Rosetta
Public Member Functions | Private Attributes | List of all members
protocols::vip::VIP_Mover Class Reference

#include <VIP_Mover.hh>

Public Member Functions

 VIP_Mover ()
 
 VIP_Mover (core::pose::Pose, core::pose::Pose, core::pose::Pose, core::pose::Pose, utility::vector1< core::conformation::ResidueOP >, utility::vector1< core::Size >, utility::vector1< core::Real >, utility::vector1< core::conformation::ResidueOP >, utility::vector1< core::Size >, utility::vector1< core::Real >, core::Size, utility::vector1< core::Size >, utility::vector1< std::string >, utility::vector1< core::Size >, utility::vector1< core::Size >, core::Real)
 
virtual ~VIP_Mover ()
 
void set_iteration (core::Size it)
 
core::Size iteration ()
 
void set_initial_pose (core::pose::Pose)
 
core::pose::Pose & get_unrelaxed_pose ()
 
void minimize_conformation ()
 
void compute_number_cavities ()
 
void get_cavity_positions ()
 
void apply_holes ()
 
void dump_pdb_to_file (core::pose::Pose &, std::string)
 
void get_neighbors ()
 
void try_point_mutants ()
 
void relax_favorable_poses ()
 
void cull_mutatable_residues ()
 
void sort_fill_energies ()
 
core::Real get_cav_approx (core::Size)
 
void skip_relax ()
 
void sort_relaxed_poses ()
 
void print_pack_report ()
 
void print_relax_report ()
 
void nook_finder ()
 
void cranny_packer ()
 
void set_excluded_positions ()
 
core::Real get_final_energy ()
 
void set_energy_to_beat (core::Real in_value)
 
void set_use_stored_energy (bool in_value)
 
core::pose::Pose get_final_pose ()
 
void apply ()
 

Private Attributes

core::pose::Pose initial_pose
 
core::pose::Pose cavity_pose
 
core::pose::Pose final_pose
 
core::pose::Pose final_unrelaxed_pose
 
utility::vector1< core::conformation::ResidueOP > temp_residues
 
utility::vector1< core::Size > temp_positions
 
utility::vector1< core::Real > temp_energies
 
utility::vector1< core::conformation::ResidueOP > favorable_residues
 
utility::vector1< core::Size > favorable_positions
 
utility::vector1< core::Real > favorable_energies
 
core::Size number_cavities
 
utility::vector1< core::Size > cavity_balls
 
utility::vector1< std::string > favorable_mutations
 
utility::vector1< core::Size > void_neighbors
 
utility::vector1< core::Size > void_mutatables
 
core::Real final_energy
 
core::Real energy_to_beat
 
utility::vector1< core::Size > excluded_positions
 
core::Size iteration_
 
bool use_stored_best_energy
 

Constructor & Destructor Documentation

◆ VIP_Mover() [1/2]

protocols::vip::VIP_Mover::VIP_Mover ( )
default

◆ VIP_Mover() [2/2]

protocols::vip::VIP_Mover::VIP_Mover ( core::pose::Pose  p,
core::pose::Pose  cp,
core::pose::Pose  fp,
core::pose::Pose  fup,
utility::vector1< core::conformation::ResidueOP >  tr,
utility::vector1< core::Size >  tp,
utility::vector1< core::Real >  te,
utility::vector1< core::conformation::ResidueOP >  vr,
utility::vector1< core::Size >  fav_p,
utility::vector1< core::Real >  fav_e,
core::Size  nc,
utility::vector1< core::Size >  cb,
utility::vector1< std::string >  fm,
utility::vector1< core::Size >  vn,
utility::vector1< core::Size >  vm,
core::Real  fe 
)

References cavity_balls, cavity_pose, energy_to_beat, favorable_energies, favorable_mutations, favorable_positions, favorable_residues, final_energy, final_pose, final_unrelaxed_pose, initial_pose, iteration_, number_cavities, temp_energies, temp_positions, temp_residues, core::chemical::tr(), use_stored_best_energy, void_mutatables, and void_neighbors.

◆ ~VIP_Mover()

protocols::vip::VIP_Mover::~VIP_Mover ( )
virtualdefault

Member Function Documentation

◆ apply()

void protocols::vip::VIP_Mover::apply ( )

References cranny_packer(), nook_finder(), and set_excluded_positions().

◆ apply_holes()

void protocols::vip::VIP_Mover::apply_holes ( )

References protocols::simple_moves::AddCavitiesMover::apply(), cavity_pose, and initial_pose.

Referenced by nook_finder().

◆ compute_number_cavities()

void protocols::vip::VIP_Mover::compute_number_cavities ( )

References core::pose::motif::a(), cavity_pose, core::conformation::Residue::name(), number_cavities, core::pose::Pose::residue(), and core::pose::Pose::size().

◆ cranny_packer()

void protocols::vip::VIP_Mover::cranny_packer ( )

References relax_favorable_poses(), skip_relax(), sort_fill_energies(), sort_relaxed_poses(), and try_point_mutants().

Referenced by apply().

◆ cull_mutatable_residues()

void protocols::vip::VIP_Mover::cull_mutatable_residues ( )

References core::conformation::Residue::aa(), core::conformation::Residue::atom_is_backbone(), excluded_positions, core::chemical::ResidueProperties::has_property(), initial_pose, core::conformation::Residue::is_polar(), core::chemical::num_canonical_aas, core::chemical::ResidueTypeBase::properties(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::chemical::SURFACE, void_mutatables, and void_neighbors.

Referenced by nook_finder().

◆ dump_pdb_to_file()

void protocols::vip::VIP_Mover::dump_pdb_to_file ( core::pose::Pose &  posey,
std::string  filename 
)

References core::pose::Pose::dump_pdb(), and protocols::abinitio::filename().

Referenced by skip_relax().

◆ get_cav_approx()

core::Real protocols::vip::VIP_Mover::get_cav_approx ( core::Size  a)

References core::pose::motif::a(), cavity_balls, cavity_pose, initial_pose, protocols::mean_field::min(), core::pose::Pose::residue(), core::pose::Pose::size(), and core::conformation::Residue::xyz().

Referenced by get_neighbors().

◆ get_cavity_positions()

void protocols::vip::VIP_Mover::get_cavity_positions ( )

References cavity_balls, cavity_pose, core::conformation::Residue::name(), core::pose::Pose::residue(), and core::pose::Pose::size().

Referenced by nook_finder().

◆ get_final_energy()

core::Real protocols::vip::VIP_Mover::get_final_energy ( )
inline

References final_energy.

◆ get_final_pose()

core::pose::Pose protocols::vip::VIP_Mover::get_final_pose ( )
inline

References final_pose.

◆ get_neighbors()

void protocols::vip::VIP_Mover::get_neighbors ( )

References core::pose::motif::a(), protocols::match::upstream::b, cavity_balls, cavity_pose, core::pose::Pose::dump_pdb(), get_cav_approx(), initial_pose, protocols::mean_field::min(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::vip::TR(), void_neighbors, and core::conformation::Residue::xyz().

Referenced by nook_finder().

◆ get_unrelaxed_pose()

core::pose::Pose& protocols::vip::VIP_Mover::get_unrelaxed_pose ( )
inline

References final_unrelaxed_pose.

◆ iteration()

core::Size protocols::vip::VIP_Mover::iteration ( )
inline

References iteration_.

◆ minimize_conformation()

void protocols::vip::VIP_Mover::minimize_conformation ( )

References core::scoring::ScoreFunctionFactory::create_score_function(), and initial_pose.

Referenced by nook_finder().

◆ nook_finder()

void protocols::vip::VIP_Mover::nook_finder ( )

References apply_holes(), cull_mutatable_residues(), get_cavity_positions(), get_neighbors(), and minimize_conformation().

Referenced by apply().

◆ print_pack_report()

void protocols::vip::VIP_Mover::print_pack_report ( )

References energy_to_beat, favorable_energies, favorable_positions, favorable_residues, protocols::vip::VIP_Report::get_GOE_repack_report(), initial_pose, and iteration_.

Referenced by sort_fill_energies().

◆ print_relax_report()

void protocols::vip::VIP_Mover::print_relax_report ( )

References energy_to_beat, favorable_energies, favorable_positions, favorable_residues, protocols::vip::VIP_Report::get_GOE_relaxed_report(), initial_pose, iteration_, and use_stored_best_energy.

Referenced by sort_relaxed_poses().

◆ relax_favorable_poses()

void protocols::vip::VIP_Mover::relax_favorable_poses ( )

References core::scoring::ScoreFunctionFactory::create_score_function(), favorable_energies, favorable_positions, favorable_residues, final_energy, final_pose, final_unrelaxed_pose, initial_pose, protocols::relax::relax_pose(), core::pose::Pose::replace_residue(), and protocols::vip::set_local_movemap().

Referenced by cranny_packer().

◆ set_energy_to_beat()

void protocols::vip::VIP_Mover::set_energy_to_beat ( core::Real  in_value)
inline

References energy_to_beat.

◆ set_excluded_positions()

void protocols::vip::VIP_Mover::set_excluded_positions ( )

References excluded_positions, initial_pose, core::conformation::Residue::is_protein(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::vip::TR().

Referenced by apply().

◆ set_initial_pose()

void protocols::vip::VIP_Mover::set_initial_pose ( core::pose::Pose  pose)

References initial_pose.

◆ set_iteration()

void protocols::vip::VIP_Mover::set_iteration ( core::Size  it)
inline

References iteration_.

◆ set_use_stored_energy()

void protocols::vip::VIP_Mover::set_use_stored_energy ( bool  in_value)
inline

References use_stored_best_energy.

◆ skip_relax()

void protocols::vip::VIP_Mover::skip_relax ( )

References dump_pdb_to_file(), favorable_energies, favorable_positions, favorable_residues, final_energy, final_pose, initial_pose, core::pose::Pose::replace_residue(), and protocols::vip::TR().

Referenced by cranny_packer().

◆ sort_fill_energies()

void protocols::vip::VIP_Mover::sort_fill_energies ( )

References core::scoring::ScoreFunctionFactory::create_score_function(), core::pose::Pose::energies(), favorable_energies, favorable_positions, favorable_residues, initial_pose, core::conformation::Residue::name(), num_stored_poses(), print_pack_report(), core::pose::Pose::residue(), temp_energies, temp_positions, temp_residues, and core::scoring::Energies::total_energy().

Referenced by cranny_packer().

◆ sort_relaxed_poses()

void protocols::vip::VIP_Mover::sort_relaxed_poses ( )

References print_relax_report().

Referenced by cranny_packer().

◆ try_point_mutants()

void protocols::vip::VIP_Mover::try_point_mutants ( )

References protocols::cluster::calibur::aa, core::conformation::Residue::clone(), core::pack::task::TaskFactory::create_packer_task(), core::scoring::ScoreFunctionFactory::create_score_function(), core::pose::Pose::energies(), initial_pose, core::pose::Pose::residue(), core::pose::Pose::size(), temp_energies, temp_positions, temp_residues, core::scoring::Energies::total_energy(), and void_mutatables.

Referenced by cranny_packer().

Member Data Documentation

◆ cavity_balls

utility::vector1<core::Size> protocols::vip::VIP_Mover::cavity_balls
private

Referenced by get_cav_approx(), get_cavity_positions(), get_neighbors(), and VIP_Mover().

◆ cavity_pose

core::pose::Pose protocols::vip::VIP_Mover::cavity_pose
private

Referenced by apply_holes(), compute_number_cavities(), get_cav_approx(), get_cavity_positions(), get_neighbors(), and VIP_Mover().

◆ energy_to_beat

core::Real protocols::vip::VIP_Mover::energy_to_beat
private

Referenced by print_pack_report(), print_relax_report(), set_energy_to_beat(), and VIP_Mover().

◆ excluded_positions

utility::vector1<core::Size> protocols::vip::VIP_Mover::excluded_positions
private

Referenced by cull_mutatable_residues(), and set_excluded_positions().

◆ favorable_energies

utility::vector1<core::Real> protocols::vip::VIP_Mover::favorable_energies
private

Referenced by print_pack_report(), print_relax_report(), relax_favorable_poses(), skip_relax(), sort_fill_energies(), and VIP_Mover().

◆ favorable_mutations

utility::vector1<std::string> protocols::vip::VIP_Mover::favorable_mutations
private

Referenced by VIP_Mover().

◆ favorable_positions

utility::vector1<core::Size> protocols::vip::VIP_Mover::favorable_positions
private

Referenced by print_pack_report(), print_relax_report(), relax_favorable_poses(), skip_relax(), sort_fill_energies(), and VIP_Mover().

◆ favorable_residues

utility::vector1<core::conformation::ResidueOP> protocols::vip::VIP_Mover::favorable_residues
private

Referenced by print_pack_report(), print_relax_report(), relax_favorable_poses(), skip_relax(), sort_fill_energies(), and VIP_Mover().

◆ final_energy

core::Real protocols::vip::VIP_Mover::final_energy
private

Referenced by get_final_energy(), relax_favorable_poses(), skip_relax(), and VIP_Mover().

◆ final_pose

core::pose::Pose protocols::vip::VIP_Mover::final_pose
private

Referenced by get_final_pose(), relax_favorable_poses(), skip_relax(), and VIP_Mover().

◆ final_unrelaxed_pose

core::pose::Pose protocols::vip::VIP_Mover::final_unrelaxed_pose
private

Referenced by get_unrelaxed_pose(), relax_favorable_poses(), and VIP_Mover().

◆ initial_pose

core::pose::Pose protocols::vip::VIP_Mover::initial_pose
private

Referenced by apply_holes(), cull_mutatable_residues(), get_cav_approx(), get_neighbors(), minimize_conformation(), print_pack_report(), print_relax_report(), relax_favorable_poses(), set_excluded_positions(), set_initial_pose(), skip_relax(), sort_fill_energies(), try_point_mutants(), and VIP_Mover().

◆ iteration_

core::Size protocols::vip::VIP_Mover::iteration_
private

Referenced by iteration(), print_pack_report(), print_relax_report(), set_iteration(), and VIP_Mover().

◆ number_cavities

core::Size protocols::vip::VIP_Mover::number_cavities
private

Referenced by compute_number_cavities(), and VIP_Mover().

◆ temp_energies

utility::vector1<core::Real> protocols::vip::VIP_Mover::temp_energies
private

Referenced by sort_fill_energies(), try_point_mutants(), and VIP_Mover().

◆ temp_positions

utility::vector1<core::Size> protocols::vip::VIP_Mover::temp_positions
private

Referenced by sort_fill_energies(), try_point_mutants(), and VIP_Mover().

◆ temp_residues

utility::vector1<core::conformation::ResidueOP> protocols::vip::VIP_Mover::temp_residues
private

Referenced by sort_fill_energies(), try_point_mutants(), and VIP_Mover().

◆ use_stored_best_energy

bool protocols::vip::VIP_Mover::use_stored_best_energy
private

Referenced by print_relax_report(), set_use_stored_energy(), and VIP_Mover().

◆ void_mutatables

utility::vector1<core::Size> protocols::vip::VIP_Mover::void_mutatables
private

Referenced by cull_mutatable_residues(), try_point_mutants(), and VIP_Mover().

◆ void_neighbors

utility::vector1<core::Size> protocols::vip::VIP_Mover::void_neighbors
private

Referenced by cull_mutatable_residues(), get_neighbors(), and VIP_Mover().

The documentation for this class was generated from the following files:
Generated on Thu Sep 11 2025 21:36:16 for Rosetta by doxygen 1.9.1