#include <LHRepulsiveRampLegacy.hh>

Inheritance diagram for protocols::antibody::LHRepulsiveRampLegacy:

[legend]

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

	LHRepulsiveRampLegacy (loops::Loops loops_in)
	constructor with arguments More...

	LHRepulsiveRampLegacy (AntibodyInfoOP antibody_in)

	LHRepulsiveRampLegacy (AntibodyInfoOP antibody_in, bool camelid)

	LHRepulsiveRampLegacy (loops::Loops loops_in, core::scoring::ScoreFunctionCOP dock_scorefxn, core::scoring::ScoreFunctionCOP pack_scorefxn)

	LHRepulsiveRampLegacy (AntibodyInfoOP antibody_in, core::scoring::ScoreFunctionCOP dock_scorefxn, core::scoring::ScoreFunctionCOP pack_scorefxn)

protocols::moves::MoverOP	clone () const override
	Return a clone of the Mover object. More...

	~LHRepulsiveRampLegacy () override
	default destructor More...

void	set_default ()

void	set_dock_score_func (core::scoring::ScoreFunctionCOP dock_scorefxn)

void	set_pack_score_func (core::scoring::ScoreFunctionCOP pack_scorefxn)

void	apply (core::pose::Pose &pose) override
	ramping up the fullatom repulsive weight slowly to allow the partners to relieve clashes and make way for each other More...

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

void	set_task_factory (core::pack::task::TaskFactoryCOP tf)

core::Real	set_rot_mag (core::Real rot_mag)

core::Real	set_trans_mag (core::Real trans_mag)

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

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

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Member Functions
void	init (loops::Loops loops_in, bool camelid)

void	setup_objects ()

void	finalize_setup (core::pose::Pose &pose)

void	snugfit_MC_min (core::pose::Pose &pose, core::scoring::ScoreFunctionOP temp_scorefxn)

void	repulsive_ramp (core::pose::Pose &pose_in, loops::Loops loops_in)

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

◆ LHRepulsiveRampLegacy() [1/6]

protocols::antibody::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy ( )

default constructor

◆ LHRepulsiveRampLegacy() [2/6]

protocols::antibody::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy ( loops::Loops loops_in )

constructor with arguments

References init(), and user_defined_.

◆ LHRepulsiveRampLegacy() [3/6]

protocols::antibody::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy ( AntibodyInfoOP antibody_in )

References init(), and user_defined_.

◆ LHRepulsiveRampLegacy() [4/6]

protocols::antibody::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy	(	AntibodyInfoOP	antibody_in,
		bool	camelid
	)

References init(), and user_defined_.

◆ LHRepulsiveRampLegacy() [5/6]

protocols::antibody::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy	(	loops::Loops	loops_in,
		core::scoring::ScoreFunctionCOP	dock_scorefxn,
		core::scoring::ScoreFunctionCOP	pack_scorefxn
	)

References dock_scorefxn_, init(), pack_scorefxn_, and user_defined_.

◆ LHRepulsiveRampLegacy() [6/6]

protocols::antibody::LHRepulsiveRampLegacy::LHRepulsiveRampLegacy	(	AntibodyInfoOP	antibody_in,
		core::scoring::ScoreFunctionCOP	dock_scorefxn,
		core::scoring::ScoreFunctionCOP	pack_scorefxn
	)

References dock_scorefxn_, init(), pack_scorefxn_, and user_defined_.

◆ ~LHRepulsiveRampLegacy()

protocols::antibody::LHRepulsiveRampLegacy::~LHRepulsiveRampLegacy ( )

overridedefault

default destructor

Member Function Documentation

◆ apply()

void protocols::antibody::LHRepulsiveRampLegacy::apply ( core::pose::Pose & pose )

overridevirtual

ramping up the fullatom repulsive weight slowly to allow the partners to relieve clashes and make way for each other

This routine is specially targetted to the coupled optimization of docking partners and the loop region. The loop modelling & all previous steps involve mainly centroid mode .On switching on fullatom mode, one is bound to end up with clashes.To relieve the clashes, it is essential to slowly dial up the repulsive weight instead of turning it on to the maximum value in one single step

Parameters

[in] input pose which is assumed to have a docking fold tree

Global Read: fa_rep : fullatom repulsive weight

Global Write: fa_rep ( It is reset to the original value at the end )

Remarks: A particular portion is commented out,which can be uncommented if one uses a low resolution homology model. Check details in the beginning of the commented out region

References:

Author: Aroop 07/13/2010

Implements protocols::moves::Mover.

References core::pose::add_variant_type_to_pose_residue(), all_loops_, benchmark_, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, dock_scorefxn_, core::scoring::fa_rep, finalize_setup(), min_threshold_, num_repeats_, protocols::loops::remove_cutpoint_variants(), rep_ramp_cycles_, snugfit_MC_min(), and protocols::antibody::TR().

◆ clone()

protocols::moves::MoverOP protocols::antibody::LHRepulsiveRampLegacy::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.

◆ finalize_setup()

void protocols::antibody::LHRepulsiveRampLegacy::finalize_setup ( core::pose::Pose & pose )

private

References all_loops_, cdr_dock_map_, protocols::loops::Loops::num_loop(), protocols::loops::select_loop_residues(), protocols::antibody::setup_packer_task(), core::pose::Pose::size(), tf_, and protocols::antibody::TR().

Referenced by apply().

◆ get_name()

std::string protocols::antibody::LHRepulsiveRampLegacy::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ init()

void protocols::antibody::LHRepulsiveRampLegacy::init	(	loops::Loops	loops_in,
		bool	camelid
	)

private

References all_loops_, is_camelid_, set_default(), and tf_.

Referenced by LHRepulsiveRampLegacy().

◆ repulsive_ramp()

void protocols::antibody::LHRepulsiveRampLegacy::repulsive_ramp	(	core::pose::Pose &	pose_in,
		loops::Loops	loops_in
	)

private

◆ set_default()

void protocols::antibody::LHRepulsiveRampLegacy::set_default ( )

References benchmark_, core::scoring::chainbreak, core::scoring::ScoreFunctionFactory::create_score_function(), dock_scorefxn_, core::scoring::get_score_function_legacy(), min_threshold_, min_type_, num_repeats_, core::scoring::overlap_chainbreak, pack_scorefxn_, core::scoring::PRE_TALARIS_2013_STANDARD_WTS, rep_ramp_cycles_, rot_mag_, temperature_, trans_mag_, and user_defined_.

Referenced by init().

◆ set_dock_score_func()

void protocols::antibody::LHRepulsiveRampLegacy::set_dock_score_func ( core::scoring::ScoreFunctionCOP dock_scorefxn )

inline

References dock_scorefxn_.

◆ set_pack_score_func()

void protocols::antibody::LHRepulsiveRampLegacy::set_pack_score_func ( core::scoring::ScoreFunctionCOP pack_scorefxn )

inline

References pack_scorefxn_.

◆ set_rot_mag()

core::Real protocols::antibody::LHRepulsiveRampLegacy::set_rot_mag ( core::Real rot_mag )

inline

References rot_mag_.

◆ set_task_factory()

void protocols::antibody::LHRepulsiveRampLegacy::set_task_factory ( core::pack::task::TaskFactoryCOP tf )

References tf_.

◆ set_trans_mag()

core::Real protocols::antibody::LHRepulsiveRampLegacy::set_trans_mag ( core::Real trans_mag )

inline

References trans_mag_.

◆ setup_objects()

void protocols::antibody::LHRepulsiveRampLegacy::setup_objects ( )

private

◆ snugfit_MC_min()

void protocols::antibody::LHRepulsiveRampLegacy::snugfit_MC_min	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunctionOP	temp_scorefxn
	)

private

References cdr_dock_map_, min_threshold_, min_type_, num_repeats_, pack_scorefxn_, protocols::rigid::partner_downstream, rot_mag_, temperature_, tf_, and trans_mag_.

Referenced by apply().

Member Data Documentation

◆ ab_info_

AntibodyInfoOP protocols::antibody::LHRepulsiveRampLegacy::ab_info_

private

◆ all_loops_

loops::Loops protocols::antibody::LHRepulsiveRampLegacy::all_loops_

private

Referenced by apply(), finalize_setup(), and init().

◆ benchmark_

bool protocols::antibody::LHRepulsiveRampLegacy::benchmark_

private

Referenced by apply(), and set_default().

◆ cdr_dock_map_

core::kinematics::MoveMapOP protocols::antibody::LHRepulsiveRampLegacy::cdr_dock_map_

private

Referenced by finalize_setup(), and snugfit_MC_min().

◆ dock_scorefxn_

core::scoring::ScoreFunctionOP protocols::antibody::LHRepulsiveRampLegacy::dock_scorefxn_

private

Referenced by apply(), LHRepulsiveRampLegacy(), set_default(), and set_dock_score_func().

◆ is_camelid_

bool protocols::antibody::LHRepulsiveRampLegacy::is_camelid_

private

Referenced by init().

◆ min_threshold_

core::Real protocols::antibody::LHRepulsiveRampLegacy::min_threshold_

private

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

◆ min_type_

std::string protocols::antibody::LHRepulsiveRampLegacy::min_type_

private

Referenced by set_default(), and snugfit_MC_min().

◆ nres_

core::Size protocols::antibody::LHRepulsiveRampLegacy::nres_

private

◆ num_repeats_

core::Size protocols::antibody::LHRepulsiveRampLegacy::num_repeats_

private

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

◆ pack_scorefxn_

core::scoring::ScoreFunctionOP protocols::antibody::LHRepulsiveRampLegacy::pack_scorefxn_

private

Referenced by LHRepulsiveRampLegacy(), set_default(), set_pack_score_func(), and snugfit_MC_min().

◆ rep_ramp_cycles_

core::Size protocols::antibody::LHRepulsiveRampLegacy::rep_ramp_cycles_

private

Referenced by apply(), and set_default().

◆ rot_mag_

core::Real protocols::antibody::LHRepulsiveRampLegacy::rot_mag_

private

Referenced by set_default(), set_rot_mag(), and snugfit_MC_min().

◆ temperature_

core::Real protocols::antibody::LHRepulsiveRampLegacy::temperature_

private

Referenced by set_default(), and snugfit_MC_min().

◆ tf_

core::pack::task::TaskFactoryOP protocols::antibody::LHRepulsiveRampLegacy::tf_

private

Referenced by finalize_setup(), init(), set_task_factory(), and snugfit_MC_min().

◆ trans_mag_

core::Real protocols::antibody::LHRepulsiveRampLegacy::trans_mag_

private

Referenced by set_default(), set_trans_mag(), and snugfit_MC_min().

◆ user_defined_

bool protocols::antibody::LHRepulsiveRampLegacy::user_defined_

private

Referenced by LHRepulsiveRampLegacy(), and set_default().

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

src/protocols/antibody_legacy/LHRepulsiveRampLegacy.hh
src/protocols/antibody_legacy/LHRepulsiveRampLegacy.cc

Private Attributes
AntibodyInfoOP	ab_info_

bool	user_defined_

bool	benchmark_

bool	is_camelid_

loops::Loops	all_loops_

core::Size	nres_

core::kinematics::MoveMapOP	cdr_dock_map_

core::Size	rep_ramp_cycles_

std::string	min_type_

core::Real	rot_mag_

core::Real	trans_mag_

core::Real	temperature_

core::Real	min_threshold_

core::Size	num_repeats_

core::scoring::ScoreFunctionOP	dock_scorefxn_

core::scoring::ScoreFunctionOP	pack_scorefxn_

core::pack::task::TaskFactoryOP	tf_

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ LHRepulsiveRampLegacy() [1/6]

◆ LHRepulsiveRampLegacy() [2/6]

◆ LHRepulsiveRampLegacy() [3/6]

◆ LHRepulsiveRampLegacy() [4/6]

◆ LHRepulsiveRampLegacy() [5/6]

◆ LHRepulsiveRampLegacy() [6/6]

◆ ~LHRepulsiveRampLegacy()

Member Function Documentation

◆ apply()

◆ clone()

◆ finalize_setup()

◆ get_name()

◆ init()

◆ repulsive_ramp()

◆ set_default()

◆ set_dock_score_func()

◆ set_pack_score_func()

◆ set_rot_mag()

◆ set_task_factory()

◆ set_trans_mag()

◆ setup_objects()

◆ snugfit_MC_min()

Member Data Documentation

◆ ab_info_

◆ all_loops_

◆ benchmark_

◆ cdr_dock_map_

◆ dock_scorefxn_

◆ is_camelid_

◆ min_threshold_

◆ min_type_

◆ nres_

◆ num_repeats_

◆ pack_scorefxn_

◆ rep_ramp_cycles_

◆ rot_mag_

◆ temperature_

◆ tf_

◆ trans_mag_

◆ user_defined_