Rosetta Core  2014.35
Public Types | Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
core::pack::rotamer_set::RotamerSets Class Reference

#include <RotamerSets.hh>

Public Types

typedef task::PackerTaskCOP PackerTaskCOP
 
- Public Types inherited from core::pack::rotamer_set::FixbbRotamerSets
typedef RotamerSetsBase parent
 
typedef utility::vector1
< RotamerSetOP > 		RotamerSetVector
 

Public Member Functions

 RotamerSets ()
 
 ~RotamerSets ()
 
void set_task (task::PackerTaskCOP task)
 
void build_rotamers (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, graph::GraphCOP packer_neighbor_graph)
 
void compute_energies (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, graph::GraphCOP packer_neighbor_graph, interaction_graph::InteractionGraphBaseOP ig)
 
void dump_pdb (pose::Pose const &pose, std::string const &filename) const
 
virtual uint nrotamers () const
 
virtual uint nrotamers_for_moltenres (uint) const
 
virtual uint nmoltenres () const
 
virtual uint total_residue () const
 
virtual uint moltenres_2_resid (uint) const
 
virtual uint resid_2_moltenres (uint) const
 
virtual uint moltenres_for_rotamer (uint) const
 
virtual uint res_for_rotamer (uint) const
 
virtual
core::conformation::ResidueCOP 		rotamer (uint) const
 
virtual
core::conformation::ResidueCOP 		rotamer_for_moltenres (uint moltenres_id, uint rotamerid) const
 
virtual uint nrotamer_offset_for_moltenres (uint) const
 
virtual RotamerSetCOP rotamer_set_for_residue (uint resid) const
 
virtual RotamerSetOP rotamer_set_for_residue (uint resid)
 
virtual RotamerSetCOP rotamer_set_for_moltenresidue (uint moltenresid) const
 
virtual RotamerSetOP rotamer_set_for_moltenresidue (uint moltenresid)
 
virtual
RotamerSetVector::const_iterator 		begin ()
 
virtual
RotamerSetVector::const_iterator 		end ()
 
virtual uint rotid_on_moltenresidue (uint rotid) const
 convert rotid in full rotamer enumeration into rotamer id on its source residue More...
 
virtual uint moltenres_rotid_2_rotid (uint moltenres, uint moltenresrotid) const
 convert moltenres rotid to id in full rotamer enumeration More...
 
PackerTaskCOP task () const
 access to packer_task_ More...
 
void prepare_sets_for_packing (pose::Pose const &pose, scoring::ScoreFunction const &)
 
void compute_one_body_energies (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, graph::GraphCOP packer_neighbor_graph, interaction_graph::InteractionGraphBaseOP ig)
 
void precompute_two_body_energies (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, graph::GraphCOP packer_neighbor_graph, interaction_graph::PrecomputedPairEnergiesInteractionGraphOP pig, bool const finalize_edges=true)
 precomputes all rotamer pair energies between neighboring RotamerSets( residues ) and stores those energies in an intereaction graph capable of storing them public so it can be used by the GreenPacker. More...
 
virtual utility::vector1< uint >
const & 		resid_2_moltenres_vector () const
 
virtual utility::vector1< uint >
const & 		moltenres_2_resid_vector () const
 
- Public Member Functions inherited from core::pack::rotamer_set::FixbbRotamerSets
 FixbbRotamerSets ()
 
virtual ~FixbbRotamerSets ()
 
- Public Member Functions inherited from core::pack::rotamer_set::RotamerSetsBase
 RotamerSetsBase ()
 
virtual ~RotamerSetsBase ()
 

Static Public Member Functions

static core::PackerEnergy get_bb_bbE (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, conformation::Residue const &res1, conformation::Residue const &res2)
 
static core::PackerEnergy get_sc_bbE (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, conformation::Residue const &res1, conformation::Residue const &res2)
 

Private Member Functions

void update_offset_data ()
 
void prepare_otf_graph (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, graph::GraphCOP packer_neighbor_graph, interaction_graph::OnTheFlyInteractionGraphOP otfig)
 Marks all protein vertices in the on-the-fly interaction graph as ones that should distinguish between the backbones and sidechains. Then, adds edges to the on-the-fly interaction graph between neighboring RotamerSets, and figures out, for those edges, which pairs of rotamer groups (e.g. ala1/arg2, ser1/phe2) are close enough to interact for their energies to need calculation. More...
 
void compute_proline_correction_energies_for_otf_graph (pose::Pose const &pose, scoring::ScoreFunction const &scfxn, graph::GraphCOP packer_neighbor_graph, interaction_graph::OnTheFlyInteractionGraphOP otfig)
 computes one body energies for the on-the-fly graph, calculating proline-correction terms for protien-residues that allow prolines and storing them on the otf edges More...
 

Private Attributes

uint nmoltenres_
 
uint total_residue_
 
uint nrotamers_
 
RotamerSetVector set_of_rotamer_sets_
 
utility::vector1< uint > resid_2_moltenres_
 
utility::vector1< uint > moltenres_2_resid_
 
utility::vector1< uint > nrotamer_offsets_
 
utility::vector1< uint > moltenres_for_rotamer_
 
utility::vector1< uint > nrotamers_for_moltenres_
 
PackerTaskCOP task_
 

Member Typedef Documentation

typedef task::PackerTaskCOP core::pack::rotamer_set::RotamerSets::PackerTaskCOP

Constructor & Destructor Documentation

core::pack::rotamer_set::RotamerSets::RotamerSets ( )
core::pack::rotamer_set::RotamerSets::~RotamerSets ( )

Member Function Documentation

virtual RotamerSetVector::const_iterator core::pack::rotamer_set::RotamerSets::begin ( )
inlinevirtual

Implements core::pack::rotamer_set::FixbbRotamerSets.

References set_of_rotamer_sets_.

void core::pack::rotamer_set::RotamerSets::build_rotamers ( pose::Pose const &  pose,
scoring::ScoreFunction const &  scfxn,
graph::GraphCOP  packer_neighbor_graph 
)

References core::pose::add_variant_type_to_residue(), core::pose::Pose::conformation(), core::conformation::Residue::copy_residue_connections(), core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(), core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::conformation::Residue::has_variant_type(), core::pose::symmetry::is_symmetric(), core::chemical::LOWER_TERMINUS_VARIANT, core::conformation::Residue::place(), core::pose::remove_variant_type_from_residue(), core::pose::Pose::residue(), core::conformation::Residue::residue_connection_partner(), runtime_assert, core::conformation::Residue::seqpos(), core::pose::symmetry::symmetry_info(), core::pose::Pose::total_residue(), and core::chemical::UPPER_TERMINUS_VARIANT.

void core::pack::rotamer_set::RotamerSets::compute_energies ( pose::Pose const &  pose,
scoring::ScoreFunction const &  scfxn,
graph::GraphCOP  packer_neighbor_graph,
interaction_graph::InteractionGraphBaseOP  ig 
)

References utility::pointer::owning_ptr< T >::get(), scoring, and utility_exit_with_message.

void core::pack::rotamer_set::RotamerSets::compute_one_body_energies ( pose::Pose const &  pose,
scoring::ScoreFunction const &  scfxn,
graph::GraphCOP  packer_neighbor_graph,
interaction_graph::InteractionGraphBaseOP  ig 
)
void core::pack::rotamer_set::RotamerSets::compute_proline_correction_energies_for_otf_graph ( pose::Pose const &  pose,
scoring::ScoreFunction const &  scfxn,
graph::GraphCOP  packer_neighbor_graph,
interaction_graph::OnTheFlyInteractionGraphOP  otfig 
)
private

computes one body energies for the on-the-fly graph, calculating proline-correction terms for protien-residues that allow prolines and storing them on the otf edges

0. Find example proline and glycine residues where possible.

  1. Iterate across all edges in the graph
    1. Calculate proline-correction terms between neighbors

References core::chemical::aa_gly, and core::chemical::aa_pro.

void core::pack::rotamer_set::RotamerSets::dump_pdb ( pose::Pose const &  pose,
std::string const &  filename 
) const

References core::io::pdb::dump_pdb_residue(), core::chemical::element::I, out, core::pose::Pose::residue(), and core::pose::Pose::total_residue().

virtual RotamerSetVector::const_iterator core::pack::rotamer_set::RotamerSets::end ( )
inlinevirtual

Implements core::pack::rotamer_set::FixbbRotamerSets.

References set_of_rotamer_sets_.

core::PackerEnergy core::pack::rotamer_set::RotamerSets::get_bb_bbE ( pose::Pose const &  pose,
scoring::ScoreFunction const &  scfxn,
conformation::Residue const &  res1,
conformation::Residue const &  res2 
)
static

References core::scoring::EMapVector::dot(), core::scoring::ScoreFunction::eval_cd_2b_bb_bb(), core::scoring::ScoreFunction::eval_ci_2b_bb_bb(), and core::scoring::ScoreFunction::weights().

core::PackerEnergy core::pack::rotamer_set::RotamerSets::get_sc_bbE ( pose::Pose const &  pose,
scoring::ScoreFunction const &  scfxn,
conformation::Residue const &  res1,
conformation::Residue const &  res2 
)
static

References core::scoring::EMapVector::dot(), core::scoring::ScoreFunction::eval_cd_2b_bb_sc(), core::scoring::ScoreFunction::eval_ci_2b_bb_sc(), and core::scoring::ScoreFunction::weights().

uint core::pack::rotamer_set::RotamerSets::moltenres_2_resid ( uint  mresid) const
virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

Referenced by core::pack::scmin::AtomTreeCollection::AtomTreeCollection(), and core::pack::get_total_energy_for_state().

virtual utility::vector1< uint > const& core::pack::rotamer_set::RotamerSets::moltenres_2_resid_vector ( ) const
inlinevirtual

Implements core::pack::rotamer_set::FixbbRotamerSets.

References moltenres_2_resid_.

uint core::pack::rotamer_set::RotamerSets::moltenres_for_rotamer ( uint  rotid) const
virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

uint core::pack::rotamer_set::RotamerSets::moltenres_rotid_2_rotid ( uint  moltenres,
uint  moltenresrotid 
) const
virtual

convert moltenres rotid to id in full rotamer enumeration

Implements core::pack::rotamer_set::RotamerSetsBase.

uint core::pack::rotamer_set::RotamerSets::nmoltenres ( ) const
virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

Referenced by core::pack::scmin::AtomTreeCollection::AtomTreeCollection(), core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph(), core::pack::get_total_energy_for_state(), core::pack::interaction_graph::DoubleDensePDInteractionGraph::initialize(), core::pack::interaction_graph::DensePDInteractionGraph::initialize(), core::pack::interaction_graph::OnTheFlyInteractionGraph::initialize(), core::pack::interaction_graph::FASTERInteractionGraph::initialize(), core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::initialize(), core::pack::interaction_graph::PDInteractionGraph::initialize(), core::pack::interaction_graph::SurfaceInteractionGraph< V, E, G >::initialize(), and core::pack::interaction_graph::HPatchInteractionGraph< V, E, G >::initialize().

uint core::pack::rotamer_set::RotamerSets::nrotamer_offset_for_moltenres ( uint  mresid) const
virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

uint core::pack::rotamer_set::RotamerSets::nrotamers ( ) const
virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

uint core::pack::rotamer_set::RotamerSets::nrotamers_for_moltenres ( uint  mresid) const
virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

void core::pack::rotamer_set::RotamerSets::precompute_two_body_energies ( pose::Pose const &  pose,
scoring::ScoreFunction const &  scfxn,
graph::GraphCOP  packer_neighbor_graph,
interaction_graph::PrecomputedPairEnergiesInteractionGraphOP  pig,
bool const  finalize_edges = true 
)

precomputes all rotamer pair energies between neighboring RotamerSets( residues ) and stores those energies in an intereaction graph capable of storing them public so it can be used by the GreenPacker.

References core::scoring::ScoreFunction::any_lr_residue_pair_energy(), core::pose::Pose::energies(), core::scoring::ScoreFunction::evaluate_rotamer_pair_energies(), core::scoring::Energies::long_range_container(), core::scoring::ScoreFunction::long_range_energies_begin(), core::scoring::ScoreFunction::long_range_energies_end(), scoring, and core::scoring::ScoreFunction::weights().

void core::pack::rotamer_set::RotamerSets::prepare_otf_graph ( pose::Pose const &  pose,
scoring::ScoreFunction const &  scfxn,
graph::GraphCOP  packer_neighbor_graph,
interaction_graph::OnTheFlyInteractionGraphOP  otfig 
)
private

Marks all protein vertices in the on-the-fly interaction graph as ones that should distinguish between the backbones and sidechains. Then, adds edges to the on-the-fly interaction graph between neighboring RotamerSets, and figures out, for those edges, which pairs of rotamer groups (e.g. ala1/arg2, ser1/phe2) are close enough to interact for their energies to need calculation.

References core::scoring::ScoreFunction::any_lr_residue_pair_energy(), numeric::xyzVector< class >::distance_squared(), core::pose::Pose::energies(), core::scoring::ScoreFunction::info(), core::scoring::Energies::long_range_container(), core::scoring::ScoreFunction::long_range_energies_begin(), core::scoring::ScoreFunction::long_range_energies_end(), core::chemical::num_canonical_aas, and scoring.

void core::pack::rotamer_set::RotamerSets::prepare_sets_for_packing ( pose::Pose const &  pose,
scoring::ScoreFunction const &  sfxn 
)

References core::scoring::ScoreFunction::prepare_rotamers_for_packing().

uint core::pack::rotamer_set::RotamerSets::res_for_rotamer ( uint  rotid) const
virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

uint core::pack::rotamer_set::RotamerSets::resid_2_moltenres ( uint  resid) const
virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

virtual utility::vector1< uint > const& core::pack::rotamer_set::RotamerSets::resid_2_moltenres_vector ( ) const
inlinevirtual

Implements core::pack::rotamer_set::FixbbRotamerSets.

References resid_2_moltenres_.

core::conformation::ResidueCOP core::pack::rotamer_set::RotamerSets::rotamer ( uint  rotid) const
virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

core::conformation::ResidueCOP core::pack::rotamer_set::RotamerSets::rotamer_for_moltenres ( uint  moltenres_id,
uint  rotamerid 
) const
virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

Referenced by core::pack::minimize_alt_rotamer().

RotamerSetCOP core::pack::rotamer_set::RotamerSets::rotamer_set_for_moltenresidue ( uint  moltenresid) const
virtual

Implements core::pack::rotamer_set::FixbbRotamerSets.

Referenced by core::pack::scmin::AtomTreeCollection::AtomTreeCollection(), core::pack::interaction_graph::InteractionGraphFactory::create_interaction_graph(), core::pack::interaction_graph::DoubleDensePDInteractionGraph::initialize(), core::pack::interaction_graph::DensePDInteractionGraph::initialize(), core::pack::interaction_graph::OnTheFlyInteractionGraph::initialize(), core::pack::interaction_graph::FASTERInteractionGraph::initialize(), core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::initialize(), and core::pack::interaction_graph::PDInteractionGraph::initialize().

RotamerSetOP core::pack::rotamer_set::RotamerSets::rotamer_set_for_moltenresidue ( uint  moltenresid)
virtual

Implements core::pack::rotamer_set::FixbbRotamerSets.

RotamerSetCOP core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue ( uint  resid) const
virtual

Implements core::pack::rotamer_set::FixbbRotamerSets.

Referenced by core::pack::rotamer_set::build_moving_O_water_rotamers_dependent(), core::pack::get_residue_current_energy(), core::pack::get_total_energy_for_state(), and core::pack::minimize_alt_rotamer().

RotamerSetOP core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue ( uint  resid)
virtual

Implements core::pack::rotamer_set::FixbbRotamerSets.

uint core::pack::rotamer_set::RotamerSets::rotid_on_moltenresidue ( uint  rotid) const
virtual

convert rotid in full rotamer enumeration into rotamer id on its source residue

Implements core::pack::rotamer_set::RotamerSetsBase.

void core::pack::rotamer_set::RotamerSets::set_task ( task::PackerTaskCOP  task)
task::PackerTaskCOP core::pack::rotamer_set::RotamerSets::task ( ) const

access to packer_task_

uint core::pack::rotamer_set::RotamerSets::total_residue ( ) const
virtual

Implements core::pack::rotamer_set::RotamerSetsBase.

void core::pack::rotamer_set::RotamerSets::update_offset_data ( )
private

Member Data Documentation

utility::vector1< uint > core::pack::rotamer_set::RotamerSets::moltenres_2_resid_
private

Referenced by moltenres_2_resid_vector().

utility::vector1< uint > core::pack::rotamer_set::RotamerSets::moltenres_for_rotamer_
private
uint core::pack::rotamer_set::RotamerSets::nmoltenres_
private
utility::vector1< uint > core::pack::rotamer_set::RotamerSets::nrotamer_offsets_
private
uint core::pack::rotamer_set::RotamerSets::nrotamers_
private
utility::vector1< uint > core::pack::rotamer_set::RotamerSets::nrotamers_for_moltenres_
private
utility::vector1< uint > core::pack::rotamer_set::RotamerSets::resid_2_moltenres_
private

Referenced by resid_2_moltenres_vector().

RotamerSetVector core::pack::rotamer_set::RotamerSets::set_of_rotamer_sets_
private

Referenced by begin(), and end().

PackerTaskCOP core::pack::rotamer_set::RotamerSets::task_
private
uint core::pack::rotamer_set::RotamerSets::total_residue_
private
The documentation for this class was generated from the following files:
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