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protocols::ub_e2c::ubi_e2c_modeler Class Reference

#include <Ubiquitin_E2C_Modeler.hh>

Inheritance diagram for protocols::ub_e2c::ubi_e2c_modeler:
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Public Member Functions

 ubi_e2c_modeler ()
 
 ~ubi_e2c_modeler () override
 
void set_default ()
 
void apply (core::pose::Pose &pose_in) override
 Main Method. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. 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 MoverOP create ()
 
MoverCOP get_self_ptr () const
 
MoverOP get_self_ptr ()
 
MoverCAP get_self_weak_ptr () const
 
MoverAP get_self_weak_ptr ()
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
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...
 
virtual bool reinitialize_for_each_job () const
 Inform 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
 Inform 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
 Generates a new Mover object freshly created with the default ctor. More...
 
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...
 
void set_type (std::string const &setting)
 Set the 'type' string. More...
 
std::string get_type () const
 
void type (const std::string &type_in)
 Set the 'type' string. More...
 
std::string const & type () const
 Get the set 'type' string. More...
 
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 parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void set_current_tag (std::string const &new_tag)
 
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...
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 
virtual core::Real last_proposal_density_ratio ()
 
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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

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::Realscore_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 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::SizeCSP_
 
utility::vector1< core::SizeCSP_trim_
 
utility::vector1< core::SizeCSP_swap_trim_
 
utility::vector1< core::Sizenon_CSP_
 
utility::vector1< core::Sizenon_CSP_trim_
 
utility::vector1< core::Sizenon_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::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
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. 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...
 

Constructor & Destructor Documentation

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

References set_default().

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

Member Function Documentation

void protocols::ub_e2c::ubi_e2c_modeler::apply ( core::pose::Pose )
overridevirtual
void protocols::ub_e2c::ubi_e2c_modeler::assign_CSPs ( const core::pose::Pose pose_in)
private
void protocols::ub_e2c::ubi_e2c_modeler::assign_non_CSPs ( const core::pose::Pose pose_in)
private
Real protocols::ub_e2c::ubi_e2c_modeler::calc_interaction_energy ( const core::pose::Pose pose_in,
bool  dimer = true 
)
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 
)
bool protocols::ub_e2c::ubi_e2c_modeler::centroid_filter ( core::pose::Pose pose_in)
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
overridevirtual

Return a clone of the Mover object.

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.

void protocols::ub_e2c::ubi_e2c_modeler::compute_swap_trim_CSPs ( )
private
void protocols::ub_e2c::ubi_e2c_modeler::compute_trim_CSPs ( )
private
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)
bool protocols::ub_e2c::ubi_e2c_modeler::fullatom_filter ( core::pose::Pose pose_in)
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
overridevirtual

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

Implements protocols::moves::Mover.

void protocols::ub_e2c::ubi_e2c_modeler::init_d77_perturbation ( core::pose::Pose pose_in)
void protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation ( core::pose::Pose pose_in)
void protocols::ub_e2c::ubi_e2c_modeler::initial_cter_perturbation ( core::pose::Pose pose_in)
Real protocols::ub_e2c::ubi_e2c_modeler::initial_perturbation ( core::pose::Pose pose_in)
void protocols::ub_e2c::ubi_e2c_modeler::initial_repack ( core::pose::Pose pose_in)
void protocols::ub_e2c::ubi_e2c_modeler::monoub_apply ( core::pose::Pose pose_in)
private
void protocols::ub_e2c::ubi_e2c_modeler::monoub_assign_CSPs ( const core::pose::Pose pose_in)
private
Real protocols::ub_e2c::ubi_e2c_modeler::monoub_calc_interaction_energy ( const core::pose::Pose pose_in)
private
core::Real protocols::ub_e2c::ubi_e2c_modeler::monoub_calc_Lrmsd ( const core::pose::Pose pose_in,
const core::pose::Pose native_pose 
)
private
bool protocols::ub_e2c::ubi_e2c_modeler::monoub_centroid_filter ( core::pose::Pose pose_in)
private
void protocols::ub_e2c::ubi_e2c_modeler::monoub_centroid_mode_perturbation ( core::pose::Pose pose_in)
private
core::Real protocols::ub_e2c::ubi_e2c_modeler::monoub_CSP_fraction ( const core::pose::Pose pose_in)
private
void protocols::ub_e2c::ubi_e2c_modeler::monoub_first_perturbation ( core::pose::Pose pose_in)
private
void protocols::ub_e2c::ubi_e2c_modeler::monoub_fold_tree ( core::pose::Pose pose_in)
private
bool protocols::ub_e2c::ubi_e2c_modeler::monoub_fullatom_filter ( core::pose::Pose pose_in)
private
void protocols::ub_e2c::ubi_e2c_modeler::monoub_fullatom_mode_perturbation ( core::pose::Pose pose_in)
private
void protocols::ub_e2c::ubi_e2c_modeler::monoub_initial_cter_perturbation ( core::pose::Pose pose_in)
private
void protocols::ub_e2c::ubi_e2c_modeler::monoub_initial_perturbation ( core::pose::Pose pose_in)
private
void protocols::ub_e2c::ubi_e2c_modeler::monoub_setup_key_residues ( const core::pose::Pose pose_in)
private
void protocols::ub_e2c::ubi_e2c_modeler::monoub_setup_move_maps ( )
private
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 
)
void protocols::ub_e2c::ubi_e2c_modeler::restrict_to_interfacial_loop_packing ( core::pose::Pose pose_in)
void protocols::ub_e2c::ubi_e2c_modeler::set_default ( )
void protocols::ub_e2c::ubi_e2c_modeler::set_e2g2_diubi_fold_tree ( core::pose::Pose pose_in)
void protocols::ub_e2c::ubi_e2c_modeler::setup_complex_fold_tree ( core::pose::Pose pose_in,
bool  trim = false 
)
void protocols::ub_e2c::ubi_e2c_modeler::setup_key_residues ( const core::pose::Pose pose_in)
void protocols::ub_e2c::ubi_e2c_modeler::setup_move_maps ( )
void protocols::ub_e2c::ubi_e2c_modeler::setup_packer_task ( core::pose::Pose pose_in)
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 
)
void protocols::ub_e2c::ubi_e2c_modeler::trim_cter ( core::pose::Pose pose_in)

Member Data Documentation

core::kinematics::MoveMapOP protocols::ub_e2c::ubi_e2c_modeler::all_dof_map_
private
bool protocols::ub_e2c::ubi_e2c_modeler::applied_fullatom_pert_
private
core::Size const protocols::ub_e2c::ubi_e2c_modeler::CA
private
core::Real const protocols::ub_e2c::ubi_e2c_modeler::cen_constraint_
private
core::Real const protocols::ub_e2c::ubi_e2c_modeler::cen_vdw_
private

Referenced by set_default().

core::Real const protocols::ub_e2c::ubi_e2c_modeler::centroid_allowed_CSP_fraction_
private
core::Real const protocols::ub_e2c::ubi_e2c_modeler::centroid_CSP_weight_
private
core::Real const protocols::ub_e2c::ubi_e2c_modeler::centroid_non_CSP_weight_
private
bool const protocols::ub_e2c::ubi_e2c_modeler::cov_bond_only_flag_
private

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

utility::vector1<core::Size> protocols::ub_e2c::ubi_e2c_modeler::CSP_
private
utility::vector1<core::Size> protocols::ub_e2c::ubi_e2c_modeler::CSP_swap_trim_
private
utility::vector1<core::Size> protocols::ub_e2c::ubi_e2c_modeler::CSP_trim_
private

Referenced by compute_trim_CSPs(), and CSP_fraction().

core::Size protocols::ub_e2c::ubi_e2c_modeler::d77_48_lys_
private
core::Size protocols::ub_e2c::ubi_e2c_modeler::d77_75g_mtsl_
private

Referenced by set_default(), and setup_key_residues().

core::Size protocols::ub_e2c::ubi_e2c_modeler::d77_ctr_of_mass_
private
core::kinematics::MoveMapOP protocols::ub_e2c::ubi_e2c_modeler::d77_docking_map_
private
core::Size protocols::ub_e2c::ubi_e2c_modeler::d77_end_
private
core::Size protocols::ub_e2c::ubi_e2c_modeler::d77_trim_ctr_mass_
private
core::Size protocols::ub_e2c::ubi_e2c_modeler::d77_trim_end_
private
core::scoring::ScoreFunctionOP protocols::ub_e2c::ubi_e2c_modeler::dock_lowres_cst_scorefxn_
private
core::scoring::ScoreFunctionOP protocols::ub_e2c::ubi_e2c_modeler::dock_lowres_scorefxn_
private
core::scoring::ScoreFunctionOP protocols::ub_e2c::ubi_e2c_modeler::dockfa_cst_min_scorefxn_
private
core::scoring::ScoreFunctionOP protocols::ub_e2c::ubi_e2c_modeler::dockfa_cst_scorefxn_
private
core::scoring::ScoreFunctionOP protocols::ub_e2c::ubi_e2c_modeler::dockfa_min_scorefxn_
private

Referenced by set_default().

core::scoring::ScoreFunctionOP protocols::ub_e2c::ubi_e2c_modeler::dockfa_scorefxn_
private

Referenced by set_default().

core::kinematics::MoveMapOP protocols::ub_e2c::ubi_e2c_modeler::docking_map_
private
core::Size protocols::ub_e2c::ubi_e2c_modeler::e2_ctr_of_mass_
private
core::Size const protocols::ub_e2c::ubi_e2c_modeler::e2_d77_jump_
private
core::Size protocols::ub_e2c::ubi_e2c_modeler::e2_end_
private
core::Size const protocols::ub_e2c::ubi_e2c_modeler::e2_k48r_jump_
private
core::Size const protocols::ub_e2c::ubi_e2c_modeler::flex_cter_
private
core::kinematics::MoveMapOP protocols::ub_e2c::ubi_e2c_modeler::flex_cter_map_
private
core::Real protocols::ub_e2c::ubi_e2c_modeler::full_constraint_
private
core::Real const protocols::ub_e2c::ubi_e2c_modeler::fullatom_allowed_CSP_fraction_
private
core::Real protocols::ub_e2c::ubi_e2c_modeler::fullatom_constraint_cutoff_
private
core::Real const protocols::ub_e2c::ubi_e2c_modeler::fullatom_CSP_weight_
private
core::Real const protocols::ub_e2c::ubi_e2c_modeler::fullatom_non_CSP_weight_
private
bool const protocols::ub_e2c::ubi_e2c_modeler::higher_d77_pert_mode_
private

Referenced by init_k48r_perturbation().

core::kinematics::MoveMapOP protocols::ub_e2c::ubi_e2c_modeler::init_all_dof_map_
private
core::kinematics::MoveMapOP protocols::ub_e2c::ubi_e2c_modeler::init_d77_docking_map_
private

Referenced by setup_move_maps().

core::kinematics::MoveMapOP protocols::ub_e2c::ubi_e2c_modeler::init_docking_map_
private

Referenced by setup_move_maps().

core::kinematics::MoveMapOP protocols::ub_e2c::ubi_e2c_modeler::init_flex_cter_map_
private

Referenced by setup_move_maps().

core::kinematics::MoveMapOP protocols::ub_e2c::ubi_e2c_modeler::init_k48r_docking_map_
private

Referenced by setup_move_maps().

core::kinematics::MoveMapOP protocols::ub_e2c::ubi_e2c_modeler::init_monoub_all_dof_map_
private

Referenced by monoub_setup_move_maps().

core::kinematics::MoveMapOP protocols::ub_e2c::ubi_e2c_modeler::init_monoub_docking_map_
private

Referenced by monoub_setup_move_maps().

core::kinematics::MoveMapOP protocols::ub_e2c::ubi_e2c_modeler::init_monoub_flex_cter_map_
private

Referenced by monoub_setup_move_maps().

core::pack::task::TaskFactoryOP protocols::ub_e2c::ubi_e2c_modeler::init_task_factory_
private

Referenced by setup_packer_task().

core::Size protocols::ub_e2c::ubi_e2c_modeler::k48r_48_lys_
private

Referenced by set_default(), and setup_key_residues().

core::Size protocols::ub_e2c::ubi_e2c_modeler::k48r_48k_mtsl_
private

Referenced by set_default(), and setup_key_residues().

core::Size protocols::ub_e2c::ubi_e2c_modeler::k48r_ctr_of_mass_
private
core::kinematics::MoveMapOP protocols::ub_e2c::ubi_e2c_modeler::k48r_docking_map_
private
core::Size protocols::ub_e2c::ubi_e2c_modeler::k48r_end_
private
bool protocols::ub_e2c::ubi_e2c_modeler::k48r_swap_
private
core::Size protocols::ub_e2c::ubi_e2c_modeler::k48r_trim_end_
private
core::scoring::ScoreFunctionOP protocols::ub_e2c::ubi_e2c_modeler::lowres_cst_scorefxn_
private
core::scoring::ScoreFunctionOP protocols::ub_e2c::ubi_e2c_modeler::lowres_scorefxn_
private

Referenced by set_default().

core::Real const protocols::ub_e2c::ubi_e2c_modeler::max_k48_cter_dist_
private
core::Size const protocols::ub_e2c::ubi_e2c_modeler::max_repeats_
private

Referenced by apply(), and monoub_apply().

core::Real protocols::ub_e2c::ubi_e2c_modeler::min_tolerance_
private
std::string protocols::ub_e2c::ubi_e2c_modeler::min_type_
private
core::kinematics::MoveMapOP protocols::ub_e2c::ubi_e2c_modeler::monoub_all_dof_map_
private
core::Size protocols::ub_e2c::ubi_e2c_modeler::monoub_ctr_of_mass_
private
core::kinematics::MoveMapOP protocols::ub_e2c::ubi_e2c_modeler::monoub_docking_map_
private
core::Size protocols::ub_e2c::ubi_e2c_modeler::monoub_end_
private
core::kinematics::MoveMapOP protocols::ub_e2c::ubi_e2c_modeler::monoub_flex_cter_map_
private
bool const protocols::ub_e2c::ubi_e2c_modeler::monoub_mode_
private

Referenced by apply(), and set_default().

bool protocols::ub_e2c::ubi_e2c_modeler::nb_list_
private
utility::vector1<core::Size> protocols::ub_e2c::ubi_e2c_modeler::non_CSP_
private
utility::vector1<core::Size> protocols::ub_e2c::ubi_e2c_modeler::non_CSP_swap_trim_
private
utility::vector1<core::Size> protocols::ub_e2c::ubi_e2c_modeler::non_CSP_trim_
private

Referenced by compute_trim_CSPs(), and CSP_fraction().

core::scoring::ScoreFunctionOP protocols::ub_e2c::ubi_e2c_modeler::output_cen_scorefxn_
private

Referenced by set_default().

core::scoring::ScoreFunctionOP protocols::ub_e2c::ubi_e2c_modeler::output_full_scorefxn_
private

Referenced by set_default().

core::scoring::ScoreFunctionOP protocols::ub_e2c::ubi_e2c_modeler::pack_cst_scorefxn_
private
core::scoring::ScoreFunctionOP protocols::ub_e2c::ubi_e2c_modeler::pack_scorefxn_
private
bool protocols::ub_e2c::ubi_e2c_modeler::passed_centroid_filter_
private

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

bool protocols::ub_e2c::ubi_e2c_modeler::passed_fullatom_filter_
private

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

bool const protocols::ub_e2c::ubi_e2c_modeler::refinement_mode_
private
std::map< std::string, core::Real > protocols::ub_e2c::ubi_e2c_modeler::score_map_
private
core::Real const protocols::ub_e2c::ubi_e2c_modeler::temperature_
private
core::pack::task::TaskFactoryOP protocols::ub_e2c::ubi_e2c_modeler::tf_
private

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