Module _core_pack_

create_packer_graph( (Pose)pose, (ScoreFunction)scfxn, (PackerTask)task, (int)total_nodes, (vector1_Real)residue_radii) -> Graph :
    core/pack/packer_neighbors.hh:49

    C++ signature :
        boost::shared_ptr<core::graph::Graph> create_packer_graph(core::pose::Pose,core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>,unsigned long,utility::vector1<double, std::allocator<double> >)

create_packer_graph( (Pose)pose, (ScoreFunction)scfxn, (PackerTask)task) -> Graph :
    core/pack/packer_neighbors.hh:40

    C++ signature :
        boost::shared_ptr<core::graph::Graph> create_packer_graph(core::pose::Pose,core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>)

figure_out_repackable_residues( (Pose)pose, (AtomID_Map_T_bool_T)to_repack, (vector1_bool)repackable) -> bool :
    return vector of bools with true for each residue that has >=1 atom in to_repack that is not VIRTUAL, ORBS or LPbb
    

    C++ signature :
        bool figure_out_repackable_residues(core::pose::Pose {lvalue},core::id::AtomID_Map<bool>,utility::vector1<bool, std::allocator<bool> > {lvalue})

find_residue_max_radii( (Pose)pose, (PackerTask)task) -> vector1_Real :
    core/pack/packer_neighbors.hh:55

    C++ signature :
        utility::vector1<double, std::allocator<double> > find_residue_max_radii(core::pose::Pose,boost::shared_ptr<core::pack::task::PackerTask const>)

make_new_symmetric_PackerTask_by_requested_method( (Pose)pose, (PackerTask)non_symmetric_task) -> PackerTask :
    core/pack/make_symmetric_task.hh:40

    C++ signature :
        boost::shared_ptr<core::pack::task::PackerTask> make_new_symmetric_PackerTask_by_requested_method(core::pose::Pose,boost::shared_ptr<core::pack::task::PackerTask const>)

make_symmetric_PackerTask_by_truncation( (Pose)pose, (PackerTask)task) -> None :
    core/pack/make_symmetric_task.hh:32

    C++ signature :
        void make_symmetric_PackerTask_by_truncation(core::pose::Pose,boost::shared_ptr<core::pack::task::PackerTask>)

min_pack( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task [, (bool)cartesian=False [, (bool)nonideal=False]]) -> None :
    Interface function to the minimize-each-rotamer-during-packing sidechain placement algorithm.
    

    C++ signature :
        void min_pack(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const> [,bool=False [,bool=False]])

min_pack_optimize( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task, (object)rotsets, (object)scminmap, (__CPP_MinimizationGraph__)mingraph, (object)atc, (object)min_options, (object)best_state) -> None :
    core/pack/min_pack.hh:76

    C++ signature :
        void min_pack_optimize(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask>,boost::shared_ptr<core::pack::rotamer_set::RotamerSets>,boost::shared_ptr<core::pack::scmin::SCMinMinimizerMap>,boost::shared_ptr<core::scoring::MinimizationGraph>,boost::shared_ptr<core::pack::scmin::AtomTreeCollection>,core::optimization::MinimizerOptions,core::pack::scmin::SidechainStateAssignment {lvalue})

min_pack_place_opt_rotamers_on_pose( (Pose)pose, (ScoreFunction)sfxn, (object)rotsets, (object)atc, (object)best_state, (float)start_score) -> None :
    core/pack/min_pack.hh:86

    C++ signature :
        void min_pack_place_opt_rotamers_on_pose(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::rotamer_set::RotamerSets>,boost::shared_ptr<core::pack::scmin::AtomTreeCollection>,core::pack::scmin::SidechainStateAssignment,double)

min_pack_setup( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task, (bool)cartesian, (bool)nonideal, (object)rotsets, (object)scminmap, (__CPP_MinimizationGraph__)mingraph, (object)atc, (object)min_options) -> None :
    core/pack/min_pack.hh:63

    C++ signature :
        void min_pack_setup(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask>,bool,bool,boost::shared_ptr<core::pack::rotamer_set::RotamerSets> {lvalue},boost::shared_ptr<core::pack::scmin::SCMinMinimizerMap> {lvalue},boost::shared_ptr<core::scoring::MinimizationGraph> {lvalue},boost::shared_ptr<core::pack::scmin::AtomTreeCollection> {lvalue},boost::shared_ptr<core::optimization::MinimizerOptions> {lvalue})

off_rotamer_pack( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task) -> None :
    Interface to a version of the packer that uses very little memory
    and simultaneously is able to go off rotamer and explore more of sidechain
    conformation space.  Quite a bit faster than the min-packer.
    

    C++ signature :
        void off_rotamer_pack(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>)

off_rotamer_pack_optimize( (object)rotsets, (object)atc, (object)ig, (object)best_state) -> None :
    core/pack/min_pack.hh:114

    C++ signature :
        void off_rotamer_pack_optimize(core::pack::rotamer_set::ContinuousRotamerSets,boost::shared_ptr<core::pack::scmin::AtomTreeCollection>,core::pack::interaction_graph::SimpleInteractionGraph {lvalue},core::pack::scmin::SidechainStateAssignment {lvalue})

off_rotamer_pack_setup( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task, (object)rotsets, (object)atc, (object)ig) -> None :
    core/pack/min_pack.hh:106

    C++ signature :
        void off_rotamer_pack_setup(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>,boost::shared_ptr<core::pack::rotamer_set::ContinuousRotamerSets> {lvalue},boost::shared_ptr<core::pack::scmin::AtomTreeCollection> {lvalue},boost::shared_ptr<core::pack::interaction_graph::SimpleInteractionGraph> {lvalue})

off_rotamer_pack_update_pose( (Pose)pose, (object)rotsets, (object)atc, (object)best_state) -> None :
    core/pack/min_pack.hh:122

    C++ signature :
        void off_rotamer_pack_update_pose(core::pose::Pose {lvalue},core::pack::rotamer_set::ContinuousRotamerSets,boost::shared_ptr<core::pack::scmin::AtomTreeCollection>,core::pack::scmin::SidechainStateAssignment)

optimizeH( (Pose)pose, (ScoreFunction)sfxn) -> None :
    This function will optimize the placement of all movable
    hydrogen atoms.  This includes the hydroxyl hydrogens as well as
    the HIS protonation state.  If the -flip_HNQ flag is on the command
    line, then it will also consider the flip states of histadine,
    asparagine and glutamine, (nearly) as described by Word et al. 1999.
    

    C++ signature :
        void optimizeH(core::pose::Pose {lvalue},core::scoring::ScoreFunction)

optimize_H_and_notify( (Pose)pose, (AtomID_Map_T_bool_T)missing) -> None :
    Call optimizeH and tell the user what chi angles have changed
    

    C++ signature :
        void optimize_H_and_notify(core::pose::Pose {lvalue},core::id::AtomID_Map<bool>)

pack_missing_sidechains( (Pose)pose, (AtomID_Map_T_bool_T)missing) -> None :
    This function runs rotamer trials on residues missing sidechain density (as described by the AtomID_Mask)
    

    C++ signature :
        void pack_missing_sidechains(core::pose::Pose {lvalue},core::id::AtomID_Map<bool>)

pack_rotamers( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task) -> None :
    core/pack/pack_rotamers.hh:53

    C++ signature :
        void pack_rotamers(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>)

pack_rotamers_loop( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task, (int)nloop) -> None :
    core/pack/pack_rotamers.hh:80

    C++ signature :
        void pack_rotamers_loop(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>,unsigned long)

pack_rotamers_loop( (Pose)pose, (ScoreFunction)scfxn, (PackerTask)task, (int)nloop, (vector1_pair_Real_string)results, (vector1_PoseOP)pose_list) -> None :
    core/pack/pack_rotamers.hh:72

    C++ signature :
        void pack_rotamers_loop(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>,unsigned long,utility::vector1<std::pair<double, std::string>, std::allocator<std::pair<double, std::string> > > {lvalue},utility::vector1<boost::shared_ptr<core::pose::Pose>, std::allocator<boost::shared_ptr<core::pose::Pose> > > {lvalue})

pack_rotamers_loop( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task, (int)nloop, (vector1_pair_Real_string)results) -> None :
    core/pack/pack_rotamers.hh:62

    C++ signature :
        void pack_rotamers_loop(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>,unsigned long,utility::vector1<std::pair<double, std::string>, std::allocator<std::pair<double, std::string> > > {lvalue})

pack_rotamers_run( (Pose)pose, (PackerTask)task, (object)rotsets, (object)ig, (vector0_T_int_std_allocator_T_int_T__T)rot_to_pack, (object)bestrotamer_at_seqpos, (float)bestenergy) -> None :
    Run simulated annealing and return the best rotamer assignment
    found.  This function does not modify the input pose.
    

    C++ signature :
        void pack_rotamers_run(core::pose::Pose,boost::shared_ptr<core::pack::task::PackerTask const>,boost::shared_ptr<core::pack::rotamer_set::FixbbRotamerSets const>,boost::shared_ptr<core::pack::interaction_graph::InteractionGraphBase>,utility::vector0<int, std::allocator<int> >,ObjexxFCL::FArray1D<int> {lvalue},float {lvalue})

pack_rotamers_run( (Pose)pose, (PackerTask)task, (object)rotsets, (object)ig, (vector0_T_int_std_allocator_T_int_T__T)rot_to_pack) -> float :
    Run simulated annealing, return the energy of the best rotamer assignment
    found, and place the best rotamers onto the input pose.
    

    C++ signature :
        double pack_rotamers_run(core::pose::Pose {lvalue},boost::shared_ptr<core::pack::task::PackerTask const>,boost::shared_ptr<core::pack::rotamer_set::FixbbRotamerSets const>,boost::shared_ptr<core::pack::interaction_graph::InteractionGraphBase>,utility::vector0<int, std::allocator<int> >)

pack_rotamers_setup( (Pose)pose, (ScoreFunction)scfxn, (PackerTask)task, (object)rotsets) -> object :
    core/pack/pack_rotamers.hh:98

    C++ signature :
        boost::shared_ptr<core::pack::interaction_graph::InteractionGraphBase> pack_rotamers_setup(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>,boost::shared_ptr<core::pack::rotamer_set::RotamerSets>)

pack_rotamers_setup( (Pose)pose, (ScoreFunction)scfxn, (PackerTask)task, (object)rotsets, (object)ig) -> None :
    core/pack/pack_rotamers.hh:89

    C++ signature :
        void pack_rotamers_setup(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>,boost::shared_ptr<core::pack::rotamer_set::RotamerSets>,boost::shared_ptr<core::pack::interaction_graph::InteractionGraphBase> {lvalue})

pack_scorefxn_pose_handshake( (Pose)pose, (ScoreFunction)scfxn) -> None :
    core/pack/packer_neighbors.hh:61

    C++ signature :
        void pack_scorefxn_pose_handshake(core::pose::Pose {lvalue},core::scoring::ScoreFunction)

reinitialize_mingraph_neighborhood_for_residue( (Pose)pose, (ScoreFunction)scorefxn, (object)bgres, (object)scminmap, (Residue)rsd, (MinimizationGraph)mingraph) -> None :
    core/pack/rtmin.hh:80

    C++ signature :
        void reinitialize_mingraph_neighborhood_for_residue(core::pose::Pose {lvalue},core::scoring::ScoreFunction,utility::vector1<boost::shared_ptr<core::conformation::Residue const>, std::allocator<boost::shared_ptr<core::conformation::Residue const> > >,core::pack::scmin::SCMinMinimizerMap,core::conformation::Residue,core::scoring::MinimizationGraph {lvalue})

repackable_residues( (PackerTask)the_task) -> vector1_Size :
    core/pack/rotamer_trials.hh:35

    C++ signature :
        utility::vector1<unsigned long, std::allocator<unsigned long> > repackable_residues(core::pack::task::PackerTask)

rotamer_trials( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)input_task) -> None :
    core/pack/rotamer_trials.hh:43

    C++ signature :
        void rotamer_trials(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>)

setup_IG_res_res_weights( (Pose)pose, (PackerTask)task, (object)rotsets, (object)ig) -> None :
    core/pack/pack_rotamers.hh:106

    C++ signature :
        void setup_IG_res_res_weights(core::pose::Pose,boost::shared_ptr<core::pack::task::PackerTask const>,boost::shared_ptr<core::pack::rotamer_set::RotamerSets const>,boost::shared_ptr<core::pack::interaction_graph::InteractionGraphBase>)

symmetric_pack_rotamers( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)task) -> None :
    core/pack/pack_rotamers.hh:138

    C++ signature :
        void symmetric_pack_rotamers(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>)

symmetric_pack_rotamers_run( (Pose)pose, (PackerTask)task, (object)rotsets, (object)ig, (vector0_T_int_std_allocator_T_int_T__T)rot_to_pack) -> float :
    core/pack/pack_rotamers.hh:165

    C++ signature :
        double symmetric_pack_rotamers_run(core::pose::Pose {lvalue},boost::shared_ptr<core::pack::task::PackerTask const>,boost::shared_ptr<core::pack::rotamer_set::symmetry::SymmetricRotamerSets const>,boost::shared_ptr<core::pack::interaction_graph::InteractionGraphBase>,utility::vector0<int, std::allocator<int> >)

symmetric_pack_rotamers_setup( (Pose)pose, (ScoreFunction)scfxn, (PackerTask)task, (object)rotsets) -> object :
    core/pack/pack_rotamers.hh:156

    C++ signature :
        boost::shared_ptr<core::pack::interaction_graph::InteractionGraphBase> symmetric_pack_rotamers_setup(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>,boost::shared_ptr<core::pack::rotamer_set::symmetry::SymmetricRotamerSets>)

symmetric_pack_rotamers_setup( (Pose)pose, (ScoreFunction)scfxn, (PackerTask)task, (object)rotsets, (object)ig) -> None :
    core/pack/pack_rotamers.hh:147

    C++ signature :
        void symmetric_pack_rotamers_setup(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>,boost::shared_ptr<core::pack::rotamer_set::symmetry::SymmetricRotamerSets>,boost::shared_ptr<core::pack::interaction_graph::InteractionGraphBase> {lvalue})

symmetric_rotamer_trials( (Pose)pose, (ScoreFunction)sfxn, (PackerTask)input_task) -> None :
    core/pack/rotamer_trials.hh:50

    C++ signature :
        void symmetric_rotamer_trials(core::pose::Pose {lvalue},core::scoring::ScoreFunction,boost::shared_ptr<core::pack::task::PackerTask const>)