zinc1_homodimer_design Class Reference

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::symmetry::SymmetricScoreFunctionOP	softrep_sym_scorefxn_
core::scoring::symmetry::SymmetricScoreFunctionOP	sym_scorefxn_
core::scoring::symmetry::SymmetricScoreFunctionOP	no_constraints_scorefxn_for_ddG_calc_
core::scoring::symmetry::SymmetricScoreFunctionOP	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::simple_moves::symmetry::SymPackRotamersMoverOP	sym_pack_mover_
protocols::simple_moves::symmetry::SymRotamerTrialsMoverOP	sym_rottrials_mover_
protocols::simple_moves::symmetry::SymMinMoverOP	softrep_min_mover_
protocols::simple_moves::symmetry::SymMinMoverOP	sc_min_mover_
protocols::simple_moves::symmetry::SymMinMoverOP	sc_bb_min_mover_
protocols::moves::MonteCarloOP	mc_
protocols::anchored_design::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::zinc1_homodimer_design ( )

inline

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

inline

virtual zinc1_homodimer_design::~zinc1_homodimer_design ( )

inlinevirtual

Member Function Documentation

virtual void zinc1_homodimer_design::apply ( Pose &  pose )

inlinevirtual

References utility::file::FileName::base(), gridsearch_rollmove_angles, nstruct_iterations, basic::options::option, basic::options::OptionKeys::broker::setup, basic::options::OptionKeys::mh::match::ss, and TR().

Referenced by src.protocols.jd2.RosettaScriptWrapper::apply_to_failure().

virtual void zinc1_homodimer_design::design_symmetric_homodimer_interface ( Pose &  pose )

inlinevirtual

References basic::options::OptionKeys::mc::mc, basic::options::OptionKeys::MonteCarlo::MonteCarlo, and TR().

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

inlinevirtual

virtual void zinc1_homodimer_design::gridsearch_rollmove_angles ( Pose &  pose )

inlinevirtual

References name, TR(), x(), y(), and z().

virtual void zinc1_homodimer_design::setup ( Pose &  pose )

inlinevirtual

References setup_movers().

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

inlinevirtual

References TR().

virtual void zinc1_homodimer_design::setup_metalsite_constraints ( Pose &  pose )

inlinevirtual

References basic::options::OptionKeys::constraints::constraints, fav_nat_bonus, clean_pdb_keep_ligand::nres, basic::options::option, TR(), and value.

virtual void zinc1_homodimer_design::setup_movemap_bb_chi ( Pose &  pose )

inlinevirtual

References TR().

virtual void zinc1_homodimer_design::setup_movers ( )

inlinevirtual

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

virtual void zinc1_homodimer_design::setup_output_tag ( )

inlinevirtual

References me.

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

inlinevirtual

References numeric::angle_of(), numeric::cross_product(), numeric::rotation_matrix(), and numeric::z_rotation_matrix().

virtual void zinc1_homodimer_design::setup_scorefunctions ( )

inlinevirtual

References pyrosetta::create_score_function, fav_nat_bonus, pyrosetta::get_score_function, basic::options::option, PyMOL_demo::scorefxn, basic::options::OptionKeys::frags::scoring::scoring, TR(), and value.

virtual void zinc1_homodimer_design::setup_taskfactory ( Pose &  pose )

inlinevirtual

References option, options, basic::options::OptionKeys::packing::resfile, app.delta_score_per_mutation::task, TR(), and basic::options::OptionKeys::inout::dbms::user.

Member Data Documentation

core::scoring::ScoreFunctionOP zinc1_homodimer_design::angle_scorefxn_

private

Real zinc1_homodimer_design::best_ddG_

private

Pose zinc1_homodimer_design::best_pose_

private

Pose zinc1_homodimer_design::centroid_

private

core::scoring::symmetry::SymmetricScoreFunctionOP zinc1_homodimer_design::centroid_scorefxn_for_ddG_calc_

private

core::scoring::ScoreFunctionOP zinc1_homodimer_design::dihed_scorefxn_

private

bool zinc1_homodimer_design::gridsearch_rollmove_angles_

private

Size zinc1_homodimer_design::highres_symmetric_design_cycles_

private

protocols::anchored_design::InterfaceAnalyzerMoverOP zinc1_homodimer_design::interface_analyzer_

private

core::kinematics::FoldTree zinc1_homodimer_design::interface_scorable_tree_

private

Size zinc1_homodimer_design::lowres_symmetric_design_cycles_

private

protocols::moves::MonteCarloOP zinc1_homodimer_design::mc_

private

core::scoring::ScoreFunctionOP zinc1_homodimer_design::metal_scorefxn_

private

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

private

core::scoring::symmetry::SymmetricScoreFunctionOP zinc1_homodimer_design::no_constraints_scorefxn_for_ddG_calc_

private

std::string zinc1_homodimer_design::output_tag_

private

std::string zinc1_homodimer_design::output_tag_base_

private

core::scoring::ScoreFunctionOP zinc1_homodimer_design::pair_scorefxn_

private

std::string zinc1_homodimer_design::pdbname_

private

std::string zinc1_homodimer_design::pdbname_base_

private

protocols::simple_moves::symmetry::SymMinMoverOP zinc1_homodimer_design::sc_bb_min_mover_

private

core::kinematics::MoveMapOP zinc1_homodimer_design::sc_bb_move_map_

private

protocols::simple_moves::symmetry::SymMinMoverOP zinc1_homodimer_design::sc_min_mover_

private

core::kinematics::MoveMapOP zinc1_homodimer_design::sc_move_map_

private

protocols::simple_moves::symmetry::SymMinMoverOP zinc1_homodimer_design::softrep_min_mover_

private

core::scoring::symmetry::SymmetricScoreFunctionOP zinc1_homodimer_design::softrep_sym_scorefxn_

private

Pose zinc1_homodimer_design::starting_centroid_pose_

private

Pose zinc1_homodimer_design::starting_fullatom_pose_

private

Pose zinc1_homodimer_design::starting_monomer_pose_

private

protocols::simple_moves::symmetry::SymPackRotamersMoverOP zinc1_homodimer_design::sym_pack_mover_

private

protocols::simple_moves::symmetry::SymRotamerTrialsMoverOP zinc1_homodimer_design::sym_rottrials_mover_

private

core::scoring::symmetry::SymmetricScoreFunctionOP zinc1_homodimer_design::sym_scorefxn_

private

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

private

protocols::rigid::RollMoverOP zinc1_homodimer_design::xmover_

private

protocols::rigid::RollMoverOP zinc1_homodimer_design::ymover_

private

protocols::rigid::RollMoverOP zinc1_homodimer_design::zmover_

private

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

• src/apps/public/design/zinc1_homodimer_design.cc