Rosetta  2020.37
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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::Poseget_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::Sizetemp_positions
 
utility::vector1< core::Realtemp_energies
 
utility::vector1
< core::conformation::ResidueOP
favorable_residues
 
utility::vector1< core::Sizefavorable_positions
 
utility::vector1< core::Realfavorable_energies
 
core::Size number_cavities
 
utility::vector1< core::Sizecavity_balls
 
utility::vector1< std::string > favorable_mutations
 
utility::vector1< core::Sizevoid_neighbors
 
utility::vector1< core::Sizevoid_mutatables
 
core::Real final_energy
 
core::Real energy_to_beat
 
utility::vector1< core::Sizeexcluded_positions
 
core::Size iteration_
 
bool use_stored_best_energy
 

Constructor & Destructor Documentation

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

Member Function Documentation

void protocols::vip::VIP_Mover::apply ( )
void protocols::vip::VIP_Mover::apply_holes ( )
void protocols::vip::VIP_Mover::compute_number_cavities ( )
void protocols::vip::VIP_Mover::cranny_packer ( )
void protocols::vip::VIP_Mover::cull_mutatable_residues ( )
void protocols::vip::VIP_Mover::dump_pdb_to_file ( core::pose::Pose posey,
std::string  filename 
)

References core::pose::Pose::dump_pdb().

Referenced by skip_relax().

core::Real protocols::vip::VIP_Mover::get_cav_approx ( core::Size  a)
void protocols::vip::VIP_Mover::get_cavity_positions ( )
core::Real protocols::vip::VIP_Mover::get_final_energy ( )
inline

References final_energy.

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

References final_pose.

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

References final_unrelaxed_pose.

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

References iteration_.

void protocols::vip::VIP_Mover::minimize_conformation ( )
void protocols::vip::VIP_Mover::nook_finder ( )
void protocols::vip::VIP_Mover::print_pack_report ( )
void protocols::vip::VIP_Mover::print_relax_report ( )
void protocols::vip::VIP_Mover::relax_favorable_poses ( )
void protocols::vip::VIP_Mover::set_energy_to_beat ( core::Real  in_value)
inline

References energy_to_beat.

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

References initial_pose.

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

References iteration_.

void protocols::vip::VIP_Mover::set_use_stored_energy ( bool  in_value)
inline
void protocols::vip::VIP_Mover::skip_relax ( )
void protocols::vip::VIP_Mover::sort_fill_energies ( )
void protocols::vip::VIP_Mover::sort_relaxed_poses ( )

References print_relax_report().

Referenced by cranny_packer().

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

Member Data Documentation

utility::vector1<core::Size> protocols::vip::VIP_Mover::cavity_balls
private
core::pose::Pose protocols::vip::VIP_Mover::cavity_pose
private
core::Real protocols::vip::VIP_Mover::energy_to_beat
private
utility::vector1<core::Size> protocols::vip::VIP_Mover::excluded_positions
private
utility::vector1<core::Real> protocols::vip::VIP_Mover::favorable_energies
private
utility::vector1<std::string> protocols::vip::VIP_Mover::favorable_mutations
private

Referenced by VIP_Mover().

utility::vector1<core::Size> protocols::vip::VIP_Mover::favorable_positions
private
utility::vector1<core::conformation::ResidueOP> protocols::vip::VIP_Mover::favorable_residues
private
core::Real protocols::vip::VIP_Mover::final_energy
private
core::pose::Pose protocols::vip::VIP_Mover::final_pose
private
core::pose::Pose protocols::vip::VIP_Mover::final_unrelaxed_pose
private
core::pose::Pose protocols::vip::VIP_Mover::initial_pose
private
core::Size protocols::vip::VIP_Mover::iteration_
private
core::Size protocols::vip::VIP_Mover::number_cavities
private
utility::vector1<core::Real> protocols::vip::VIP_Mover::temp_energies
private
utility::vector1<core::Size> protocols::vip::VIP_Mover::temp_positions
private
utility::vector1<core::conformation::ResidueOP> protocols::vip::VIP_Mover::temp_residues
private
bool protocols::vip::VIP_Mover::use_stored_best_energy
private
utility::vector1<core::Size> protocols::vip::VIP_Mover::void_mutatables
private
utility::vector1<core::Size> protocols::vip::VIP_Mover::void_neighbors
private

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