Inheritance diagram for zinc1_homodimer_design:

Public Member Functions
	zinc1_homodimer_design ()

	zinc1_homodimer_design (Size lowres_symmetric_design_cycles, Size highres_symmetric_design_cycles, bool gridsearch_rollmove_angles)

virtual	~zinc1_homodimer_design ()

virtual void	apply (Pose &pose)

virtual void	setup (Pose &pose)

virtual void	setup_output_tag ()

virtual void	setup_metalsite (Pose const &pose)

virtual void	setup_metalsite_constraints (Pose &pose)

virtual void	setup_taskfactory (Pose &pose)

virtual void	setup_scorefunctions ()

virtual void	setup_movemap_bb_chi (Pose &pose)

virtual void	setup_movers ()

virtual void	setup_rollmoving (Pose const &pose)

virtual void	gridsearch_rollmove_angles (Pose &pose)

virtual void	design_symmetric_homodimer_interface (Pose &pose)

virtual std::string	get_name () const

Private Attributes
Size	lowres_symmetric_design_cycles_

Size	highres_symmetric_design_cycles_

bool	gridsearch_rollmove_angles_

Pose	starting_monomer_pose_

Pose	centroid_

Pose	starting_centroid_pose_

Pose	starting_fullatom_pose_

utility::vector1< protocols::metal_interface::MetalSiteResidueOP >	msr_

core::pack::task::TaskFactoryCOP	taskfactory_

core::scoring::ScoreFunctionOP	softrep_sym_scorefxn_

core::scoring::ScoreFunctionOP	sym_scorefxn_

core::scoring::ScoreFunctionOP	no_constraints_scorefxn_for_ddG_calc_

core::scoring::ScoreFunctionOP	centroid_scorefxn_for_ddG_calc_

core::scoring::ScoreFunctionOP	metal_scorefxn_

core::scoring::ScoreFunctionOP	pair_scorefxn_

core::scoring::ScoreFunctionOP	angle_scorefxn_

core::scoring::ScoreFunctionOP	dihed_scorefxn_

core::kinematics::FoldTree	interface_scorable_tree_

core::kinematics::MoveMapOP	sc_move_map_

core::kinematics::MoveMapOP	sc_bb_move_map_

protocols::minimization_packing::PackRotamersMoverOP	sym_pack_mover_

protocols::minimization_packing::RotamerTrialsMoverOP	sym_rottrials_mover_

protocols::minimization_packing::MinMoverOP	softrep_min_mover_

protocols::minimization_packing::MinMoverOP	sc_min_mover_

protocols::minimization_packing::MinMoverOP	sc_bb_min_mover_

protocols::moves::MonteCarloOP	mc_

protocols::analysis::InterfaceAnalyzerMoverOP	interface_analyzer_

protocols::rigid::RollMoverOP	zmover_

protocols::rigid::RollMoverOP	ymover_

protocols::rigid::RollMoverOP	xmover_

Pose	best_pose_

Real	best_ddG_

std::string	output_tag_

std::string	output_tag_base_

std::string	pdbname_

std::string	pdbname_base_

Constructor & Destructor Documentation

◆ zinc1_homodimer_design() [1/2]

zinc1_homodimer_design::zinc1_homodimer_design ( )

inline

◆ zinc1_homodimer_design() [2/2]

zinc1_homodimer_design::zinc1_homodimer_design	(	Size	lowres_symmetric_design_cycles,
		Size	highres_symmetric_design_cycles,
		bool	gridsearch_rollmove_angles
	)

inline

◆ ~zinc1_homodimer_design()

virtual zinc1_homodimer_design::~zinc1_homodimer_design ( )

inlinevirtual

Member Function Documentation

◆ apply()

virtual void zinc1_homodimer_design::apply ( Pose & pose )

inlinevirtual

References utility::file::FileName::base(), gridsearch_rollmove_angles, kmeans_adaptive_kernel_density_bb_dependent_rotlib::n, nstruct_iterations, basic::options::option, beta_nonlocal::pose, basic::options::OptionKeys::broker::setup, challenge::ss, and TR.

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

◆ design_symmetric_homodimer_interface()

virtual void zinc1_homodimer_design::design_symmetric_homodimer_interface ( Pose & pose )

inlinevirtual

References create_a3b_hbs::i, beta_nonlocal::pose, and TR.

◆ get_name()

virtual std::string zinc1_homodimer_design::get_name ( ) const

inlinevirtual

◆ gridsearch_rollmove_angles()

virtual void zinc1_homodimer_design::gridsearch_rollmove_angles ( Pose & pose )

inlinevirtual

References beta_nonlocal::pose, TR, x, predPRE::y, and predPRE::z.

◆ setup()

virtual void zinc1_homodimer_design::setup ( Pose & pose )

inlinevirtual

References beta_nonlocal::pose, and setup_movers().

Referenced by pyrosetta.distributed.tasks.taskbase.TaskBase::maybe_setup().

◆ setup_metalsite()

virtual void zinc1_homodimer_design::setup_metalsite ( Pose const & pose )

inlinevirtual

References beta_nonlocal::pose, and TR.

◆ setup_metalsite_constraints()

virtual void zinc1_homodimer_design::setup_metalsite_constraints ( Pose & pose )

inlinevirtual

References basic::options::OptionKeys::constraints::constraints, erraser_util::copy(), fav_nat_bonus, create_a3b_hbs::i, create_a3b_hbs::nres, basic::options::option, beta_nonlocal::pose, TR, and value.

◆ setup_movemap_bb_chi()

virtual void zinc1_homodimer_design::setup_movemap_bb_chi ( Pose & pose )

inlinevirtual

References TR.

◆ setup_movers()

virtual void zinc1_homodimer_design::setup_movers ( )

inlinevirtual

References basic::options::OptionKeys::symmetry::symmetry, and TR.

◆ setup_output_tag()

virtual void zinc1_homodimer_design::setup_output_tag ( )

inlinevirtual

References localrmsd::output_name.

◆ setup_rollmoving()

virtual void zinc1_homodimer_design::setup_rollmoving ( Pose const & pose )

inlinevirtual

References numeric::angle_of(), chain_begin(), chain_end(), vector::cross_product(), beta_nonlocal::pose, numeric::rotation_matrix(), and numeric::z_rotation_matrix().

◆ setup_scorefunctions()

virtual void zinc1_homodimer_design::setup_scorefunctions ( )

inlinevirtual

References pyrosetta::create_score_function, fav_nat_bonus, basic::options::option, oop_conformations::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, TR, and value.

◆ setup_taskfactory()

virtual void zinc1_homodimer_design::setup_taskfactory ( Pose & pose )

inlinevirtual

References create_a3b_hbs::i, option, beta_nonlocal::pose, basic::options::OptionKeys::packing::resfile, vancomycin::task, TR, and basic::options::OptionKeys::inout::dbms::user.

Member Data Documentation

◆ angle_scorefxn_

core::scoring::ScoreFunctionOP zinc1_homodimer_design::angle_scorefxn_

private

◆ best_ddG_

Real zinc1_homodimer_design::best_ddG_

private

◆ best_pose_

Pose zinc1_homodimer_design::best_pose_

private

◆ centroid_

Pose zinc1_homodimer_design::centroid_

private

◆ centroid_scorefxn_for_ddG_calc_

core::scoring::ScoreFunctionOP zinc1_homodimer_design::centroid_scorefxn_for_ddG_calc_

private

◆ dihed_scorefxn_

core::scoring::ScoreFunctionOP zinc1_homodimer_design::dihed_scorefxn_

private

◆ gridsearch_rollmove_angles_

bool zinc1_homodimer_design::gridsearch_rollmove_angles_

private

◆ highres_symmetric_design_cycles_

Size zinc1_homodimer_design::highres_symmetric_design_cycles_

private

◆ interface_analyzer_

protocols::analysis::InterfaceAnalyzerMoverOP zinc1_homodimer_design::interface_analyzer_

private

◆ interface_scorable_tree_

core::kinematics::FoldTree zinc1_homodimer_design::interface_scorable_tree_

private

◆ lowres_symmetric_design_cycles_

Size zinc1_homodimer_design::lowres_symmetric_design_cycles_

private

◆ mc_

protocols::moves::MonteCarloOP zinc1_homodimer_design::mc_

private

◆ metal_scorefxn_

core::scoring::ScoreFunctionOP zinc1_homodimer_design::metal_scorefxn_

private

◆ msr_

utility::vector1< protocols::metal_interface::MetalSiteResidueOP > zinc1_homodimer_design::msr_

private

◆ no_constraints_scorefxn_for_ddG_calc_

core::scoring::ScoreFunctionOP zinc1_homodimer_design::no_constraints_scorefxn_for_ddG_calc_

private

◆ output_tag_

std::string zinc1_homodimer_design::output_tag_

private

◆ output_tag_base_

std::string zinc1_homodimer_design::output_tag_base_

private

◆ pair_scorefxn_

core::scoring::ScoreFunctionOP zinc1_homodimer_design::pair_scorefxn_

private

◆ pdbname_

std::string zinc1_homodimer_design::pdbname_

private

◆ pdbname_base_

std::string zinc1_homodimer_design::pdbname_base_

private

◆ sc_bb_min_mover_

protocols::minimization_packing::MinMoverOP zinc1_homodimer_design::sc_bb_min_mover_

private

◆ sc_bb_move_map_

core::kinematics::MoveMapOP zinc1_homodimer_design::sc_bb_move_map_

private

◆ sc_min_mover_

protocols::minimization_packing::MinMoverOP zinc1_homodimer_design::sc_min_mover_

private

◆ sc_move_map_

core::kinematics::MoveMapOP zinc1_homodimer_design::sc_move_map_

private

◆ softrep_min_mover_

protocols::minimization_packing::MinMoverOP zinc1_homodimer_design::softrep_min_mover_

private

◆ softrep_sym_scorefxn_

core::scoring::ScoreFunctionOP zinc1_homodimer_design::softrep_sym_scorefxn_

private

◆ starting_centroid_pose_

Pose zinc1_homodimer_design::starting_centroid_pose_

private

◆ starting_fullatom_pose_

Pose zinc1_homodimer_design::starting_fullatom_pose_

private

◆ starting_monomer_pose_

Pose zinc1_homodimer_design::starting_monomer_pose_

private

◆ sym_pack_mover_

protocols::minimization_packing::PackRotamersMoverOP zinc1_homodimer_design::sym_pack_mover_

private

◆ sym_rottrials_mover_

protocols::minimization_packing::RotamerTrialsMoverOP zinc1_homodimer_design::sym_rottrials_mover_

private

◆ sym_scorefxn_

core::scoring::ScoreFunctionOP zinc1_homodimer_design::sym_scorefxn_

private

◆ taskfactory_

core::pack::task::TaskFactoryCOP zinc1_homodimer_design::taskfactory_

private

◆ xmover_

protocols::rigid::RollMoverOP zinc1_homodimer_design::xmover_

private

◆ ymover_

protocols::rigid::RollMoverOP zinc1_homodimer_design::ymover_

private

◆ zmover_

protocols::rigid::RollMoverOP zinc1_homodimer_design::zmover_

private

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

src/apps/public/design/zinc1_homodimer_design.cc

Public Member Functions

Private Attributes

Constructor & Destructor Documentation

◆ zinc1_homodimer_design() [1/2]

◆ zinc1_homodimer_design() [2/2]

◆ ~zinc1_homodimer_design()

Member Function Documentation

◆ apply()

◆ design_symmetric_homodimer_interface()

◆ get_name()

◆ gridsearch_rollmove_angles()

◆ setup()

◆ setup_metalsite()

◆ setup_metalsite_constraints()

◆ setup_movemap_bb_chi()

◆ setup_movers()

◆ setup_output_tag()

◆ setup_rollmoving()

◆ setup_scorefunctions()

◆ setup_taskfactory()

Member Data Documentation

◆ angle_scorefxn_

◆ best_ddG_

◆ best_pose_

◆ centroid_

◆ centroid_scorefxn_for_ddG_calc_

◆ dihed_scorefxn_

◆ gridsearch_rollmove_angles_

◆ highres_symmetric_design_cycles_

◆ interface_analyzer_

◆ interface_scorable_tree_

◆ lowres_symmetric_design_cycles_

◆ mc_

◆ metal_scorefxn_

◆ msr_

◆ no_constraints_scorefxn_for_ddG_calc_

◆ output_tag_

◆ output_tag_base_

◆ pair_scorefxn_

◆ pdbname_

◆ pdbname_base_

◆ sc_bb_min_mover_

◆ sc_bb_move_map_

◆ sc_min_mover_

◆ sc_move_map_

◆ softrep_min_mover_

◆ softrep_sym_scorefxn_

◆ starting_centroid_pose_

◆ starting_fullatom_pose_

◆ starting_monomer_pose_

◆ sym_pack_mover_

◆ sym_rottrials_mover_

◆ sym_scorefxn_

◆ taskfactory_

◆ xmover_

◆ ymover_

◆ zmover_