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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:
Inheritance graph
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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::Poseget_conformer (core::Size conf_num)
 
core::pose::Poseget_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::Reallowres_reference_energies_
 
utility::vector1< core::Realhighres_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

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

Automatically generated virtual destructor for class deriving directly from VirtualBase.

Auto-generated virtual destructor

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

Member Function Documentation

void protocols::docking::DockingEnsemble::calculate_highres_ref_energy ( core::Size  conf_num)
void protocols::docking::DockingEnsemble::calculate_highres_ref_energy ( core::pose::Pose pose,
std::string  partner_num 
)
void protocols::docking::DockingEnsemble::calculate_lowres_ref_energy ( core::pose::Pose pose)
core::Size protocols::docking::DockingEnsemble::conf_size ( )
inline

References conf_size_.

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

References end_res_.

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

References ensemble_list_.

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

References ensemble_list_cen_.

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

References conf_num_.

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

References jump_id_.

void protocols::docking::DockingEnsemble::load_ensemble ( )
private
core::Real protocols::docking::DockingEnsemble::lowres_reference_energy ( core::Size  conf_num)
inline
core::Real protocols::docking::DockingEnsemble::lowres_reference_energy ( )
inline
std::string protocols::docking::DockingEnsemble::partner ( )
inline

References partner_.

void protocols::docking::DockingEnsemble::recover_and_pack_conformer_sidechains ( core::pose::Pose pose)
core::scoring::ScoreFunctionCOP protocols::docking::DockingEnsemble::scorefxn_low ( )
inline

References scorefxn_low_.

Referenced by DockingEnsemble().

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

References conf_num_.

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

References pack_operations_.

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

References ensemble_size_.

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

References start_res_.

void protocols::docking::DockingEnsemble::update_pdblist_file ( std::string  partner_num)

Member Data Documentation

core::Size protocols::docking::DockingEnsemble::conf_num_
private
core::Size protocols::docking::DockingEnsemble::conf_size_
private

Referenced by conf_size(), and DockingEnsemble().

core::Size protocols::docking::DockingEnsemble::end_res_
private
std::string protocols::docking::DockingEnsemble::ensemble_file_path_
private
utility::vector1< core::pose::Pose > protocols::docking::DockingEnsemble::ensemble_list_
private
utility::vector1< core::pose::Pose > protocols::docking::DockingEnsemble::ensemble_list_cen_
private

Referenced by get_conformer_cen(), and load_ensemble().

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

Referenced by DockingEnsemble(), and size().

utility::vector1< core::Real > protocols::docking::DockingEnsemble::highres_reference_energies_
private
core::Size protocols::docking::DockingEnsemble::jump_id_
private

Referenced by jump_id().

utility::vector1< core::Real > protocols::docking::DockingEnsemble::lowres_reference_energies_
private
protocols::moves::SequenceMoverOP protocols::docking::DockingEnsemble::pack_operations_
private
std::string protocols::docking::DockingEnsemble::partner_
private
utility::vector1< std::string > protocols::docking::DockingEnsemble::pdb_filenames_
private
core::scoring::ScoreFunctionCOP protocols::docking::DockingEnsemble::scorefxn_high_
private

Referenced by DockingEnsemble().

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

Referenced by DockingEnsemble(), and scorefxn_low().

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

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