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Namespaces | Functions
util.hh File Reference
#include <core/types.hh>
#include <core/fragment/FragSet.fwd.hh>
#include <core/fragment/SecondaryStructure.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <protocols/loops/Loops.fwd.hh>
#include <protocols/loops/Loop.fwd.hh>
#include <utility/vector1.hh>
#include <string>

Namespaces

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

Functions

void protocols::loops::fix_with_coord_cst (Loops const &rigid, core::pose::Pose &pose, bool bCstAllAtom, utility::vector1< core::Real > &weights)
 
void protocols::loops::select_loop_frags (loops::Loops const &loops, core::fragment::FragSet &source, core::fragment::FragSet &loop_frags, core::Size shorten)
 get frags that are fully within the Loop — shorten(=true/false) frags that are close to the end of loops. More...
 
void protocols::loops::set_extended_torsions_and_idealize_loops (core::pose::Pose &pose, loops::Loops loops)
 
void protocols::loops::safe_set_extended_torsions_and_idealize_loops (const protocols::loops::Loops &loops, core::pose::Pose *pose)
 Identical to set_extended_torsions_and_idealize_loops() without the irrational behavior surrounding empty loops. More...
 
void protocols::loops::addScoresForLoopParts (core::pose::Pose &pose, loops::Loops loops, const core::scoring::ScoreFunction &scorefxn, core::pose::Pose &native_pose, core::Size nloops)
 
loops::Loops protocols::loops::compute_ss_regions (core::Real max_loop_frac, core::Size min_length, core::fragment::SecondaryStructure const &ss)
 
core::scoring::ScoreFunctionOP protocols::loops::get_fa_scorefxn ()
 
core::scoring::ScoreFunctionOP protocols::loops::get_cen_scorefxn ()
 
void protocols::loops::add_coordinate_constraints_to_pose (core::pose::Pose &pose, const core::pose::Pose &constraint_target_pose, protocols::loops::Loops &exclude_regions)
 
LoopsOP protocols::loops::loops_from_string (std::string const &loop_str, core::pose::Pose const &pose)
 loop_str has the format: start:end:cut,start:end:cut and can use rosetta or pdb numbering. The return value is an owning pointer to a Loops object encoding that loop More...
 
SerializedLoopList protocols::loops::serialized_loops_from_string (std::string const &loop_str, core::pose::Pose const &pose)
 
void protocols::loops::define_scorable_core_from_secondary_structure (core::fragment::SecondaryStructure const &ss_def, protocols::loops::Loops &scored_core)
 
protocols::loops::Loops protocols::loops::extract_secondary_structure_chunks (core::pose::Pose const &pose, std::string extracted_ss_types="HE", core::Size gap_size=1, core::Size minimum_length_of_chunk_helix=5, core::Size minimum_length_of_chunk_strand=3, core::Size minimum_length_of_chunk_loop=3, core::Real CA_CA_distance_cutoff=4)
 Extract secondary structure chunks from the pose, using multiple secondary structure types this function requires that the pose object already have secstruct information to get this information from structure (DSSP), call protocols::jumping::Dssp dssp_obj( *pose ); dssp_obj.insert_ss_into_pose( *pose ); or from secondary structure prediction (psipred_ss2 file), call core::pose::read_psipred_ss2_file(pose);. More...
 
protocols::loops::Loops protocols::loops::extract_secondary_structure_chunks (core::pose::Pose const &pose, char const extracted_ss_type)
 Extract secondary structure chunks from the secondary structure. More...
 
protocols::loops::Loops protocols::loops::split_by_resSeq (core::pose::Pose const &pose)
 
protocols::loops::Loops protocols::loops::split_by_resSeq (core::pose::Pose const &pose, protocols::loops::Loops const &input_chunks)
 
protocols::loops::Loops protocols::loops::find_non_protein_chunks (core::pose::Pose const &pose)
 
protocols::loops::Loops protocols::loops::split_by_ca_ca_dist (core::pose::Pose const &pose, Loops const &input_chunks, core::Real const CA_CA_distance_cutoff=4)
 Split into separate chunks if CA-CA distance is over the cutoff. More...
 
protocols::loops::Loops protocols::loops::remove_small_gaps (Loops const &input_chunks, core::Size gap_size=1)
 If two chunks are separated by a small gap of size <= <gap_size>, combine them. More...
 
protocols::loops::Loops protocols::loops::remove_short_chunks (Loops const &input_chunks, core::Size min_length=3)
 Remove small chunks. More...
 
protocols::loops::Loops protocols::loops::extract_continuous_chunks (core::pose::Pose const &pose, core::Size const minimum_size, core::Real const CA_CA_distance_cutoff)
 
std::pair< bool, core::Sizeprotocols::loops::has_severe_pep_bond_geom_issues (core::pose::Pose const &pose, const Loop &loop, bool check_bonds=true, bool check_angles=true, core::Real max_c_n_dis=2.0, core::Real allowed_ca_c_n_deviation=25.0, core::Real allowed_c_n_ca_deviation=25.0)
 Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residues if outside cutoff. Returns boolean and the position of found wonky peptide bond (0 if none found). Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1. More...
 
std::pair< bool, core::Sizeprotocols::loops::has_severe_pep_bond_geom_issues (core::pose::Pose const &pose, core::Size resnum, bool check_bonds=true, bool check_angles=true, core::Real max_c_n_dis=2.0, core::Real allowed_ca_c_n_deviation=25.0, core::Real allowed_c_n_ca_deviation=25.0)
 Measures C-N distance and N-Ca-C, C-N-CA bond angles to detect chainbreak/poory resolved loop residue outside cutoff. Returns boolean and the position of found wonky peptide bond (0 if none found). Does not use AtomTree to get angles/lengths, assumes resnum is connected to resnum +1. More...
 
LoopsOP protocols::loops::pick_loops_unaligned (core::Size nres, utility::vector1< core::Size > const &unaligned_residues, core::Size min_loop_size)
 
LoopsOP protocols::loops::pick_loops_chainbreak (core::pose::Pose &query_pose, core::Size min_loop_size)