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protocols::fold_from_loops::utils Namespace Reference

Classes

class  Nub
 
struct  NubSegment
 

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

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

Function Documentation

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().

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().

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 
)
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 
)
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::pack::dunbrack::c, 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().

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(), core::pose::Pose::sequence(), core::sequence::SequenceAlignment::sequence_mapping(), core::pose::Pose::size(), core::id::to_string(), core::id::SequenceMapping::to_string(), and TR().

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

void protocols::fold_from_loops::utils::report_unfolded ( core::pose::Pose const &  pose,
core::kinematics::MoveMapOP  movemap 
)
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(), core::select::residue_selector::ResidueRange::start(), protocols::loops::start, core::select::residue_selector::ResidueRange::stop(), core::select::residue_selector::ResidueRange::to_string(), and TR().

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