#include <VIP_Mover.hh>

Collaboration diagram for protocols::vip::VIP_Mover:

Public Member Functions
	VIP_Mover ()

	VIP_Mover (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_initial_pose (core::pose::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 ()

core::pose::Pose	get_final_pose ()

void	apply ()

Detailed Description

Definition at line 18 of file VIP_Mover.hh.

Constructor & Destructor Documentation

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

Definition at line 55 of file VIP_Mover.cc.

protocols::vip::VIP_Mover::VIP_Mover	(	core::pose::Pose	p,
		core::pose::Pose	cp,
		core::pose::Pose	fp,
		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
	)

Definition at line 56 of file VIP_Mover.cc.

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

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

virtual

Definition at line 89 of file VIP_Mover.cc.

Member Function Documentation

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

Definition at line 435 of file VIP_Mover.cc.

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

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

Definition at line 129 of file VIP_Mover.cc.

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

Referenced by nook_finder().

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

Definition at line 117 of file VIP_Mover.cc.

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

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

Definition at line 421 of file VIP_Mover.cc.

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

Referenced by apply().

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

Definition at line 197 of file VIP_Mover.cc.

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().

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

Definition at line 149 of file VIP_Mover.cc.

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

Referenced by skip_relax().

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

Definition at line 155 of file VIP_Mover.cc.

References cavity_balls, cavity_pose, initial_pose, core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

Referenced by get_neighbors().

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

Definition at line 138 of file VIP_Mover.cc.

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

Referenced by nook_finder().

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

inline

Definition at line 81 of file VIP_Mover.hh.

References final_energy.

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

inline

Definition at line 83 of file VIP_Mover.hh.

References final_pose.

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

Definition at line 168 of file VIP_Mover.cc.

References protocols::match::upstream::b, cavity_balls, cavity_pose, core::pose::Pose::dump_pdb(), get_cav_approx(), initial_pose, core::conformation::Residue::nheavyatoms(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), void_neighbors, and core::conformation::Residue::xyz().

Referenced by nook_finder().

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

Definition at line 100 of file VIP_Mover.cc.

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

Referenced by nook_finder().

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

Definition at line 413 of file VIP_Mover.cc.

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

Referenced by apply().

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

Definition at line 270 of file VIP_Mover.cc.

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

Referenced by sort_fill_energies().

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

Definition at line 309 of file VIP_Mover.cc.

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

Referenced by sort_relaxed_poses().

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

Definition at line 343 of file VIP_Mover.cc.

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

Referenced by cranny_packer().

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

Definition at line 442 of file VIP_Mover.cc.

References excluded_positions, initial_pose, and core::pose::Pose::pdb_info().

Referenced by apply().

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

Definition at line 91 of file VIP_Mover.cc.

References initial_pose.

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

Definition at line 317 of file VIP_Mover.cc.

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

Referenced by cranny_packer().

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

Definition at line 278 of file VIP_Mover.cc.

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::replace_residue(), core::pose::Pose::residue(), temp_energies, temp_positions, temp_residues, and core::scoring::Energies::total_energy().

Referenced by cranny_packer().

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

Definition at line 404 of file VIP_Mover.cc.

References print_relax_report().

Referenced by cranny_packer().

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

Definition at line 228 of file VIP_Mover.cc.

References 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(), temp_energies, temp_positions, temp_residues, core::scoring::Energies::total_energy(), core::pose::Pose::total_residue(), and void_mutatables.

Referenced by cranny_packer().

Member Data Documentation

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

private

Definition at line 31 of file VIP_Mover.hh.

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

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

private

Definition at line 22 of file VIP_Mover.hh.

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

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

private

Definition at line 37 of file VIP_Mover.hh.

Referenced by cull_mutatable_residues(), and set_excluded_positions().

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

private

Definition at line 29 of file VIP_Mover.hh.

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

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

private

Definition at line 32 of file VIP_Mover.hh.

Referenced by VIP_Mover().

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

private

Definition at line 28 of file VIP_Mover.hh.

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

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

private

Definition at line 27 of file VIP_Mover.hh.

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

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

private

Definition at line 35 of file VIP_Mover.hh.

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

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

private

Definition at line 23 of file VIP_Mover.hh.

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

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

private

Definition at line 21 of file VIP_Mover.hh.

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().

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

private

Definition at line 30 of file VIP_Mover.hh.

Referenced by compute_number_cavities(), and VIP_Mover().

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

private

Definition at line 26 of file VIP_Mover.hh.

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

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

private

Definition at line 25 of file VIP_Mover.hh.

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

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

private

Definition at line 24 of file VIP_Mover.hh.

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

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

private

Definition at line 34 of file VIP_Mover.hh.

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

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

private

Definition at line 33 of file VIP_Mover.hh.

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

Private Attributes
core::pose::Pose	initial_pose

core::pose::Pose	cavity_pose

core::pose::Pose	final_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

utility::vector1< core::Size >	excluded_positions

Public Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation