protocols::docking::DockingEnsemble Class Reference

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:

Public Member Functions
	~DockingEnsemble () override
	Automatically generated virtual destructor for class deriving directly from VirtualBase. More...
	DockingEnsemble ()
	DockingEnsemble (core::Size start_res, core::Size end_res, core::Size jump_id, std::string const &ensemble_file_path, std::string const &partner, core::scoring::ScoreFunctionCOP scorefxn_low, core::scoring::ScoreFunctionCOP scorefxn_high)
void	recover_and_pack_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	calculate_highres_ref_energy (core::pose::Pose &pose, std::string partner_num)
void	update_pdblist_file (std::string partner_num)
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
core::Size	start_res_
core::Size	end_res_
core::Size	conf_size_
core::Size	jump_id_
core::Size	ensemble_size_
core::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.

Constructor & Destructor Documentation

~DockingEnsemble()

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

overridedefault

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

DockingEnsemble() [1/2]

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

inline

DockingEnsemble() [2/2]

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

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

Member Function Documentation

calculate_highres_ref_energy() [1/2]

void protocols::docking::DockingEnsemble::calculate_highres_ref_energy	(	core::pose::Pose &	pose,
		std::string	partner_num
	)

References core::pose::Pose::conformation(), core::pose::Pose::delete_residue_slow(), core::pose::Pose::dump_pdb(), protocols::abinitio::filename(), highres_reference_energies_, core::conformation::Conformation::is_membrane(), pack_operations_, protocols::hybridization::path, pdb_filenames_, core::pose::Pose::size(), and protocols::docking::TR().

calculate_highres_ref_energy() [2/2]

void protocols::docking::DockingEnsemble::calculate_highres_ref_energy

(

core::Size

conf_num

)

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

calculate_lowres_ref_energy()

void protocols::docking::DockingEnsemble::calculate_lowres_ref_energy

(

core::pose::Pose &

pose

)

References lowres_reference_energies_, and protocols::docking::TR().

conf_size()

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

inline

References conf_size_.

end_res()

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

inline

References end_res_.

get_conformer()

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

inline

References ensemble_list_.

get_conformer_cen()

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

inline

References ensemble_list_cen_.

get_current_confnum()

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

inline

References conf_num_.

highres_reference_energy() [1/2]

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

inline

References conf_num_, and highres_reference_energies_.

highres_reference_energy() [2/2]

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

inline

References highres_reference_energies_.

jump_id()

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

inline

References jump_id_.

load_ensemble()

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

private

References core::chemical::CENTROID, ensemble_file_path_, ensemble_list_, ensemble_list_cen_, highres_reference_energies_, lowres_reference_energies_, core::import_pose::PDB_file, pdb_filenames_, core::import_pose::poses_from_files(), protocols::medal::to_centroid(), and protocols::docking::TR().

Referenced by DockingEnsemble().

lowres_reference_energy() [1/2]

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

inline

References conf_num_, and lowres_reference_energies_.

lowres_reference_energy() [2/2]

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

inline

References lowres_reference_energies_.

partner()

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

inline

References partner_.

recover_and_pack_conformer_sidechains()

void protocols::docking::DockingEnsemble::recover_and_pack_conformer_sidechains

(

core::pose::Pose &

pose

)

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

scorefxn_low()

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

inline

References scorefxn_low_.

Referenced by DockingEnsemble().

set_current_confnum()

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

inline

References conf_num_.

set_packer()

void protocols::docking::DockingEnsemble::set_packer

(

protocols::moves::SequenceMoverOP

packer

)

References pack_operations_.

size()

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

inline

References ensemble_size_.

start_res()

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

inline

References start_res_.

update_pdblist_file()

void protocols::docking::DockingEnsemble::update_pdblist_file

(

std::string

partner_num

)

References ensemble_file_path_, protocols::abinitio::filename(), highres_reference_energies_, lowres_reference_energies_, protocols::mean_field::min(), protocols::hybridization::path, pdb_filenames_, and protocols::docking::TR().

Member Data Documentation

conf_num_

core::Size protocols::docking::DockingEnsemble::conf_num_

private

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

conf_size_

core::Size protocols::docking::DockingEnsemble::conf_size_

private

Referenced by conf_size(), and DockingEnsemble().

end_res_

core::Size protocols::docking::DockingEnsemble::end_res_

private

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

ensemble_file_path_

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

private

Referenced by load_ensemble(), and update_pdblist_file().

ensemble_list_

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

private

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

ensemble_list_cen_

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

private

Referenced by get_conformer_cen(), and load_ensemble().

ensemble_size_

core::Size protocols::docking::DockingEnsemble::ensemble_size_

private

Referenced by DockingEnsemble(), and size().

highres_reference_energies_

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

private

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

jump_id_

core::Size protocols::docking::DockingEnsemble::jump_id_

private

Referenced by jump_id().

lowres_reference_energies_

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

private

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

pack_operations_

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

private

Referenced by calculate_highres_ref_energy(), and set_packer().

partner_

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

private

Referenced by partner(), and recover_and_pack_conformer_sidechains().

pdb_filenames_

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

private

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

scorefxn_high_

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

private

Referenced by DockingEnsemble().

scorefxn_low_

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

private

Referenced by DockingEnsemble(), and scorefxn_low().

start_res_

core::Size protocols::docking::DockingEnsemble::start_res_

private

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

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

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