Rosetta: PhDocking Class Reference

Rosetta

Inheritance diagram for PhDocking:

Inheritance graph

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Public Member Functions
	PhDocking ()

virtual	~PhDocking ()

void	set_default ()

void	init_options ()

void	set_file_name (std::string pdb_file_name)

void	set_partners (std::string partner_info)

void	set_pH_mode (bool pH_mode)

void	set_resfile (bool resfile)

void	set_unbound_pdbs (utility::vector1< utility::file::FileName > unbound_pdbs)

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

void	setup_foldtree (core::pose::Pose &pose, std::string partner_chainID)

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

utility::vector1< core::Real >	calc_energies (const core::pose::Pose &pose, core::scoring::ScoreFunctionOP scorefxn, utility::vector1_int movable_jumps)

void	setup_pH_mode (core::pose::Pose &pose, core::scoring::ScoreFunctionOP score_fxn)

core::Real	calc_unbound_score (core::scoring::ScoreFunctionOP score_fxn)

virtual void	apply (core::pose::Pose &pose)

std::string	get_name () const

virtual protocols::moves::MoverOP	fresh_instance () const

virtual bool	reinitialize_for_each_job () const

virtual bool	reinitialize_for_new_input () const

Private Attributes
std::string	pdb_file_name_

std::string	partner_info_

utility::vector1_int	movable_jumps_

bool	pH_mode_

bool	resfile_

bool	unbound_avail_

utility::vector1< utility::file::FileName >	unbound_pdbs_

Constructor & Destructor Documentation

◆ PhDocking()

PhDocking::PhDocking ( )

inline

References init_options().

Referenced by fresh_instance().

◆ ~PhDocking()

virtual PhDocking::~PhDocking ( )

inlinevirtual

Member Function Documentation

◆ apply()

virtual void PhDocking::apply ( core::pose::Pose & pose )

inlinevirtual

References calc_energies(), pyrosetta::create_score_function, bin_torsions::job, test.T400_Refinement::minmover, movable_jumps_, basic::options::OptionKeys::in::file::movemap, partner_info_, pH_mode_, beta_nonlocal::pose, resfile_, beta_nonlocal::score_fxn, basic::options::OptionKeys::frags::scoring::scoring, setup_foldtree(), and setup_pH_mode().

Referenced by pyrosetta.distributed.tasks.rosetta_scripts.BaseRosettaScriptsTask::execute().

◆ calc_energies()

utility::vector1< core::Real > PhDocking::calc_energies	(	const core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	scorefxn,
		utility::vector1_int	movable_jumps
	)

inline

References calc_unbound_score(), movable_jumps_, beta_nonlocal::pose, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, setup_task_and_repack(), basic::options::OptionKeys::enzdes::trans_magnitude, and unbound_avail_.

Referenced by apply().

◆ calc_unbound_score()

core::Real PhDocking::calc_unbound_score ( core::scoring::ScoreFunctionOP score_fxn )

inline

References pyrosetta.distributed.io::pose_from_file, beta_nonlocal::score_fxn, setup_task_and_repack(), and unbound_pdbs_.

Referenced by calc_energies().

◆ fresh_instance()

virtual protocols::moves::MoverOP PhDocking::fresh_instance ( ) const

inlinevirtual

References PhDocking().

◆ get_name()

std::string PhDocking::get_name ( ) const

inline

◆ init_options()

void PhDocking::init_options ( )

inline

References option, basic::options::OptionKeys::docking::partners, basic::options::OptionKeys::pH::pH_mode, basic::options::OptionKeys::pH::pH_unbound, basic::options::OptionKeys::packing::resfile, docking::s, set_default(), set_file_name(), set_partners(), set_pH_mode(), set_resfile(), set_unbound_pdbs(), and basic::options::OptionKeys::inout::dbms::user.

Referenced by PhDocking().

◆ print_hbonds()

void PhDocking::print_hbonds ( core::pose::Pose & pose )

inline

References utility::io::oc::cout, beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

◆ reinitialize_for_each_job()

virtual bool PhDocking::reinitialize_for_each_job ( ) const

inlinevirtual

◆ reinitialize_for_new_input()

virtual bool PhDocking::reinitialize_for_new_input ( ) const

inlinevirtual

◆ set_default()

void PhDocking::set_default ( )

inline

References pH_mode_, resfile_, and unbound_avail_.

Referenced by init_options().

◆ set_file_name()

void PhDocking::set_file_name ( std::string pdb_file_name )

inline

References pdb_file_name_.

Referenced by init_options().

◆ set_partners()

void PhDocking::set_partners ( std::string partner_info )

inline

References partner_info_.

Referenced by init_options().

◆ set_pH_mode()

void PhDocking::set_pH_mode ( bool pH_mode )

inline

References basic::options::OptionKeys::pH::pH_mode, and pH_mode_.

Referenced by init_options().

◆ set_resfile()

void PhDocking::set_resfile ( bool resfile )

inline

References basic::options::OptionKeys::packing::resfile, and resfile_.

Referenced by init_options().

◆ set_unbound_pdbs()

void PhDocking::set_unbound_pdbs ( utility::vector1< utility::file::FileName > unbound_pdbs )

inline

References unbound_avail_, and unbound_pdbs_.

Referenced by init_options().

◆ setup_foldtree()

void PhDocking::setup_foldtree	(	core::pose::Pose &	pose,
		std::string	partner_chainID
	)

inline

References chain_begin(), chain_end(), loops::cutpoint, create_a3b_hbs::f, create_a3b_hbs::i, movable_jumps_, create_a3b_hbs::pdb_info, and beta_nonlocal::pose.

Referenced by apply().

◆ setup_pH_mode()

void PhDocking::setup_pH_mode	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	score_fxn
	)

inline

References create_a3b_hbs::ii, test.Workshop6test::pack_mover, pdb_file_name_, beta_nonlocal::pose, beta_nonlocal::score_fxn, basic::options::OptionKeys::frags::scoring::scoring, vancomycin::task, and TR.

Referenced by apply().

◆ setup_task_and_repack()

void PhDocking::setup_task_and_repack ( core::pose::Pose & pose )

inline

References pyrosetta::create_score_function, create_a3b_hbs::ii, beta_nonlocal::pose, and basic::options::OptionKeys::frags::scoring::scoring.

Referenced by calc_energies(), and calc_unbound_score().

Member Data Documentation

◆ movable_jumps_

utility::vector1_int PhDocking::movable_jumps_

private

Referenced by apply(), calc_energies(), and setup_foldtree().

◆ partner_info_

std::string PhDocking::partner_info_

private

Referenced by apply(), and set_partners().

◆ pdb_file_name_

std::string PhDocking::pdb_file_name_

private

Referenced by set_file_name(), and setup_pH_mode().

◆ pH_mode_

bool PhDocking::pH_mode_

private

Referenced by apply(), set_default(), and set_pH_mode().

◆ resfile_

bool PhDocking::resfile_

private

Referenced by apply(), set_default(), and set_resfile().

◆ unbound_avail_

bool PhDocking::unbound_avail_

private

Referenced by calc_energies(), set_default(), and set_unbound_pdbs().

◆ unbound_pdbs_

utility::vector1< utility::file::FileName > PhDocking::unbound_pdbs_

private

Referenced by calc_unbound_score(), and set_unbound_pdbs().

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

src/apps/pilot/krishna/pH_docking.cc