#include <H3PerturbCCD.hh>

Inheritance diagram for protocols::antibody::H3PerturbCCD:

[legend]

Public Member Functions
	H3PerturbCCD ()
	default constructor More...

	H3PerturbCCD (AntibodyInfoOP antibody_in)
	constructor with arguments More...

	H3PerturbCCD (AntibodyInfoOP antibody_in, core::scoring::ScoreFunctionCOP highres_scorefxn)
	constructor with arguments More...

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

	~H3PerturbCCD () override
	default destructor More...

void	apply (core::pose::Pose &pose) override
	Main Method. More...

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

void	read_and_store_fragments ()

void	pass_the_loop (loops::Loop &input_loop)

void	turn_off_H3_filter ()

void	set_lowres_score_func (core::scoring::ScoreFunctionCOP lowres_scorefxn)
	set scorefunction for low resolution of CDR H3 modeling More...

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	set_default ()

void	init ()

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

void	build_centroid_loop (core::pose::Pose &pose)
	Build centroid mode CDR H3 loop. More...

void	scored_frag_close (core::pose::Pose &pose_in, loops::Loop const trimmed_cdr_h3)

Private Attributes
AntibodyInfoOP	ab_info_

loops::Loop	input_loop_

bool	user_defined_

bool	is_camelid_

core::Size	cutoff_9_
	size of loop above which 9mer frags are used More...

core::Size	cutoff_3_
	size of loop above which 3mer frags are used More...

core::scoring::ScoreFunctionOP	lowres_scorefxn_

core::Real	cen_cst_

bool	current_loop_is_H3_
	flag indicating that current loop being modeled is CDR H3 More...

bool	H3_filter_
	actually enables H3 filter for H3 operations More...

core::Size	num_cycles1_

core::Size	max_ccd_cycles_

utility::vector1< core::fragment::FragSetOP >	cdr_h3_frags_

core::Real	h3_fraction_

core::Real	ccd_threshold_

core::Real	Temperature_

protocols::moves::MonteCarloOP	mc_

protocols::moves::MonteCarloOP	outer_mc_

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

◆ H3PerturbCCD() [1/3]

protocols::antibody::H3PerturbCCD::H3PerturbCCD ( )

default constructor

References user_defined_.

◆ H3PerturbCCD() [2/3]

protocols::antibody::H3PerturbCCD::H3PerturbCCD ( AntibodyInfoOP antibody_in )

constructor with arguments

References ab_info_, init(), and user_defined_.

◆ H3PerturbCCD() [3/3]

protocols::antibody::H3PerturbCCD::H3PerturbCCD	(	AntibodyInfoOP	antibody_in,
		core::scoring::ScoreFunctionCOP	highres_scorefxn
	)

constructor with arguments

References ab_info_, init(), lowres_scorefxn_, and user_defined_.

◆ ~H3PerturbCCD()

protocols::antibody::H3PerturbCCD::~H3PerturbCCD ( )

overridedefault

default destructor

Member Function Documentation

◆ apply()

void protocols::antibody::H3PerturbCCD::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References ab_info_, core::pose::add_variant_type_to_pose_residue(), ccd_threshold_, protocols::antibody::CDR_H3_cter_filter(), cdr_h3_frags_, current_loop_is_H3_, protocols::loops::Loop::cut(), cutoff_9_, core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, protocols::antibody::Extended, finalize_setup(), core::pose::Pose::fold_tree(), H3_filter_, h3_fraction_, core::conformation::Residue::has_variant_type(), input_loop_, is_camelid_, core::conformation::Residue::is_upper_terminus(), max_ccd_cycles_, mc_, num_cycles1_, outer_mc_, protocols::loops::remove_cutpoint_variants(), core::pose::Pose::residue(), core::scoring::rg, protocols::antibody::simple_one_loop_fold_tree(), protocols::loops::Loop::size(), protocols::loops::Loop::start(), protocols::loops::Loop::stop(), and protocols::antibody::TR().

◆ build_centroid_loop()

void protocols::antibody::H3PerturbCCD::build_centroid_loop ( core::pose::Pose & pose )

private

Build centroid mode CDR H3 loop.

◆ clone()

protocols::moves::MoverOP protocols::antibody::H3PerturbCCD::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::H3PerturbCCD::finalize_setup ( core::pose::Pose & pose )

private

References lowres_scorefxn_, mc_, outer_mc_, read_and_store_fragments(), and Temperature_.

Referenced by apply().

◆ get_name()

std::string protocols::antibody::H3PerturbCCD::get_name ( ) const

inlineoverridevirtual

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

Implements protocols::moves::Mover.

◆ init()

void protocols::antibody::H3PerturbCCD::init ( void )

private

References set_default().

Referenced by H3PerturbCCD().

◆ pass_the_loop()

void protocols::antibody::H3PerturbCCD::pass_the_loop ( loops::Loop & input_loop )

inline

References input_loop_.

◆ read_and_store_fragments()

void protocols::antibody::H3PerturbCCD::read_and_store_fragments ( )

References ab_info_, cdr_h3_frags_, protocols::antibody::h3, protocols::loops::read_loop_fragments(), and protocols::antibody::TR().

Referenced by finalize_setup().

◆ scored_frag_close()

void protocols::antibody::H3PerturbCCD::scored_frag_close	(	core::pose::Pose &	pose_in,
		loops::Loop const	trimmed_cdr_h3
	)

private

◆ set_default()

void protocols::antibody::H3PerturbCCD::set_default ( )

private

References core::scoring::atom_pair_constraint, ccd_threshold_, cen_cst_, core::scoring::chainbreak, current_loop_is_H3_, cutoff_3_, cutoff_9_, H3_filter_, h3_fraction_, is_camelid_, lowres_scorefxn_, max_ccd_cycles_, num_cycles1_, Temperature_, and user_defined_.

Referenced by init().

◆ set_lowres_score_func()

void protocols::antibody::H3PerturbCCD::set_lowres_score_func ( core::scoring::ScoreFunctionCOP lowres_scorefxn )

inline

set scorefunction for low resolution of CDR H3 modeling

References lowres_scorefxn_.

◆ turn_off_H3_filter()

void protocols::antibody::H3PerturbCCD::turn_off_H3_filter ( )

inline

References H3_filter_.

Member Data Documentation

◆ ab_info_

AntibodyInfoOP protocols::antibody::H3PerturbCCD::ab_info_

private

Referenced by apply(), H3PerturbCCD(), and read_and_store_fragments().

◆ ccd_threshold_

core::Real protocols::antibody::H3PerturbCCD::ccd_threshold_

private

Referenced by apply(), and set_default().

◆ cdr_h3_frags_

utility::vector1< core::fragment::FragSetOP > protocols::antibody::H3PerturbCCD::cdr_h3_frags_

private

Referenced by apply(), and read_and_store_fragments().

◆ cen_cst_

core::Real protocols::antibody::H3PerturbCCD::cen_cst_

private

Referenced by set_default().

◆ current_loop_is_H3_

bool protocols::antibody::H3PerturbCCD::current_loop_is_H3_

private

flag indicating that current loop being modeled is CDR H3

Referenced by apply(), and set_default().

◆ cutoff_3_

core::Size protocols::antibody::H3PerturbCCD::cutoff_3_

private

size of loop above which 3mer frags are used

Referenced by set_default().

◆ cutoff_9_

core::Size protocols::antibody::H3PerturbCCD::cutoff_9_

private

size of loop above which 9mer frags are used

Referenced by apply(), and set_default().

◆ H3_filter_

bool protocols::antibody::H3PerturbCCD::H3_filter_

private

actually enables H3 filter for H3 operations

Referenced by apply(), set_default(), and turn_off_H3_filter().

◆ h3_fraction_

core::Real protocols::antibody::H3PerturbCCD::h3_fraction_

private

Referenced by apply(), and set_default().

◆ input_loop_

loops::Loop protocols::antibody::H3PerturbCCD::input_loop_

private

Referenced by apply(), and pass_the_loop().

◆ is_camelid_

bool protocols::antibody::H3PerturbCCD::is_camelid_

private

Referenced by apply(), and set_default().

◆ lowres_scorefxn_

core::scoring::ScoreFunctionOP protocols::antibody::H3PerturbCCD::lowres_scorefxn_

private

Referenced by finalize_setup(), H3PerturbCCD(), set_default(), and set_lowres_score_func().

◆ max_ccd_cycles_

core::Size protocols::antibody::H3PerturbCCD::max_ccd_cycles_

private

Referenced by apply(), and set_default().

◆ mc_

protocols::moves::MonteCarloOP protocols::antibody::H3PerturbCCD::mc_

private

Referenced by apply(), and finalize_setup().

◆ num_cycles1_

core::Size protocols::antibody::H3PerturbCCD::num_cycles1_

private

Referenced by apply(), and set_default().

◆ outer_mc_

protocols::moves::MonteCarloOP protocols::antibody::H3PerturbCCD::outer_mc_

private

Referenced by apply(), and finalize_setup().

◆ Temperature_

core::Real protocols::antibody::H3PerturbCCD::Temperature_

private

Referenced by finalize_setup(), and set_default().

◆ user_defined_

bool protocols::antibody::H3PerturbCCD::user_defined_

private

Referenced by H3PerturbCCD(), and set_default().

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

src/protocols/antibody/H3PerturbCCD.hh
src/protocols/antibody/H3PerturbCCD.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ H3PerturbCCD() [1/3]

◆ H3PerturbCCD() [2/3]

◆ H3PerturbCCD() [3/3]

◆ ~H3PerturbCCD()

Member Function Documentation

◆ apply()

◆ build_centroid_loop()

◆ clone()

◆ finalize_setup()

◆ get_name()

◆ init()

◆ pass_the_loop()

◆ read_and_store_fragments()

◆ scored_frag_close()

◆ set_default()

◆ set_lowres_score_func()

◆ turn_off_H3_filter()

Member Data Documentation

◆ ab_info_

◆ ccd_threshold_

◆ cdr_h3_frags_

◆ cen_cst_

◆ current_loop_is_H3_

◆ cutoff_3_

◆ cutoff_9_

◆ H3_filter_

◆ h3_fraction_

◆ input_loop_

◆ is_camelid_

◆ lowres_scorefxn_

◆ max_ccd_cycles_

◆ mc_

◆ num_cycles1_

◆ outer_mc_

◆ Temperature_

◆ user_defined_