) const

core::Size	evaluate (ObjexxFCL::FArray2D_double &, std::string &best_decoy, core::Real &best_rmsd, core::Size index) const

void	add (ObjexxFCL::FArray2D_double const &, core::Size nres, std::string new_tag)

void	set_excluded_residues (utility::vector1< core::Size > const &excluded_residues)

Private Member Functions
void	send_receive_and_write_structures (bool winning_rank, core::pose::Pose const &pose)

void	write_decoys_to_hierarchy (core::io::silent::SilentFileData &sfd, core::io::silent::SilentStructOP &ss, Address &ss_addr, core::Size new_level_begins)

void	write_headers_to_hierarchy (core::io::silent::SilentStructOP &ss)

void	buf_to_address (Address &addr, int *addr_buf, core::Size index)

void	address_to_buf (Address &addr, int *addr_buf, core::Size index)

bool	is_my_structure ()

core::Size	any_node_finished ()

void	update_comm (core::Size newsize)

void	create_comm (int *ranks_to_include, int new_size)

void	initialize ()

void	resolve_address_and_assign_tag (Address &new_addr, core::Size &new_level_start, std::string &new_candidate_tag)

void	receive_and_output_structures (core::io::silent::SilentFileData &, core::Size num_structures_to_write)

void	assign_tag (std::string const &address_tag, core::Size assigned_id_num, std::string &newtag)

void	assign_tag (Address &address_tag, core::Size assigned_id_num, std::string &newtag)

bool	get_next_candidate ()

void	receive_silent_struct_any_source (core::io::silent::SilentFileData &, core::io::silent::SilentStructOP &ss, Address &ss_addr, core::Size &new_level)

void	send_silent_struct_to_rank (core::io::silent::SilentFileData &, core::io::silent::SilentStructOP &ss, Address &ss_addr, core::Size &new_level_begins)

void	send_silent_struct_to_rank (core::io::silent::SilentFileData &, core::io::silent::SilentStructOP &ss, Address &ss_addr, core::Size &new_level_begins, core::Size rank)

void	prepare_send_new_coords (bool send_coords)

void	scan_output_and_setup_to_receive ()

void	address_to_string (Address &address_buf, core::Size index, std::string &address_tag)

void	string_to_address (Address &address_buf, core::Size index, std::string &address_tag)

Additional Inherited Members
Protected Member Functions inherited from protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD
core::Size	natom () const

ObjexxFCL::FArray3D_double const &	coords () const

std::string const &	tag (core::Size index) const

Detailed Description

Definition at line 39 of file MPIHPool_ConvergenceCheck.hh.

Member Typedef Documentation

typedef utility::vector1< core::Size > protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::Address

Definition at line 43 of file MPIHPool_ConvergenceCheck.hh.

Constructor & Destructor Documentation

protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::MPIHPool_RMSD	(	std::string const &	silent_file,
		core::Size	levels
	)

Member Function Documentation

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::address_to_buf	(	Address &	addr,
		int *	addr_buf,
		core::Size	index
	)

private

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::address_to_string	(	Address &	address_buf,
		core::Size	index,
		std::string &	address_tag
	)

private

core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::any_node_finished ( )

private

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::assign_tag	(	std::string const &	address_tag,
		core::Size	assigned_id_num,
		std::string &	newtag
	)

private

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::assign_tag	(	Address &	address_tag,
		core::Size	assigned_id_num,
		std::string &	newtag
	)

private

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::buf_to_address	(	Address &	addr,
		int *	addr_buf,
		core::Size	index
	)

private

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::create_comm	(	int *	ranks_to_include,
		int	new_size
	)

private

core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::evaluate_and_add	(	core::pose::Pose const &	pose,
		std::string &	best_decoy,
		core::Real &	best_rmsd
	)

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::finalize ( )

virtual

Reimplemented from protocols::canonical_sampling::mc_convergence_checks::Pool_RMSD.

core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::find_address	(	Address &	query_addr,
		utility::vector1< Address > &	address_database
	)

std::string const& protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::get_discovered_out ( )

bool protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::get_next_candidate ( )

private

core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::get_nresidues ( )

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::initialize ( )

private

bool protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::is_in_neighborhood	(	Address &	q_address,
		Address &	ref_address
	)

bool protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::is_my_structure ( )

private

bool protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::is_new_structure	(	Address &	address,
		utility::vector1< core::Real > &	radii,
		utility::vector1< core::Real > &	rmsds
	)

bool protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::is_new_structure	(	Address &	address,
		utility::vector1< core::Real > &	radii,
		core::Real &	rmsds
	)

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::max_cache_size ( core::Size max_cache)

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::prepare_send_new_coords ( bool send_coords)

private

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::print_address ( Address & addr)

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::receive_and_output_structures	(	core::io::silent::SilentFileData &	,
		core::Size	num_structures_to_write
	)

private

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::receive_silent_struct_any_source	(	core::io::silent::SilentFileData &	,
		core::io::silent::SilentStructOP &	ss,
		Address &	ss_addr,
		core::Size &	new_level
	)

private

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::resolve_address_and_assign_tag	(	Address &	new_addr,
		core::Size &	new_level_start,
		std::string &	new_candidate_tag
	)

private

core::Real protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::resolved_level_best_rmsd	(	Address &	addr,
		utility::vector1< core::Real > &	rmsd
	)

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::scan_output_and_setup_to_receive ( )

private

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::send_receive_and_write_structures	(	bool	winning_rank,
		core::pose::Pose const &	pose
	)

private

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::send_silent_struct_to_rank	(	core::io::silent::SilentFileData &	,
		core::io::silent::SilentStructOP &	ss,
		Address &	ss_addr,
		core::Size &	new_level_begins
	)

private

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::send_silent_struct_to_rank	(	core::io::silent::SilentFileData &	,
		core::io::silent::SilentStructOP &	ss,
		Address &	ss_addr,
		core::Size &	new_level_begins,
		core::Size	rank
	)

private

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::set_discovered_out ( std::string const & newout)

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::set_nresidues ( core::Size nres)

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::set_transition_threshold ( core::Real threshold)

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::string_to_address	(	Address &	address_buf,
		core::Size	index,
		std::string &	address_tag
	)

private

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::update_comm ( core::Size newsize)

private

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::write_decoys_to_hierarchy	(	core::io::silent::SilentFileData &	sfd,
		core::io::silent::SilentStructOP &	ss,
		Address &	ss_addr,
		core::Size	new_level_begins
	)

private

void protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::write_headers_to_hierarchy ( core::io::silent::SilentStructOP & ss)

private

Member Data Documentation

Address protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::best_address_

private

Definition at line 170 of file MPIHPool_ConvergenceCheck.hh.

DataBuffer protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::buf_

private

Definition at line 173 of file MPIHPool_ConvergenceCheck.hh.

Address protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::current_address_

private

Definition at line 168 of file MPIHPool_ConvergenceCheck.hh.

std::string protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::current_address_str_

private

Definition at line 171 of file MPIHPool_ConvergenceCheck.hh.

utility::vector1< core::Real > protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::current_best_rmsds_

private

Definition at line 169 of file MPIHPool_ConvergenceCheck.hh.

core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::current_trajectory_state_

private

Definition at line 174 of file MPIHPool_ConvergenceCheck.hh.

bool protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::first_time_writing_

private

Definition at line 165 of file MPIHPool_ConvergenceCheck.hh.

protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::hlevel_

private

Definition at line 154 of file MPIHPool_ConvergenceCheck.hh.

utility::vector1< core::Real > protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::level_radii_

private

Definition at line 167 of file MPIHPool_ConvergenceCheck.hh.

std::string protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::new_decoys_out_

private

Definition at line 161 of file MPIHPool_ConvergenceCheck.hh.

core::Size const protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::nlevels_

private

Definition at line 163 of file MPIHPool_ConvergenceCheck.hh.

core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::npes_

private

Definition at line 157 of file MPIHPool_ConvergenceCheck.hh.

core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::nresidues_

private

Definition at line 162 of file MPIHPool_ConvergenceCheck.hh.

core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::num_structures_added_

private

Definition at line 156 of file MPIHPool_ConvergenceCheck.hh.

core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::pool_npes_

private

Definition at line 159 of file MPIHPool_ConvergenceCheck.hh.

core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::pool_rank_

private

Definition at line 160 of file MPIHPool_ConvergenceCheck.hh.

core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::pool_size_

private

Definition at line 155 of file MPIHPool_ConvergenceCheck.hh.

core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::rank_

private

Definition at line 158 of file MPIHPool_ConvergenceCheck.hh.

bool protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::tracer_visible_

private

Definition at line 164 of file MPIHPool_ConvergenceCheck.hh.

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

src/protocols/canonical_sampling/mc_convergence_checks/MPIHPool_ConvergenceCheck.hh

Private Attributes
protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel	hlevel_

core::Size	pool_size_

core::Size	num_structures_added_

core::Size	npes_

core::Size	rank_

core::Size	pool_npes_

core::Size	pool_rank_

std::string	new_decoys_out_

core::Size	nresidues_

core::Size const	nlevels_

bool	tracer_visible_

bool	first_time_writing_

utility::vector1< core::Real >	level_radii_

Address	current_address_

utility::vector1< core::Real >	current_best_rmsds_

Address	best_address_

std::string	current_address_str_

DataBuffer	buf_

core::Size	current_trajectory_state_

Public Types

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Member Typedef Documentation

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation