#include <SubMotifLibrary.hh>

Inheritance diagram for protocols::stepwise::monte_carlo::submotif::SubMotifLibrary:

Public Member Functions
	SubMotifLibrary (core::chemical::ResidueTypeSetCOP rsd_set, bool const include_submotifs_from_jump_library=false, bool const use_first_jump_for_submotif=false, utility::vector1< std::string > const &exclude_submotif_list=utility::vector1< std::string >())

	~SubMotifLibrary () override

core::pose::PoseOP	create_new_submotif (SequenceMapping const &sequence_mapping, PoseTag const &submotif_tag, core::pose::Pose const &pose, bool const &seed=false) const

utility::vector1 < monte_carlo::mover::StepWiseMove >	get_submotif_moves (core::pose::Pose const &pose) const

Private Member Functions
void	initialize ()

void	initialize_from_directory (std::string const &dir_name)

void	initialize_from_jump_library ()

SubMotifSequenceSet	get_submotif_sequence_set (core::pose::Pose const &pose, bool sort_sequences=true) const

void	save_pose_as_submotif (core::pose::PoseOP pose, std::string const &tag)

utility::vector1< SequenceMapping >	get_matches_for_one_submotif_sequence_set (SubMotifSequenceSet const &submotif_sequence_set, core::pose::Pose const &pose, bool const use_full_model_info=true) const

void	get_moves_for_one_submotif (core::pose::PoseCOP submotif_pose, core::pose::Pose const &pose) const

void	get_matches (utility::vector1< SequenceMapping > &all_matches, SequenceMapping const &matching_residues, std::string const &submotif_sequence, utility::vector1< core::Size > const &submotif_cutpoints, std::string const &pose_sequence, utility::vector1< core::Size > const &pose_cutpoints, utility::vector1< core::Size > const &pose_domain_map) const

void	output_tags () const

Private Attributes
core::chemical::ResidueTypeSetCOP	rsd_set_

bool const	include_submotifs_from_jump_library_

bool const	use_first_jump_for_submotif_

utility::vector1< PoseTag >	exclude_submotif_list_

std::set< SubMotifSequenceSet >	submotif_sequence_sets_

std::map< SubMotifSequenceSet, utility::vector1< std::pair < PoseTag, SequenceMapping > > >	submotif_mappings_by_sequence_set_

std::map< PoseTag, core::pose::PoseCOP >	submotif_poses_by_tag_

Constructor & Destructor Documentation

protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::SubMotifLibrary	(	core::chemical::ResidueTypeSetCOP	rsd_set,
		bool const	include_submotifs_from_jump_library = `false`,
		bool const	use_first_jump_for_submotif = `false`,
		utility::vector1< std::string > const &	exclude_submotif_list = `utility::vector1< std::string >()`
	)

References initialize().

protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::~SubMotifLibrary ( )

overridedefault

Member Function Documentation

pose::PoseOP protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::create_new_submotif	(	SequenceMapping const &	sequence_mapping,
		PoseTag const &	submotif_tag,
		core::pose::Pose const &	pose,
		bool const &	seed = `false`
	)		const

References core::pose::full_model_info::const_full_model_info(), core::chemical::FA_STANDARD, core::pose::fix_up_residue_type_variants(), core::pose::full_model_info::FullModelInfo::full_model_parameters(), core::pose::full_model_info::FullModelInfo::full_sequence(), core::chemical::ResidueTypeFinder::get_representative_type(), output_tags(), core::chemical::ResidueTypeFinder::residue_base_name(), core::pose::full_model_info::set_full_model_info(), submotif_poses_by_tag_, and protocols::TR().

void protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_matches	(	utility::vector1< SequenceMapping > &	all_matches,
		SequenceMapping const &	matching_residues,
		std::string const &	submotif_sequence,
		utility::vector1< core::Size > const &	submotif_cutpoints,
		std::string const &	pose_sequence,
		utility::vector1< core::Size > const &	pose_cutpoints,
		utility::vector1< core::Size > const &	pose_domain_map
	)		const

private

Referenced by get_matches_for_one_submotif_sequence_set().

utility::vector1< SequenceMapping > protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_matches_for_one_submotif_sequence_set	(	SubMotifSequenceSet const &	submotif_sequence_set,
		core::pose::Pose const &	pose,
		bool const	use_full_model_info = `true`
	)		const

private

References core::pose::full_model_info::const_full_model_info(), core::pose::full_model_info::FullModelInfo::cutpoint_open_in_full_model(), core::pose::full_model_info::figure_out_pose_domain_map_const(), core::pose::Pose::fold_tree(), core::pose::full_model_info::full_model_info_defined(), core::pose::full_model_info::FullModelInfo::full_sequence(), get_matches(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::sequence(), and core::pose::Pose::size().

Referenced by get_submotif_moves(), and save_pose_as_submotif().

void protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_moves_for_one_submotif	(	core::pose::PoseCOP	submotif_pose,
		core::pose::Pose const &	pose
	)		const

private

utility::vector1< StepWiseMove > protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_submotif_moves ( core::pose::Pose const & pose ) const

References protocols::stepwise::monte_carlo::mover::FROM_SCRATCH, get_matches_for_one_submotif_sequence_set(), core::chemical::rings::q, submotif_mappings_by_sequence_set_, and submotif_sequence_sets_.

SubMotifSequenceSet protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::get_submotif_sequence_set	(	core::pose::Pose const &	pose,
		bool	sort_sequences = `true`
	)		const

private

References core::pose::Pose::fold_tree(), core::kinematics::FoldTree::is_cutpoint(), core::pose::Pose::sequence(), and core::pose::Pose::size().

Referenced by output_tags(), and save_pose_as_submotif().

void protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::initialize ( )

private

References include_submotifs_from_jump_library_, initialize_from_directory(), and initialize_from_jump_library().

Referenced by SubMotifLibrary().

void protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::initialize_from_directory ( std::string const & dir_name )

private

References exclude_submotif_list_, core::import_pose::get_pdb_and_cleanup(), rsd_set_, save_pose_as_submotif(), and protocols::TR().

Referenced by initialize().

void protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::initialize_from_jump_library ( )

private

References core::import_pose::cleanup(), core::pose::rna::fill_in_default_jump_atoms(), core::pose::make_pose_from_sequence(), core::kinematics::FoldTree::new_jump(), core::chemical::rna::rna_nts(), rsd_set_, save_pose_as_submotif(), core::import_pose::libraries::BasePairType::tag(), protocols::TR(), and use_first_jump_for_submotif_.

Referenced by initialize().

void protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::output_tags ( ) const

private

References get_submotif_sequence_set(), submotif_poses_by_tag_, and protocols::TR().

Referenced by create_new_submotif().

void protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::save_pose_as_submotif	(	core::pose::PoseOP	pose,
		std::string const &	tag
	)

private

References get_matches_for_one_submotif_sequence_set(), get_submotif_sequence_set(), submotif_mappings_by_sequence_set_, submotif_poses_by_tag_, submotif_sequence_sets_, and core::pose::tag_into_pose().

Referenced by initialize_from_directory(), and initialize_from_jump_library().

Member Data Documentation

utility::vector1< PoseTag > protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::exclude_submotif_list_

private

Referenced by initialize_from_directory().

bool const protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::include_submotifs_from_jump_library_

private

Referenced by initialize().

core::chemical::ResidueTypeSetCOP protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::rsd_set_

private

Referenced by initialize_from_directory(), and initialize_from_jump_library().

std::map< SubMotifSequenceSet, utility::vector1< std::pair< PoseTag, SequenceMapping > > > protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::submotif_mappings_by_sequence_set_

private

Referenced by get_submotif_moves(), and save_pose_as_submotif().

std::map< PoseTag, core::pose::PoseCOP > protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::submotif_poses_by_tag_

private

Referenced by create_new_submotif(), output_tags(), and save_pose_as_submotif().

std::set< SubMotifSequenceSet > protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::submotif_sequence_sets_

private

Referenced by get_submotif_moves(), and save_pose_as_submotif().

bool const protocols::stepwise::monte_carlo::submotif::SubMotifLibrary::use_first_jump_for_submotif_

private

Referenced by initialize_from_jump_library().

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