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util.cc File Reference

Align a random jump to template. More...

#include <protocols/hybridization/util.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/chemical/ResidueType.hh>
#include <core/conformation/Residue.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/fragment/ConstantLengthFragSet.hh>
#include <core/fragment/FragSet.hh>
#include <core/fragment/Frame.hh>
#include <core/fragment/IndependentBBTorsionSRFD.hh>
#include <core/kinematics/FoldTree.hh>
#include <core/kinematics/Jump.hh>
#include <core/kinematics/Edge.hh>
#include <core/types.hh>
#include <numeric/model_quality/rms.hh>
#include <numeric/model_quality/maxsub.hh>
#include <ObjexxFCL/FArray1D.hh>
#include <ObjexxFCL/FArray2D.hh>
#include <ObjexxFCL/format.hh>
#include <core/scoring/constraints/Constraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/constraints/ConstraintIO.hh>
#include <protocols/constraint_movers/AddConstraintsToCurrentConformationMover.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/CoordinateConstraint.hh>
#include <core/scoring/func/ScalarWeightedFunc.hh>
#include <core/scoring/func/USOGFunc.hh>
#include <core/scoring/func/SOGFunc.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/util.hh>
#include <core/scoring/dssp/Dssp.hh>
#include <core/pose/PDBInfo.hh>
#include <protocols/moves/DsspMover.hh>
#include <core/fragment/picking_old/vall/util.hh>
#include <core/pose/symmetry/util.hh>
#include <core/optimization/symmetry/SymAtomTreeMinimizer.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/scoring/rms_util.hh>
#include <core/sequence/Sequence.hh>
#include <core/sequence/util.hh>
#include <protocols/comparative_modeling/coord_util.hh>
#include <list>
#include <numeric/xyzVector.hh>
#include <basic/Tracer.hh>

Namespaces

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

Functions

static basic::Tracer TR ("protocols.hybridization.util")
 
core::Size protocols::hybridization::get_num_residues_nonvirt (core::pose::Pose const &pose)
 
core::Size protocols::hybridization::get_num_residues_prot (core::pose::Pose const &pose)
 
void protocols::hybridization::setup_centroid_constraints (core::pose::Pose &pose, utility::vector1< core::pose::PoseCOP > const &templates, utility::vector1< core::Real > const &template_weights, std::string const &cen_cst_file, std::set< core::Size > const &ignore_res_for_AUTO)
 
void protocols::hybridization::setup_fullatom_constraints (core::pose::Pose &pose, utility::vector1< core::pose::PoseCOP > const &templates, utility::vector1< core::Real > const &template_weights, std::string const &cen_cst_file, std::string const &fa_cst_file)
 
void protocols::hybridization::setup_constraints (core::pose::Pose &pose, std::string &cst_in)
 
void protocols::hybridization::generate_centroid_constraints (core::pose::Pose &pose, utility::vector1< core::pose::PoseCOP > templates, utility::vector1< core::Real >, std::set< core::Size > ignore_res)
 
void protocols::hybridization::setup_user_coordinate_constraints (core::pose::Pose &pose, utility::vector1< core::Size > reses)
 
void protocols::hybridization::generate_fullatom_constraints (core::pose::Pose &pose, utility::vector1< core::pose::PoseCOP > templates, utility::vector1< core::Real > template_weights)
 
void protocols::hybridization::add_strand_pairs_cst (core::pose::Pose &pose, utility::vector1< std::pair< core::Size, core::Size > > const strand_pairs)
 
void protocols::hybridization::add_non_protein_cst (core::pose::Pose &pose, core::pose::Pose &tmpl, core::Real const self_cst_weight, core::Real const het_prot_cst_weight)
 
bool protocols::hybridization::discontinued_upper (core::pose::Pose const &pose, core::Size const seqpos)
 
bool protocols::hybridization::discontinued_lower (core::pose::Pose const &pose, core::Size const seqpos)
 
std::list< core::Sizeprotocols::hybridization::downstream_residues_from_jump (core::pose::Pose const &pose, core::Size const jump_number)
 
void protocols::hybridization::partial_align (core::pose::Pose &pose, core::pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map, bool iterate_convergence, utility::vector1< core::Real > distance_thresholds, core::Real min_coverage)
 
void protocols::hybridization::partial_align (core::pose::Pose &pose, core::pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map, std::list< core::Size > const &residue_list, bool iterate_convergence, utility::vector1< core::Real > distance_thresholds, core::Real min_coverage)
 
core::Size protocols::hybridization::atom_map_valid_size (core::pose::Pose const &pose, core::id::AtomID_Map< core::id::AtomID > const &atom_map)
 
core::id::AtomID_Map
< core::id::AtomID
protocols::hybridization::update_atom_map (core::pose::Pose &pose, core::pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map, core::Real distance_squared_threshold)
 
Size protocols::hybridization::natom_aligned (core::pose::Pose &pose, core::pose::Pose const &ref_pose, id::AtomID_Map< id::AtomID > const &atom_map, core::Real distance_squared_threshold)
 
void protocols::hybridization::get_superposition_transformation (pose::Pose const &mod_pose, pose::Pose const &ref_pose, core::id::AtomID_Map< core::id::AtomID > const &atom_map, numeric::xyzMatrix< core::Real > &R, numeric::xyzVector< core::Real > &preT, numeric::xyzVector< core::Real > &postT)
 
void protocols::hybridization::apply_transformation (pose::Pose &mod_pose, std::list< core::Size > const &residue_list, numeric::xyzMatrix< core::Real > const &R, numeric::xyzVector< core::Real > const &preT, numeric::xyzVector< core::Real > const &postT)
 
core::fragment::FragSetOP protocols::hybridization::create_fragment_set (core::pose::Pose const &pose, core::Size len, core::Size nfrag)
 
core::fragment::FragSetOP protocols::hybridization::create_fragment_set_no_ssbias (core::pose::Pose const &pose, core::Size len, core::Size nfrag, char force_ss)
 
core::fragment::FragSetOP protocols::hybridization::create_fragment_set_no_ssbias (core::pose::Pose const &pose, std::set< core::Size > user_pos, core::Size len, core::Size nfrag, char force_ss)
 
core::fragment::FragSetOP protocols::hybridization::create_fragment_set_no_ssbias (std::string tgt_seq, core::Size len, core::Size nfrag, char force_ss)
 
protocols::loops::Loops protocols::hybridization::renumber_with_pdb_info (protocols::loops::Loops &template_chunk, core::pose::PoseCOP template_pose)
 
core::Real protocols::hybridization::get_gdtmm (core::pose::Pose &native, core::pose::Pose &pose, core::sequence::SequenceAlignmentOP &aln)
 

Detailed Description

Align a random jump to template.

Author
Yifan Song

Function Documentation

static basic::Tracer TR ( "protocols.hybridization.util"  )
static