#include <refinable_lattice.hh>

Inheritance diagram for protocols::cryst::DockLatticeMover:

[legend]

Public Member Functions
	DockLatticeMover ()

	DockLatticeMover (core::scoring::ScoreFunctionOP sf_cen_in)

void	set_defaults ()

void	initialize (core::pose::Pose &pose, core::Real contact_dist_scale=1.0)

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

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

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

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

void	repack (core::pose::Pose &pose, bool rottrials=false)

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

bool	regenerate_lattice (core::pose::Pose &pose)

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

void	set_rot_mag (core::Real rot_mag_in)

void	set_trans_mag (core::Real trans_mag_in)

void	set_ncycles (core::Size ncycles_in)

void	set_scorefunction (core::scoring::ScoreFunctionOP sf_new)

void	set_temp (core::Real val)

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

protocols::moves::MoverOP	fresh_instance () const override
	Generates a new Mover object freshly created with the default ctor. More...

void	parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...

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

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

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...

Static Public Member Functions
static std::string	mover_name ()

static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

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 Attributes
core::scoring::ScoreFunctionOP	sf_

std::map< core::Size, core::conformation::symmetry::SymDof >	symdofs_

core::Size	SUBjump_

core::Size	Ajump_

core::Size	Bjump_

core::Size	Cjump_

core::Real	rot_mag_

core::Real	trans_mag_

core::Real	chi_mag_

core::Real	kT_

core::Real	contact_dist_

core::Real	init_score_cut_

numeric::xyzVector< core::Real >	lattice_mag_

core::Size	ncycles_

std::string	spacegroup_

core::Size	mult_

bool	randomize_

bool	min_

bool	min_lattice_

bool	final_min_

bool	pack_

bool	perturb_chi_

bool	verbose_

bool	recover_low_

core::pose::PoseOP	native_

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

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

◆ DockLatticeMover() [1/2]

protocols::cryst::DockLatticeMover::DockLatticeMover ( )

References core::scoring::get_score_function().

◆ DockLatticeMover() [2/2]

protocols::cryst::DockLatticeMover::DockLatticeMover ( core::scoring::ScoreFunctionOP sf_cen_in )

Member Function Documentation

◆ apply()

void protocols::cryst::DockLatticeMover::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References core::io::CrystInfo::A(), core::pose::add_score_line_string(), protocols::cryst::UpdateCrystInfo::apply(), core::io::CrystInfo::B(), core::io::CrystInfo::C(), protocols::cryst::crystRMS(), core::pose::get_score_line_string(), core::pose::symmetry::make_symmetric_movemap(), protocols::antibody::design::repack, protocols::hybridization::score, core::pose::setPoseExtraScore(), and protocols::cryst::TR().

◆ clone()

protocols::moves::MoverOP protocols::cryst::DockLatticeMover::clone ( ) const

inlineoverridevirtual

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.

◆ fresh_instance()

protocols::moves::MoverOP protocols::cryst::DockLatticeMover::fresh_instance ( ) const

inlineoverridevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

◆ get_name()

std::string protocols::cryst::DockLatticeMover::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

◆ initialize()

void protocols::cryst::DockLatticeMover::initialize	(	core::pose::Pose &	pose,
		core::Real	contact_dist_scale = `1.0`
	)

◆ mover_name()

std::string protocols::cryst::DockLatticeMover::mover_name ( )

static

Referenced by protocols::cryst::DockLatticeMoverCreator::keyname().

◆ parse_my_tag()

void protocols::cryst::DockLatticeMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

References core::scoring::parse_score_function().

◆ perturb_chis()

void protocols::cryst::DockLatticeMover::perturb_chis ( core::pose::Pose & pose )

References core::pose::Pose::chi(), core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), core::pose::Pose::residue(), core::scoring::rg, core::pose::Pose::set_chi(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::pose::Pose::total_residue().

◆ perturb_lattice()

void protocols::cryst::DockLatticeMover::perturb_lattice ( core::pose::Pose & pose )

References core::kinematics::Jump::get_translation(), core::pose::Pose::jump(), core::scoring::rg, core::pose::Pose::set_jump(), and core::kinematics::Jump::set_translation().

◆ perturb_rb()

void protocols::cryst::DockLatticeMover::perturb_rb ( core::pose::Pose & pose )

References core::conformation::symmetry::SymDof::allow_dof(), core::kinematics::Jump::gaussian_move_single_rb(), core::pose::Pose::jump(), and core::pose::Pose::set_jump().

◆ provide_xml_schema()

void protocols::cryst::DockLatticeMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References core::scoring::attributes_for_parse_score_function(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::cryst::DockLatticeMoverCreator::provide_xml_schema().

◆ randomize_chis()

void protocols::cryst::DockLatticeMover::randomize_chis ( core::pose::Pose & pose )

References core::pose::Pose::conformation(), core::pose::symmetry::is_symmetric(), core::pose::Pose::residue(), core::scoring::rg, core::pose::Pose::set_chi(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and core::pose::Pose::total_residue().

◆ regenerate_lattice()

bool protocols::cryst::DockLatticeMover::regenerate_lattice ( core::pose::Pose & pose )

References core::io::CrystInfo::A(), core::io::CrystInfo::alpha(), protocols::cryst::UpdateCrystInfo::apply(), protocols::cryst::MakeLatticeMover::apply(), core::io::CrystInfo::B(), core::io::CrystInfo::beta(), core::io::CrystInfo::C(), core::pose::Pose::conformation(), protocols::cryst::MakeLatticeMover::contact_dist(), core::pose::Pose::fold_tree(), core::io::CrystInfo::gamma(), protocols::cryst::getMW(), protocols::cryst::getVolume(), core::pose::symmetry::is_symmetric(), core::pose::Pose::pdb_info(), protocols::cryst::MakeLatticeMover::set_refinable_lattice(), core::conformation::symmetry::SymmetricConformation::Symmetry_Info(), and protocols::cryst::TR().

◆ repack()

void protocols::cryst::DockLatticeMover::repack	(	core::pose::Pose &	pose,
		bool	rottrials = `false`
	)

◆ set_defaults()

void protocols::cryst::DockLatticeMover::set_defaults ( )

References protocols::cryst::MakeLatticeMover::contact_dist(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), and protocols::cryst::MakeLatticeMover::set_refinable_lattice().

◆ set_ncycles()

void protocols::cryst::DockLatticeMover::set_ncycles ( core::Size ncycles_in )

inline

References ncycles_.

◆ set_rot_mag()

void protocols::cryst::DockLatticeMover::set_rot_mag ( core::Real rot_mag_in )

inline

References rot_mag_.

◆ set_scorefunction()

void protocols::cryst::DockLatticeMover::set_scorefunction ( core::scoring::ScoreFunctionOP sf_new )

inline

References sf_.

◆ set_temp()

void protocols::cryst::DockLatticeMover::set_temp ( core::Real val )

inline

References kT_, and protocols::hybridization::val.

◆ set_trans_mag()

void protocols::cryst::DockLatticeMover::set_trans_mag ( core::Real trans_mag_in )

inline

References trans_mag_.

◆ slide_lattice()

void protocols::cryst::DockLatticeMover::slide_lattice ( core::pose::Pose & pose )

References core::pose::symmetry::make_symmetric_movemap().

Member Data Documentation

◆ Ajump_

core::Size protocols::cryst::DockLatticeMover::Ajump_

private

◆ Bjump_

core::Size protocols::cryst::DockLatticeMover::Bjump_

private

◆ chi_mag_

core::Real protocols::cryst::DockLatticeMover::chi_mag_

private

◆ Cjump_

core::Size protocols::cryst::DockLatticeMover::Cjump_

private

◆ contact_dist_

core::Real protocols::cryst::DockLatticeMover::contact_dist_

private

◆ final_min_

bool protocols::cryst::DockLatticeMover::final_min_

private

◆ init_score_cut_

core::Real protocols::cryst::DockLatticeMover::init_score_cut_

private

◆ kT_

core::Real protocols::cryst::DockLatticeMover::kT_

private

Referenced by set_temp().

◆ lattice_mag_

numeric::xyzVector< core::Real > protocols::cryst::DockLatticeMover::lattice_mag_

private

◆ min_

bool protocols::cryst::DockLatticeMover::min_

private

◆ min_lattice_

bool protocols::cryst::DockLatticeMover::min_lattice_

private

◆ mult_

core::Size protocols::cryst::DockLatticeMover::mult_

private

◆ native_

core::pose::PoseOP protocols::cryst::DockLatticeMover::native_

private

◆ ncycles_

core::Size protocols::cryst::DockLatticeMover::ncycles_

private

Referenced by set_ncycles().

◆ pack_

bool protocols::cryst::DockLatticeMover::pack_

private

◆ perturb_chi_

bool protocols::cryst::DockLatticeMover::perturb_chi_

private

◆ randomize_

bool protocols::cryst::DockLatticeMover::randomize_

private

◆ recover_low_

bool protocols::cryst::DockLatticeMover::recover_low_

private

◆ rot_mag_

core::Real protocols::cryst::DockLatticeMover::rot_mag_

private

Referenced by set_rot_mag().

◆ sf_

core::scoring::ScoreFunctionOP protocols::cryst::DockLatticeMover::sf_

private

Referenced by set_scorefunction().

◆ spacegroup_

std::string protocols::cryst::DockLatticeMover::spacegroup_

private

◆ SUBjump_

core::Size protocols::cryst::DockLatticeMover::SUBjump_

private

◆ symdofs_

std::map< core::Size, core::conformation::symmetry::SymDof > protocols::cryst::DockLatticeMover::symdofs_

private

◆ trans_mag_

core::Real protocols::cryst::DockLatticeMover::trans_mag_

private

Referenced by set_trans_mag().

◆ verbose_

bool protocols::cryst::DockLatticeMover::verbose_

private

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

src/protocols/cryst/refinable_lattice.hh
src/protocols/cryst/refinable_lattice.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ DockLatticeMover() [1/2]

◆ DockLatticeMover() [2/2]

Member Function Documentation

◆ apply()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ initialize()

◆ mover_name()

◆ parse_my_tag()

◆ perturb_chis()

◆ perturb_lattice()

◆ perturb_rb()

◆ provide_xml_schema()

◆ randomize_chis()

◆ regenerate_lattice()

◆ repack()

◆ set_defaults()

◆ set_ncycles()

◆ set_rot_mag()

◆ set_scorefunction()

◆ set_temp()

◆ set_trans_mag()

◆ slide_lattice()

Member Data Documentation

◆ Ajump_

◆ Bjump_

◆ chi_mag_

◆ Cjump_

◆ contact_dist_

◆ final_min_

◆ init_score_cut_

◆ kT_

◆ lattice_mag_

◆ min_

◆ min_lattice_

◆ mult_

◆ native_

◆ ncycles_

◆ pack_

◆ perturb_chi_

◆ randomize_

◆ recover_low_

◆ rot_mag_

◆ sf_

◆ spacegroup_

◆ SUBjump_

◆ symdofs_

◆ trans_mag_

◆ verbose_