Classes
struct	NubSegment

class	Nub

Typedefs
typedef utility::pointer::shared_ptr< Nub >	NubOP

typedef utility::pointer::shared_ptr< Nub const >	NubCOP

Functions
static basic::Tracer	TR ("protocols.fold_from_loops.Nub", basic::t_debug)

static basic::Tracer	TR ("protocols.fold_from_loops.utils", basic::t_trace)

core::select::residue_selector::ResidueRanges	split_mid_ranges (std::string structure, core::select::residue_selector::ResidueRanges const &ranges)
	It will take each range that is not the first or the last one and split it into two, following the logic of `find_cutpoint_from_secondary_structure` Input Ranges are not modified, a new ResidueRanges is returned. WARNING1: When splitting a range of 1 residue, it splits into 1 range of 1 and another from 0 to 0, so that it is easy to filter afterwards ( for the purpose of NubInitio, this means adding and empty pose to the vector, for example ). WARNING2: If the first ResidueRange does not start with 1, an empty_range (0,0) is set at the begining too. WARNING3: If the final number of ranges is odds, we will assume that the last insertion is C-terminal and add a final empty range at the end. More...

core::Size	find_cutpoint_from_secondary_structure (std::string structure)
	Given a Secondary Structure definition as a string, it finds what it considers the optimal cutpoint. This means that, if there is no loop 'L' segment it will return the middle point as a residue; otherwise it will try to split the larger loop 'L' region. More...

void	attach_n_and_c_unfolded_poses_to_pose (core::pose::Pose const &n_insert, core::pose::Pose &scaffold, core::pose::Pose const &c_insert)
	To a given scaffold it attaches a unfolded version of a pose to the N-terminal and another to the C-terminal Generates a FoldTree that goes from the middle of 'scaffold' towards both directions. More...

void	attach_unfolded_pose_to_pose_n_term (core::pose::Pose const &insert, core::pose::Pose &scaffold, core::chemical::ResidueTypeSetCOP rsd_set)
	adds the 'insert' unfolded pose to the N-terminal of the provided pose More...

void	attach_unfolded_pose_to_pose_c_term (core::pose::Pose const &insert, core::pose::Pose &scaffold, core::chemical::ResidueTypeSetCOP rsd_set)
	adds the 'insert' unfolded pose to the C-terminal of the provided pose More...

void	append_pose_to_pose_keep_fold_tree (core::pose::Pose &scaffold, core::pose::Pose const &insert, bool new_chain)
	Basically works as 'core::pose::append_pose_to_pose' but the FoldTree is build by joining by jump the root of 'insert' FoldTree to that of 'scaffold' FoldTree. More...

core::id::SequenceMapping	map_by_residue_subsets (core::pose::Pose const &p1, core::select::residue_selector::ResidueSubset const &r1, core::pose::Pose const &p2, core::select::residue_selector::ResidueSubset const &r2)
	Creates a sequence mapping between two proteins assuming that the False selections on a ResidueSubset marks the residues that are the same for both of them. Assumes the same number of non-selected patches for each pose. More...

void	report_unfolded (core::pose::Pose const &pose, core::kinematics::MoveMapOP movemap)
	@ brief reports the conditions of the pose More...

Typedef Documentation

◆ NubCOP

typedef utility::pointer::shared_ptr< Nub const > protocols::fold_from_loops::utils::NubCOP

◆ NubOP

typedef utility::pointer::shared_ptr< Nub > protocols::fold_from_loops::utils::NubOP

Function Documentation

◆ append_pose_to_pose_keep_fold_tree()

void protocols::fold_from_loops::utils::append_pose_to_pose_keep_fold_tree	(	core::pose::Pose &	scaffold,
		core::pose::Pose const &	insert,
		bool	new_chain
	)

Basically works as 'core::pose::append_pose_to_pose' but the FoldTree is build by joining by jump the root of 'insert' FoldTree to that of 'scaffold' FoldTree.

Basically works as 'core::pose::append_pose_to_pose' but the FoldTree is build by joining by jump the root of 'insert' FoldTree to that of 'scaffold' FoldTree. PDBInfo is lost.

References core::pose::append_pose_to_pose(), core::pose::Pose::empty(), core::pose::Pose::fold_tree(), core::kinematics::FoldTree::insert_fold_tree_by_jump(), core::pose::Pose::pdb_info(), core::kinematics::FoldTree::root(), core::pose::Pose::secstruct(), core::pose::Pose::set_secstruct(), core::pose::Pose::size(), and TR().

Referenced by protocols::fold_from_loops::utils::Nub::add_binders(), and protocols::fold_from_loops::utils::Nub::join_pieces().

◆ attach_n_and_c_unfolded_poses_to_pose()

void protocols::fold_from_loops::utils::attach_n_and_c_unfolded_poses_to_pose	(	core::pose::Pose const &	n_insert,
		core::pose::Pose &	scaffold,
		core::pose::Pose const &	c_insert
	)

To a given scaffold it attaches a unfolded version of a pose to the N-terminal and another to the C-terminal Generates a FoldTree that goes from the middle of 'scaffold' towards both directions.

References core::kinematics::FoldTree::add_edge(), attach_unfolded_pose_to_pose_c_term(), attach_unfolded_pose_to_pose_n_term(), core::chemical::FA_STANDARD, core::pose::Pose::fold_tree(), core::pose::Pose::pdb_info(), core::kinematics::Edge::PEPTIDE, core::pose::Pose::secstruct(), core::pose::Pose::sequence(), core::pose::Pose::size(), and TR().

Referenced by protocols::fold_from_loops::utils::Nub::join_pieces().

◆ attach_unfolded_pose_to_pose_c_term()

void protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_c_term	(	core::pose::Pose const &	insert,
		core::pose::Pose &	scaffold,
		core::chemical::ResidueTypeSetCOP	rsd_set
	)

adds the 'insert' unfolded pose to the C-terminal of the provided pose

References core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::chemical::LOWER_TERMINUS_VARIANT, core::conformation::Residue::name1(), core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), core::pose::Pose::secstruct(), core::pose::Pose::set_omega(), core::pose::Pose::set_secstruct(), core::pose::Pose::size(), core::id::to_string(), and TR().

Referenced by attach_n_and_c_unfolded_poses_to_pose().

◆ attach_unfolded_pose_to_pose_n_term()

void protocols::fold_from_loops::utils::attach_unfolded_pose_to_pose_n_term	(	core::pose::Pose const &	insert,
		core::pose::Pose &	scaffold,
		core::chemical::ResidueTypeSetCOP	rsd_set
	)

adds the 'insert' unfolded pose to the N-terminal of the provided pose

References core::pose::Pose::conformation(), core::conformation::ResidueFactory::create_residue(), core::conformation::Residue::name1(), core::conformation::Residue::name3(), core::pose::Pose::pdb_info(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue(), core::conformation::Conformation::safely_prepend_polymer_residue_before_seqpos(), core::pose::Pose::secstruct(), core::pose::Pose::set_omega(), core::pose::Pose::set_secstruct(), core::pose::Pose::size(), core::id::to_string(), TR(), and core::chemical::UPPER_TERMINUS_VARIANT.

Referenced by attach_n_and_c_unfolded_poses_to_pose().

◆ find_cutpoint_from_secondary_structure()

core::Size protocols::fold_from_loops::utils::find_cutpoint_from_secondary_structure ( std::string structure )

Given a Secondary Structure definition as a string, it finds what it considers the optimal cutpoint. This means that, if there is no loop 'L' segment it will return the middle point as a residue; otherwise it will try to split the larger loop 'L' region.

References core::kinematics::distance(), protocols::mean_field::max(), protocols::loops::start, protocols::loops::stop, and TR().

Referenced by protocols::fold_from_loops::NubInitioMover::make_template_ranges(), and split_mid_ranges().

◆ map_by_residue_subsets()

core::id::SequenceMapping protocols::fold_from_loops::utils::map_by_residue_subsets	(	core::pose::Pose const &	p1,
		core::select::residue_selector::ResidueSubset const &	r1,
		core::pose::Pose const &	p2,
		core::select::residue_selector::ResidueSubset const &	r2
	)

Creates a sequence mapping between two proteins assuming that the False selections on a ResidueSubset marks the residues that are the same for both of them. Assumes the same number of non-selected patches for each pose.

Creates a sequence mapping betwee two proteins assuming that the False selections on a ResidueSubset marks the residues that are the same for both of them. Assumes the same number of non-selected patches for each pose.

References core::sequence::SequenceAlignment::add_sequence(), core::select::residue_selector::are_selections_equal(), protocols::hybridization::r1, protocols::hybridization::r2, core::pose::Pose::sequence(), core::sequence::SequenceAlignment::sequence_mapping(), core::pose::Pose::size(), core::id::SequenceMapping::to_string(), core::id::to_string(), and TR().

Referenced by protocols::fold_from_loops::utils::Nub::apply().

◆ report_unfolded()

void protocols::fold_from_loops::utils::report_unfolded	(	core::pose::Pose const &	pose,
		core::kinematics::MoveMapOP	movemap
	)

@ brief reports the conditions of the pose

References core::pose::Pose::annotated_sequence(), core::pose::Pose::fold_tree(), core::sequence::left, core::pose::Pose::pdb_info(), core::select::residue_selector::represent_residue_selector(), core::pose::Pose::secstruct(), core::pose::Pose::sequence(), and TR().

◆ split_mid_ranges()

core::select::residue_selector::ResidueRanges protocols::fold_from_loops::utils::split_mid_ranges	(	std::string	structure,
		core::select::residue_selector::ResidueRanges const &	ranges
	)

It will take each range that is not the first or the last one and split it into two, following the logic of find_cutpoint_from_secondary_structure Input Ranges are not modified, a new ResidueRanges is returned. WARNING1: When splitting a range of 1 residue, it splits into 1 range of 1 and another from 0 to 0, so that it is easy to filter afterwards ( for the purpose of NubInitio, this means adding and empty pose to the vector, for example ). WARNING2: If the first ResidueRange does not start with 1, an empty_range (0,0) is set at the begining too. WARNING3: If the final number of ranges is odds, we will assume that the last insertion is C-terminal and add a final empty range at the end.

It will take each range that is not the first or the last one and split it into two, following the logic of find_cutpoint_from_secondary_structure Input Ranges are not modified, a new ResidueRanges is returned. WARNING1: When splitting a range of 1 residue, it splits into 1 range of 1 and another from 0 to 0, so that it is easy to filter afterwards ( for the purpose of NubInitio, this means adding and empty pose to the vector, for example ). WARNING2: If the first ResidueRange does not start with 1, an empty_range (0,0) is set at the begining too.

References find_cutpoint_from_secondary_structure(), protocols::sic_dock::range(), protocols::loops::start, core::select::residue_selector::ResidueRange::to_string(), and TR().

◆ TR() [1/2]

static basic::Tracer protocols::fold_from_loops::utils::TR	(	"protocols.fold_from_loops.Nub"	,
		basic::t_debug
	)

static

◆ TR() [2/2]

static basic::Tracer protocols::fold_from_loops::utils::TR	(	"protocols.fold_from_loops.utils"	,
		basic::t_trace
	)