this mover does the conformer swap in RosettaDock's ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction. More...

#include <DockingEnsemble.hh>

Inheritance diagram for protocols::docking::DockingEnsemble:

[legend]

Collaboration diagram for protocols::docking::DockingEnsemble:

[legend]

Public Member Functions
virtual	~DockingEnsemble ()
	Automatically generated virtual destructor for class deriving directly from ReferenceCount. More...

	DockingEnsemble ()

	DockingEnsemble (Size start_res, Size end_res, Size jump_id, std::string ensemble_file_path, std::string partner, core::scoring::ScoreFunctionCOP scorefxn_low, core::scoring::ScoreFunctionCOP scorefxn_high)

void	recover_conformer_sidechains (core::pose::Pose &pose)

void	calculate_lowres_ref_energy (core::pose::Pose &pose)

void	calculate_highres_ref_energy (core::Size conf_num)

void	update_pdblist_file ()

void	set_packer (protocols::moves::SequenceMoverOP packer)

void	set_current_confnum (core::Size conf_num)

core::Size	get_current_confnum ()

core::pose::Pose &	get_conformer (core::Size conf_num)

core::pose::Pose &	get_conformer_cen (core::Size conf_num)

core::Size	size ()

core::Size	jump_id ()

core::Size	start_res ()

core::Size	end_res ()

core::Size	conf_size ()

std::string	partner ()

core::Real	lowres_reference_energy (core::Size conf_num)

core::Real	lowres_reference_energy ()

core::Real	highres_reference_energy (core::Size conf_num)

core::Real	highres_reference_energy ()

core::scoring::ScoreFunctionCOP	scorefxn_low ()

Private Member Functions
void	load_ensemble ()

Private Attributes
Size	start_res_

Size	end_res_

Size	conf_size_

Size	jump_id_

Size	ensemble_size_

Size	conf_num_

std::string	ensemble_file_path_

std::string	partner_

core::scoring::ScoreFunctionCOP	scorefxn_low_

core::scoring::ScoreFunctionCOP	scorefxn_high_

utility::vector1< std::string >	pdb_filenames_

utility::vector1 < core::pose::Pose >	ensemble_list_

utility::vector1 < core::pose::Pose >	ensemble_list_cen_

utility::vector1< core::Real >	lowres_reference_energies_

utility::vector1< core::Real >	highres_reference_energies_

protocols::moves::SequenceMoverOP	pack_operations_

Detailed Description

this mover does the conformer swap in RosettaDock's ensemble docking. It takes in a multi-model PDB file as an ensemble, and does swaps conformers by superpositioning over interface residues, and selects a conformer based on a partition function using a ScoreFunction.

Definition at line 51 of file DockingEnsemble.hh.

Constructor & Destructor Documentation

protocols::docking::DockingEnsemble::~DockingEnsemble ( )

virtual

Automatically generated virtual destructor for class deriving directly from ReferenceCount.

Auto-generated virtual destructor

Definition at line 66 of file DockingEnsemble.cc.

protocols::docking::DockingEnsemble::DockingEnsemble ( )

inline

Definition at line 58 of file DockingEnsemble.hh.

protocols::docking::DockingEnsemble::DockingEnsemble	(	Size	start_res,
		Size	end_res,
		Size	jump_id,
		std::string	ensemble_file_path,
		std::string	partner,
		core::scoring::ScoreFunctionCOP	scorefxn_low,
		core::scoring::ScoreFunctionCOP	scorefxn_high
	)

Definition at line 70 of file DockingEnsemble.cc.

References conf_num_, conf_size_, end_res_, ensemble_list_, ensemble_size_, load_ensemble(), scorefxn_high_, scorefxn_low(), scorefxn_low_, start_res_, and protocols::TR().

Member Function Documentation

void protocols::docking::DockingEnsemble::calculate_highres_ref_energy ( core::Size conf_num)

Definition at line 172 of file DockingEnsemble.cc.

References protocols::simple_moves::SwitchResidueTypeSetMover::apply(), core::pose::Pose::dump_pdb(), ensemble_list_, core::chemical::FA_STANDARD, protocols::abinitio::filename(), highres_reference_energies_, pack_operations_, pdb_filenames_, and protocols::TR().

void protocols::docking::DockingEnsemble::calculate_lowres_ref_energy ( core::pose::Pose & pose)

Definition at line 165 of file DockingEnsemble.cc.

References lowres_reference_energies_, and protocols::TR().

core::Size protocols::docking::DockingEnsemble::conf_size ( )

inline

Definition at line 102 of file DockingEnsemble.hh.

References conf_size_.

core::Size protocols::docking::DockingEnsemble::end_res ( )

inline

Definition at line 101 of file DockingEnsemble.hh.

References end_res_.

core::pose::Pose& protocols::docking::DockingEnsemble::get_conformer ( core::Size conf_num)

inline

Definition at line 94 of file DockingEnsemble.hh.

References ensemble_list_.

core::pose::Pose& protocols::docking::DockingEnsemble::get_conformer_cen ( core::Size conf_num)

inline

Definition at line 95 of file DockingEnsemble.hh.

References ensemble_list_cen_.

core::Size protocols::docking::DockingEnsemble::get_current_confnum ( )

inline

Definition at line 91 of file DockingEnsemble.hh.

References conf_num_.

core::Real protocols::docking::DockingEnsemble::highres_reference_energy ( core::Size conf_num)

inline

Definition at line 110 of file DockingEnsemble.hh.

References highres_reference_energies_.

core::Real protocols::docking::DockingEnsemble::highres_reference_energy ( )

inline

Definition at line 111 of file DockingEnsemble.hh.

References conf_num_, and highres_reference_energies_.

core::Size protocols::docking::DockingEnsemble::jump_id ( )

inline

Definition at line 99 of file DockingEnsemble.hh.

References jump_id_.

void protocols::docking::DockingEnsemble::load_ensemble ( )

private

Definition at line 104 of file DockingEnsemble.cc.

References protocols::simple_moves::SwitchResidueTypeSetMover::apply(), core::chemical::CENTROID, ensemble_file_path_, ensemble_list_, ensemble_list_cen_, highres_reference_energies_, lowres_reference_energies_, pdb_filenames_, core::import_pose::poses_from_pdbs(), protocols::medal::to_centroid(), and protocols::TR().

Referenced by DockingEnsemble().

core::Real protocols::docking::DockingEnsemble::lowres_reference_energy ( core::Size conf_num)

inline

Definition at line 108 of file DockingEnsemble.hh.

References lowres_reference_energies_.

core::Real protocols::docking::DockingEnsemble::lowres_reference_energy ( )

inline

Definition at line 109 of file DockingEnsemble.hh.

References conf_num_, and lowres_reference_energies_.

std::string protocols::docking::DockingEnsemble::partner ( )

inline

Definition at line 103 of file DockingEnsemble.hh.

References partner_.

void protocols::docking::DockingEnsemble::recover_conformer_sidechains ( core::pose::Pose & pose)

Definition at line 140 of file DockingEnsemble.cc.

References core::pose::datacache::CacheableDataType::ARBITRARY_FLOAT_DATA, conf_num_, core::pose::Pose::data(), end_res_, ensemble_list_, highres_reference_energies_, partner_, and start_res_.

core::scoring::ScoreFunctionCOP protocols::docking::DockingEnsemble::scorefxn_low ( )

inline

Definition at line 113 of file DockingEnsemble.hh.

References scorefxn_low_.

Referenced by DockingEnsemble().

void protocols::docking::DockingEnsemble::set_current_confnum ( core::Size conf_num)

inline

Definition at line 90 of file DockingEnsemble.hh.

References conf_num_.

void protocols::docking::DockingEnsemble::set_packer ( protocols::moves::SequenceMoverOP packer)

Definition at line 227 of file DockingEnsemble.cc.

References pack_operations_.

core::Size protocols::docking::DockingEnsemble::size ( )

inline

Definition at line 98 of file DockingEnsemble.hh.

References ensemble_size_.

core::Size protocols::docking::DockingEnsemble::start_res ( )

inline

Definition at line 100 of file DockingEnsemble.hh.

References start_res_.

void protocols::docking::DockingEnsemble::update_pdblist_file ( )

Definition at line 191 of file DockingEnsemble.cc.

References ensemble_file_path_, highres_reference_energies_, lowres_reference_energies_, and pdb_filenames_.

Member Data Documentation

Size protocols::docking::DockingEnsemble::conf_num_

private

Definition at line 118 of file DockingEnsemble.hh.

Referenced by DockingEnsemble(), get_current_confnum(), highres_reference_energy(), lowres_reference_energy(), recover_conformer_sidechains(), and set_current_confnum().

Size protocols::docking::DockingEnsemble::conf_size_

private

Definition at line 118 of file DockingEnsemble.hh.

Referenced by conf_size(), and DockingEnsemble().

Size protocols::docking::DockingEnsemble::end_res_

private

Definition at line 118 of file DockingEnsemble.hh.

Referenced by DockingEnsemble(), end_res(), and recover_conformer_sidechains().

std::string protocols::docking::DockingEnsemble::ensemble_file_path_

private

Definition at line 119 of file DockingEnsemble.hh.

Referenced by load_ensemble(), and update_pdblist_file().

utility::vector1< core::pose::Pose > protocols::docking::DockingEnsemble::ensemble_list_

private

Definition at line 123 of file DockingEnsemble.hh.

Referenced by calculate_highres_ref_energy(), DockingEnsemble(), get_conformer(), load_ensemble(), and recover_conformer_sidechains().

utility::vector1< core::pose::Pose > protocols::docking::DockingEnsemble::ensemble_list_cen_

private

Definition at line 124 of file DockingEnsemble.hh.

Referenced by get_conformer_cen(), and load_ensemble().

Size protocols::docking::DockingEnsemble::ensemble_size_

private

Definition at line 118 of file DockingEnsemble.hh.

Referenced by DockingEnsemble(), and size().

utility::vector1< core::Real > protocols::docking::DockingEnsemble::highres_reference_energies_

private

Definition at line 125 of file DockingEnsemble.hh.

Referenced by calculate_highres_ref_energy(), highres_reference_energy(), load_ensemble(), recover_conformer_sidechains(), and update_pdblist_file().

Size protocols::docking::DockingEnsemble::jump_id_

private

Definition at line 118 of file DockingEnsemble.hh.

Referenced by jump_id().

utility::vector1< core::Real > protocols::docking::DockingEnsemble::lowres_reference_energies_

private

Definition at line 125 of file DockingEnsemble.hh.

Referenced by calculate_lowres_ref_energy(), load_ensemble(), lowres_reference_energy(), and update_pdblist_file().

protocols::moves::SequenceMoverOP protocols::docking::DockingEnsemble::pack_operations_

private

Definition at line 127 of file DockingEnsemble.hh.

Referenced by calculate_highres_ref_energy(), and set_packer().

std::string protocols::docking::DockingEnsemble::partner_

private

Definition at line 120 of file DockingEnsemble.hh.

Referenced by partner(), and recover_conformer_sidechains().

utility::vector1< std::string > protocols::docking::DockingEnsemble::pdb_filenames_

private

Definition at line 122 of file DockingEnsemble.hh.

Referenced by calculate_highres_ref_energy(), load_ensemble(), and update_pdblist_file().

core::scoring::ScoreFunctionCOP protocols::docking::DockingEnsemble::scorefxn_high_

private

Definition at line 121 of file DockingEnsemble.hh.

Referenced by DockingEnsemble().

core::scoring::ScoreFunctionCOP protocols::docking::DockingEnsemble::scorefxn_low_

private

Definition at line 121 of file DockingEnsemble.hh.

Referenced by DockingEnsemble(), and scorefxn_low().

Size protocols::docking::DockingEnsemble::start_res_

private

Definition at line 118 of file DockingEnsemble.hh.

Referenced by DockingEnsemble(), recover_conformer_sidechains(), and start_res().

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

src/protocols/docking/DockingEnsemble.hh
src/protocols/docking/DockingEnsemble.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation