util functions for denovo design of structures More...

#include <protocols/denovo_design/util.hh>
#include <protocols/denovo_design/components/StructureData.hh>
#include <protocols/denovo_design/components/Segment.hh>
#include <protocols/forge/methods/pose_mod.hh>
#include <protocols/simple_moves/MutateResidue.hh>
#include <protocols/toolbox/pose_manipulation/pose_manipulation.hh>
#include <core/chemical/util.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/conformation/util.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/scoring/EnergyMap.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/energy_methods/LinearChainbreakEnergy.hh>
#include <core/select/residue_selector/ResidueSelector.fwd.hh>
#include <core/select/residue_selector/util.hh>
#include <core/pose/PDBInfo.hh>
#include <core/pose/Pose.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Edge.hh>
#include <basic/Tracer.hh>
#include <basic/datacache/DataMap.fwd.hh>
#include <boost/algorithm/string.hpp>
#include <boost/lexical_cast.hpp>
#include <utility/stream_util.hh>

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

	protocols::denovo_design

Functions
static basic::Tracer	TR ("protocols.denovo_design.components.util")

bool	protocols::denovo_design::same_pose (core::pose::Pose const &pose1, core::pose::Pose const &pose2)
	Tells whether the two given poses are identical based on # resides and dihedrals. More...

core::kinematics::FoldTree	protocols::denovo_design::remove_all_jump_atoms (core::kinematics::FoldTree const &orig)

core::kinematics::FoldTree	protocols::denovo_design::remove_missing_jump_atoms (core::pose::Pose const &pose, core::kinematics::FoldTree const &orig)
	removes atoms missing from the current pose More...

void	protocols::denovo_design::construct_poly_ala_pose (core::pose::Pose &pose, bool const keep_disulf, core::select::residue_selector::ResidueSubset const &set1, core::select::residue_selector::ResidueSubset const &set2, bool const keep_chirality)
	creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine More...

void	protocols::denovo_design::construct_poly_ala_pose (core::pose::Pose &pose, bool const keep_disulf, std::set< core::Size > const &res_set, bool const keep_chirality)
	creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine More...

core::pose::PoseOP	protocols::denovo_design::construct_dummy_pose (std::string const &restype_name)
	builds an extended-conformation poly-XXX pose More...

core::pose::PoseOP	protocols::denovo_design::construct_dummy_pose (std::string const &restype_name, core::Size const length)

core::pose::PoseOP	protocols::denovo_design::construct_dummy_pose (core::chemical::ResidueType const &restype)

core::pose::PoseOP	protocols::denovo_design::construct_dummy_pose (core::chemical::ResidueType const &restype, core::Size length)

core::select::residue_selector::ResidueSelectorCOP	protocols::denovo_design::get_residue_selector (basic::datacache::DataMap const &data, std::string const &name)

std::string	protocols::denovo_design::abego_str (utility::vector1< std::string > const &abego)

utility::vector1< std::string >	protocols::denovo_design::abego_vector (std::string const &ab)

std::string	protocols::denovo_design::get_remark_line (core::io::Remarks::const_iterator &it_rem, core::io::Remarks::const_iterator const &end)

void	protocols::denovo_design::add_remark (core::io::Remarks &remarks, core::Size const num, std::string const &str_val)
	adds a remark to a Remarks object, splitting it into multiple remarks if it is too long More...

core::Size	protocols::denovo_design::loop_stop_without_overlap (core::pose::Pose const &pose, core::Size stopres, core::Size const overlap)

core::Size	protocols::denovo_design::loop_start_without_overlap (core::pose::Pose const &pose, core::Size startres, core::Size const overlap)

void	protocols::denovo_design::rebuild_missing_atoms (core::pose::Pose &pose, core::Size const resi)
	given a residue, rebuilds all missing atoms More...

int	protocols::denovo_design::find_jump_rec (core::kinematics::FoldTree const &ft, core::Size const residue)
	helper function that looks for the given residue in a fold tree and returns the jump that controls its 6D-DoFs More...

void	protocols::denovo_design::insert_peptide_edges (core::kinematics::FoldTree &ft, core::kinematics::Edge const &jedge)
	inserts the peptide edges to accomodate the new jump edge given More...

core::Size	protocols::denovo_design::extract_int (core::Real &num, core::Size const m, core::Size const n)
	given a number 0 <= x < 1, calculate an integer M <= x <= N NOTE THAT THIS FUNCTION MODIFIES THE PARAMETER More...

std::pair< std::string, std::string >	protocols::denovo_design::parse_strand_pair (std::string const &strand_pair_str)

core::Size	protocols::denovo_design::count_bulges (components::StructureData const &perm, std::string const &segment)
	counts the beta-bulges in the given segment. This simply counts all abego A's in the segment More...

void	protocols::denovo_design::add_chain_from_pose (core::pose::PoseCOP to_add, core::pose::PoseOP combined)
	dumps a pose into another pose as a new chain More...

void	protocols::denovo_design::add_residues_to_pose (core::pose::Pose &pose, core::pose::Pose const &template_pose, bool const new_chain)
	adds residues from template_pose to pose. If new_chain == true, creates covalent bond More...

core::Size	protocols::denovo_design::get_resid (components::StructureData const &perm, std::string const &resid_str)

core::Real	protocols::denovo_design::linear_chainbreak (core::pose::Pose const &pose, core::Size const pos)
	evaluate linear chainbreak at a position More...

core::kinematics::FoldTree	protocols::denovo_design::slide_jump (core::kinematics::FoldTree const &ft_orig, core::Size const jump_idx, core::Size const new_start, core::Size const new_stop)

void	protocols::denovo_design::add_cutpoints (core::pose::Pose &pose, components::StructureData const &sd)

std::string	protocols::denovo_design::symmetric_secstruct (core::pose::Pose const &pose, std::string const &asymm_secstruct)
	Given a symmetric pose and a secstruct for the asymmetric unit, constructs and returns a secondary structure string compatible with the symmetric pose based on the secondary structure of the asymmetric unit. More...

core::kinematics::FoldTree	protocols::denovo_design::symmetric_fold_tree (core::pose::Pose const &pose, core::kinematics::FoldTree const &asymm_ft)
	Given a symmetric pose, and a fold tree for the asymmetric unit, constructs and returns a symmetric fold tree while preserving the topology of the aysmmetric unit's fold tree. More...

core::select::residue_selector::ResidueSubset	protocols::denovo_design::symmetric_residue_subset (core::pose::Pose const &pose, core::select::residue_selector::ResidueSubset const &asymm_subset)
	Given a symmetric pose and a ResidueSubset for the asymmetric unit, constructs and returns a residue subset compatible with the symmetric pose based on the given asymmetric unit residue subset. More...

void	protocols::denovo_design::parse_motif_string (std::string const &motif_str, std::string &secstruct, std::string &abego)
	Computes secondary structure string from the given motifs. More...

Detailed Description

util functions for denovo design of structures

Author: Tom Linsky

Function Documentation

◆ TR()

static basic::Tracer TR ( "protocols.denovo_design.components.util" )

static

Namespaces

Functions

Detailed Description

Function Documentation

◆ TR()