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, initial_pose, core::conformation::Residue::is_polar(), core::conformation::Residue::is_surface(), core::chemical::num_canonical_aas, core::pose::Pose::residue(), 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:

• src/protocols/vip/VIP_Mover.hh
• src/protocols/vip/VIP_Mover.cc