#include <Ubiquitin_E2C_Modeler.hh>

Inheritance diagram for protocols::ub_e2c::ubi_e2c_modeler:

Collaboration diagram for protocols::ub_e2c::ubi_e2c_modeler:

Public Member Functions
	ubi_e2c_modeler ()

	~ubi_e2c_modeler ()

void	set_default ()

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

virtual std::string	get_name () const
	Each derived class must specify its name. The class name. More...

virtual protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected. More...

void	setup_key_residues (const core::pose::Pose &pose_in)

void	setup_move_maps ()

void	setup_complex_fold_tree (core::pose::Pose &pose_in, bool trim=false)

void	initial_cter_perturbation (core::pose::Pose &pose_in)

void	setup_simple_fold_tree (core::Size jumppoint1, core::Size cutpoint, core::Size jumppoint2, core::Size nres, core::pose::Pose &pose_in)

void	trim_cter (core::pose::Pose &pose_in)

void	restore_cter (core::pose::Pose &pose_in, core::pose::Pose without_cter)

void	init_k48r_perturbation (core::pose::Pose &pose_in)

void	init_d77_perturbation (core::pose::Pose &pose_in)

core::Real	initial_perturbation (core::pose::Pose &pose_in)

core::Real	centroid_mode_perturbation (core::pose::Pose &pose_in)

core::Real	fullatom_mode_perturbation (core::pose::Pose &pose_in)

void	initial_repack (core::pose::Pose &pose_in)

void	setup_packer_task (core::pose::Pose &pose_in)

void	restrict_to_interfacial_loop_packing (core::pose::Pose &pose_in)

void	set_e2g2_diubi_fold_tree (core::pose::Pose &pose_in)

core::Real	calc_interaction_energy (const core::pose::Pose &pose_in, bool dimer=true)

core::Real	CSP_fraction (const core::pose::Pose &pose_in, bool non_CSP=false, bool trim=false, bool swap=false)

bool	centroid_filter (core::pose::Pose &pose_in)

bool	fullatom_filter (core::pose::Pose &pose_in)

core::Real	calc_Lrmsd (const core::pose::Pose &pose_in, const core::pose::Pose &native_pose, core::Size ubiquitin)

void	evaluate_native (core::pose::Pose &pose_in)

void	optimize_cov_bond (core::pose::Pose &pose_in)

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

virtual void	apply (core::io::serialization::PipeMap &pmap)

virtual void	parse_state (SerializableState const &state)

virtual void	parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)

virtual void	save_state (SerializableState &state)

	Mover (std::string const &type_name)
	sets the type for a mover; name_ has been removed (2010/05/14) More...

	Mover (Mover const &other)

Mover &	operator= (Mover const &other)
	assignment operator More...

virtual core::Real	last_proposal_density_ratio ()

std::string const &	type () const

std::string	get_current_tag () const
	A tag is a unique identifier used to identify structures produced by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor. More...

void	set_current_tag (std::string const &new_tag)

virtual void	set_input_pose (PoseCOP pose)
	setter for poses contained for rms More...

virtual void	set_native_pose (PoseCOP pose)
	setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...

PoseCOP	get_input_pose () const

PoseCOP	get_native_pose () const

virtual void	test_move (Pose &pose)
	: Unit test support function. Apply one move to a given pose. Allows extra test specific functions to be called before applying More...

void	type (const std::string &type_in)

virtual void	parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

std::string	get_type () const

MoverStatus	get_last_move_status () const
	end parser interface, start Job Distributor interface///////////// More...

void	reset_status ()
	resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s. More...

virtual core::pose::PoseOP	get_additional_output ()
	Mechanism by which a mover may return multiple output poses from a single input pose. More...

virtual void	clear_info ()
	Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file. More...

virtual Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual bool	reinitialize_for_each_job () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be freshly regenerated on each use. More...

virtual bool	reinitialize_for_new_input () const
	this function informs the job distributor (august 08 vintage) whether this object needs to be regenerated when the input pose is about to change (for example, if the mover has special code on the first apply() that is only valid for that one input pose). More...

virtual MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...

void	set_current_job (protocols::jobdist::BasicJobCOP job)

jobdist::BasicJobCOP	get_current_job () const

Private Member Functions
void	compute_trim_CSPs ()

void	compute_swap_trim_CSPs ()

void	assign_CSPs (const core::pose::Pose &pose_in)

void	assign_non_CSPs (const core::pose::Pose &pose_in)

void	monoub_assign_CSPs (const core::pose::Pose &pose_in)

void	monoub_apply (core::pose::Pose &pose_in)

void	monoub_setup_key_residues (const core::pose::Pose &pose_in)

void	monoub_setup_move_maps ()

void	monoub_fold_tree (core::pose::Pose &pose_in)

void	monoub_initial_cter_perturbation (core::pose::Pose &pose_in)

void	monoub_first_perturbation (core::pose::Pose &pose_in)

void	monoub_initial_perturbation (core::pose::Pose &pose_in)

void	monoub_centroid_mode_perturbation (core::pose::Pose &pose_in)

void	monoub_fullatom_mode_perturbation (core::pose::Pose &pose_in)

core::Real	monoub_calc_interaction_energy (const core::pose::Pose &pose_in)

core::Real	monoub_CSP_fraction (const core::pose::Pose &pose_in)

bool	monoub_centroid_filter (core::pose::Pose &pose_in)

bool	monoub_fullatom_filter (core::pose::Pose &pose_in)

core::Real	monoub_calc_Lrmsd (const core::pose::Pose &pose_in, const core::pose::Pose &native_pose)

Private Attributes
core::Size	e2_ctr_of_mass_

core::Size	k48r_ctr_of_mass_

core::Size	d77_ctr_of_mass_

core::Size	e2_end_

core::Size	k48r_end_

core::Size	d77_end_

core::Size	k48r_48_lys_

core::Size	d77_48_lys_

core::Size	k48r_trim_end_

core::Size	d77_trim_end_

core::Size	d77_trim_ctr_mass_

bool	k48r_swap_

core::kinematics::MoveMapOP	k48r_docking_map_

core::kinematics::MoveMapOP	d77_docking_map_

core::kinematics::MoveMapOP	docking_map_

core::kinematics::MoveMapOP	flex_cter_map_

core::kinematics::MoveMapOP	all_dof_map_

core::kinematics::MoveMapOP	init_k48r_docking_map_

core::kinematics::MoveMapOP	init_d77_docking_map_

core::kinematics::MoveMapOP	init_docking_map_

core::kinematics::MoveMapOP	init_flex_cter_map_

core::kinematics::MoveMapOP	init_all_dof_map_

core::Size const	e2_k48r_jump_

core::Size const	e2_d77_jump_

core::Real const	max_k48_cter_dist_

core::Real const	temperature_

std::map< std::string, core::Real >	score_map_

core::Size const	flex_cter_

core::Size const	CA

core::Size const	max_repeats_

core::Real	fullatom_constraint_cutoff_

core::Real const	centroid_allowed_CSP_fraction_

core::Real const	fullatom_allowed_CSP_fraction_

core::Real const	centroid_CSP_weight_

core::Real const	centroid_non_CSP_weight_

core::Real const	fullatom_CSP_weight_

core::Real const	fullatom_non_CSP_weight_

core::Real const	cen_vdw_

core::Real const	cen_constraint_

core::Real const	full_vdw_

core::Real	full_constraint_

bool const	refinement_mode_

bool const	cov_bond_only_flag_

bool const	monoub_mode_

bool const	higher_d77_pert_mode_

core::Size	k48r_48k_mtsl_

core::Size	d77_75g_mtsl_

bool	passed_centroid_filter_

bool	passed_fullatom_filter_

bool	applied_fullatom_pert_

core::pack::task::TaskFactoryOP	tf_

core::pack::task::TaskFactoryOP	init_task_factory_

core::Real	min_tolerance_

std::string	min_type_

bool	nb_list_

utility::vector1< core::Size >	CSP_

utility::vector1< core::Size >	CSP_trim_

utility::vector1< core::Size >	CSP_swap_trim_

utility::vector1< core::Size >	non_CSP_

utility::vector1< core::Size >	non_CSP_trim_

utility::vector1< core::Size >	non_CSP_swap_trim_

core::scoring::ScoreFunctionOP	dock_lowres_scorefxn_

core::scoring::ScoreFunctionOP	lowres_scorefxn_

core::scoring::ScoreFunctionOP	dock_lowres_cst_scorefxn_

core::scoring::ScoreFunctionOP	lowres_cst_scorefxn_

core::scoring::ScoreFunctionOP	pack_scorefxn_

core::scoring::ScoreFunctionOP	dockfa_scorefxn_

core::scoring::ScoreFunctionOP	dockfa_cst_scorefxn_

core::scoring::ScoreFunctionOP	dockfa_min_scorefxn_

core::scoring::ScoreFunctionOP	dockfa_cst_min_scorefxn_

core::scoring::ScoreFunctionOP	pack_cst_scorefxn_

core::scoring::ScoreFunctionOP	output_cen_scorefxn_

core::scoring::ScoreFunctionOP	output_full_scorefxn_

core::Size	monoub_end_

core::Size	monoub_ctr_of_mass_

core::kinematics::MoveMapOP	monoub_all_dof_map_

core::kinematics::MoveMapOP	monoub_docking_map_

core::kinematics::MoveMapOP	monoub_flex_cter_map_

core::kinematics::MoveMapOP	init_monoub_all_dof_map_

core::kinematics::MoveMapOP	init_monoub_docking_map_

core::kinematics::MoveMapOP	init_monoub_flex_cter_map_

Additional Inherited Members
Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr	TagPtr

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

typedef std::list< std::string >	Strings

Static Public Member Functions inherited from protocols::moves::Mover
static std::string	name ()

static void	register_options ()
	overload this static method if you access options within the mover. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...

Protected Member Functions inherited from protocols::moves::Mover
void	set_last_move_status (MoverStatus status)
	nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...

Detailed Description

Definition at line 35 of file Ubiquitin_E2C_Modeler.hh.

Constructor & Destructor Documentation

protocols::ub_e2c::ubi_e2c_modeler::ubi_e2c_modeler ( )

Definition at line 110 of file Ubiquitin_E2C_Modeler.cc.

References set_default().

Referenced by clone().

protocols::ub_e2c::ubi_e2c_modeler::~ubi_e2c_modeler ( )

Definition at line 137 of file Ubiquitin_E2C_Modeler.cc.

Member Function Documentation

void protocols::ub_e2c::ubi_e2c_modeler::apply ( core::pose::Pose & pose_in)

virtual

Implements protocols::moves::Mover.

Definition at line 628 of file Ubiquitin_E2C_Modeler.cc.

References applied_fullatom_pert_, protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), assign_CSPs(), calc_Lrmsd(), core::chemical::CENTROID, centroid_filter(), centroid_mode_perturbation(), cov_bond_only_flag_, core::pose::Pose::data(), e2_d77_jump_, e2_k48r_jump_, core::chemical::FA_STANDARD, flex_cter_, fullatom_filter(), fullatom_mode_perturbation(), lowres_cst_scorefxn_, max_repeats_, monoub_apply(), monoub_mode_, protocols::jd2::ScoreMap::nonzero_energies(), optimize_cov_bond(), output_cen_scorefxn_, output_full_scorefxn_, pack_cst_scorefxn_, passed_centroid_filter_, passed_fullatom_filter_, refinement_mode_, core::pose::datacache::CacheableDataType::SCORE_MAP, score_map_, setup_key_residues(), setup_move_maps(), protocols::medal::to_centroid(), and protocols::TR().

void protocols::ub_e2c::ubi_e2c_modeler::assign_CSPs ( const core::pose::Pose & pose_in)

private

Definition at line 315 of file Ubiquitin_E2C_Modeler.cc.

References assign_non_CSPs(), compute_swap_trim_CSPs(), compute_trim_CSPs(), CSP_, core::pose::Pose::pdb_info(), and protocols::TR().

Referenced by apply().

void protocols::ub_e2c::ubi_e2c_modeler::assign_non_CSPs ( const core::pose::Pose & pose_in)

private

Definition at line 407 of file Ubiquitin_E2C_Modeler.cc.

References non_CSP_, core::pose::Pose::pdb_info(), and protocols::TR().

Referenced by assign_CSPs().

Real protocols::ub_e2c::ubi_e2c_modeler::calc_interaction_energy	(	const core::pose::Pose &	pose_in,
		bool	dimer = `true`
	)

Definition at line 1821 of file Ubiquitin_E2C_Modeler.cc.

References core::scoring::ScoreFunctionFactory::create_score_function(), e2_d77_jump_, e2_k48r_jump_, core::pose::Pose::is_fullatom(), set_e2g2_diubi_fold_tree(), setup_complex_fold_tree(), and protocols::TR().

Referenced by fullatom_filter().

core::Real protocols::ub_e2c::ubi_e2c_modeler::calc_Lrmsd	(	const core::pose::Pose &	pose_in,
		const core::pose::Pose &	native_pose,
		core::Size	ubiquitin
	)

Definition at line 2117 of file Ubiquitin_E2C_Modeler.cc.

References d77_end_, e2_d77_jump_, e2_end_, e2_k48r_jump_, flex_cter_, core::scoring::is_protein_CA(), k48r_end_, core::scoring::rmsd_no_super_subset(), and core::pose::Pose::total_residue().

Referenced by apply().

bool protocols::ub_e2c::ubi_e2c_modeler::centroid_filter ( core::pose::Pose & pose_in)

Definition at line 1953 of file Ubiquitin_E2C_Modeler.cc.

References core::scoring::atom_pair_constraint, cen_constraint_, centroid_allowed_CSP_fraction_, CSP_fraction(), dock_lowres_cst_scorefxn_, core::pose::Pose::energies(), fullatom_constraint_cutoff_, max_k48_cter_dist_, score_map_, core::scoring::Energies::total_energies(), and protocols::TR().

Referenced by apply().

Real protocols::ub_e2c::ubi_e2c_modeler::centroid_mode_perturbation ( core::pose::Pose & pose_in)

protocols::moves::MoverOP protocols::ub_e2c::ubi_e2c_modeler::clone ( ) const

virtual

clone has to be overridden only if clone invocation is expected.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

Definition at line 140 of file Ubiquitin_E2C_Modeler.cc.

References ubi_e2c_modeler().

void protocols::ub_e2c::ubi_e2c_modeler::compute_swap_trim_CSPs ( )

private

Definition at line 286 of file Ubiquitin_E2C_Modeler.cc.

References CSP_, CSP_swap_trim_, d77_end_, d77_trim_end_, e2_end_, flex_cter_, k48r_end_, k48r_trim_end_, non_CSP_, non_CSP_swap_trim_, and protocols::TR().

Referenced by assign_CSPs().

void protocols::ub_e2c::ubi_e2c_modeler::compute_trim_CSPs ( )

private

Definition at line 263 of file Ubiquitin_E2C_Modeler.cc.

References CSP_, CSP_trim_, e2_end_, flex_cter_, k48r_end_, non_CSP_, non_CSP_trim_, and protocols::TR().

Referenced by assign_CSPs().

core::Real protocols::ub_e2c::ubi_e2c_modeler::CSP_fraction	(	const core::pose::Pose &	pose_in,
		bool	non_CSP = `false`,
		bool	trim = `false`,
		bool	swap = `false`
	)

void protocols::ub_e2c::ubi_e2c_modeler::evaluate_native ( core::pose::Pose & pose_in)

Definition at line 2151 of file Ubiquitin_E2C_Modeler.cc.

References protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), core::chemical::CENTROID, core::scoring::ScoreFunctionFactory::create_score_function(), core::pose::Pose::data(), e2_d77_jump_, e2_k48r_jump_, core::chemical::FA_STANDARD, core::pose::datacache::CacheableDataType::INTERFACE_INFO, set_e2g2_diubi_fold_tree(), setup_complex_fold_tree(), setup_key_residues(), setup_packer_task(), tf_, protocols::medal::to_centroid(), and protocols::TR().

bool protocols::ub_e2c::ubi_e2c_modeler::fullatom_filter ( core::pose::Pose & pose_in)

Definition at line 2031 of file Ubiquitin_E2C_Modeler.cc.

References core::scoring::atom_pair_constraint, calc_interaction_energy(), CSP_fraction(), dockfa_cst_scorefxn_, core::pose::Pose::energies(), full_constraint_, fullatom_allowed_CSP_fraction_, fullatom_constraint_cutoff_, max_k48_cter_dist_, refinement_mode_, score_map_, core::scoring::Energies::total_energies(), and protocols::TR().

Referenced by apply().

Real protocols::ub_e2c::ubi_e2c_modeler::fullatom_mode_perturbation ( core::pose::Pose & pose_in)

std::string protocols::ub_e2c::ubi_e2c_modeler::get_name ( ) const

virtual

Each derived class must specify its name. The class name.

Implements protocols::moves::Mover.

Definition at line 765 of file Ubiquitin_E2C_Modeler.cc.

void protocols::ub_e2c::ubi_e2c_modeler::init_d77_perturbation ( core::pose::Pose & pose_in)

Definition at line 1267 of file Ubiquitin_E2C_Modeler.cc.

References protocols::simple_moves::SwitchResidueTypeSetMover::apply(), core::chemical::CENTROID, core::pose::Pose::copy_segment(), d77_trim_end_, e2_end_, init_k48r_perturbation(), k48r_trim_end_, protocols::medal::to_centroid(), and protocols::TR().

Referenced by initial_perturbation().

void protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation ( core::pose::Pose & pose_in)

Definition at line 1115 of file Ubiquitin_E2C_Modeler.cc.

References protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::docking::DockingSlideIntoContact::apply(), protocols::rigid::RigidBodyPerturbMover::apply(), protocols::rigid::RigidBodySpinMover::apply(), core::chemical::CENTROID, centroid_CSP_weight_, centroid_non_CSP_weight_, core::pose::Pose::copy_segment(), CSP_fraction(), d77_trim_ctr_mass_, d77_trim_end_, core::pose::Pose::data(), dock_lowres_scorefxn_, docking, e2_ctr_of_mass_, e2_d77_jump_, e2_end_, e2_k48r_jump_, higher_d77_pert_mode_, core::pose::datacache::CacheableDataType::INTERFACE_INFO, k48r_ctr_of_mass_, k48r_swap_, k48r_trim_end_, protocols::rigid::random, protocols::geometry::residue_center_of_mass(), setup_complex_fold_tree(), setup_simple_fold_tree(), temperature_, protocols::medal::to_centroid(), and protocols::TR().

Referenced by init_d77_perturbation(), and initial_perturbation().

void protocols::ub_e2c::ubi_e2c_modeler::initial_cter_perturbation ( core::pose::Pose & pose_in)

Definition at line 949 of file Ubiquitin_E2C_Modeler.cc.

References core::pose::Pose::conformation(), d77_end_, flex_cter_, core::conformation::idealize_position(), k48r_end_, lowres_cst_scorefxn_, min_tolerance_, nb_list_, core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), setup_complex_fold_tree(), temperature_, and protocols::TR().

Referenced by initial_perturbation().

Real protocols::ub_e2c::ubi_e2c_modeler::initial_perturbation ( core::pose::Pose & pose_in)

Definition at line 1306 of file Ubiquitin_E2C_Modeler.cc.

References CA, d77_48_lys_, core::pose::Pose::data(), docking, e2_d77_jump_, e2_k48r_jump_, init_d77_perturbation(), init_k48r_perturbation(), initial_cter_perturbation(), core::pose::datacache::CacheableDataType::INTERFACE_INFO, k48r_end_, k48r_swap_, core::pose::Pose::residue(), restore_cter(), protocols::TR(), trim_cter(), and core::conformation::Residue::xyz().

Referenced by centroid_mode_perturbation().

void protocols::ub_e2c::ubi_e2c_modeler::initial_repack ( core::pose::Pose & pose_in)

Definition at line 1692 of file Ubiquitin_E2C_Modeler.cc.

References pack_scorefxn_, refinement_mode_, setup_packer_task(), temperature_, tf_, and protocols::TR().

Referenced by fullatom_mode_perturbation(), and monoub_fullatom_mode_perturbation().

void protocols::ub_e2c::ubi_e2c_modeler::monoub_apply ( core::pose::Pose & pose_in)

private

Definition at line 2443 of file Ubiquitin_E2C_Modeler.cc.

References applied_fullatom_pert_, protocols::simple_moves::SwitchResidueTypeSetMover::apply(), protocols::simple_moves::ReturnSidechainMover::apply(), core::chemical::CENTROID, core::pose::Pose::data(), core::chemical::FA_STANDARD, lowres_cst_scorefxn_, max_repeats_, monoub_assign_CSPs(), monoub_calc_Lrmsd(), monoub_centroid_filter(), monoub_centroid_mode_perturbation(), monoub_fullatom_filter(), monoub_fullatom_mode_perturbation(), monoub_setup_key_residues(), monoub_setup_move_maps(), protocols::jd2::ScoreMap::nonzero_energies(), output_cen_scorefxn_, output_full_scorefxn_, pack_cst_scorefxn_, passed_centroid_filter_, passed_fullatom_filter_, core::pose::datacache::CacheableDataType::SCORE_MAP, score_map_, protocols::medal::to_centroid(), and protocols::TR().

Referenced by apply().

void protocols::ub_e2c::ubi_e2c_modeler::monoub_assign_CSPs ( const core::pose::Pose & pose_in)

private

Definition at line 2371 of file Ubiquitin_E2C_Modeler.cc.

References CSP_, core::pose::Pose::pdb_info(), and protocols::TR().

Referenced by monoub_apply().

Real protocols::ub_e2c::ubi_e2c_modeler::monoub_calc_interaction_energy ( const core::pose::Pose & pose_in)

private

Definition at line 3032 of file Ubiquitin_E2C_Modeler.cc.

References core::scoring::ScoreFunctionFactory::create_score_function(), core::pose::Pose::is_fullatom(), monoub_fold_tree(), and protocols::TR().

Referenced by monoub_fullatom_filter().

core::Real protocols::ub_e2c::ubi_e2c_modeler::monoub_calc_Lrmsd	(	const core::pose::Pose &	pose_in,
		const core::pose::Pose &	native_pose
	)

private

Definition at line 3226 of file Ubiquitin_E2C_Modeler.cc.

References e2_end_, core::scoring::is_protein_CA(), monoub_end_, and core::scoring::rmsd_no_super_subset().

Referenced by monoub_apply().

bool protocols::ub_e2c::ubi_e2c_modeler::monoub_centroid_filter ( core::pose::Pose & pose_in)

private

Definition at line 3105 of file Ubiquitin_E2C_Modeler.cc.

References core::scoring::atom_pair_constraint, cen_constraint_, centroid_allowed_CSP_fraction_, dock_lowres_cst_scorefxn_, core::pose::Pose::energies(), fullatom_constraint_cutoff_, monoub_CSP_fraction(), score_map_, core::scoring::Energies::total_energies(), and protocols::TR().

Referenced by monoub_apply().

void protocols::ub_e2c::ubi_e2c_modeler::monoub_centroid_mode_perturbation ( core::pose::Pose & pose_in)

private

Definition at line 2808 of file Ubiquitin_E2C_Modeler.cc.

References centroid_CSP_weight_, docking, lowres_cst_scorefxn_, min_tolerance_, monoub_CSP_fraction(), monoub_flex_cter_map_, monoub_fold_tree(), monoub_initial_perturbation(), nb_list_, protocols::rigid::random, temperature_, and protocols::TR().

Referenced by monoub_apply().

core::Real protocols::ub_e2c::ubi_e2c_modeler::monoub_CSP_fraction ( const core::pose::Pose & pose_in)

private

Definition at line 3068 of file Ubiquitin_E2C_Modeler.cc.

References protocols::scoring::Interface::calculate(), CSP_, CSP_fraction(), protocols::scoring::Interface::distance(), protocols::scoring::Interface::is_interface(), and core::pose::Pose::total_residue().

Referenced by monoub_centroid_filter(), monoub_centroid_mode_perturbation(), monoub_first_perturbation(), monoub_fullatom_filter(), and monoub_fullatom_mode_perturbation().

void protocols::ub_e2c::ubi_e2c_modeler::monoub_first_perturbation ( core::pose::Pose & pose_in)

private

Definition at line 2724 of file Ubiquitin_E2C_Modeler.cc.

References protocols::simple_moves::SwitchResidueTypeSetMover::apply(), core::chemical::CENTROID, centroid_CSP_weight_, core::pose::Pose::data(), docking, core::pose::datacache::CacheableDataType::INTERFACE_INFO, monoub_CSP_fraction(), protocols::rigid::random, temperature_, protocols::medal::to_centroid(), and protocols::TR().

Referenced by monoub_initial_perturbation().

void protocols::ub_e2c::ubi_e2c_modeler::monoub_fold_tree ( core::pose::Pose & pose_in)

private

Definition at line 2624 of file Ubiquitin_E2C_Modeler.cc.

References e2_ctr_of_mass_, e2_end_, core::pose::Pose::fold_tree(), monoub_ctr_of_mass_, monoub_end_, and protocols::TR().

Referenced by monoub_calc_interaction_energy(), and monoub_centroid_mode_perturbation().

bool protocols::ub_e2c::ubi_e2c_modeler::monoub_fullatom_filter ( core::pose::Pose & pose_in)

private

Definition at line 3171 of file Ubiquitin_E2C_Modeler.cc.

References core::scoring::atom_pair_constraint, dockfa_cst_scorefxn_, core::pose::Pose::energies(), full_constraint_, fullatom_allowed_CSP_fraction_, fullatom_constraint_cutoff_, monoub_calc_interaction_energy(), monoub_CSP_fraction(), refinement_mode_, score_map_, core::scoring::Energies::total_energies(), and protocols::TR().

Referenced by monoub_apply().

void protocols::ub_e2c::ubi_e2c_modeler::monoub_fullatom_mode_perturbation ( core::pose::Pose & pose_in)

private

Definition at line 2905 of file Ubiquitin_E2C_Modeler.cc.

References applied_fullatom_pert_, dockfa_cst_min_scorefxn_, dockfa_cst_scorefxn_, fullatom_CSP_weight_, initial_repack(), min_tolerance_, min_type_, monoub_all_dof_map_, monoub_CSP_fraction(), monoub_docking_map_, monoub_flex_cter_map_, nb_list_, pack_scorefxn_, protocols::rigid::partner_downstream, protocols::rigid::random, temperature_, tf_, and protocols::TR().

Referenced by monoub_apply().

void protocols::ub_e2c::ubi_e2c_modeler::monoub_initial_cter_perturbation ( core::pose::Pose & pose_in)

private

Definition at line 2652 of file Ubiquitin_E2C_Modeler.cc.

References core::pose::Pose::conformation(), flex_cter_, core::conformation::idealize_position(), lowres_cst_scorefxn_, min_tolerance_, monoub_end_, nb_list_, core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), temperature_, and protocols::TR().

Referenced by monoub_initial_perturbation().

void protocols::ub_e2c::ubi_e2c_modeler::monoub_initial_perturbation ( core::pose::Pose & pose_in)

private

Definition at line 2787 of file Ubiquitin_E2C_Modeler.cc.

References core::pose::Pose::data(), docking, core::pose::datacache::CacheableDataType::INTERFACE_INFO, monoub_first_perturbation(), monoub_initial_cter_perturbation(), and protocols::TR().

Referenced by monoub_centroid_mode_perturbation().

void protocols::ub_e2c::ubi_e2c_modeler::monoub_setup_key_residues ( const core::pose::Pose & pose_in)

private

Definition at line 2537 of file Ubiquitin_E2C_Modeler.cc.

References e2_ctr_of_mass_, e2_end_, monoub_ctr_of_mass_, monoub_end_, core::pose::Pose::pdb_info(), protocols::geometry::residue_center_of_mass(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by monoub_apply().

void protocols::ub_e2c::ubi_e2c_modeler::monoub_setup_move_maps ( )

private

Definition at line 2572 of file Ubiquitin_E2C_Modeler.cc.

References flex_cter_, init_all_dof_map_, init_monoub_all_dof_map_, init_monoub_docking_map_, init_monoub_flex_cter_map_, monoub_all_dof_map_, monoub_docking_map_, monoub_end_, monoub_flex_cter_map_, and protocols::TR().

Referenced by monoub_apply().

void protocols::ub_e2c::ubi_e2c_modeler::optimize_cov_bond ( core::pose::Pose & pose_in)

void protocols::ub_e2c::ubi_e2c_modeler::restore_cter	(	core::pose::Pose &	pose_in,
		core::pose::Pose	without_cter
	)

Definition at line 1079 of file Ubiquitin_E2C_Modeler.cc.

References protocols::simple_moves::SwitchResidueTypeSetMover::apply(), core::chemical::CENTROID, core::pose::Pose::conformation(), core::pose::Pose::copy_segment(), d77_end_, d77_trim_end_, e2_end_, flex_cter_, k48r_end_, k48r_trim_end_, core::pose::Pose::residue(), core::conformation::Conformation::safely_append_polymer_residue_after_seqpos(), setup_complex_fold_tree(), protocols::medal::to_centroid(), and protocols::TR().

Referenced by initial_perturbation().

void protocols::ub_e2c::ubi_e2c_modeler::restrict_to_interfacial_loop_packing ( core::pose::Pose & pose_in)

Definition at line 1763 of file Ubiquitin_E2C_Modeler.cc.

References d77_end_, e2_d77_jump_, e2_k48r_jump_, flex_cter_, k48r_end_, tf_, core::pose::Pose::total_residue(), and protocols::TR().

void protocols::ub_e2c::ubi_e2c_modeler::set_default ( )

Definition at line 144 of file Ubiquitin_E2C_Modeler.cc.

References applied_fullatom_pert_, core::scoring::atom_pair_constraint, core::scoring::cbeta, cen_constraint_, cen_vdw_, cov_bond_only_flag_, core::scoring::ScoreFunctionFactory::create_score_function(), d77_48_lys_, d77_75g_mtsl_, d77_ctr_of_mass_, d77_end_, d77_trim_ctr_mass_, d77_trim_end_, dock_lowres_cst_scorefxn_, dock_lowres_scorefxn_, dockfa_cst_min_scorefxn_, dockfa_cst_scorefxn_, dockfa_min_scorefxn_, dockfa_scorefxn_, e2_ctr_of_mass_, e2_end_, full_constraint_, fullatom_constraint_cutoff_, core::scoring::interchain_contact, core::scoring::interchain_vdw, k48r_48_lys_, k48r_48k_mtsl_, k48r_ctr_of_mass_, k48r_end_, k48r_swap_, k48r_trim_end_, lowres_cst_scorefxn_, lowres_scorefxn_, min_tolerance_, min_type_, monoub_mode_, nb_list_, output_cen_scorefxn_, output_full_scorefxn_, pack_cst_scorefxn_, pack_scorefxn_, passed_centroid_filter_, passed_fullatom_filter_, protocols::TR(), and core::scoring::vdw.

Referenced by ubi_e2c_modeler().

void protocols::ub_e2c::ubi_e2c_modeler::set_e2g2_diubi_fold_tree ( core::pose::Pose & pose_in)

Definition at line 1790 of file Ubiquitin_E2C_Modeler.cc.

References d77_end_, e2_ctr_of_mass_, e2_end_, core::pose::Pose::fold_tree(), protocols::geometry::residue_center_of_mass(), and protocols::TR().

Referenced by calc_interaction_energy(), and evaluate_native().

void protocols::ub_e2c::ubi_e2c_modeler::setup_complex_fold_tree	(	core::pose::Pose &	pose_in,
		bool	trim = `false`
	)

Definition at line 906 of file Ubiquitin_E2C_Modeler.cc.

References d77_ctr_of_mass_, d77_end_, e2_ctr_of_mass_, e2_d77_jump_, e2_end_, e2_k48r_jump_, flex_cter_, core::pose::Pose::fold_tree(), k48r_ctr_of_mass_, k48r_end_, and protocols::TR().

Referenced by calc_interaction_energy(), centroid_mode_perturbation(), evaluate_native(), init_k48r_perturbation(), initial_cter_perturbation(), optimize_cov_bond(), and restore_cter().

void protocols::ub_e2c::ubi_e2c_modeler::setup_key_residues ( const core::pose::Pose & pose_in)

Definition at line 770 of file Ubiquitin_E2C_Modeler.cc.

References d77_48_lys_, d77_75g_mtsl_, d77_ctr_of_mass_, d77_end_, d77_trim_ctr_mass_, d77_trim_end_, e2_ctr_of_mass_, e2_end_, k48r_48_lys_, k48r_48k_mtsl_, k48r_ctr_of_mass_, k48r_end_, k48r_trim_end_, core::pose::Pose::pdb_info(), protocols::geometry::residue_center_of_mass(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by apply(), and evaluate_native().

void protocols::ub_e2c::ubi_e2c_modeler::setup_move_maps ( )

Definition at line 825 of file Ubiquitin_E2C_Modeler.cc.

References all_dof_map_, cov_bond_only_flag_, d77_docking_map_, d77_end_, docking_map_, e2_d77_jump_, e2_k48r_jump_, flex_cter_, flex_cter_map_, init_all_dof_map_, init_d77_docking_map_, init_docking_map_, init_flex_cter_map_, init_k48r_docking_map_, k48r_docking_map_, k48r_end_, and protocols::TR().

Referenced by apply().

void protocols::ub_e2c::ubi_e2c_modeler::setup_packer_task ( core::pose::Pose & pose_in)

Definition at line 1721 of file Ubiquitin_E2C_Modeler.cc.

References init_task_factory_, core::pack::dunbrack::load_unboundrot(), tf_, and protocols::TR().

Referenced by evaluate_native(), initial_repack(), and optimize_cov_bond().

void protocols::ub_e2c::ubi_e2c_modeler::setup_simple_fold_tree	(	core::Size	jumppoint1,
		core::Size	cutpoint,
		core::Size	jumppoint2,
		core::Size	nres,
		core::pose::Pose &	pose_in
	)