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protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD Class Reference

#include <MPIHPool_ConvergenceCheck.hh>

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

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::Reallevel_radii_
 
Address current_address_
 
utility::vector1< core::Realcurrent_best_rmsds_
 
Address best_address_
 
std::string current_address_str_
 
DataBuffer buf_
 
core::Size current_trajectory_state_
 

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
 

Member Typedef Documentation

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
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
DataBuffer protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::buf_
private
Address protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::current_address_
private
std::string protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::current_address_str_
private
utility::vector1< core::Real > protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::current_best_rmsds_
private
core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::current_trajectory_state_
private
bool protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::first_time_writing_
private
protocols::canonical_sampling::mc_convergence_checks::HierarchicalLevel protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::hlevel_
private
utility::vector1< core::Real > protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::level_radii_
private
std::string protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::new_decoys_out_
private
core::Size const protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::nlevels_
private
core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::npes_
private
core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::nresidues_
private
core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::num_structures_added_
private
core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::pool_npes_
private
core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::pool_rank_
private
core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::pool_size_
private
core::Size protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::rank_
private
bool protocols::canonical_sampling::mc_convergence_checks::MPIHPool_RMSD::tracer_visible_
private

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