#include <TransformEnsemble.hh>

Inheritance diagram for protocols::ligand_docking::TransformEnsemble:

[legend]

Public Member Functions
	TransformEnsemble ()

	TransformEnsemble (protocols::qsar::scoring_grid::GridSetCOP grid_set_prototype, utility::vector1< std::string > const &chains, core::Real const &box_size, core::Real const &move_distance, core::Real const &angle, core::Size const &cycles, core::Real const &temp)

	TransformEnsemble (TransformEnsemble const &other)

	~TransformEnsemble () override

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

core::Vector	weighted_center (utility::vector1< core::conformation::UltraLightResidue > &residues)

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

void	translate_ligand (utility::vector1< core::conformation::UltraLightResidue > &ligand_residues, utility::vector1< core::conformation::UltraLightResidue > &reference_residues, core::Real distance)

void	transform_ligand (utility::vector1< core::conformation::UltraLightResidue > &ligand_residues, utility::vector1< core::conformation::UltraLightResidue > &reference_residues)

void	change_conformers (utility::vector1< core::conformation::UltraLightResidue > &ligand_residues, const utility::vector1< core::conformation::UltraLightResidue > &reference_residues)

void	change_conformer (core::conformation::UltraLightResidue &ligand_residue, const core::conformation::UltraLightResidue &reference_residue, core::Size resid)

void	dump_conformer (core::conformation::UltraLightResidue const &residue, utility::io::ozstream &output)

void	print_xyz (core::Vector vector)

bool	monte_carlo (core::Real &current, core::Real &last)

bool	check_grid (utility::vector1< core::conformation::UltraLightResidue > &ligand_residues, core::Real distance=0)

core::Real	score_ligands (utility::vector1< core::conformation::UltraLightResidue > &ligand_residues)
	Calculate unconstrained score for given ligands. More...

void	make_multi_pose_grids (core::Vector center)
	Generate all extra grids. More...

core::Real	convert_to_full_pose (core::pose::Pose &pose, core::Size &best_pose_count)
	copy the ligand into the desired receptor model and update conformation using the best model More...

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

void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const override
	Provide the citation. 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...

Static Public Member Functions
static void	provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)

static std::string	mover_name ()

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
protocols::qsar::scoring_grid::GridSetCOP	grid_set_prototype_

utility::vector1< std::pair< std::string, qsar::scoring_grid::GridSetCOP > >	grid_sets_

std::map< std::string, core::pose::Pose >	grid_set_poses_

TransformEnsemble_info	transform_info_

utility::vector1< core::conformation::UltraLightResidue >	best_ligands_

utility::vector1< core::conformation::UltraLightResidue >	ligand_residues_

utility::vector1< core::conformation::UltraLightResidue >	reference_residues_

utility::vector1< core::conformation::UltraLightResidue >	last_accepted_ligand_residues_

utility::vector1< core::conformation::UltraLightResidue >	last_accepted_reference_residues_

std::map< core::Size, utility::vector1< core::conformation::ResidueOP > >	ligand_conformers_

std::string	ensemble_proteins_ = ""

bool	optimize_until_score_is_negative_ = false

bool	output_sampled_space_ = false

bool	use_conformers_ = true

bool	use_main_model_ = false

std::string	sampled_space_file_

core::Real	initial_perturb_ = 0.0

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

◆ TransformEnsemble() [1/3]

protocols::ligand_docking::TransformEnsemble::TransformEnsemble ( )

◆ TransformEnsemble() [2/3]

protocols::ligand_docking::TransformEnsemble::TransformEnsemble	(	protocols::qsar::scoring_grid::GridSetCOP	grid_set_prototype,
		utility::vector1< std::string > const &	chains,
		core::Real const &	box_size,
		core::Real const &	move_distance,
		core::Real const &	angle,
		core::Size const &	cycles,
		core::Real const &	temp
	)

References protocols::ligand_docking::TransformEnsemble_info::angle, protocols::ligand_docking::TransformEnsemble_info::box_size, protocols::ligand_docking::TransformEnsemble_info::chains, protocols::ligand_docking::TransformEnsemble_info::cycles, protocols::ligand_docking::TransformEnsemble_info::move_distance, protocols::ligand_docking::TransformEnsemble_info::temperature, and transform_info_.

◆ TransformEnsemble() [3/3]

protocols::ligand_docking::TransformEnsemble::TransformEnsemble ( TransformEnsemble const & other )

default

◆ ~TransformEnsemble()

protocols::ligand_docking::TransformEnsemble::~TransformEnsemble ( )

overridedefault

Member Function Documentation

◆ apply()

void protocols::ligand_docking::TransformEnsemble::apply ( core::pose::Pose & )

overridevirtual

Main Method.

Implements protocols::moves::Mover.

◆ change_conformer()

void protocols::ligand_docking::TransformEnsemble::change_conformer	(	core::conformation::UltraLightResidue &	ligand_residue,
		const core::conformation::UltraLightResidue &	reference_residue,
		core::Size	resid
	)

References core::conformation::UltraLightResidue::align_to_residue(), ligand_conformers_, and protocols::ligand_docking::transform_tracer().

Referenced by apply(), and change_conformers().

◆ change_conformers()

void protocols::ligand_docking::TransformEnsemble::change_conformers	(	utility::vector1< core::conformation::UltraLightResidue > &	ligand_residues,
		const utility::vector1< core::conformation::UltraLightResidue > &	reference_residues
	)

References change_conformer().

◆ check_grid()

bool protocols::ligand_docking::TransformEnsemble::check_grid	(	utility::vector1< core::conformation::UltraLightResidue > &	ligand_residues,
		core::Real	distance = `0`
	)

References protocols::ligand_docking::TransformEnsemble_info::box_size, core::kinematics::distance(), grid_sets_, transform_info_, and protocols::ligand_docking::transform_tracer().

Referenced by apply().

◆ clone()

protocols::moves::MoverOP protocols::ligand_docking::TransformEnsemble::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.

◆ convert_to_full_pose()

core::Real protocols::ligand_docking::TransformEnsemble::convert_to_full_pose	(	core::pose::Pose &	pose,
		core::Size &	best_pose_count
	)

copy the ligand into the desired receptor model and update conformation using the best model

References best_ligands_, core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), protocols::ligand_docking::TransformEnsemble_info::chain_ids(), core::pose::Pose::conformation(), grid_set_poses_, grid_sets_, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), transform_info_, protocols::ligand_docking::transform_tracer(), and use_main_model_.

Referenced by apply().

◆ dump_conformer()

void protocols::ligand_docking::TransformEnsemble::dump_conformer	(	core::conformation::UltraLightResidue const &	residue,
		utility::io::ozstream &	output
	)

References protocols::simple_filters::coords(), core::chemical::element::F, core::chemical::element::I, and core::conformation::UltraLightResidue::natoms().

Referenced by apply().

◆ fresh_instance()

protocols::moves::MoverOP protocols::ligand_docking::TransformEnsemble::fresh_instance ( ) const

overridevirtual

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::ligand_docking::TransformEnsemble::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ make_multi_pose_grids()

void protocols::ligand_docking::TransformEnsemble::make_multi_pose_grids ( core::Vector center )

Generate all extra grids.

References core::conformation::membrane::center, protocols::ligand_docking::TransformEnsemble_info::chains, protocols::qsar::scoring_grid::GridManager::get_grids(), grid_set_poses_, grid_set_prototype_, grid_sets_, and transform_info_.

Referenced by apply().

◆ monte_carlo()

bool protocols::ligand_docking::TransformEnsemble::monte_carlo	(	core::Real &	current,
		core::Real &	last
	)

References protocols::simple_moves::bb_sampler::probability, protocols::ligand_docking::TransformEnsemble_info::temperature, transform_info_, and protocols::ligand_docking::transform_tracer().

Referenced by apply().

◆ mover_name()

std::string protocols::ligand_docking::TransformEnsemble::mover_name ( )

static

Referenced by get_name(), protocols::ligand_docking::TransformEnsembleCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::ligand_docking::TransformEnsemble::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 protocols::ligand_docking::TransformEnsemble_info::angle, protocols::ligand_docking::TransformEnsemble_info::box_size, protocols::ligand_docking::TransformEnsemble_info::chains, protocols::ligand_docking::TransformEnsemble_info::cycles, ensemble_proteins_, grid_set_poses_, grid_set_prototype_, initial_perturb_, protocols::ligand_docking::TransformEnsemble_info::move_distance, optimize_until_score_is_negative_, output_sampled_space_, protocols::qsar::scoring_grid::parse_grid_set_from_tag(), core::import_pose::PDB_file, core::import_pose::pose_from_file(), protocols::ligand_docking::TransformEnsemble_info::repeats, sampled_space_file_, protocols::ligand_docking::TransformEnsemble_info::temperature, transform_info_, use_conformers_, and use_main_model_.

◆ print_xyz()

void protocols::ligand_docking::TransformEnsemble::print_xyz ( core::Vector vector )

References protocols::ligand_docking::transform_tracer().

◆ provide_citation_info()

void protocols::ligand_docking::TransformEnsemble::provide_citation_info ( basic::citation_manager::CitationCollectionList & citations ) const

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

◆ provide_xml_schema()

void protocols::ligand_docking::TransformEnsemble::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References protocols::qsar::scoring_grid::attributes_for_parse_grid_set_from_tag(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::ligand_docking::TransformEnsembleCreator::provide_xml_schema().

◆ score_ligands()

core::Real protocols::ligand_docking::TransformEnsemble::score_ligands ( utility::vector1< core::conformation::UltraLightResidue > & ligand_residues )

Calculate unconstrained score for given ligands.

References grid_sets_, protocols::hybridization::score, and protocols::ligand_docking::transform_tracer().

Referenced by apply().

◆ transform_ligand()

void protocols::ligand_docking::TransformEnsemble::transform_ligand	(	utility::vector1< core::conformation::UltraLightResidue > &	ligand_residues,
		utility::vector1< core::conformation::UltraLightResidue > &	reference_residues
	)

References protocols::ligand_docking::TransformEnsemble_info::angle, protocols::ligand_docking::TransformEnsemble_info::move_distance, transform_info_, protocols::ligand_docking::transform_tracer(), and weighted_center().

Referenced by apply().

◆ translate_ligand()

void protocols::ligand_docking::TransformEnsemble::translate_ligand	(	utility::vector1< core::conformation::UltraLightResidue > &	ligand_residues,
		utility::vector1< core::conformation::UltraLightResidue > &	reference_residues,
		core::Real	distance
	)

References core::kinematics::distance(), and weighted_center().

Referenced by apply().

◆ weighted_center()

core::Vector protocols::ligand_docking::TransformEnsemble::weighted_center ( utility::vector1< core::conformation::UltraLightResidue > & residues )

TransformEnsemble_info protocols::ligand_docking::TransformEnsemble::transform_info_

private

Referenced by apply(), check_grid(), convert_to_full_pose(), make_multi_pose_grids(), monte_carlo(), parse_my_tag(), transform_ligand(), and TransformEnsemble().

◆ use_conformers_

bool protocols::ligand_docking::TransformEnsemble::use_conformers_ = true

private

Referenced by apply(), and parse_my_tag().

◆ use_main_model_

bool protocols::ligand_docking::TransformEnsemble::use_main_model_ = false

private

Referenced by convert_to_full_pose(), and parse_my_tag().

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

src/protocols/ligand_docking/TransformEnsemble.hh
src/protocols/ligand_docking/TransformEnsemble.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ TransformEnsemble() [1/3]

◆ TransformEnsemble() [2/3]

◆ TransformEnsemble() [3/3]

◆ ~TransformEnsemble()

Member Function Documentation

◆ apply()

◆ change_conformer()

◆ change_conformers()

◆ check_grid()

◆ clone()

◆ convert_to_full_pose()

◆ dump_conformer()

◆ fresh_instance()

◆ get_name()

◆ make_multi_pose_grids()

◆ monte_carlo()

◆ mover_name()

◆ parse_my_tag()

◆ print_xyz()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ score_ligands()

◆ transform_ligand()

◆ translate_ligand()

◆ weighted_center()

Member Data Documentation

◆ best_ligands_

◆ ensemble_proteins_

◆ grid_set_poses_

◆ grid_set_prototype_

◆ grid_sets_

◆ initial_perturb_

◆ last_accepted_ligand_residues_

◆ last_accepted_reference_residues_

◆ ligand_conformers_

◆ ligand_residues_

◆ optimize_until_score_is_negative_

◆ output_sampled_space_

◆ reference_residues_

◆ sampled_space_file_

◆ transform_info_

◆ use_conformers_

◆ use_main_model_