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rotamer_building_functions.cc File Reference
#include <core/pack/rotamer_set/rotamer_building_functions.hh>
#include <core/pack/rotamer_set/RotamerCouplings.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/rotamer_set/RotamerSet_.hh>
#include <core/pack/rotamer_set/RotamerSets.hh>
#include <core/pack/rotamer_set/WaterAnchorInfo.hh>
#include <core/pack/rotamer_set/WaterPackingInfo.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/task/RotamerSampleOptions.hh>
#include <core/pack/dunbrack/ChiSet.hh>
#include <core/pack/dunbrack/DunbrackRotamer.hh>
#include <core/chemical/ResidueTypeSet.hh>
#include <core/chemical/AtomType.hh>
#include <core/conformation/Atom.hh>
#include <core/conformation/Residue.hh>
#include <core/conformation/ResidueMatcher.hh>
#include <core/conformation/ResidueFactory.hh>
#include <core/kinematics/Stub.hh>
#include <core/kinematics/MoveMap.hh>
#include <core/scoring/hbonds/HBEvalTuple.hh>
#include <core/scoring/hbonds/HBondDatabase.hh>
#include <core/scoring/hbonds/HBondOptions.hh>
#include <core/scoring/hbonds/hbonds_geom.hh>
#include <core/scoring/func/Func.hh>
#include <core/scoring/func/HarmonicFunc.hh>
#include <core/scoring/constraints/AtomPairConstraint.hh>
#include <core/scoring/constraints/AngleConstraint.hh>
#include <core/scoring/constraints/ConstraintSet.hh>
#include <core/scoring/ScoreFunction.hh>
#include <core/scoring/hbonds/HBondTypeManager.hh>
#include <utility/graph/Graph.hh>
#include <core/pose/Pose.hh>
#include <core/pose/util.hh>
#include <core/pose/datacache/CacheableDataType.hh>
#include <core/optimization/AtomTreeMinimizer.hh>
#include <core/optimization/MinimizerOptions.hh>
#include <basic/Tracer.hh>
#include <basic/datacache/BasicDataCache.hh>
#include <basic/database/open.hh>
#include <basic/options/option.hh>
#include <basic/options/keys/hydrate.OptionKeys.gen.hh>
#include <basic/options/keys/score.OptionKeys.gen.hh>
#include <numeric/random/random.hh>
#include <numeric/xyz.functions.hh>
#include <numeric/constants.hh>
#include <utility/io/izstream.hh>
#include <utility/vector1.hh>
#include <ObjexxFCL/format.hh>
#include <ObjexxFCL/FArray3D.hh>
#include <string>
#include <iostream>
#include <fstream>

Namespaces

 core
 A class for reading in the atom type properties.
 
 core::pack
 
 core::pack::rotamer_set
 

Functions

static basic::Tracer core::pack::rotamer_set::tt ("core.pack.rotamer_set.rotamer_building_functions", basic::t_info)
 
void core::pack::rotamer_set::read_DNA_rotlib (utility::io::izstream &lib_stream, utility::vector1< DihedralSet * > &library)
 
void core::pack::rotamer_set::build_lib_dna_rotamers (utility::vector1< DihedralSet * > const &library, Size const resid, pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, utility::vector1< conformation::ResidueOP > &rotamers)
 
void core::pack::rotamer_set::build_random_dna_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, pack::task::ExtraRotSample const &level, utility::vector1< conformation::ResidueOP > &rotamers)
 
void core::pack::rotamer_set::build_dna_rotamers (Size const resid, pose::Pose const &pose, chemical::ResidueTypeCOP concrete_residue, pack::task::PackerTask const &task, utility::vector1< conformation::ResidueOP > &rotamers)
 
void core::pack::rotamer_set::build_rotamers_from_rotamer_bins (conformation::Residue const &residue, utility::vector1< conformation::ResidueOP > &rotamers, uint current_chi_index, utility::vector1< uint > &current_bin_indices)
 Internal, recursive function to implement the external interface of build_rotamers_from_rotamer_bins(), below. More...
 
void core::pack::rotamer_set::build_rotamers_from_rotamer_bins (conformation::Residue const &residue, utility::vector1< conformation::ResidueOP > &rotamers)
 Make a rotamer (Residue) for every combination of torsion angle in the rotamer bins listed in the params file for the given Residue. More...
 
void core::pack::rotamer_set::debug_dump_rotamers (utility::vector1< conformation::ResidueOP > &rotamers)
 
conformation::ResidueOP core::pack::rotamer_set::create_oriented_water_rotamer (chemical::ResidueType const &h2o_type, Vector const &xyz_atom1, Vector const &xyz_O, Vector const &xyz_atom2, std::string const &name1, std::string const &name2, conformation::Residue const &tp5)
 
void core::pack::rotamer_set::build_fixed_O_water_rotamers_independent (Size const seqpos, chemical::ResidueType const &h2o_type, pose::Pose const &pose, utility::graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers)
 
Vector core::pack::rotamer_set::build_water_O_on_donor (Vector const &hxyz, Vector const &dxyz, Real phi, Real theta)
 
Vector core::pack::rotamer_set::build_optimal_water_O_on_donor (Vector const &hxyz, Vector const &dxyz)
 
Vector core::pack::rotamer_set::build_optimal_hyp_H_for_donor (Vector const &o1, Vector const &hatm1_xyz, Vector const &reference, Real angle)
 
Vector core::pack::rotamer_set::build_optimal_hyp_H_for_acceptor (Vector const &o2, Vector const &aatm2_xyz, Vector const &reference, Real angle)
 
void core::pack::rotamer_set::build_optimal_water_Os_on_acceptor (Vector const &a_xyz, Vector b1_xyz, Vector const &b2_xyz, chemical::Hybridization const &hybrid, utility::vector1< Vector > &O_list)
 
core::PackerEnergy core::pack::rotamer_set::pre_bump_check (Size const &seqpos_water, conformation::ResidueOP rot, scoring::ScoreFunction const &score_fxn, pose::Pose const &pose, task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph)
 
void core::pack::rotamer_set::build_donor_donor_waters (Size const &seqpos_water, conformation::Residue const &rsd1, Size const hatm1, conformation::Residue const &rsd2, Size const hatm2, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, Size const nstep, utility::vector1< conformation::ResidueOP > &new_waters, pose::Pose const &pose, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &score_fxn)
 
void core::pack::rotamer_set::build_sew_waters_to_donor (Size const &seqpos_water, conformation::Residue const &rsd, Size const hatm, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, utility::vector1< conformation::ResidueOP > &new_waters, pose::Pose const &pose, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &score_fxn)
 
void core::pack::rotamer_set::build_sew_waters_to_acceptor (Size const &seqpos_water, conformation::Residue const &rsd, Size const aatm, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, utility::vector1< conformation::ResidueOP > &new_waters, pose::Pose const &pose, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &score_fxn)
 
void core::pack::rotamer_set::build_donor_acceptor_waters (Size const &seqpos_water, conformation::Residue const &rsd1, Size const hatm1, conformation::Residue const &rsd2, Size const aatm2, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, Size const nstep, utility::vector1< conformation::ResidueOP > &new_waters, pose::Pose const &pose, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &score_fxn)
 
void core::pack::rotamer_set::build_acceptor_acceptor_waters (Size const &seqpos_water, conformation::Residue const &rsd1, Size const aatm1, conformation::Residue const &rsd2, Size const aatm2, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, Size const nstep, utility::vector1< conformation::ResidueOP > &new_waters, pose::Pose const &pose, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &score_fxn)
 
void core::pack::rotamer_set::build_single_edge_waters (Size const &seqpos_water, conformation::Residue const &rsd, Size anchor_atom, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, utility::vector1< conformation::ResidueOP > &new_rotamers, pose::Pose const &pose, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &score_fxn)
 
void core::pack::rotamer_set::build_moving_O_bridge_waters (Size const &seqpos_water, conformation::Residue const &rsd1, Size anchor_atom, conformation::Residue const &rsd2, chemical::ResidueType const &h2o_type, conformation::Residue const &tp5, Size const nstep, utility::vector1< conformation::ResidueOP > &new_rotamers, pose::Pose const &pose, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &scorefxn, bool is_first_rsd)
 
void core::pack::rotamer_set::build_moving_O_water_rotamers_dependent (RotamerSets const &rotsets, Size const seqpos_water, WaterAnchorInfo const &water_info, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, utility::graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers, scoring::ScoreFunction const &scorefxn)
 
void core::pack::rotamer_set::build_anchorless_water_rotamers (Size const seqpos, chemical::ResidueType const &h2o_type, pose::Pose const &pose, utility::vector1< conformation::ResidueOP > &new_rotamers, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &score_fxn)
 builds water molecule rotamers on top of cubic lattice in hydrate/SPaDES protocol More...
 
void core::pack::rotamer_set::build_moving_O_water_rotamers_independent (Size const &seqpos_water, WaterAnchorInfo const &water_info, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, utility::graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers, scoring::ScoreFunction const &scorefxn)
 
void core::pack::rotamer_set::build_single_anchor_water_rotamers_independet (Size const &seqpos_water, WaterAnchorInfo const &water_info, chemical::ResidueType const &h2o_type, pose::Pose const &pose, utility::vector1< conformation::ResidueOP > &new_rotamers, pack::task::PackerTask const &task, utility::graph::GraphCOP packer_neighbor_graph, scoring::ScoreFunction const &score_fxn)
 
void core::pack::rotamer_set::build_independent_water_rotamers (Size const seqpos_water, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, utility::graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers, scoring::ScoreFunction const &scorefxn)
 
void core::pack::rotamer_set::build_dependent_water_rotamers (RotamerSets const &rotsets, Size const seqpos_water, chemical::ResidueType const &h2o_type, pack::task::PackerTask const &task, pose::Pose const &pose, utility::graph::GraphCOP packer_neighbor_graph, utility::vector1< conformation::ResidueOP > &new_rotamers, scoring::ScoreFunction const &scorefxn)