#include <RemodelMover.hh>

Classes
struct	instruction_flags

Public Types
typedef std::string	String

typedef core::Real	Real

typedef core::Size	Size

typedef core::pack::task::TaskFactoryOP	TaskFactoryOP

typedef core::pose::Pose	Pose

typedef core::scoring::ScoreFunction	ScoreFunction

typedef core::scoring::ScoreFunctionOP	ScoreFunctionOP

typedef protocols::forge::build::BuildInstructionOP	BuildInstructionOP

typedef protocols::forge::build::BuildManager	BuildManager

typedef protocols::forge::build::BuildManager::Original2Modified	Original2Modified

typedef protocols::forge::build::Interval	Interval

typedef protocols::moves::MoverOP	MoverOP

typedef protocols::forge::components::VarLengthBuildOP	VarLengthBuildOP

typedef protocols::forge::components::VarLengthBuild	VarLengthBuild

typedef protocols::forge::remodel::RemodelData	RemodelData

typedef protocols::forge::remodel::RemodelWorkingSet	RemodelWorkingSet

typedef std::pair< Interval, String >	OriginalInterval2DesignString
	A pair storing a instruction's original interval and a string denoting the sequence during design. More...

typedef utility::vector1 < OriginalInterval2DesignString >	DesignInfo

typedef utility::tag::TagCOP	TagCOP

typedef protocols::filters::Filters_map	Filters_map

typedef basic::datacache::DataMap	DataMap

typedef protocols::moves::Movers_map	Movers_map

Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP	TagCOP

typedef core::pose::Pose	Pose

typedef core::pose::PoseCOP	PoseCOP

typedef protocols::filters::Filters_map	Filters_map

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

Public Member Functions
	RemodelMover ()
	default constructor More...

	RemodelMover (RemodelMover const &rval)
	copy constructor More...

virtual	~RemodelMover ()
	default destructor More...

virtual MoverOP	clone () const
	clone this object, for parser More...

virtual MoverOP	fresh_instance () const
	create this type of object, for parser More...

virtual MoverOP	clone ()
	clone this object More...

virtual MoverOP	fresh_instance ()
	create this type of object More...

ScoreFunction const &	centroid_scorefunction () const
	the centroid level score function, default "remodel_cen" More...

ScoreFunction const &	fullatom_scorefunction () const
	the full-atom level score function More...

void	max_linear_chainbreak (Real const threshold)
	add instruction to the manager of this RemodelMover (no copy) More...

void	centroid_loop_mover_str (String const &loop_mover_str)
	the loop mover string to use during centroid build More...

void	redesign_loop_neighborhood (bool const flag)
	redesign the neighborhood around the loop? if false, then just repacks during the design phase More...

void	dr_cycles (Size const cycles)
	set the number of design-refine cycles to perform More...

void	centroid_scorefunction (ScoreFunction const &sfx)
	set the centroid level score function More...

void	centroid_scorefunction (ScoreFunctionOP const &sfx)
	set the centroid level score function More...

void	fullatom_scorefunction (ScoreFunction const &sfx)
	set the full-atom level score function More...

void	fullatom_scorefunction (ScoreFunctionOP const &sfx)
	set the full-atom level score function More...

virtual void	apply (Pose &pose)
	apply defined moves to given Pose More...

virtual std::string	get_name () const
	get_name function for JobDistributor More...

bool	confirm_sequence (core::pose::Pose &pose)
	As best as I can tell, does some loop closure and calculates RMSD to native. Returns true. NOTE: CURRENTLY ALWAYS RETURNS TRUE regardless of rmsd value, because this stage is not being used as a filter Checks the value of -remodelswap_refine_confirm_protocols. More...

virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data, Filters_map const &, Movers_map const &, Pose const &)
	parse xml More...

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)

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
	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...

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

jobdist::BasicJobCOP	get_current_job () const

virtual void	show (std::ostream &output=std::cout) const
	Outputs details about the Mover, including current settings. More...

Static Public Member Functions
static String	neighborhood_calc_name ()
	the name for the loops' neighborhood calculator More...

static String	loops_buns_polar_calc_name ()
	the name for the loops' buried unsatisfied polars calculator More...

static String	neighborhood_buns_polar_calc_name ()
	the name for the loops' neighborhood buried unsatisfied polars calculator More...

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...

Private Types
typedef protocols::moves::Mover	Super

Private Member Functions
RemodelMover &	operator= (RemodelMover const &rval)
	copy assignment More...

bool	SamePose (Pose const &pose1, Pose const &pose2)
	Apply method for Mover. Checks the values of the following options -remodelcheckpoint -remodel::domainFusion::insert_segment_from_pdb -remodelbypass_fragments, -remodelnum_trajectory, -remodelrepeat_structure -remodelbuild_disulf -remodelquick_and_dirty -remodeluse_pose_relax -remodelrun_confirmation -enzdescstfile -symmetrysymmetry_definition -runshow_simulation_in_pymol. More...

void	register_user_options ()
	Checks for presence of any score term weight override options and calls set_weight on the centroid scorefunction. Note: options only get applied to centroid scorefunction - fullatom scorefunction left as is. More...

bool	centroid_build (Pose &pose, protocols::forge::build::BuildManager &manager)
	Does the same as function below, but takes in a BuildManager object. Also checks the value of the option -remodelbypass_fragments. More...

bool	centroid_build (Pose &pose)
	run the centroid level build stage More...

bool	design_refine_seq_relax (Pose &pose, RemodelDesignMover &designMover)
	Sets up constraints and a modified scorefunction and run design/relax cycles. Checks the value of -remodel:repeat_structure. More...

bool	design_refine_cart_relax (Pose &pose, RemodelDesignMover &designMover)

bool	design_refine (Pose &pose, RemodelDesignMover &designMover)
	run the design-refine stage More...

TaskFactoryOP	generic_taskfactory ()
	return a TaskFactory useable as a starting point for either design or refinement More...

void	process_continuous_design_string (Interval const &original_interval, String const &design_str, Original2Modified const &original2modified_interval_endpoints, TaskFactoryOP design_tf)
	process a continuous design string, adding appropriate operations to the TaskFactory More...

void	process_insert_design_string (Interval const &original_interval, String const &design_str, Original2Modified const &original2modified_interval_endpoints, TaskFactoryOP design_tf)
	process a design string containing an insert, adding appropriate operations to the TaskFactory More...

void	set_param_from_options ()

Static Private Member Functions
static utility::vector1< bool > const &	allowed_surface_aa ()
	return a boolean vector specifying allowed a.a. when designing on the surface More...

Private Attributes
BuildManager	manager_
	the BuildManager More...

Pose	native_pose_

RemodelData	remodel_data_
	holds all the blueprint info, contains build manager More...

RemodelWorkingSet	working_model_
	working set holds all the modified index that is required for the remodeling task More...

DesignInfo	design_info_
	Stores instructions' original interval and a string denoting the sequence during design. More...

Real	max_linear_chainbreak_
	use sequence biased fragments when building the loop? (default false) bool use_sequence_bias_; More...

String	centroid_loop_mover_str_
	the loop mover string to use during centroid build (default "RemodelLoopMover") More...

bool	redesign_loop_neighborhood_
	redesign the neighborhood around the loop? if false, then just repacks during the design phase (default true) More...

Size	dr_cycles_
	name of the resfile to use during design-refine; empty string implies no resfile String resfile_; More...

ScoreFunctionOP	centroid_sfx_
	the centroid scorefunction to use, default "remodel_cen" More...

ScoreFunctionOP	fullatom_sfx_
	the full-atom scorefunction to use More...

String	blueprint_

bool	rosetta_scripts_quick_and_dirty_

bool	rosetta_scripts_build_disulfide_

bool	rosetta_scripts_fast_disulfide_

bool	rosetta_scripts_bypass_fragments_

core::Real	rosetta_scripts_match_rt_limit_

Size	rosetta_scripts_min_disulfides_

Size	rosetta_scripts_max_disulfides_

bool	rosetta_scripts_include_current_ds_

bool	rosetta_scripts_keep_current_ds_

Size	rosetta_scripts_min_loop_

bool	rosetta_scripts_

core::pose::PoseOP	last_input_pose_

forge::remodel::RemodelAccumulator	accumulator_

VarLengthBuildOP	vlb_
	VLB for centroid_build. More...

Additional Inherited Members
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...

Member Typedef Documentation

typedef protocols::forge::build::BuildInstructionOP protocols::forge::remodel::RemodelMover::BuildInstructionOP

typedef protocols::forge::build::BuildManager protocols::forge::remodel::RemodelMover::BuildManager

typedef basic::datacache::DataMap protocols::forge::remodel::RemodelMover::DataMap

typedef utility::vector1< OriginalInterval2DesignString > protocols::forge::remodel::RemodelMover::DesignInfo

typedef protocols::filters::Filters_map protocols::forge::remodel::RemodelMover::Filters_map

typedef protocols::forge::build::Interval protocols::forge::remodel::RemodelMover::Interval

typedef protocols::moves::MoverOP protocols::forge::remodel::RemodelMover::MoverOP

typedef protocols::moves::Movers_map protocols::forge::remodel::RemodelMover::Movers_map

typedef protocols::forge::build::BuildManager::Original2Modified protocols::forge::remodel::RemodelMover::Original2Modified

typedef std::pair< Interval, String > protocols::forge::remodel::RemodelMover::OriginalInterval2DesignString

A pair storing a instruction's original interval and a string denoting the sequence during design.

Remarks: This is only for instructions such as SegmentRebuild or SegmentInsert. Non-applicable instructions will not have any data stored here.

typedef core::pose::Pose protocols::forge::remodel::RemodelMover::Pose

typedef core::Real protocols::forge::remodel::RemodelMover::Real

typedef protocols::forge::remodel::RemodelData protocols::forge::remodel::RemodelMover::RemodelData

typedef protocols::forge::remodel::RemodelWorkingSet protocols::forge::remodel::RemodelMover::RemodelWorkingSet

typedef core::scoring::ScoreFunction protocols::forge::remodel::RemodelMover::ScoreFunction

typedef core::scoring::ScoreFunctionOP protocols::forge::remodel::RemodelMover::ScoreFunctionOP

typedef core::Size protocols::forge::remodel::RemodelMover::Size

typedef std::string protocols::forge::remodel::RemodelMover::String

typedef protocols::moves::Mover protocols::forge::remodel::RemodelMover::Super

private

typedef utility::tag::TagCOP protocols::forge::remodel::RemodelMover::TagCOP

typedef core::pack::task::TaskFactoryOP protocols::forge::remodel::RemodelMover::TaskFactoryOP

typedef protocols::forge::components::VarLengthBuild protocols::forge::remodel::RemodelMover::VarLengthBuild

typedef protocols::forge::components::VarLengthBuildOP protocols::forge::remodel::RemodelMover::VarLengthBuildOP

Constructor & Destructor Documentation

protocols::forge::remodel::RemodelMover::RemodelMover ( )

default constructor

Default constructor. Checks values of options packing::soft_rep_design, and remodel::dr_cycles Creates and sets the centroid and fullatom score functions.

RemodelMover::RemodelMover

References blueprint_, centroid_loop_mover_str_, centroid_sfx_, core::scoring::ScoreFunctionFactory::create_score_function(), dr_cycles_, fullatom_sfx_, core::scoring::getScoreFunction(), last_input_pose_, max_linear_chainbreak_, option, redesign_loop_neighborhood_, register_user_options(), rosetta_scripts_, rosetta_scripts_build_disulfide_, rosetta_scripts_bypass_fragments_, rosetta_scripts_fast_disulfide_, rosetta_scripts_include_current_ds_, rosetta_scripts_keep_current_ds_, rosetta_scripts_match_rt_limit_, rosetta_scripts_max_disulfides_, rosetta_scripts_min_disulfides_, rosetta_scripts_min_loop_, rosetta_scripts_quick_and_dirty_, SOFT_REP_DESIGN_WTS, and protocols::forge::remodel::TR.

Referenced by clone(), and fresh_instance().

protocols::forge::remodel::RemodelMover::RemodelMover ( RemodelMover const & rval )

copy constructor

Copy constructor.

RemodelMover::RemodelMover( RemodelMover )

References clone(), utility::pointer::owning_ptr< T >::get(), and vlb_.

protocols::forge::remodel::RemodelMover::~RemodelMover ( )

virtual

default destructor

Default destructor. Does this need to free the VarLengthBuild memory?

RemodelMover::~RemodelMover

Member Function Documentation

utility::vector1< bool > const & protocols::forge::remodel::RemodelMover::allowed_surface_aa ( )

staticprivate

return a boolean vector specifying allowed a.a. when designing on the surface

RemodelMover::process_insert_design_string

References core::chemical::aa_from_oneletter_code(), and aa_from_oneletter_code().

Referenced by process_continuous_design_string(), and process_insert_design_string().

void protocols::forge::remodel::RemodelMover::apply ( Pose & pose )

virtual

apply defined moves to given Pose

Implements protocols::moves::Mover.

bool protocols::forge::remodel::RemodelMover::centroid_build	(	Pose &	pose,
		protocols::forge::build::BuildManager &	manager
	)

private

Does the same as function below, but takes in a BuildManager object. Also checks the value of the option -remodelbypass_fragments.

RemodelMover::centroid_build

References manager_, option, rosetta_scripts_bypass_fragments_, rosetta_scripts_fast_disulfide_, and protocols::forge::remodel::TR.

Referenced by apply().

bool protocols::forge::remodel::RemodelMover::centroid_build ( Pose & pose )

private

run the centroid level build stage

Runs the centroid level build state. Returns true if loop was closed, false if not. Also checks the value of options -remodel:use_same_length_fragments, -remodel:use_blueprint_sequence and -remodel:repeat_structure.

Returns: true if loop closed, false otherwise

RemodelMover::centroid_build

References protocols::forge::remodel::RemodelWorkingSet::abego, protocols::simple_moves::symmetry::SetupForSymmetryMover::apply(), protocols::forge::remodel::RemodelData::blueprint, centroid_loop_mover_str_, centroid_sfx_, core::scoring::Energies::clear(), protocols::forge::components::VLB_VallMemoryUsage::CLEAR_IF_CACHING_FRAGMENTS, core::pose::Pose::energies(), core::chemical::FA_STANDARD, utility::pointer::owning_ptr< T >::get(), protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::methods::intervals_to_loops(), loops, manager_, max_linear_chainbreak_, protocols::moves::MS_SUCCESS, option, remodel_data_, protocols::forge::remodel::RemodelLoopMover::repeat_generation_with_additional_residue(), protocols::forge::methods::restore_residues(), protocols::forge::remodel::RemodelData::sequence, protocols::forge::remodel::RemodelLoopMover::set_repeat_tail_length(), protocols::forge::remodel::RemodelWorkingSet::ss, core::util::switch_to_residue_type_set(), protocols::forge::remodel::TR, user, vlb_, and working_model_.

void protocols::forge::remodel::RemodelMover::centroid_loop_mover_str ( String const & loop_mover_str )

inline

the loop mover string to use during centroid build

Remarks: set to either a string the create_loop_mover() LoopMoverFactory recognizes or the "RemodelLoopMover"

References centroid_loop_mover_str_.

ScoreFunction const & protocols::forge::remodel::RemodelMover::centroid_scorefunction ( ) const

the centroid level score function, default "remodel_cen"

References centroid_sfx_.

void protocols::forge::remodel::RemodelMover::centroid_scorefunction ( ScoreFunction const & sfx )

set the centroid level score function

References centroid_sfx_, and core::scoring::ScoreFunction::clone().

void protocols::forge::remodel::RemodelMover::centroid_scorefunction ( ScoreFunctionOP const & sfx )

set the centroid level score function

References centroid_sfx_, and core::scoring::ScoreFunction::clone().

RemodelMover::MoverOP protocols::forge::remodel::RemodelMover::clone ( ) const

virtual

clone this object, for parser

clone for parser

Reimplemented from protocols::moves::Mover.

References RemodelMover().

RemodelMover::MoverOP protocols::forge::remodel::RemodelMover::clone ( )

virtual

clone this object

References RemodelMover().

bool protocols::forge::remodel::RemodelMover::confirm_sequence ( core::pose::Pose & pose )

As best as I can tell, does some loop closure and calculates RMSD to native. Returns true. NOTE: CURRENTLY ALWAYS RETURNS TRUE regardless of rmsd value, because this stage is not being used as a filter Checks the value of -remodelswap_refine_confirm_protocols.

RemodelMover::confirm_sequence

References protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), end, protocols::loops::loop_mover::LoopMover::false_movemap(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), fullatom_sfx_, generic_taskfactory(), core::kinematics::MoveMap::import(), protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::methods::intervals_to_confirmation_loops(), core::conformation::Residue::is_DNA(), manager_, protocols::forge::build::BuildManager::movemap(), native_pose_, protocols::forge::remodel::RemodelData::natro_movemap_, neighborhood_calc_name(), option, core::pose::Pose::pdb_info(), core::pack::task::TaskFactory::push_back(), refine, remodel_data_, core::pose::Pose::residue(), rmsd, core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_task_factory(), utility::to_string(), core::pose::Pose::total_residue(), protocols::forge::remodel::TR, user, core::pose::RemarkInfo::value, and core::conformation::Residue::xyz().

Referenced by apply().

bool protocols::forge::remodel::RemodelMover::design_refine	(	Pose &	pose,
		RemodelDesignMover &	designMover
	)

private

run the design-refine stage

Run the design-refine stage. Checks the value of -remodel:repeat_structure and -remodel:swap_refine_confirm_protocols NOTE: CURRENTLY ALWAYS RETURNS TRUE regardless of if chain breaks test passes or fails.

Returns: currently always true

RemodelMover::design_refine

References protocols::loops::loop_mover::refine::LoopMover_Refine_KIC::apply(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::forge::remodel::RemodelDesignMover::apply(), core::scoring::atom_pair_constraint, c, core::scoring::Energies::clear(), core::scoring::coordinate_constraint, core::scoring::dihedral_constraint, dr_cycles_, core::pose::Pose::dump_pdb(), core::pose::Pose::energies(), protocols::loops::loop_mover::LoopMover::false_movemap(), core::pose::Pose::fold_tree(), protocols::loops::fold_tree_from_loops(), generic_taskfactory(), core::kinematics::MoveMap::get_chi(), core::scoring::getScoreFunction(), core::kinematics::MoveMap::import(), protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::methods::intervals_to_loops(), core::conformation::Residue::is_DNA(), l, protocols::forge::methods::linear_chainbreak(), loops, manager_, max_linear_chainbreak_, protocols::forge::build::BuildManager::movemap(), protocols::forge::remodel::RemodelData::natro_movemap_, neighborhood_calc_name(), option, protocols::forge::build::BuildManager::original2modified_interval_endpoints(), refine, remodel_data_, protocols::loops::remove_cutpoint_variants(), core::pose::Pose::residue(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_chi(), protocols::forge::remodel::RemodelDesignMover::set_state(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_task_factory(), core::pose::Pose::total_residue(), protocols::forge::remodel::TR, and user.

Referenced by apply().

bool protocols::forge::remodel::RemodelMover::design_refine_cart_relax	(	Pose &	pose,
		RemodelDesignMover &	designMover
	)

private

Referenced by apply().

bool protocols::forge::remodel::RemodelMover::design_refine_seq_relax	(	Pose &	pose,
		RemodelDesignMover &	designMover
	)

private

Sets up constraints and a modified scorefunction and run design/relax cycles. Checks the value of -remodel:repeat_structure.

RemodelMover::design_refine_seq_relax

References core::scoring::angle_constraint, protocols::forge::remodel::RemodelDesignMover::apply(), protocols::relax::FastRelax::apply(), core::scoring::atom_pair_constraint, core::scoring::Energies::clear(), core::pose::Pose::constraint_set(), core::scoring::coordinate_constraint, protocols::forge::methods::cyclize_pose(), core::scoring::dihedral_constraint, dr_cycles_, core::pose::Pose::energies(), protocols::forge::methods::fill_non_loop_cst_set(), core::scoring::getScoreFunction(), protocols::forge::build::BuildManager::intervals_containing_undefined_positions(), protocols::forge::methods::intervals_to_loops(), is_symmetric(), loops, manager_, option, protocols::forge::build::BuildManager::original2modified_interval_endpoints(), core::scoring::res_type_constraint, core::scoring::res_type_linking_constraint, protocols::forge::remodel::RemodelDesignMover::set_state(), core::pose::symmetry::symmetry_info(), core::pose::Pose::total_residue(), protocols::forge::remodel::TR, and user.

Referenced by apply().

void protocols::forge::remodel::RemodelMover::dr_cycles ( Size const cycles )

inline

set the number of design-refine cycles to perform

Remarks: set this to 0 to skip design-refine

References dr_cycles_.

RemodelMover::MoverOP protocols::forge::remodel::RemodelMover::fresh_instance ( ) const

virtual

create this type of object, for parser

fresh instance for parser

Reimplemented from protocols::moves::Mover.

References RemodelMover().

RemodelMover::MoverOP protocols::forge::remodel::RemodelMover::fresh_instance ( )

virtual

create this type of object

References RemodelMover().

ScoreFunction const & protocols::forge::remodel::RemodelMover::fullatom_scorefunction ( ) const

the full-atom level score function

References fullatom_sfx_.

void protocols::forge::remodel::RemodelMover::fullatom_scorefunction ( ScoreFunction const & sfx )

set the full-atom level score function

References core::scoring::ScoreFunction::clone(), and fullatom_sfx_.

void protocols::forge::remodel::RemodelMover::fullatom_scorefunction ( ScoreFunctionOP const & sfx )

set the full-atom level score function

References core::scoring::ScoreFunction::clone(), and fullatom_sfx_.

RemodelMover::TaskFactoryOP protocols::forge::remodel::RemodelMover::generic_taskfactory ( )

private

return a TaskFactory useable as a starting point for either design or refinement

Returns a TaskFactory useable as a starting point for either design or refinement. Only adds the NoRepackDisulfides, IncludeCurrent, and Init from command line ops. ReadResfile is not included.

RemodelMover::generic_taskfactory

References option, tf, and user.

Referenced by confirm_sequence(), and design_refine().

std::string protocols::forge::remodel::RemodelMover::get_name ( ) const

virtual

get_name function for JobDistributor

Implements protocols::moves::Mover.

static String protocols::forge::remodel::RemodelMover::loops_buns_polar_calc_name ( )

inlinestatic

the name for the loops' buried unsatisfied polars calculator

Referenced by apply().

void protocols::forge::remodel::RemodelMover::max_linear_chainbreak ( Real const threshold )

inline

add instruction to the manager of this RemodelMover (no copy)

Parameters

[in]	bi	BuildInstruction
[in]	aa_during_design_refine	The allowed amino acid sequence during design. Only applicable to BuildInstructions like SegmentRebuild and SegmentInsert. Make sure the length of this string matches up properly, and remember to use any special characters, e.g. the insertion character for SegmentInsert the maximum allowed linear chainbreak

References max_linear_chainbreak_.

static String protocols::forge::remodel::RemodelMover::neighborhood_buns_polar_calc_name ( )

inlinestatic

the name for the loops' neighborhood buried unsatisfied polars calculator

Referenced by apply().

static String protocols::forge::remodel::RemodelMover::neighborhood_calc_name ( )

inlinestatic

the name for the loops' neighborhood calculator

Referenced by apply(), confirm_sequence(), and design_refine().

RemodelMover& protocols::forge::remodel::RemodelMover::operator= ( RemodelMover const & rval )

private

copy assignment

Remarks: Mover base class prevents this from working properly...

void protocols::forge::remodel::RemodelMover::parse_my_tag	(	TagCOP	tag,
		basic::datacache::DataMap &	data,
		Filters_map const &	,
		Movers_map const &	,
		Pose const &
	)

virtual

parse xml

Reimplemented from protocols::moves::Mover.

References blueprint_, rosetta_scripts_, rosetta_scripts_build_disulfide_, rosetta_scripts_bypass_fragments_, rosetta_scripts_fast_disulfide_, rosetta_scripts_include_current_ds_, rosetta_scripts_keep_current_ds_, rosetta_scripts_match_rt_limit_, rosetta_scripts_max_disulfides_, rosetta_scripts_min_disulfides_, rosetta_scripts_min_loop_, rosetta_scripts_quick_and_dirty_, and protocols::forge::remodel::TR.

void protocols::forge::remodel::RemodelMover::process_continuous_design_string	(	Interval const &	original_interval,
		String const &	design_str,
		Original2Modified const &	original2modified_interval_endpoints,
		TaskFactoryOP	design_tf
	)

private

process a continuous design string, adding appropriate operations to the TaskFactory

RemodelMover::process_continuous_design_string

References allowed_surface_aa(), protocols::forge::build::Interval::left, and core::pack::task::TaskFactory::push_back().

void protocols::forge::remodel::RemodelMover::process_insert_design_string	(	Interval const &	original_interval,
		String const &	design_str,
		Original2Modified const &	original2modified_interval_endpoints,
		TaskFactoryOP	design_tf
	)

private

process a design string containing an insert, adding appropriate operations to the TaskFactory

RemodelMover::process_insert_design_string

References allowed_surface_aa(), protocols::forge::build::SegmentInsert::insertion_char(), interval, protocols::forge::build::Interval::left, core::pack::task::TaskFactory::push_back(), and protocols::forge::build::Interval::right.

void protocols::forge::remodel::RemodelMover::redesign_loop_neighborhood ( bool const flag )

inline

redesign the neighborhood around the loop? if false, then just repacks during the design phase

References redesign_loop_neighborhood_.

void protocols::forge::remodel::RemodelMover::register_user_options ( )

private

Checks for presence of any score term weight override options and calls set_weight on the centroid scorefunction. Note: options only get applied to centroid scorefunction - fullatom scorefunction left as is.

RemodelMover::register_user_options

References cbeta, cenpack, centroid_sfx_, hbond_lr_bb, hbond_sr_bb, option, rama, protocols::simple_moves::rg, rg_local, rsigma, ss_pair, protocols::forge::remodel::TR, user, and vdw.