protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased Class Reference

#include <StepWiseLegacyClustererSilentBased.hh>

Inheritance diagram for protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased:

Public Member Functions
	StepWiseLegacyClustererSilentBased (utility::vector1< std::string > const &silent_files_in)
	StepWiseLegacyClustererSilentBased (std::string const &silent_file_in)
	StepWiseLegacyClustererSilentBased (core::io::silent::SilentFileDataOP &sfd)
	StepWiseLegacyClustererSilentBased (core::io::silent::SilentFileDataOP silent_file_data, utility::vector1< core::Size > const &moving_res_list, options::StepWiseModelerOptionsCOP options, bool const force_align)
	~StepWiseLegacyClustererSilentBased () override
void	set_max_decoys (core::Size const &setting)
	Filter a list of poses by score. More...
void	set_cluster_radius (core::Real const &setting)
void	set_cluster_by_all_atom_rmsd (core::Real const &setting)
void	set_rename_tags (core::Real const &setting)
void	set_score_diff_cut (core::Real const &setting)
void	set_auto_tune (bool const auto_tune)
void	set_force_align (bool const force_align)
void	set_numbered_pdb_output (bool const numbered_pdb_output)
void	set_calc_rms_res (utility::vector1< core::Size > const &calc_rms_res)
void	set_silent_file_data (core::io::silent::SilentFileDataOP &sfd)
void	set_rsd_type_set (std::string const &setting)
void	cluster ()
core::io::silent::SilentFileDataOP	silent_file_data ()
void	output_silent_file (std::string const &silent_file)
PoseList	clustered_pose_list ()
utility::vector1< core::pose::PoseOP >	get_pose_list ()
utility::vector1< core::io::silent::SilentStructOP > &	silent_struct_output_list ()

Private Member Functions
void	initialize_parameters_and_input ()
void	initialize_cluster_list ()
void	initialize_corresponding_atom_id_map (core::pose::Pose const &pose)
void	do_some_clustering ()
core::Size	check_for_closeness (core::pose::PoseOP const &pose_op)
void	cluster_with_auto_tune ()
void	recluster_current_pose_list ()
void	initialize_auto_tune_cluster_rmsds ()
core::io::silent::SilentStructOP	setup_silent_struct (core::Size const n)

Private Attributes
utility::vector1< std::string >	silent_files_
core::Size	max_decoys_
core::Real	cluster_radius_
bool	cluster_by_all_atom_rmsd_
core::Real	score_diff_cut_
bool	auto_tune_
bool	rename_tags_
bool	force_align_
bool	numbered_pdb_output_ = false
std::string	rsd_type_set_
core::Real	score_min_
bool	score_min_defined_
utility::vector1< core::pose::PoseOP >	pose_output_list_
utility::vector1< std::string >	tag_output_list_
utility::vector1< core::io::silent::SilentStructOP >	silent_struct_output_list_
utility::vector1< core::Size >	num_pose_in_cluster_
core::import_pose::pose_stream::SilentFilePoseInputStreamOP	input_
utility::vector1< core::Real >	cluster_rmsds_to_try_with_auto_tune_
bool	hit_score_cutoff_
bool	initialized_atom_id_map_for_rmsd_
utility::vector1< core::Size >	calc_rms_res_
std::map< core::id::AtomID, core::id::AtomID >	corresponding_atom_id_map_
core::chemical::ResidueTypeSetCAP	rsd_set_

Constructor & Destructor Documentation

StepWiseLegacyClustererSilentBased() [1/4]

protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::StepWiseLegacyClustererSilentBased

(

utility::vector1< std::string > const &

silent_files_in

)

StepWiseLegacyClustererSilentBased() [2/4]

protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::StepWiseLegacyClustererSilentBased

(

std::string const &

silent_file_in

)

StepWiseLegacyClustererSilentBased() [3/4]

protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::StepWiseLegacyClustererSilentBased

(

core::io::silent::SilentFileDataOP &

sfd

)

StepWiseLegacyClustererSilentBased() [4/4]

protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::StepWiseLegacyClustererSilentBased	(	core::io::silent::SilentFileDataOP	silent_file_data,
		utility::vector1< core::Size > const &	moving_res_list,
		options::StepWiseModelerOptionsCOP	options,
		bool const	force_align
	)

~StepWiseLegacyClustererSilentBased()

protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::~StepWiseLegacyClustererSilentBased ( )

overridedefault

Member Function Documentation

check_for_closeness()

Size protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::check_for_closeness ( core::pose::PoseOP const &  pose_op )

private

References core::scoring::rms_at_corresponding_atoms(), and core::scoring::rms_at_corresponding_atoms_no_super().

cluster()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::cluster

(

)

References core::pose::TR().

Referenced by protocols::stepwise::sampler::protein::generate_beta_database_test().

cluster_with_auto_tune()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::cluster_with_auto_tune ( )

private

References core::pose::TR().

clustered_pose_list()

PoseList protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::clustered_pose_list

(

)

Referenced by protocols::stepwise::sampler::protein::generate_beta_database_test().

do_some_clustering()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::do_some_clustering ( )

private

References core::pose::Pose::clone(), core::pose::Pose::dump_pdb(), core::pose::getPoseExtraScore(), core::pose::pdbslice(), protocols::hybridization::score, and core::pose::TR().

get_pose_list()

utility::vector1< PoseOP > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::get_pose_list

(

)

References core::pose::tag_into_pose().

initialize_auto_tune_cluster_rmsds()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::initialize_auto_tune_cluster_rmsds ( )

private

initialize_cluster_list()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::initialize_cluster_list ( )

private

initialize_corresponding_atom_id_map()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::initialize_corresponding_atom_id_map ( core::pose::Pose const &  pose )

private

References core::scoring::setup_matching_heavy_atoms(), and core::scoring::setup_matching_protein_backbone_heavy_atoms().

initialize_parameters_and_input()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::initialize_parameters_and_input ( )

private

output_silent_file()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::output_silent_file

(

std::string const &

silent_file

)

References core::io::silent::SilentFileData::write_silent_struct().

Referenced by protocols::stepwise::sampler::protein::generate_beta_database_test().

recluster_current_pose_list()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::recluster_current_pose_list ( )

private

References core::pose::TR().

set_auto_tune()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_auto_tune ( bool const  auto_tune )

inline

References auto_tune_.

set_calc_rms_res()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_calc_rms_res

(

utility::vector1< core::Size > const &

calc_rms_res

)

Referenced by protocols::stepwise::sampler::protein::generate_beta_database_test().

set_cluster_by_all_atom_rmsd()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_cluster_by_all_atom_rmsd ( core::Real const &  setting )

inline

References cluster_by_all_atom_rmsd_.

set_cluster_radius()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_cluster_radius ( core::Real const &  setting )

inline

References cluster_radius_.

Referenced by protocols::stepwise::sampler::protein::generate_beta_database_test().

set_force_align()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_force_align ( bool const  force_align )

inline

References force_align_.

set_max_decoys()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_max_decoys ( core::Size const &  setting )

inline

Filter a list of poses by score.

References max_decoys_.

Referenced by protocols::stepwise::sampler::protein::generate_beta_database_test().

set_numbered_pdb_output()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_numbered_pdb_output ( bool const  numbered_pdb_output )

inline

References numbered_pdb_output_.

set_rename_tags()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_rename_tags ( core::Real const &  setting )

inline

References rename_tags_.

Referenced by protocols::stepwise::sampler::protein::generate_beta_database_test().

set_rsd_type_set()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_rsd_type_set ( std::string const &  setting )

inline

References rsd_type_set_.

set_score_diff_cut()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_score_diff_cut ( core::Real const &  setting )

inline

References score_diff_cut_.

Referenced by protocols::stepwise::sampler::protein::generate_beta_database_test().

set_silent_file_data()

void protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_silent_file_data

(

core::io::silent::SilentFileDataOP &

sfd

)

setup_silent_struct()

core::io::silent::SilentStructOP protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::setup_silent_struct ( core::Size const  n )

private

References core::chemical::element::I.

silent_file_data()

core::io::silent::SilentFileDataOP protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::silent_file_data

(

)

silent_struct_output_list()

utility::vector1< core::io::silent::SilentStructOP >& protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::silent_struct_output_list ( )

inline

References silent_struct_output_list_.

Member Data Documentation

auto_tune_

bool protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::auto_tune_

private

Referenced by set_auto_tune().

calc_rms_res_

utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::calc_rms_res_

private

cluster_by_all_atom_rmsd_

bool protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::cluster_by_all_atom_rmsd_

private

Referenced by set_cluster_by_all_atom_rmsd().

cluster_radius_

core::Real protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::cluster_radius_

private

Referenced by set_cluster_radius().

cluster_rmsds_to_try_with_auto_tune_

utility::vector1< core::Real > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::cluster_rmsds_to_try_with_auto_tune_

private

corresponding_atom_id_map_

std::map< core::id::AtomID, core::id::AtomID > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::corresponding_atom_id_map_

private

force_align_

bool protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::force_align_

private

Referenced by set_force_align().

hit_score_cutoff_

bool protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::hit_score_cutoff_

private

initialized_atom_id_map_for_rmsd_

bool protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::initialized_atom_id_map_for_rmsd_

private

input_

core::import_pose::pose_stream::SilentFilePoseInputStreamOP protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::input_

private

max_decoys_

core::Size protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::max_decoys_

private

Referenced by set_max_decoys().

num_pose_in_cluster_

utility::vector1< core::Size > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::num_pose_in_cluster_

private

numbered_pdb_output_

bool protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::numbered_pdb_output_ = false

private

Referenced by set_numbered_pdb_output().

pose_output_list_

utility::vector1< core::pose::PoseOP > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::pose_output_list_

private

rename_tags_

bool protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::rename_tags_

private

Referenced by set_rename_tags().

rsd_set_

core::chemical::ResidueTypeSetCAP protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::rsd_set_

private

rsd_type_set_

std::string protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::rsd_type_set_

private

Referenced by set_rsd_type_set().

score_diff_cut_

core::Real protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::score_diff_cut_

private

Referenced by set_score_diff_cut().

score_min_

core::Real protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::score_min_

private

score_min_defined_

bool protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::score_min_defined_

private

silent_files_

utility::vector1< std::string > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::silent_files_

private

silent_struct_output_list_

utility::vector1< core::io::silent::SilentStructOP > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::silent_struct_output_list_

private

Referenced by silent_struct_output_list().

tag_output_list_

utility::vector1< std::string > protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::tag_output_list_

private

---

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

• src/protocols/stepwise/modeler/align/StepWiseLegacyClustererSilentBased.hh
• src/protocols/stepwise/modeler/align/StepWiseLegacyClustererSilentBased.cc