Rosetta Protocols  2014.35
Public Types | Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::flexpack::rotamer_set::FlexbbRotamerSet Class Reference

#include <FlexbbRotamerSet.hh>

Public Types

typedef
core::pack::rotamer_set::RotamerSet_ 
parent
 
- Public Types inherited from core::pack::rotamer_set::RotamerSet_
typedef conformation::ResidueOP ResidueOP
 
typedef conformation::ResidueCOP ResidueCOP
 
typedef pack::dunbrack::ChiSetOP ChiSetOP
 
typedef
scoring::trie::RotamerTrieBaseOP 
RotamerTrieBaseOP
 

Public Member Functions

 FlexbbRotamerSet ()
 
virtual ~FlexbbRotamerSet ()
 
void set_owner (FlexbbRotamerSetsCAP owner)
 
virtual void build_dependent_rotamers (core::pack::rotamer_set::RotamerSets const &rotamer_sets, core::pose::Pose const &pose, core::scoring::ScoreFunction const &scorefxn, core::pack::task::PackerTask const &task, core::graph::GraphCOP packer_neighbor_graph)
 Build rotamers that depend on positions of rotamers built in a previous pass This function won't work... More...
 
void set_existing_residue (core::conformation::ResidueCOP residue)
 
- Public Member Functions inherited from core::pack::rotamer_set::RotamerSet_
 RotamerSet_ ()
 
virtual ~RotamerSet_ ()
 
virtual void build_rotamers (pose::Pose const &the_pose, scoring::ScoreFunction const &scorefxn, task::PackerTask const &task, graph::GraphCOP packer_neighbor_graph, bool use_neighbor_context=true)
 
virtual void add_rotamer (conformation::Residue const &rotamer)
 
virtual Size get_n_residue_types () const
 
virtual Size get_n_residue_groups () const
 
virtual Size get_residue_type_begin (Size which_restype) const
 
virtual Size get_residue_group_begin (Size which_resgroup) const
 
virtual Size get_n_rotamers_for_residue_type (Size which_resgroup) const
 
virtual Size get_n_rotamers_for_residue_group (Size which_resgroup) const
 
virtual Size get_residue_type_index_for_rotamer (Size which_rotamer) const
 
virtual Size get_residue_group_index_for_rotamer (Size which_rotamer) const
 
virtual void compute_one_body_energies (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, task::PackerTask const &task, graph::GraphCOP packer_neighbor_graph, utility::vector1< core::PackerEnergy > &energies) const
 
virtual void compute_one_body_energy_maps (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, task::PackerTask const &task, graph::GraphCOP packer_neighbor_graph, utility::vector1< scoring::EnergyMap > &energies) const
 
virtual Size num_rotamers () const
 
virtual Size id_for_current_rotamer () const
 
virtual conformation::ResidueCOP rotamer (Size rot_id) const
 
virtual Rotamers::const_iterator begin () const
 
virtual Rotamers::const_iterator end () const
 
virtual conformation::ResidueOP nonconst_rotamer (Size rot_id)
 
virtual void store_trie (Size method_enum_id, conformation::AbstractRotamerTrieOP trie)
 
virtual
conformation::AbstractRotamerTrieCOP 
get_trie (Size method_enum_id) const
 
virtual void drop_rotamer (Size rot_id)
 
virtual void drop_rotamers (utility::vector1< bool > const &rotamers_to_delete)
 
virtual void drop_rotamers_by_index (utility::vector1< Size > const &rotamer_indices_to_delete)
 
void set_extra_samples (task::PackerTask const &task, int num_10A_neighbors, int chi, chemical::ResidueTypeCOP concrete_residue, utility::vector1< Real > &extra_chi_steps) const
 

Protected Member Functions

virtual void build_rotamers_for_concrete_virt (core::pose::Pose const &pose, core::scoring::ScoreFunction const &scorefxn, core::pack::task::PackerTask const &task, core::chemical::ResidueTypeCOP concrete_residue, core::graph::GraphCOP packer_neighbor_graph, bool use_neighbor_context=true)
 Creates a set of rotamers for a particular residue type (the concrete residue type) while relying on the rotamer- building instructions within the PackerTask. Use the residue in the input pose at position resid_ as the existing residue. More...
 
virtual core::PackerEnergy bump_check (core::conformation::ResidueCOP rotamer, core::scoring::ScoreFunction const &sf, core::pose::Pose const &pose, core::pack::task::PackerTask const &task, core::graph::GraphCOP packer_neighbor_graph) const
 Computes the "bump energy" of a rotamer: the bump energy is the sum of rotamer's interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization. More...
 
- Protected Member Functions inherited from core::pack::rotamer_set::RotamerSet_
void build_rotamers_for_concrete (pose::Pose const &pose, scoring::ScoreFunction const &scorefxn, task::PackerTask const &task, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, graph::GraphCOP packer_neighbor_graph, bool use_neighbor_context=true)
 
void build_dependent_rotamers_for_concrete (RotamerSets const &rotamer_sets, pose::Pose const &pose, scoring::ScoreFunction const &, task::PackerTask const &task, conformation::Residue const &existing_residue, chemical::ResidueTypeCOP concrete_residue, graph::GraphCOP packer_neighbor_graph)
 
void build_optimize_H_rotamers (pose::Pose const &pose, task::PackerTask const &task, chemical::ResidueTypeCOP concrete_residue, conformation::Residue const &existing_residue, graph::GraphCOP packer_neighbor_graph)
 

Private Attributes

ResidueCOP existing_residue_
 
FlexbbRotamerSetsCAP owner_
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::flexpack::rotamer_set::FlexbbRotamerSet::FlexbbRotamerSet ( )
protocols::flexpack::rotamer_set::FlexbbRotamerSet::~FlexbbRotamerSet ( )
virtual

Member Function Documentation

void protocols::flexpack::rotamer_set::FlexbbRotamerSet::build_dependent_rotamers ( core::pack::rotamer_set::RotamerSets const &  rotamer_sets,
core::pose::Pose const &  pose,
core::scoring::ScoreFunction const &  scorefxn,
core::pack::task::PackerTask const &  task,
core::graph::GraphCOP  packer_neighbor_graph 
)
virtual

Build rotamers that depend on positions of rotamers built in a previous pass This function won't work...

Reimplemented from core::pack::rotamer_set::RotamerSet_.

References utility_exit_with_message.

void protocols::flexpack::rotamer_set::FlexbbRotamerSet::build_rotamers_for_concrete_virt ( core::pose::Pose const &  pose,
core::scoring::ScoreFunction const &  scorefxn,
core::pack::task::PackerTask const &  task,
core::chemical::ResidueTypeCOP  concrete_residue,
core::graph::GraphCOP  packer_neighbor_graph,
bool  use_neighbor_context = true 
)
protectedvirtual

Creates a set of rotamers for a particular residue type (the concrete residue type) while relying on the rotamer- building instructions within the PackerTask. Use the residue in the input pose at position resid_ as the existing residue.

Reimplemented from core::pack::rotamer_set::RotamerSet_.

References core::pack::rotamer_set::RotamerSet_::build_rotamers_for_concrete(), and existing_residue_.

core::PackerEnergy protocols::flexpack::rotamer_set::FlexbbRotamerSet::bump_check ( core::conformation::ResidueCOP  rotamer,
core::scoring::ScoreFunction const &  sf,
core::pose::Pose const &  pose,
core::pack::task::PackerTask const &  task,
core::graph::GraphCOP  packer_neighbor_graph 
) const
protectedvirtual

Computes the "bump energy" of a rotamer: the bump energy is the sum of rotamer's interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

Reimplemented from core::pack::rotamer_set::RotamerSet_.

References owner_, core::pack::task::PackerTask::pack_residue(), and core::pose::Pose::residue().

void protocols::flexpack::rotamer_set::FlexbbRotamerSet::set_existing_residue ( core::conformation::ResidueCOP  residue)

References existing_residue_.

void protocols::flexpack::rotamer_set::FlexbbRotamerSet::set_owner ( FlexbbRotamerSetsCAP  owner)

References owner_.

Member Data Documentation

ResidueCOP protocols::flexpack::rotamer_set::FlexbbRotamerSet::existing_residue_
private
FlexbbRotamerSetsCAP protocols::flexpack::rotamer_set::FlexbbRotamerSet::owner_
private

Referenced by bump_check(), and set_owner().


The documentation for this class was generated from the following files: