protocols::splice::SpliceManager Class Reference

#include <SpliceManager.hh>

Inheritance diagram for protocols::splice::SpliceManager:

Public Member Functions
	SpliceManager ()
	~SpliceManager () override
void	fold_tree (core::pose::Pose &pose, utility::vector1< std::array< int, 3 >> positions) const
	set the fold tree around start/stop/cut sites. More...
void	set_BB_dofs (core::pose::Pose &pose)
core::sequence::SequenceProfileOP	generate_sequence_profile (core::pose::Pose &pose)
void	generate_profile_from_seq (std::map< std::string, std::string > segment_seq_map, std::string segmentName, std::string sourcename, SpliceSegmentOP SpliceSegment)
void	add_sequence_constraints (core::pose::Pose &pose)
void	rb_adjust_template (core::pose::Pose const &pose) const
void	adjust_stem_positions_by_template (core::pose::Pose const &pose)
core::Size	template_from_res ()
void	template_from_res (core::Size const i)
core::Size	template_to_res ()
void	template_to_res (core::Size const i)
core::Size	pose_from_res ()
void	pose_from_res (core::Size const i)
core::Size	pose_to_res ()
void	pose_to_res (core::Size const i)
void	chain_num (core::Size const i)
core::Size	chain_num () const
void	use_sequence_profiles (bool const b)
core::Size	use_sequence_profiles ()
void	add_sequence_constraints_only (bool const b)
bool	add_sequence_constraints_only ()
void	segment_type (std::string const &s)
std::string	segment_type ()
void	source_pdb_name (std::string const &s)
std::string	source_pdb_name ()
void	pdb_segments (std::map< std::string, std::string > const &m)
std::map< std::string, std::string > &	pdb_segments ()
void	segment_names_ordered (utility::vector1< std::string > SegNameOrder)
utility::vector1< std::string > &	segment_names_ordered ()
std::map< std::string, SpliceSegmentOP > &	splice_segments ()
void	splice_segments (std::map< std::string, SpliceSegmentOP > const &m)
core::pose::PoseOP	template_pose ()
void	template_pose (core::pose::PoseOP const pose)
void	rb_sensitive (bool const b)
bool	rb_sensitive () const
void	dofs (ResidueBBDofs const &d)
ResidueBBDofs &	dofs ()
core::Real	profile_weight_away_from_interface () const
void	profile_weight_away_from_interface (core::Real const p)
void	scorefxn (core::scoring::ScoreFunctionOP sf)
core::scoring::ScoreFunctionOP	scorefxn () const
void	cut_site (core::Size const c)
core::Size	cut_site ()
void	residue_diff (core::Size const c)
int	residue_diff ()
std::string	tail_seg ()
void	tail_seg (std::string const &s)
core::kinematics::MoveMapOP	mm ()
void	mm (core::kinematics::MoveMapOP const m)
void	update_pose_stem_positions ()
void	check_sequence_profile (core::pose::Pose &pose, core::id::SequenceMappingOP smap, core::sequence::SequenceProfileOP seqprof)
void	parse_tags (TagCOP const tag, basic::datacache::DataMap &data)
core::pack::task::TaskFactoryOP	task_factory () const
void	task_factory (core::pack::task::TaskFactoryOP tf)
void	dbase_file_name (std::string const &s)
std::string	dbase_file_name () const
void	design_shell (core::Real const c)
void	repack_shell (core::Real const c)
core::Real	design_shell () const
core::Real	repack_shell () const
std::string	template_file () const
void	template_file (std::string const &s)
bool	thread_original_sequence () const
void	thread_original_sequence (bool const s)
bool	debug () const
void	debug (bool const s)
std::string	mover_name () const
void	mover_name (std::string const &s)
void	modify_pdb_segments_with_current_segment (std::string const &pdb_name)
void	chainbreak_check (core::pose::Pose const &pose, core::Real const tolerance, bool fail_retry_if_found, bool crash_if_found)
core::Size	allowed_cuts () const
void	allowed_cuts (core::Size const s)
void	add_dihedral_constraints (core::pose::Pose &pose, core::pose::Pose const &source_pose, core::Size nearest_to_from, core::Size nearest_to_to)
void	add_coordinate_constraints (core::pose::Pose &pose, core::pose::Pose const &source_pose, core::Size nearest_to_from, core::Size nearest_to_to, core::Size anchor, std::string atom_type="CA", core::pack::task::PackerTaskOP task=nullptr)
void	parse_segments (utility::vector1< TagCOP > const &sub_tags, TagCOP const tag, basic::datacache::DataMap &data)
core::Size	anchor_res ()
void	anchor_res (core::Size const c)

Public Attributes
bool	adjust_stem_positions_by_template_

Private Attributes
core::Size	template_from_res_
core::Size	template_to_res_
core::Size	pose_from_res_
core::Size	pose_to_res_
std::string	tail_seg_
int	residue_diff_
core::Size	chain_num_
ResidueBBDofs	dofs_
bool	use_sequence_profiles_
std::string	segment_type_
bool	add_sequence_constraints_only_
std::string	source_pdb_name_
std::map< std::string, std::string >	pdb_segments_
std::map< std::string, SpliceSegmentOP >	splice_segments_
core::Real	profile_weight_away_from_interface_
core::scoring::ScoreFunctionOP	scorefxn_
utility::vector1< std::string >	segment_names_ordered_
core::pose::PoseOP	template_pose_
bool	rb_sensitive_
core::Size	cut_site_
core::kinematics::MoveMapOP	mm_
core::pack::task::TaskFactoryOP	task_factory_
std::string	dbase_file_name_
core::Real	design_shell_
core::Real	repack_shell_
std::string	mover_name_
bool	debug_
std::string	template_file_
bool	thread_original_sequence_
core::Size	allowed_cuts_
core::Size	anchor_res_

Constructor & Destructor Documentation

SpliceManager()

protocols::splice::SpliceManager::SpliceManager

(

)

References protocols::splice::ResidueBBDofs::clear(), dofs_, pdb_segments_, and splice_segments_.

~SpliceManager()

protocols::splice::SpliceManager::~SpliceManager ( )

override

Member Function Documentation

add_coordinate_constraints()

void protocols::splice::SpliceManager::add_coordinate_constraints	(	core::pose::Pose &	pose,
		core::pose::Pose const &	source_pose,
		core::Size	nearest_to_from,
		core::Size	nearest_to_to,
		core::Size	anchor,
		std::string	atom_type = "CA",
		core::pack::task::PackerTaskOP	task = nullptr
	)

References core::pose::Pose::aa(), core::pose::Pose::add_constraints(), core::conformation::Residue::atom(), core::conformation::Residue::atom_index(), core::conformation::Residue::atom_is_hydrogen(), core::conformation::Residue::atom_name(), core::pose::Pose::chi(), core::conformation::Residue::chi_atoms(), core::kinematics::distance(), protocols::rosetta_scripts::find_nearest_res(), core::conformation::Residue::first_sidechain_atom(), core::pose::Pose::fold_tree(), core::membrane::intersect(), core::kinematics::FoldTree::is_cutpoint(), core::conformation::Residue::name1(), core::conformation::Residue::name3(), core::conformation::Residue::natoms(), protocols::splice::report_coordinate_constraints(), core::pose::Pose::residue(), core::pose::Pose::set_chi(), protocols::splice::TR(), protocols::splice::TR_constraints(), core::conformation::Atom::xyz(), and core::conformation::Residue::xyz().

Referenced by protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), and protocols::splice::SpliceOut::apply().

add_dihedral_constraints()

void protocols::splice::SpliceManager::add_dihedral_constraints	(	core::pose::Pose &	pose,
		core::pose::Pose const &	source_pose,
		core::Size	nearest_to_from,
		core::Size	nearest_to_to
	)

References core::pose::Pose::aa(), core::pose::Pose::add_constraints(), anchor_res_, core::conformation::Residue::atom(), core::chemical::ResidueType::atom_index(), core::scoring::dihedral_constraint, protocols::rosetta_scripts::find_nearest_res(), core::pose::Pose::omega(), core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue(), residue_diff(), core::pose::Pose::residue_type(), scorefxn(), protocols::splice::TR(), protocols::splice::TR_constraints(), and core::conformation::Atom::xyz().

Referenced by protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), and protocols::splice::SpliceOut::apply().

add_sequence_constraints()

void protocols::splice::SpliceManager::add_sequence_constraints

(

core::pose::Pose &

pose

)

References core::pose::add_comment(), core::pose::Pose::add_constraint(), add_sequence_constraints_only_, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), chain_num(), check_sequence_profile(), core::pose::Pose::conformation(), core::pose::Pose::constraint_set(), protocols::splice::find_residues_on_chain1_inside_interface(), generate_sequence_profile(), profile_weight_away_from_interface(), core::pose::Pose::remove_constraint(), core::scoring::res_type_constraint, scorefxn(), segment_type(), source_pdb_name(), core::pose::Pose::total_residue(), protocols::splice::TR(), and use_sequence_profiles().

Referenced by protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), and protocols::splice::SpliceOut::apply().

add_sequence_constraints_only() [1/2]

bool protocols::splice::SpliceManager::add_sequence_constraints_only ( )

inline

References add_sequence_constraints_only_.

Referenced by parse_segments().

add_sequence_constraints_only() [2/2]

void protocols::splice::SpliceManager::add_sequence_constraints_only ( bool const  b )

inline

References add_sequence_constraints_only_, and protocols::match::upstream::b.

adjust_stem_positions_by_template()

void protocols::splice::SpliceManager::adjust_stem_positions_by_template

(

core::pose::Pose const &

pose

)

References adjust_stem_positions_by_template_, core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), protocols::rosetta_scripts::find_nearest_res(), pose_from_res(), pose_to_res(), rb_adjust_template(), tail_seg(), template_from_res(), template_pose(), template_pose_, template_to_res(), and protocols::splice::TR().

Referenced by protocols::splice::SpliceOut::apply().

allowed_cuts() [1/2]

core::Size protocols::splice::SpliceManager::allowed_cuts ( ) const

inline

References allowed_cuts_.

Referenced by protocols::splice::SpliceOut::abstract_parse_tag(), protocols::splice::SpliceIn::parse_my_tag(), protocols::splice::SpliceInAntibody::parse_my_tag(), and protocols::splice::SpliceInTail::parse_my_tag().

allowed_cuts() [2/2]

void protocols::splice::SpliceManager::allowed_cuts ( core::Size const  s )

inline

References allowed_cuts_.

anchor_res() [1/2]

core::Size protocols::splice::SpliceManager::anchor_res ( )

inline

References anchor_res_.

Referenced by protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), and protocols::splice::SpliceOutTail::superimpose_source_on_pose().

anchor_res() [2/2]

void protocols::splice::SpliceManager::anchor_res ( core::Size const  c )

inline

References anchor_res_.

chain_num() [1/2]

core::Size protocols::splice::SpliceManager::chain_num ( ) const

inline

References chain_num_.

Referenced by add_sequence_constraints(), chainbreak_check(), and parse_tags().

chain_num() [2/2]

void protocols::splice::SpliceManager::chain_num ( core::Size const  i )

inline

References chain_num_.

chainbreak_check()

void protocols::splice::SpliceManager::chainbreak_check	(	core::pose::Pose const &	pose,
		core::Real const	tolerance,
		bool	fail_retry_if_found,
		bool	crash_if_found
	)

References allowed_cuts_, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), chain_num(), core::pose::Pose::conformation(), core::kinematics::distance(), core::pose::Pose::dump_pdb(), mover_name(), core::pose::Pose::residue(), protocols::splice::TR(), and core::conformation::Residue::xyz().

Referenced by protocols::splice::SpliceIn::apply(), and protocols::splice::SpliceInTail::apply().

check_sequence_profile()

void protocols::splice::SpliceManager::check_sequence_profile	(	core::pose::Pose &	pose,
		core::id::SequenceMappingOP	smap,
		core::sequence::SequenceProfileOP	seqprof
	)

References core::kinematics::distance(), core::sequence::end, core::conformation::Residue::name1(), core::pose::Pose::residue(), and protocols::splice::TR().

Referenced by add_sequence_constraints().

cut_site() [1/2]

core::Size protocols::splice::SpliceManager::cut_site ( )

inline

References cut_site_.

cut_site() [2/2]

void protocols::splice::SpliceManager::cut_site ( core::Size const  c )

inline

References cut_site_.

Referenced by protocols::splice::SpliceOut::abstract_parse_tag(), protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::splice::SpliceOutAntibody::apply(), protocols::splice::SpliceIn::assign_from_res_to_res(), protocols::splice::SpliceInAntibody::assign_from_res_to_res(), protocols::splice::SpliceOut::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceOut::ccd_mover(), protocols::splice::fix_chain_break_residue(), protocols::splice::SpliceIn::minimize_segment(), protocols::splice::SpliceOut::place_cut_site_in_segment(), protocols::splice::SpliceOutTail::place_cut_site_in_segment(), protocols::splice::SpliceOut::set_fold_tree_nodes(), protocols::splice::SpliceIn::set_fold_tree_nodes(), protocols::splice::SpliceOut::set_loop_length_change(), protocols::splice::SpliceIn::set_loop_length_change(), protocols::splice::SpliceOut::SpliceOutFilter(), and protocols::splice::SpliceOut::write_database_to_file().

dbase_file_name() [1/2]

std::string protocols::splice::SpliceManager::dbase_file_name ( ) const

inline

References dbase_file_name_.

Referenced by parse_tags().

dbase_file_name() [2/2]

void protocols::splice::SpliceManager::dbase_file_name ( std::string const &  s )

inline

References dbase_file_name_.

Referenced by protocols::splice::SpliceInAntibody::apply(), protocols::splice::SpliceIn::parse_my_tag(), protocols::splice::SpliceInAntibody::parse_my_tag(), protocols::splice::SpliceInTail::parse_my_tag(), protocols::splice::SpliceIn::read_torsion_database(), protocols::splice::SpliceOut::write_database_to_file(), and protocols::splice::SpliceOutTail::write_database_to_file().

debug() [1/2]

bool protocols::splice::SpliceManager::debug ( ) const

inline

References debug_.

Referenced by protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::splice::SpliceOut::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceOutTail::build_ideal_segment(), protocols::splice::SpliceOut::ccd_mover(), protocols::splice::fix_chain_break_residue(), protocols::splice::SpliceOut::min_mover(), protocols::splice::SpliceIn::minimize_segment(), protocols::splice::SpliceOut::minimize_segment(), protocols::splice::SpliceIn::rtmin(), protocols::splice::SpliceOut::superimpose_source_on_pose(), and protocols::splice::SpliceOut::tail_mover().

debug() [2/2]

void protocols::splice::SpliceManager::debug ( bool const  s )

inline

References debug_.

design_shell() [1/2]

core::Real protocols::splice::SpliceManager::design_shell ( ) const

inline

References design_shell_.

Referenced by parse_tags().

design_shell() [2/2]

void protocols::splice::SpliceManager::design_shell ( core::Real const  c )

inline

References design_shell_.

Referenced by protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::splice::SpliceIn::SpliceIn(), protocols::splice::SpliceInAntibody::SpliceInAntibody(), and protocols::splice::SpliceInTail::SpliceInTail().

dofs() [1/2]

ResidueBBDofs& protocols::splice::SpliceManager::dofs ( )

inline

References dofs_.

Referenced by set_BB_dofs().

dofs() [2/2]

void protocols::splice::SpliceManager::dofs ( ResidueBBDofs const &  d )

inline

References dofs_.

Referenced by protocols::splice::SpliceInAntibody::adjust_n_ter_tail_length(), protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInAntibody::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::splice::SpliceIn::assign_from_res_to_res(), protocols::splice::SpliceInAntibody::assign_from_res_to_res(), protocols::splice::SpliceInTail::assign_from_res_to_res(), protocols::splice::SpliceOut::copy_dofs_from_source(), protocols::splice::SpliceIn::find_dbase_entry(), protocols::splice::SpliceInTail::find_dbase_entry(), and protocols::splice::SpliceOut::SpliceOutRMSDFilter().

fold_tree()

void protocols::splice::SpliceManager::fold_tree	(	core::pose::Pose &	pose,
		utility::vector1< std::array< int, 3 >>	positions
	)		const

set the fold tree around start/stop/cut sites.

References core::kinematics::FoldTree::add_edge(), anchor_res_, core::kinematics::FoldTree::check_fold_tree(), core::kinematics::FoldTree::clear(), core::kinematics::FoldTree::delete_self_edges(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::reorder(), and protocols::splice::TR().

Referenced by protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), and protocols::splice::SpliceOut::apply().

generate_profile_from_seq()

void protocols::splice::SpliceManager::generate_profile_from_seq	(	std::map< std::string, std::string >	segment_seq_map,
		std::string	segmentName,
		std::string	sourcename,
		SpliceSegmentOP	SpliceSegment
	)

References protocols::splice::SpliceSegment::add_profile(), and core::sequence::Sequence::sequence().

generate_sequence_profile()

core::sequence::SequenceProfileOP protocols::splice::SpliceManager::generate_sequence_profile

(

core::pose::Pose &

pose

)

References core::pose::add_comment(), add_sequence_constraints_only_, protocols::splice::concatenate_profiles(), core::pose::get_all_comments(), protocols::splice::load_pdb_segments_from_pose_comments(), pdb_segments(), pdb_segments_, segment_names_ordered_, segment_type(), source_pdb_name(), splice_segments_, protocols::splice::TR(), and use_sequence_profiles_.

Referenced by add_sequence_constraints().

mm() [1/2]

core::kinematics::MoveMapOP protocols::splice::SpliceManager::mm ( )

inline

References mm_.

Referenced by protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::splice::SpliceIn::minimize_segment(), protocols::splice::SpliceOut::minimize_segment(), protocols::splice::SpliceIn::set_fold_tree_nodes(), and protocols::splice::SpliceInTail::set_fold_tree_nodes().

mm() [2/2]

void protocols::splice::SpliceManager::mm ( core::kinematics::MoveMapOP const  m )

inline

References mm_.

modify_pdb_segments_with_current_segment()

void protocols::splice::SpliceManager::modify_pdb_segments_with_current_segment

(

std::string const &

pdb_name

)

References pdb_segments(), and segment_type().

Referenced by protocols::splice::SpliceIn::apply(), and protocols::splice::SpliceInTail::apply().

mover_name() [1/2]

std::string protocols::splice::SpliceManager::mover_name ( ) const

inline

References mover_name_.

Referenced by protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::splice::SpliceOut::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceOutTail::build_ideal_segment(), protocols::splice::SpliceOut::ccd_mover(), chainbreak_check(), protocols::splice::SpliceIn::find_dbase_entry(), protocols::splice::SpliceInTail::find_dbase_entry(), protocols::splice::SpliceOut::min_mover(), protocols::splice::SpliceIn::minimize_segment(), protocols::splice::SpliceOut::minimize_segment(), protocols::splice::SpliceIn::rtmin(), and protocols::splice::SpliceOut::tail_mover().

mover_name() [2/2]

void protocols::splice::SpliceManager::mover_name ( std::string const &  s )

inline

References mover_name_.

parse_segments()

void protocols::splice::SpliceManager::parse_segments	(	utility::vector1< TagCOP > const &	sub_tags,
		TagCOP const	tag,
		basic::datacache::DataMap &	data
	)

References add_sequence_constraints_only(), profile_weight_away_from_interface(), segment_names_ordered(), segment_type(), splice_segments(), protocols::splice::TR(), and use_sequence_profiles().

Referenced by protocols::splice::SpliceIn::parse_my_tag(), protocols::splice::SpliceInTail::parse_my_tag(), and protocols::splice::SpliceOut::parse_my_tag().

parse_tags()

void protocols::splice::SpliceManager::parse_tags	(	TagCOP const	tag,
		basic::datacache::DataMap &	data
	)

References chain_num(), dbase_file_name(), debug_, design_shell(), mover_name_, core::pack::task::parse_task_operations(), core::import_pose::pose_from_file(), rb_sensitive(), repack_shell(), task_factory(), template_file(), template_file_, template_pose_, thread_original_sequence(), and protocols::splice::TR().

Referenced by protocols::splice::SpliceIn::parse_my_tag(), protocols::splice::SpliceInAntibody::parse_my_tag(), protocols::splice::SpliceInTail::parse_my_tag(), protocols::splice::SpliceOut::parse_my_tag(), and protocols::splice::SpliceOutAntibody::parse_my_tag().

pdb_segments() [1/2]

std::map< std::string, std::string >& protocols::splice::SpliceManager::pdb_segments ( )

inline

References pdb_segments_.

Referenced by generate_sequence_profile(), and modify_pdb_segments_with_current_segment().

pdb_segments() [2/2]

void protocols::splice::SpliceManager::pdb_segments ( std::map< std::string, std::string > const &  m )

inline

References pdb_segments_.

Referenced by protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), and protocols::splice::SpliceOut::load_pdb_segments_from_pose_comments().

pose_from_res() [1/2]

core::Size protocols::splice::SpliceManager::pose_from_res ( )

inline

References pose_from_res_.

Referenced by adjust_stem_positions_by_template(), protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::splice::SpliceOutAntibody::apply(), protocols::splice::SpliceIn::assign_from_res_to_res(), protocols::splice::SpliceOutAntibody::assign_from_res_to_res(), protocols::splice::SpliceInAntibody::assign_from_res_to_res(), protocols::splice::SpliceInTail::assign_from_res_to_res(), protocols::splice::SpliceOut::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceOutTail::build_ideal_segment(), protocols::splice::SpliceOut::ccd_mover(), protocols::splice::SpliceIn::find_dbase_entry(), protocols::splice::SpliceInTail::find_dbase_entry(), protocols::splice::SpliceOut::place_cut_site_in_segment(), protocols::splice::SpliceOut::retrieve_values(), protocols::splice::SpliceOut::save_values(), protocols::splice::SpliceOut::set_anchor_res(), protocols::splice::SpliceIn::set_anchor_res(), protocols::splice::SpliceInTail::set_anchor_res(), protocols::splice::SpliceOutTail::set_anchor_res(), set_BB_dofs(), protocols::splice::SpliceOut::set_fold_tree_nodes(), protocols::splice::SpliceIn::set_fold_tree_nodes(), protocols::splice::SpliceInTail::set_fold_tree_nodes(), protocols::splice::SpliceOutTail::set_fold_tree_nodes(), protocols::splice::SpliceOut::set_loop_length_change(), protocols::splice::SpliceIn::set_loop_length_change(), protocols::splice::SpliceInTail::set_loop_length_change(), protocols::splice::SpliceOutTail::set_loop_length_change(), protocols::splice::SpliceOut::SpliceOutRMSDFilter(), protocols::splice::SpliceOut::write_database_to_file(), and protocols::splice::SpliceOutTail::write_database_to_file().

pose_from_res() [2/2]

void protocols::splice::SpliceManager::pose_from_res ( core::Size const  i )

inline

References pose_from_res_.

pose_to_res() [1/2]

core::Size protocols::splice::SpliceManager::pose_to_res ( )

inline

References pose_to_res_.

Referenced by adjust_stem_positions_by_template(), protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInAntibody::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::splice::SpliceOutAntibody::apply(), protocols::splice::SpliceIn::assign_from_res_to_res(), protocols::splice::SpliceOutAntibody::assign_from_res_to_res(), protocols::splice::SpliceInAntibody::assign_from_res_to_res(), protocols::splice::SpliceInTail::assign_from_res_to_res(), protocols::splice::SpliceOut::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceOutTail::build_ideal_segment(), protocols::splice::SpliceOut::ccd_mover(), protocols::splice::SpliceIn::find_dbase_entry(), protocols::splice::SpliceInTail::find_dbase_entry(), protocols::splice::SpliceOut::place_cut_site_in_segment(), protocols::splice::SpliceOut::retrieve_values(), protocols::splice::SpliceOut::save_values(), protocols::splice::SpliceInTail::set_anchor_res(), protocols::splice::SpliceOutTail::set_anchor_res(), protocols::splice::SpliceOut::set_fold_tree_nodes(), protocols::splice::SpliceIn::set_fold_tree_nodes(), protocols::splice::SpliceInTail::set_fold_tree_nodes(), protocols::splice::SpliceOutTail::set_fold_tree_nodes(), protocols::splice::SpliceInTail::set_loop_length_change(), protocols::splice::SpliceOutTail::set_loop_length_change(), update_pose_stem_positions(), protocols::splice::SpliceOut::write_database_to_file(), and protocols::splice::SpliceOutTail::write_database_to_file().

pose_to_res() [2/2]

void protocols::splice::SpliceManager::pose_to_res ( core::Size const  i )

inline

References pose_to_res_.

profile_weight_away_from_interface() [1/2]

core::Real protocols::splice::SpliceManager::profile_weight_away_from_interface ( ) const

inline

References profile_weight_away_from_interface_.

Referenced by add_sequence_constraints(), protocols::splice::SpliceInAntibody::parse_my_tag(), protocols::splice::SpliceOutAntibody::parse_my_tag(), parse_segments(), protocols::splice::SpliceIn::SpliceIn(), protocols::splice::SpliceInAntibody::SpliceInAntibody(), protocols::splice::SpliceInTail::SpliceInTail(), protocols::splice::SpliceOut::SpliceOut(), protocols::splice::SpliceOutAntibody::SpliceOutAntibody(), and protocols::splice::SpliceOutTail::SpliceOutTail().

profile_weight_away_from_interface() [2/2]

void protocols::splice::SpliceManager::profile_weight_away_from_interface ( core::Real const  p )

inline

References profile_weight_away_from_interface_.

rb_adjust_template()

void protocols::splice::SpliceManager::rb_adjust_template

(

core::pose::Pose const &

pose

)

const

References protocols::splice::RBOutMover::get_disulf_jump(), rb_sensitive(), protocols::splice::RBInMover::set_fold_tree(), core::pose::Pose::split_by_chain(), template_pose_, and protocols::splice::TR().

Referenced by adjust_stem_positions_by_template().

rb_sensitive() [1/2]

bool protocols::splice::SpliceManager::rb_sensitive ( ) const

inline

References rb_sensitive_.

Referenced by parse_tags(), and rb_adjust_template().

rb_sensitive() [2/2]

void protocols::splice::SpliceManager::rb_sensitive ( bool const  b )

inline

References protocols::match::upstream::b, and rb_sensitive_.

Referenced by protocols::splice::SpliceIn::SpliceIn(), protocols::splice::SpliceInAntibody::SpliceInAntibody(), protocols::splice::SpliceInTail::SpliceInTail(), protocols::splice::SpliceOut::SpliceOut(), protocols::splice::SpliceOutAntibody::SpliceOutAntibody(), and protocols::splice::SpliceOutTail::SpliceOutTail().

repack_shell() [1/2]

core::Real protocols::splice::SpliceManager::repack_shell ( ) const

inline

References repack_shell_.

Referenced by parse_tags().

repack_shell() [2/2]

void protocols::splice::SpliceManager::repack_shell ( core::Real const  c )

inline

References repack_shell_.

Referenced by protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::splice::SpliceIn::SpliceIn(), protocols::splice::SpliceInAntibody::SpliceInAntibody(), and protocols::splice::SpliceInTail::SpliceInTail().

residue_diff() [1/2]

int protocols::splice::SpliceManager::residue_diff ( )

inline

References residue_diff_.

Referenced by add_dihedral_constraints(), and update_pose_stem_positions().

residue_diff() [2/2]

void protocols::splice::SpliceManager::residue_diff ( core::Size const  c )

inline

References residue_diff_.

Referenced by protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::splice::SpliceIn::assign_from_res_to_res(), protocols::splice::SpliceInAntibody::assign_from_res_to_res(), protocols::splice::SpliceOutTail::place_cut_site_in_segment(), protocols::splice::SpliceOut::set_loop_length_change(), protocols::splice::SpliceIn::set_loop_length_change(), protocols::splice::SpliceInTail::set_loop_length_change(), protocols::splice::SpliceOutTail::set_loop_length_change(), protocols::splice::SpliceInAntibody::update_vl_vh_cut(), and protocols::splice::SpliceOutAntibody::update_vl_vh_cut().

scorefxn() [1/2]

core::scoring::ScoreFunctionOP protocols::splice::SpliceManager::scorefxn ( ) const

inline

References scorefxn_.

Referenced by add_dihedral_constraints(), and add_sequence_constraints().

scorefxn() [2/2]

void protocols::splice::SpliceManager::scorefxn ( core::scoring::ScoreFunctionOP  sf )

inline

References scorefxn_.

Referenced by protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInAntibody::apply(), protocols::splice::SpliceInTail::apply(), and protocols::splice::SpliceOut::apply().

segment_names_ordered() [1/2]

utility::vector1< std::string >& protocols::splice::SpliceManager::segment_names_ordered ( )

inline

References segment_names_ordered_.

Referenced by parse_segments().

segment_names_ordered() [2/2]

void protocols::splice::SpliceManager::segment_names_ordered ( utility::vector1< std::string >  SegNameOrder )

inline

References segment_names_ordered_.

Referenced by protocols::splice::SpliceInAntibody::parse_my_tag(), protocols::splice::SpliceOutAntibody::parse_my_tag(), protocols::splice::SpliceInAntibody::SpliceInAntibody(), and protocols::splice::SpliceOutAntibody::SpliceOutAntibody().

segment_type() [1/2]

std::string protocols::splice::SpliceManager::segment_type ( )

inline

References segment_type_.

Referenced by add_sequence_constraints(), generate_sequence_profile(), modify_pdb_segments_with_current_segment(), and parse_segments().

segment_type() [2/2]

void protocols::splice::SpliceManager::segment_type ( std::string const &  s )

inline

References segment_type_.

Referenced by protocols::splice::SpliceInAntibody::adjust_n_ter_tail_length(), protocols::splice::SpliceOutAntibody::adjust_n_ter_tail_length(), protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInAntibody::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOutAntibody::apply(), protocols::splice::SpliceOutAntibody::assign_from_res_to_res(), protocols::splice::SpliceInAntibody::assign_from_res_to_res(), protocols::splice::SpliceInAntibody::build_ideal_segment(), protocols::splice::SpliceOutAntibody::build_ideal_segment(), protocols::splice::SpliceInAntibody::find_dbase_entry(), protocols::splice::SpliceOut::find_non_active_site_cut_site(), protocols::splice::SpliceOutAntibody::name_for_filter(), protocols::splice::SpliceInAntibody::parse_my_tag(), protocols::splice::SpliceOutAntibody::parse_my_tag(), protocols::splice::SpliceOutAntibody::place_cut_site_in_segment(), protocols::splice::SpliceInAntibody::set_anchor_res(), protocols::splice::SpliceOutAntibody::set_anchor_res(), protocols::splice::SpliceInAntibody::set_fold_tree_nodes(), protocols::splice::SpliceOutAntibody::set_fold_tree_nodes(), protocols::splice::SpliceInAntibody::set_loop_length_change(), protocols::splice::SpliceOutAntibody::set_loop_length_change(), protocols::splice::SpliceOutAntibody::set_source_from_to_res(), protocols::splice::SpliceOutAntibody::superimpose_source_on_pose(), protocols::splice::SpliceInAntibody::update_vl_vh_cut(), protocols::splice::SpliceOutAntibody::update_vl_vh_cut(), and protocols::splice::SpliceOutAntibody::write_database_to_file().

set_BB_dofs()

void protocols::splice::SpliceManager::set_BB_dofs

(

core::pose::Pose &

pose

)

References dofs(), core::pose::Pose::omega(), core::scoring::omega, core::pose::Pose::phi(), pose_from_res(), core::pose::Pose::psi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::splice::ResidueBBDofs::size(), and protocols::splice::TR().

Referenced by protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), and protocols::splice::SpliceOut::apply().

source_pdb_name() [1/2]

std::string protocols::splice::SpliceManager::source_pdb_name ( )

inline

References source_pdb_name_.

Referenced by add_sequence_constraints(), and generate_sequence_profile().

source_pdb_name() [2/2]

void protocols::splice::SpliceManager::source_pdb_name ( std::string const &  s )

inline

References source_pdb_name_.

Referenced by protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInAntibody::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::splice::SpliceOut::check_pose_pssm_match(), protocols::splice::SpliceOut::write_database_to_file(), and protocols::splice::SpliceOutTail::write_database_to_file().

splice_segments() [1/2]

std::map< std::string, SpliceSegmentOP >& protocols::splice::SpliceManager::splice_segments ( )

inline

References splice_segments_.

Referenced by protocols::splice::SpliceOut::find_non_active_site_cut_site(), protocols::splice::SpliceInAntibody::parse_my_tag(), protocols::splice::SpliceOutAntibody::parse_my_tag(), and parse_segments().

splice_segments() [2/2]

void protocols::splice::SpliceManager::splice_segments ( std::map< std::string, SpliceSegmentOP > const &  m )

inline

References splice_segments_.

tail_seg() [1/2]

std::string protocols::splice::SpliceManager::tail_seg ( )

inline

References tail_seg_.

Referenced by protocols::splice::SpliceOutTail::abstract_parse_tag(), adjust_stem_positions_by_template(), protocols::splice::SpliceInAntibody::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOutAntibody::apply(), protocols::splice::SpliceInAntibody::assign_from_res_to_res(), protocols::splice::SpliceInAntibody::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceOutAntibody::build_ideal_segment(), protocols::splice::SpliceOutTail::build_ideal_segment(), protocols::splice::SpliceInAntibody::find_dbase_entry(), protocols::splice::SpliceOutAntibody::name_for_filter(), protocols::splice::SpliceOutAntibody::parse_my_tag(), protocols::splice::SpliceOutAntibody::place_cut_site_in_segment(), protocols::splice::SpliceOutTail::place_cut_site_in_segment(), protocols::splice::SpliceInAntibody::set_anchor_res(), protocols::splice::SpliceInTail::set_anchor_res(), protocols::splice::SpliceOutAntibody::set_anchor_res(), protocols::splice::SpliceOutTail::set_anchor_res(), protocols::splice::SpliceInAntibody::set_fold_tree_nodes(), protocols::splice::SpliceInTail::set_fold_tree_nodes(), protocols::splice::SpliceOutAntibody::set_fold_tree_nodes(), protocols::splice::SpliceOutTail::set_fold_tree_nodes(), protocols::splice::SpliceInAntibody::set_loop_length_change(), protocols::splice::SpliceInTail::set_loop_length_change(), protocols::splice::SpliceOutAntibody::set_loop_length_change(), protocols::splice::SpliceOutTail::set_loop_length_change(), protocols::splice::SpliceOutAntibody::set_source_from_to_res(), protocols::splice::SpliceOutTail::set_source_from_to_res(), protocols::splice::SpliceOutAntibody::SpliceOutAntibody(), protocols::splice::SpliceOutAntibody::superimpose_source_on_pose(), protocols::splice::SpliceOutTail::superimpose_source_on_pose(), protocols::splice::SpliceOutAntibody::write_database_to_file(), and protocols::splice::SpliceOutTail::write_database_to_file().

tail_seg() [2/2]

void protocols::splice::SpliceManager::tail_seg ( std::string const &  s )

inline

References tail_seg_.

task_factory() [1/2]

core::pack::task::TaskFactoryOP protocols::splice::SpliceManager::task_factory ( ) const

inline

References task_factory_.

Referenced by protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), protocols::splice::SpliceOut::apply(), protocols::splice::SpliceOut::ccd_mover(), parse_tags(), and protocols::splice::SpliceOut::tail_mover().

task_factory() [2/2]

void protocols::splice::SpliceManager::task_factory ( core::pack::task::TaskFactoryOP  tf )

inline

References task_factory_.

template_file() [1/2]

std::string protocols::splice::SpliceManager::template_file ( ) const

inline

References template_file_.

Referenced by parse_tags(), and protocols::splice::SpliceOut::SpliceOut().

template_file() [2/2]

void protocols::splice::SpliceManager::template_file ( std::string const &  s )

inline

References template_file_.

template_from_res() [1/2]

core::Size protocols::splice::SpliceManager::template_from_res ( )

inline

References template_from_res_.

Referenced by protocols::splice::SpliceOut::abstract_parse_tag(), protocols::splice::SpliceOutTail::abstract_parse_tag(), adjust_stem_positions_by_template(), protocols::splice::SpliceOutAntibody::apply(), protocols::splice::SpliceOutAntibody::assign_from_res_to_res(), protocols::splice::SpliceOut::set_source_from_to_res(), protocols::splice::SpliceOutTail::set_source_from_to_res(), protocols::splice::SpliceOut::superimpose_source_on_pose(), protocols::splice::SpliceOutTail::superimpose_source_on_pose(), protocols::splice::SpliceOut::write_database_to_file(), and protocols::splice::SpliceOutTail::write_database_to_file().

template_from_res() [2/2]

void protocols::splice::SpliceManager::template_from_res ( core::Size const  i )

inline

References template_from_res_.

template_pose() [1/2]

core::pose::PoseOP protocols::splice::SpliceManager::template_pose ( )

inline

References template_pose_.

Referenced by protocols::splice::SpliceOut::abstract_parse_tag(), protocols::splice::SpliceOutTail::abstract_parse_tag(), adjust_stem_positions_by_template(), protocols::splice::SpliceInAntibody::adjust_template_jump(), protocols::splice::SpliceOutAntibody::apply(), protocols::splice::SpliceIn::assign_from_res_to_res(), protocols::splice::SpliceInTail::assign_from_res_to_res(), protocols::splice::SpliceOut::set_source_from_to_res(), protocols::splice::SpliceOutTail::set_source_from_to_res(), and protocols::splice::SpliceOutTail::superimpose_source_on_pose().

template_pose() [2/2]

void protocols::splice::SpliceManager::template_pose ( core::pose::PoseOP const  pose )

inline

References template_pose_.

template_to_res() [1/2]

core::Size protocols::splice::SpliceManager::template_to_res ( )

inline

References template_to_res_.

Referenced by protocols::splice::SpliceOut::abstract_parse_tag(), protocols::splice::SpliceOutTail::abstract_parse_tag(), adjust_stem_positions_by_template(), protocols::splice::SpliceOutAntibody::apply(), protocols::splice::SpliceOutAntibody::assign_from_res_to_res(), protocols::splice::SpliceOut::set_source_from_to_res(), protocols::splice::SpliceOutTail::set_source_from_to_res(), protocols::splice::SpliceOut::superimpose_source_on_pose(), and protocols::splice::SpliceOut::write_database_to_file().

template_to_res() [2/2]

void protocols::splice::SpliceManager::template_to_res ( core::Size const  i )

inline

References template_to_res_.

thread_original_sequence() [1/2]

bool protocols::splice::SpliceManager::thread_original_sequence ( ) const

inline

References thread_original_sequence_.

Referenced by parse_tags().

thread_original_sequence() [2/2]

void protocols::splice::SpliceManager::thread_original_sequence ( bool const  s )

inline

References thread_original_sequence_.

update_pose_stem_positions()

void protocols::splice::SpliceManager::update_pose_stem_positions

(

)

References pose_to_res(), and residue_diff().

Referenced by protocols::splice::SpliceOut::apply().

use_sequence_profiles() [1/2]

core::Size protocols::splice::SpliceManager::use_sequence_profiles ( )

inline

References use_sequence_profiles_.

Referenced by add_sequence_constraints(), and parse_segments().

use_sequence_profiles() [2/2]

void protocols::splice::SpliceManager::use_sequence_profiles ( bool const  b )

inline

References protocols::match::upstream::b, and use_sequence_profiles_.

Referenced by protocols::splice::SpliceInAntibody::parse_my_tag(), and protocols::splice::SpliceOutAntibody::parse_my_tag().

Member Data Documentation

add_sequence_constraints_only_

bool protocols::splice::SpliceManager::add_sequence_constraints_only_

private

Referenced by add_sequence_constraints(), add_sequence_constraints_only(), and generate_sequence_profile().

adjust_stem_positions_by_template_

bool protocols::splice::SpliceManager::adjust_stem_positions_by_template_

Referenced by adjust_stem_positions_by_template(), protocols::splice::SpliceOutAntibody::apply(), protocols::splice::SpliceOut::SpliceOut(), and protocols::splice::SpliceOutTail::SpliceOutTail().

allowed_cuts_

core::Size protocols::splice::SpliceManager::allowed_cuts_

private

Referenced by allowed_cuts(), and chainbreak_check().

anchor_res_

core::Size protocols::splice::SpliceManager::anchor_res_

private

Referenced by add_dihedral_constraints(), anchor_res(), and fold_tree().

chain_num_

core::Size protocols::splice::SpliceManager::chain_num_

private

Referenced by chain_num().

cut_site_

core::Size protocols::splice::SpliceManager::cut_site_

private

Referenced by cut_site().

dbase_file_name_

std::string protocols::splice::SpliceManager::dbase_file_name_

private

Referenced by dbase_file_name().

debug_

bool protocols::splice::SpliceManager::debug_

private

Referenced by debug(), and parse_tags().

design_shell_

core::Real protocols::splice::SpliceManager::design_shell_

private

Referenced by design_shell().

dofs_

ResidueBBDofs protocols::splice::SpliceManager::dofs_

private

Referenced by dofs(), and SpliceManager().

mm_

core::kinematics::MoveMapOP protocols::splice::SpliceManager::mm_

private

Referenced by mm().

mover_name_

std::string protocols::splice::SpliceManager::mover_name_

private

Referenced by mover_name(), and parse_tags().

pdb_segments_

std::map< std::string, std::string > protocols::splice::SpliceManager::pdb_segments_

private

Referenced by generate_sequence_profile(), pdb_segments(), and SpliceManager().

pose_from_res_

core::Size protocols::splice::SpliceManager::pose_from_res_

private

Referenced by pose_from_res().

pose_to_res_

core::Size protocols::splice::SpliceManager::pose_to_res_

private

Referenced by pose_to_res().

profile_weight_away_from_interface_

core::Real protocols::splice::SpliceManager::profile_weight_away_from_interface_

private

Referenced by profile_weight_away_from_interface().

rb_sensitive_

bool protocols::splice::SpliceManager::rb_sensitive_

private

Referenced by rb_sensitive().

repack_shell_

core::Real protocols::splice::SpliceManager::repack_shell_

private

Referenced by repack_shell().

residue_diff_

int protocols::splice::SpliceManager::residue_diff_

private

Referenced by residue_diff().

scorefxn_

core::scoring::ScoreFunctionOP protocols::splice::SpliceManager::scorefxn_

private

Referenced by scorefxn().

segment_names_ordered_

utility::vector1< std::string > protocols::splice::SpliceManager::segment_names_ordered_

private

Referenced by generate_sequence_profile(), and segment_names_ordered().

segment_type_

std::string protocols::splice::SpliceManager::segment_type_

private

Referenced by segment_type().

source_pdb_name_

std::string protocols::splice::SpliceManager::source_pdb_name_

private

Referenced by source_pdb_name().

splice_segments_

std::map< std::string, SpliceSegmentOP > protocols::splice::SpliceManager::splice_segments_

private

Referenced by generate_sequence_profile(), splice_segments(), and SpliceManager().

tail_seg_

std::string protocols::splice::SpliceManager::tail_seg_

private

Referenced by tail_seg().

task_factory_

core::pack::task::TaskFactoryOP protocols::splice::SpliceManager::task_factory_

private

Referenced by task_factory().

template_file_

std::string protocols::splice::SpliceManager::template_file_

private

Referenced by parse_tags(), and template_file().

template_from_res_

core::Size protocols::splice::SpliceManager::template_from_res_

private

Referenced by template_from_res().

template_pose_

core::pose::PoseOP protocols::splice::SpliceManager::template_pose_

private

Referenced by adjust_stem_positions_by_template(), parse_tags(), rb_adjust_template(), and template_pose().

template_to_res_

core::Size protocols::splice::SpliceManager::template_to_res_

private

Referenced by template_to_res().

thread_original_sequence_

bool protocols::splice::SpliceManager::thread_original_sequence_

private

Referenced by thread_original_sequence().

use_sequence_profiles_

bool protocols::splice::SpliceManager::use_sequence_profiles_

private

Referenced by generate_sequence_profile(), and use_sequence_profiles().

---

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

• src/protocols/splice/SpliceManager.hh
• src/protocols/splice/SpliceManager.cc