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core::pack::rotamer_set::RotamerSets Class Reference

#include <RotamerSets.hh>

Inheritance diagram for core::pack::rotamer_set::RotamerSets:
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Collaboration diagram for core::pack::rotamer_set::RotamerSets:
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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_
 

Detailed Description

Definition at line 54 of file RotamerSets.hh.

Member Typedef Documentation

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

Definition at line 57 of file RotamerSets.hh.

Constructor & Destructor Documentation

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

Definition at line 63 of file RotamerSets.cc.

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

Definition at line 64 of file RotamerSets.cc.

Member Function Documentation

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

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

Definition at line 135 of file RotamerSets.hh.

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 
)

Definition at line 141 of file RotamerSets.cc.

References core::pose::add_variant_type_to_residue(), core::pose::Pose::conformation(), 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, core::pose::remove_variant_type_from_residue(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::chemical::UPPER_TERMINUS.

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 
)

Definition at line 336 of file RotamerSets.cc.

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 
)

Definition at line 369 of file RotamerSets.cc.

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

Definition at line 616 of file RotamerSets.cc.

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

Definition at line 67 of file RotamerSets.cc.

References core::io::pdb::dump_pdb_residue(), 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.

Definition at line 139 of file RotamerSets.hh.

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

Definition at line 854 of file RotamerSets.cc.

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().

Referenced by protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_sr_one_body_energies_for_flexsets(), and protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_projected_deltaE_of_considered_substitution().

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

Definition at line 868 of file RotamerSets.cc.

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().

Referenced by protocols::flexpack::rotamer_set::FlexbbRotamerSets::compute_sr_one_body_energies_for_flexsets(), and protocols::flexpack::interaction_graph::OTFFlexbbInteractionGraph::debug_note_projected_deltaE_of_considered_substitution().

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

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

Definition at line 781 of file RotamerSets.cc.

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.

Definition at line 238 of file RotamerSets.hh.

References moltenres_2_resid_.

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

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

Definition at line 787 of file RotamerSets.cc.

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.

Definition at line 830 of file RotamerSets.cc.

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

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

Definition at line 776 of file RotamerSets.cc.

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::PDInteractionGraph::initialize(), core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::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.

Definition at line 806 of file RotamerSets.cc.

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

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

Definition at line 770 of file RotamerSets.cc.

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

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

Definition at line 771 of file RotamerSets.cc.

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.

Definition at line 387 of file RotamerSets.cc.

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(), 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.

Definition at line 481 of file RotamerSets.cc.

References core::scoring::ScoreFunction::any_lr_residue_pair_energy(), 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::conformation::Residue::nbr_radius(), and core::chemical::num_canonical_aas.

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

Definition at line 843 of file RotamerSets.cc.

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.

Definition at line 790 of file RotamerSets.cc.

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

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

Definition at line 784 of file RotamerSets.cc.

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

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

Definition at line 232 of file RotamerSets.hh.

References resid_2_moltenres_.

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

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

Definition at line 793 of file RotamerSets.cc.

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

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

Definition at line 799 of file RotamerSets.cc.

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.

Definition at line 815 of file RotamerSets.cc.

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::PDInteractionGraph::initialize(), and core::pack::interaction_graph::SymmOnTheFlyInteractionGraph::initialize().

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

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

Definition at line 819 of file RotamerSets.cc.

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

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

Definition at line 809 of file RotamerSets.cc.

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.

Definition at line 812 of file RotamerSets.cc.

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.

Definition at line 823 of file RotamerSets.cc.

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

Definition at line 111 of file RotamerSets.cc.

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

access to packer_task_

Definition at line 837 of file RotamerSets.cc.

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

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

Definition at line 778 of file RotamerSets.cc.

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

Definition at line 302 of file RotamerSets.cc.

Member Data Documentation

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

Definition at line 250 of file RotamerSets.hh.

Referenced by moltenres_2_resid_vector().

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

Definition at line 254 of file RotamerSets.hh.

uint core::pack::rotamer_set::RotamerSets::nmoltenres_
private

Definition at line 243 of file RotamerSets.hh.

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

Definition at line 251 of file RotamerSets.hh.

uint core::pack::rotamer_set::RotamerSets::nrotamers_
private

Definition at line 246 of file RotamerSets.hh.

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

Definition at line 255 of file RotamerSets.hh.

utility::vector1< uint > core::pack::rotamer_set::RotamerSets::resid_2_moltenres_
private

Definition at line 249 of file RotamerSets.hh.

Referenced by resid_2_moltenres_vector().

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

Definition at line 248 of file RotamerSets.hh.

Referenced by begin(), and end().

PackerTaskCOP core::pack::rotamer_set::RotamerSets::task_
private

Definition at line 257 of file RotamerSets.hh.

uint core::pack::rotamer_set::RotamerSets::total_residue_
private

Definition at line 244 of file RotamerSets.hh.

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