pack_rotamers.hh File Reference

pack rotamers module header More...

#include <core/pack/task/PackerTask.fwd.hh>
#include <core/types.hh>
#include <core/pack/rotamer_set/FixbbRotamerSets.fwd.hh>
#include <core/pack/interaction_graph/AnnealableGraphBase.fwd.hh>
#include <core/pose/Pose.fwd.hh>
#include <core/scoring/ScoreFunction.fwd.hh>
#include <core/pack/annealer/AnnealerObserver.fwd.hh>
#include <utility/vector0.hh>
#include <ObjexxFCL/FArray1D.fwd.hh>
#include <utility/vector1.hh>
#include <core/scoring/annealing/RotamerSets.fwd.hh>

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

Functions
void	core::pack::pack_rotamers (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task)
	The entry point to calling the packer, which optimizes side-chain identities and conformations (if you're designing) or conformations alone (if you're predicting structures). More...
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)
	Run the FixbbSimAnnealer multiple times using the same InteractionGraph, storing the results. More...
void	core::pack::pack_rotamers_loop (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, Size const nloop)
void	core::pack::pack_rotamers_setup (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, rotamer_set::RotamerSetsOP rotsets, interaction_graph::AnnealableGraphBaseOP &ig, core::Size const nloop)
	Get rotamers, compute energies. More...
interaction_graph::AnnealableGraphBaseOP	core::pack::pack_rotamers_setup (pose::Pose &pose, scoring::ScoreFunction const &scfxn, task::PackerTaskCOP task, rotamer_set::RotamerSetsOP rotsets)
	PyRosetta compatible version. More...
Real	core::pack::pack_rotamers_run (pose::Pose &pose, task::PackerTaskCOP task, rotamer_set::FixbbRotamerSetsCOP rotsets, interaction_graph::AnnealableGraphBaseOP ig, utility::vector0< int > rot_to_pack=utility::vector0< int >(), annealer::AnnealerObserverOP observer=nullptr)
	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::AnnealableGraphBaseOP ig, utility::vector0< int > rot_to_pack, annealer::AnnealerObserverOP observer, ObjexxFCL::FArray1D_int &bestrotamer_at_seqpos, core::PackerEnergy &bestenergy)
	Runs simulated annealing and returns the best identified rotamers and energies. More...
void	core::pack::pack_rotamers_cleanup (core::pose::Pose &pose, core::pack::interaction_graph::AnnealableGraphBaseOP annealable_graph)
	Provide the opportunity to clean up cached data from the pose or scorefunction after packing. More...

Detailed Description

pack rotamers module header

Author

Andrew Leaver-Fay (aleav.nosp@m.erfa.nosp@m.y@gma.nosp@m.il.c.nosp@m.om) @modified Vikram K. Mulligan (vmull.nosp@m.igan.nosp@m.@flat.nosp@m.iron.nosp@m.insti.nosp@m.tue..nosp@m.org) to allow multi-threaded interaction graph setup.