#include <Transform.hh>

Inheritance diagram for protocols::ligand_docking::Transform:

[legend]

Public Member Functions
	Transform ()

	Transform (qsar::scoring_grid::GridSetCOP grid_prototype, std::string const &chain, core::Real const &box_size, core::Real const &move_distance, core::Real const &angle, core::Size const &cycles, core::Real const &temp)

	Transform (Transform const &other)

	~Transform () 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...

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	randomize_ligand (core::conformation::UltraLightResidue &residue, core::Real distance, core::Real angle)
	Performa a randomization of the ligand residue, translating by some random value within a uniform distribution with a max of distance, and rotating around a random axis with a uniformly random angle of between -angle/2 and +angle/2 (in degrees). Also randomizes starting conformer if available. More...

void	transform_ligand (core::conformation::UltraLightResidue &residue)
	translate and rotate a random value by the distances specified in the Transform_info object, using a gaussian distribution More...

void	setup_conformers (core::pose::Pose &pose, core::Size begin)
	setup conformers for use More...

bool	check_conformers (core::conformation::UltraLightResidue &starting_residue) const
	Check that conformers are safely within the grids. Returns true if good, false if bad. More...

core::Real	recommended_grid_size (core::Real success_rate=-1) const
	Return the recommended minimum size of the ligand grids for this particular setup. More...

core::Real	recommended_box_size (core::Real success_rate=-1) const
	Return the recommended minimum box size for this particular setup. More...

void	change_conformer (core::conformation::UltraLightResidue &residue)
	randomly change the ligand conformation More...

void	dump_conformer (core::conformation::UltraLightResidue &residue, utility::io::ozstream &output)
	output the ligand residues to a pdb file More...

bool	check_rmsd (core::conformation::UltraLightResidue const &start, core::conformation::UltraLightResidue const &current) const
	return true if the rmsd is within the specified cutoff More...

bool	check_grid (core::conformation::UltraLightResidue &ligand_residue, core::Real distance=0)
	check ligand still inside the grid More...

core::Real	score_ligand (core::conformation::UltraLightResidue &ligand_residue)
	Calculate unconstrained score for given ligand. More...

core::Real	score_constraints (core::pose::Pose &pose, core::conformation::UltraLightResidue &residue, core::scoring::ScoreFunctionOP &sfxn)
	score constraints by updating pose and applying score_function_ 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::conformation::UltraLightResidue &residue, core::Size chain_id)
	copy the ligand into the desired receptor model and update conformation using the best model 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 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 Member Functions
core::Real	estimate_mc_travel (core::Real success_rate=-1) const
	Estimate how much the ligand will travel during the MC translation. More...

Private Attributes
Transform_info	transform_info_

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

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

utility::vector1< core::conformation::UltraLightResidueOP >	ligand_conformers_

protocols::qsar::scoring_grid::GridSetCOP	grid_set_prototype_

bool	optimize_until_score_is_negative_ = false

bool	output_sampled_space_ = false

bool	check_rmsd_ = false

bool	use_conformers_ = true

bool	use_constraints_ = false

bool	use_main_model_ = false

std::string	ensemble_proteins_ = ""

std::string	cst_fa_file_ = ""

core::Real	cst_fa_weight_ = 1.0

std::string	sampled_space_file_

core::Real	initial_perturb_ = 0.0

core::Real	initial_angle_perturb_ = -360.0

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

◆ Transform() [1/3]

protocols::ligand_docking::Transform::Transform ( )

◆ Transform() [2/3]

protocols::ligand_docking::Transform::Transform	(	qsar::scoring_grid::GridSetCOP	grid_prototype,
		std::string const &	chain,
		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::Transform_info::angle, protocols::ligand_docking::Transform_info::box_size, protocols::ligand_docking::Transform_info::chain, protocols::ligand_docking::Transform_info::cycles, protocols::ligand_docking::Transform_info::move_distance, protocols::ligand_docking::Transform_info::temperature, and transform_info_.

◆ Transform() [3/3]

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

default

◆ ~Transform()

protocols::ligand_docking::Transform::~Transform ( )

overridedefault

Member Function Documentation

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::jd2::add_string_real_pair_to_current_job(), core::scoring::angle_constraint, core::scoring::atom_pair_constraint, protocols::ligand_docking::Transform_info::box_size, core::conformation::membrane::center, core::conformation::UltraLightResidue::center(), protocols::ligand_docking::Transform_info::chain, core::conformation::Conformation::chain_begin(), change_conformer(), check_conformers(), check_grid(), check_rmsd(), check_rmsd_, core::pose::Pose::clone(), core::pose::Pose::conformation(), convert_to_full_pose(), core::scoring::coordinate_constraint, cst_fa_file_, cst_fa_weight_, protocols::ligand_docking::Transform_info::cycles, core::scoring::dihedral_constraint, core::kinematics::distance(), protocols::geometry::downstream_centroid_by_jump(), dump_conformer(), ensemble_proteins_, protocols::moves::FAIL_RETRY, core::pose::get_chain_id_from_chain(), core::pose::get_jump_id_from_chain_id(), core::conformation::Residue::get_self_ptr(), grid_set_prototype_, grid_sets_, initial_angle_perturb_, initial_perturb_, ligand_conformers_, make_multi_pose_grids(), core::conformation::Residue::nbr_atom(), optimize_until_score_is_negative_, output_sampled_space_, protocols::simple_moves::bb_sampler::probability, randomize_ligand(), recommended_box_size(), recommended_grid_size(), protocols::ligand_docking::Transform_info::repeats, core::pose::Pose::residue(), core::scoring::rg, sampled_space_file_, score_constraints(), score_ligand(), protocols::moves::Mover::set_last_move_status(), setup_conformers(), protocols::ligand_docking::Transform_info::temperature, protocols::ligand_docking::TR(), transform_info_, transform_ligand(), use_conformers_, use_constraints_, and core::conformation::Residue::xyz().

◆ change_conformer()

void protocols::ligand_docking::Transform::change_conformer ( core::conformation::UltraLightResidue & residue )

randomly change the ligand conformation

References core::conformation::UltraLightResidue::align_to_residue(), ligand_conformers_, and core::scoring::rg.

Referenced by apply().

◆ check_conformers()

bool protocols::ligand_docking::Transform::check_conformers ( core::conformation::UltraLightResidue & starting_residue ) const

Check that conformers are safely within the grids. Returns true if good, false if bad.

References core::conformation::UltraLightResidue::align_to_residue(), grid_sets_, ligand_conformers_, recommended_grid_size(), and protocols::ligand_docking::TR().

Referenced by apply().

◆ check_grid()

bool protocols::ligand_docking::Transform::check_grid	(	core::conformation::UltraLightResidue &	ligand_residue,
		core::Real	distance = `0`
	)

check ligand still inside the grid

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

Referenced by apply().

◆ check_rmsd()

bool protocols::ligand_docking::Transform::check_rmsd	(	core::conformation::UltraLightResidue const &	start,
		core::conformation::UltraLightResidue const &	current
	)		const

return true if the rmsd is within the specified cutoff

References core::conformation::UltraLightResidue::natoms(), protocols::ligand_docking::Transform_info::rmsd, protocols::loops::start, and transform_info_.

Referenced by apply().

◆ clone()

protocols::moves::MoverOP protocols::ligand_docking::Transform::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::Transform::convert_to_full_pose	(	core::pose::Pose &	pose,
		core::conformation::UltraLightResidue &	residue,
		core::Size	chain_id
	)

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

References core::pose::Pose::append_residue_by_jump(), core::conformation::Conformation::chain_begin(), core::conformation::Conformation::chain_end(), core::pose::Pose::conformation(), grid_set_poses_, grid_sets_, core::pose::Pose::pdb_info(), core::pose::Pose::residue(), core::pose::Pose::size(), protocols::ligand_docking::TR(), core::conformation::UltraLightResidue::update_conformation(), and use_main_model_.

Referenced by apply().

◆ dump_conformer()

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

output the ligand residues to a pdb file

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

Referenced by apply().

◆ estimate_mc_travel()

core::Real protocols::ligand_docking::Transform::estimate_mc_travel ( core::Real success_rate = -1 ) const

private

Estimate how much the ligand will travel during the MC translation.

success_rate is the MC success rate. Will be bumped to a reasonable minimum

References protocols::ligand_docking::Transform_info::cycles, ligand_conformers_, protocols::ligand_docking::Transform_info::move_distance, transform_info_, and use_conformers_.

Referenced by recommended_box_size(), and recommended_grid_size().

◆ fresh_instance()

protocols::moves::MoverOP protocols::ligand_docking::Transform::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::Transform::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::Transform::make_multi_pose_grids ( core::Vector center )

Generate all extra grids.

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

Referenced by apply().

◆ mover_name()

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

static

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

◆ parse_my_tag()

void protocols::ligand_docking::Transform::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.

◆ provide_citation_info()

void protocols::ligand_docking::Transform::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::Transform::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::TransformCreator::provide_xml_schema().

◆ randomize_ligand()

void protocols::ligand_docking::Transform::randomize_ligand	(	core::conformation::UltraLightResidue &	residue,
		core::Real	distance,
		core::Real	angle
	)

Performa a randomization of the ligand residue, translating by some random value within a uniform distribution with a max of distance, and rotating around a random axis with a uniformly random angle of between -angle/2 and +angle/2 (in degrees). Also randomizes starting conformer if available.

References core::conformation::UltraLightResidue::center(), core::kinematics::distance(), core::scoring::rg, and core::conformation::UltraLightResidue::transform().

Referenced by apply().

◆ recommended_box_size()

core::Real protocols::ligand_docking::Transform::recommended_box_size ( core::Real success_rate = -1 ) const

Return the recommended minimum box size for this particular setup.

success_rate is the MC success rate. Will be bumped to a reasonable minimum

References estimate_mc_travel(), and initial_perturb_.

Referenced by apply().

◆ recommended_grid_size()

core::Real protocols::ligand_docking::Transform::recommended_grid_size ( core::Real success_rate = -1 ) const

Return the recommended minimum size of the ligand grids for this particular setup.

success_rate is the MC success rate. Will be bumped to a reasonable minimum

References estimate_mc_travel(), initial_perturb_, and ligand_conformers_.

Referenced by apply(), and check_conformers().

◆ score_constraints()

core::Real protocols::ligand_docking::Transform::score_constraints	(	core::pose::Pose &	pose,
		core::conformation::UltraLightResidue &	residue,
		core::scoring::ScoreFunctionOP &	sfxn
	)

score constraints by updating pose and applying score_function_

References core::pose::Pose::conformation(), and core::conformation::UltraLightResidue::update_conformation().

Referenced by apply().

◆ score_ligand()

core::Real protocols::ligand_docking::Transform::score_ligand ( core::conformation::UltraLightResidue & ligand_residue )

Calculate unconstrained score for given ligand.

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

Referenced by apply().

◆ setup_conformers()

void protocols::ligand_docking::Transform::setup_conformers	(	core::pose::Pose &	pose,
		core::Size	begin
	)

setup conformers for use

References core::pack::task::TaskFactory::create_packer_task(), core::conformation::Residue::get_self_ptr(), ligand_conformers_, core::pose::Pose::residue(), protocols::ligand_docking::rotamers_for_trials(), and protocols::ligand_docking::TR().

Referenced by apply().

◆ transform_ligand()

void protocols::ligand_docking::Transform::transform_ligand ( core::conformation::UltraLightResidue & residue )

translate and rotate a random value by the distances specified in the Transform_info object, using a gaussian distribution

References protocols::ligand_docking::Transform_info::angle, core::conformation::UltraLightResidue::center(), protocols::ligand_docking::Transform_info::move_distance, core::scoring::rg, protocols::ligand_docking::TR(), core::conformation::UltraLightResidue::transform(), and transform_info_.

Referenced by apply().

Member Data Documentation

◆ check_rmsd_

bool protocols::ligand_docking::Transform::check_rmsd_ = false

private

Referenced by apply(), and parse_my_tag().

◆ cst_fa_file_

std::string protocols::ligand_docking::Transform::cst_fa_file_ = ""

private

Referenced by apply(), and parse_my_tag().

◆ cst_fa_weight_

core::Real protocols::ligand_docking::Transform::cst_fa_weight_ = 1.0

private

Referenced by apply(), and parse_my_tag().

◆ ensemble_proteins_

std::string protocols::ligand_docking::Transform::ensemble_proteins_ = ""

private

Referenced by apply(), and parse_my_tag().

◆ grid_set_poses_

std::map<std::string, core::pose::Pose> protocols::ligand_docking::Transform::grid_set_poses_

private

Referenced by convert_to_full_pose(), make_multi_pose_grids(), and parse_my_tag().

◆ grid_set_prototype_

protocols::qsar::scoring_grid::GridSetCOP protocols::ligand_docking::Transform::grid_set_prototype_

private

Referenced by apply(), make_multi_pose_grids(), and parse_my_tag().

◆ grid_sets_

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

private

Referenced by apply(), check_conformers(), check_grid(), convert_to_full_pose(), make_multi_pose_grids(), and score_ligand().

◆ initial_angle_perturb_

core::Real protocols::ligand_docking::Transform::initial_angle_perturb_ = -360.0

private

Referenced by apply(), and parse_my_tag().

◆ initial_perturb_

core::Real protocols::ligand_docking::Transform::initial_perturb_ = 0.0

private

Referenced by apply(), parse_my_tag(), recommended_box_size(), and recommended_grid_size().

◆ ligand_conformers_

utility::vector1< core::conformation::UltraLightResidueOP > protocols::ligand_docking::Transform::ligand_conformers_

private

Referenced by apply(), change_conformer(), check_conformers(), estimate_mc_travel(), recommended_grid_size(), and setup_conformers().

◆ optimize_until_score_is_negative_

bool protocols::ligand_docking::Transform::optimize_until_score_is_negative_ = false

private

Referenced by apply(), and parse_my_tag().

◆ output_sampled_space_

bool protocols::ligand_docking::Transform::output_sampled_space_ = false

private

Referenced by apply(), and parse_my_tag().

◆ sampled_space_file_

std::string protocols::ligand_docking::Transform::sampled_space_file_

private

Referenced by apply(), and parse_my_tag().

◆ transform_info_

Transform_info protocols::ligand_docking::Transform::transform_info_

private

Referenced by apply(), check_grid(), check_rmsd(), estimate_mc_travel(), make_multi_pose_grids(), parse_my_tag(), Transform(), and transform_ligand().

◆ use_conformers_

bool protocols::ligand_docking::Transform::use_conformers_ = true

private

Referenced by apply(), estimate_mc_travel(), and parse_my_tag().

◆ use_constraints_

bool protocols::ligand_docking::Transform::use_constraints_ = false

private

Referenced by apply(), and parse_my_tag().

◆ use_main_model_

bool protocols::ligand_docking::Transform::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/Transform.hh
src/protocols/ligand_docking/Transform.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ Transform() [1/3]

◆ Transform() [2/3]

◆ Transform() [3/3]

◆ ~Transform()

Member Function Documentation

◆ apply()

◆ change_conformer()

◆ check_conformers()

◆ check_grid()

◆ check_rmsd()

◆ clone()

◆ convert_to_full_pose()

◆ dump_conformer()

◆ estimate_mc_travel()

◆ fresh_instance()

◆ get_name()

◆ make_multi_pose_grids()

◆ mover_name()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ randomize_ligand()

◆ recommended_box_size()

◆ recommended_grid_size()

◆ score_constraints()

◆ score_ligand()

◆ setup_conformers()

◆ transform_ligand()

Member Data Documentation

◆ check_rmsd_

◆ cst_fa_file_

◆ cst_fa_weight_

◆ ensemble_proteins_

◆ grid_set_poses_

◆ grid_set_prototype_

◆ grid_sets_

◆ initial_angle_perturb_

◆ initial_perturb_

◆ ligand_conformers_

◆ optimize_until_score_is_negative_

◆ output_sampled_space_

◆ sampled_space_file_

◆ transform_info_

◆ use_conformers_

◆ use_constraints_

◆ use_main_model_