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util.hh File Reference
#include <protocols/denovo_design/components/StructureData.fwd.hh>
#include <core/chemical/ResidueType.fwd.hh>
#include <core/kinematics/Edge.fwd.hh>
#include <core/kinematics/FoldTree.fwd.hh>
#include <core/select/residue_selector/ResidueSelector.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/io/Remarks.hh>
#include <core/types.hh>
#include <basic/datacache/DataMap.fwd.hh>
#include <utility/excn/Exceptions.hh>
#include <utility/string_util.hh>
#include <boost/lexical_cast.hpp>
#include <set>
#include <list>
#include <map>


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


typedef std::map< std::string,


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...
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)
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::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...
template<class T >
utility::vector1< T > protocols::denovo_design::parse_length_string (std::string const &len_str)
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...
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)
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...
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::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...
template<typename Container , typename T >
Container protocols::denovo_design::set_difference (typename std::set< T >::const_iterator begin1, typename std::set< T >::const_iterator const &end1, typename std::set< T >::const_iterator begin2, typename std::set< T >::const_iterator const &end2)
 Returns vector of elements found in v1 but not in v2. More...
template<typename Container >
Container protocols::denovo_design::csv_to_container (std::string const &csv, char const delim=',')
 Given a comma-seperated string, convert to container. More...