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utils.hh File Reference
#include <core/pose/Pose.fwd.hh>
#include <core/id/SequenceMapping.fwd.hh>
#include <core/select/residue_selector/ResidueRanges.hh>
#include <core/select/residue_selector/ResidueSelector.fwd.hh>
#include <core/types.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/chemical/ResidueTypeSet.fwd.hh>
#include <basic/Tracer.hh>
#include <utility/vector1.hh>
#include <string>


 The instance of Loops contained by AbrelaxApplication should be replaced by a LoopsOP.


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