pack_rotamers.cc File Reference

pack rotamers module More...

#include <core/pack/pack_rotamers.hh>
#include <core/pack/packer_neighbors.hh>
#include <core/pack/task/PackerTask.hh>
#include <core/pack/make_symmetric_task.hh>
#include <core/pack/rotamer_set/RotamerSet.hh>
#include <core/pack/rotamer_set/RotamerSets.hh>
#include <core/pack/rotamer_set/symmetry/SymmetricRotamerSets.hh>
#include <core/pack/task/IGEdgeReweightContainer.hh>
#include <core/pack/annealer/AnnealerFactory.hh>
#include <core/pack/annealer/SimAnnealerBase.hh>
#include <core/pack/interaction_graph/InteractionGraphFactory.hh>
#include <core/pack/interaction_graph/InteractionGraphBase.hh>
#include <core/conformation/symmetry/SymmetryInfo.hh>
#include <core/pose/symmetry/util.hh>
#include <core/conformation/Residue.hh>
#include <core/graph/Graph.hh>
#include <core/pose/Pose.hh>
#include <core/scoring/ScoreFunction.hh>
#include <basic/prof.hh>
#include <basic/Tracer.hh>
#include <ObjexxFCL/format.hh>
#include <basic/options/keys/packing.OptionKeys.gen.hh>
#include <core/conformation/symmetry/SymmetricConformation.hh>
#include <utility/vector0.hh>
#include <utility/vector1.hh>

Namespaces
	core
	A class for defining atom parameters, known as atom_types.
	core::pack

Functions
void	core::pack::pack_rotamers (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task)
void	core::pack::pack_rotamers_loop (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, Size const nloop)
void	core::pack::pack_rotamers_loop (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, Size const nloop, utility::vector1< std::pair< Real, std::string > > &results)
void	core::pack::pack_rotamers_loop (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, Size const nloop, utility::vector1< std::pair< Real, std::string > > &results, utility::vector1< pose::PoseOP > &pose_list)
void	core::pack::pack_rotamers_setup (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, rotamer_set::RotamerSetsOP rotsets, interaction_graph::InteractionGraphBaseOP &ig)
interaction_graph::InteractionGraphBaseOP	core::pack::pack_rotamers_setup (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, rotamer_set::RotamerSetsOP rotsets)
void	core::pack::setup_IG_res_res_weights (pose::Pose const &pose, task::PackerTaskCOP task, rotamer_set::RotamerSetsCOP rotsets, interaction_graph::InteractionGraphBaseOP ig)
	upweights certain edges in the interaction graph if this is specified in the task More...
Real	core::pack::pack_rotamers_run (pose::Pose &pose, task::PackerTaskCOP task, rotamer_set::FixbbRotamerSetsCOP rotsets, interaction_graph::InteractionGraphBaseOP ig, utility::vector0< int > rot_to_pack=utility::vector0< int >())
	Run simulated annealing, return the energy of the best rotamer assignment found, and place the best rotamers onto the input pose. More...
void	core::pack::pack_rotamers_run (pose::Pose const &pose, task::PackerTaskCOP task, rotamer_set::FixbbRotamerSetsCOP rotsets, interaction_graph::InteractionGraphBaseOP ig, utility::vector0< int > rot_to_pack, ObjexxFCL::FArray1D_int &bestrotamer_at_seqpos, core::PackerEnergy &bestenergy)
	Runs simulated annealing and returns the. More...
void	core::pack::symmetric_pack_rotamers (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP non_symmetric_task)
void	core::pack::symmetric_pack_rotamers_setup (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, rotamer_set::symmetry::SymmetricRotamerSetsOP rotsets, interaction_graph::InteractionGraphBaseOP &ig)
interaction_graph::InteractionGraphBaseOP	core::pack::symmetric_pack_rotamers_setup (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, rotamer_set::symmetry::SymmetricRotamerSetsOP rotsets)
Real	core::pack::symmetric_pack_rotamers_run (pose::Pose &pose, task::PackerTaskCOP task, rotamer_set::symmetry::SymmetricRotamerSetsCOP rotsets, interaction_graph::InteractionGraphBaseOP ig, utility::vector0< int > rot_to_pack)

Variables
static basic::Tracer	core::pack::tt ("core.pack.pack_rotamers", basic::t_info)

Detailed Description

pack rotamers module

Author

Andrew Leaver-Fay (aleav.nosp@m.erfa.nosp@m.y@gma.nosp@m.il.c.nosp@m.om)