#include <HighResDocker.hh>

Inheritance diagram for protocols::ligand_docking::HighResDocker:

[legend]

Public Member Functions
	HighResDocker ()

	~HighResDocker () override

	HighResDocker (HighResDocker const &that)

	HighResDocker (core::Size num_cycles, core::Size repack_every_Nth, core::scoring::ScoreFunctionOP score_fxn, MoveMapBuilderOP movemap_builder, std::string const &resfile="")

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 &) override
	parse XML (specifically in the context of the parser/scripting scheme) More...

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

void	apply (utility::vector1< core::pose::Pose > &poses, utility::vector1< core::Real > &current_scores, utility::vector1< char > qsar_chars, core::Size cycle)

void	apply (core::pose::Pose &pose, core::Real &current_score, char qsar_char, core::Size cycle)

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

void	set_allow_repacking (bool input)

void	set_all_residues (bool input)

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...

Protected Member Functions
MinimizeLigandOPs	setup_ligands_to_minimize (core::pose::Pose &pose, char chain=0)

void	remove_ligand_dihedral_restraints (core::pose::Pose &pose, MinimizeLigandOPs &minimized_ligands) const

TetherLigandOPs	tether_ligands (core::pose::Pose &pose, char chain=0)

void	remove_ligand_tethers (core::pose::Pose pose, TetherLigandOPs ligand_tethers)

void	enable_ligand_rotamer_packing (core::pose::Pose const &pose, core::Size const ligand_residue_id, core::pack::task::PackerTaskOP &pack_task) const

core::pack::task::PackerTaskOP	make_packer_task (core::pose::Pose const &pose, bool all_residues=false) const

core::pack::task::PackerTaskOP	make_packer_task_from_vector (core::pose::Pose const &pose, ligand_options::Interface const &allow_repack) const

utility::vector1< protocols::moves::MoverOP >	create_rigid_body_movers (core::pose::Pose const &pose) const

void	apply_rigid_body_moves (core::pose::Pose &pose, utility::vector1< protocols::moves::MoverOP > &rigid_body_movers)

void	initialize_from_options ()
	function to be called by constructors to assign values to allow_minimization_, allow_repacking, and all_residues 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...

Private Attributes
core::Size	num_cycles_

core::Size	repack_every_Nth_

std::vector< std::string >	chains_

core::scoring::ScoreFunctionOP	score_fxn_

MoveMapBuilderOP	movemap_builder_

std::string	resfile_

bool	allow_minimization_ = true

bool	allow_repacking_ = true

bool	all_residues_ = false

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

Constructor & Destructor Documentation

◆ HighResDocker() [1/3]

protocols::ligand_docking::HighResDocker::HighResDocker ( )

References initialize_from_options(), and resfile_.

◆ ~HighResDocker()

protocols::ligand_docking::HighResDocker::~HighResDocker ( )

overridedefault

◆ HighResDocker() [2/3]

protocols::ligand_docking::HighResDocker::HighResDocker ( HighResDocker const & that )

References initialize_from_options().

◆ HighResDocker() [3/3]

protocols::ligand_docking::HighResDocker::HighResDocker	(	core::Size	num_cycles,
		core::Size	repack_every_Nth,
		core::scoring::ScoreFunctionOP	score_fxn,
		MoveMapBuilderOP	movemap_builder,
		std::string const &	resfile = `""`
	)

References initialize_from_options().

Member Function Documentation

◆ apply() [1/3]

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References all_residues_, allow_repacking_, apply_rigid_body_moves(), create_rigid_body_movers(), make_packer_task(), movemap_builder_, num_cycles_, remove_ligand_dihedral_restraints(), remove_ligand_tethers(), repack_every_Nth_, score_fxn_, setup_ligands_to_minimize(), tether_ligands(), and protocols::ligand_docking::TR().

◆ apply() [2/3]

void protocols::ligand_docking::HighResDocker::apply	(	core::pose::Pose &	pose,
		core::Real &	current_score,
		char	qsar_char,
		core::Size	cycle
	)

References all_residues_, allow_minimization_, allow_repacking_, apply_rigid_body_moves(), create_rigid_body_movers(), make_packer_task(), movemap_builder_, repack_every_Nth_, score_fxn_, setup_ligands_to_minimize(), tether_ligands(), and protocols::ligand_docking::TR().

◆ apply() [3/3]

void protocols::ligand_docking::HighResDocker::apply	(	utility::vector1< core::pose::Pose > &	poses,
		utility::vector1< core::Real > &	current_scores,
		utility::vector1< char >	qsar_chars,
		core::Size	cycle
	)

References all_residues_, allow_minimization_, allow_repacking_, apply_rigid_body_moves(), create_rigid_body_movers(), make_packer_task(), movemap_builder_, num_cycles_, repack_every_Nth_, score_fxn_, setup_ligands_to_minimize(), tether_ligands(), and protocols::ligand_docking::TR().

◆ apply_rigid_body_moves()

void protocols::ligand_docking::HighResDocker::apply_rigid_body_moves	(	core::pose::Pose &	pose,
		utility::vector1< protocols::moves::MoverOP > &	rigid_body_movers
	)

protected

Referenced by apply().

◆ clone()

protocols::moves::MoverOP protocols::ligand_docking::HighResDocker::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.

◆ create_rigid_body_movers()

utility::vector1< protocols::moves::MoverOP > protocols::ligand_docking::HighResDocker::create_rigid_body_movers ( core::pose::Pose const & pose ) const

protected

References core::pose::get_jump_ids_from_chain(), and movemap_builder_.

Referenced by apply().

◆ enable_ligand_rotamer_packing()

void protocols::ligand_docking::HighResDocker::enable_ligand_rotamer_packing	(	core::pose::Pose const &	pose,
		core::Size const	ligand_residue_id,
		core::pack::task::PackerTaskOP &	pack_task
	)		const

protected

References core::chemical::ResidueTypeBase::base_name(), protocols::vip::base_name(), core::chemical::ResidueTypeFinder::get_all_possible_residue_types(), core::chemical::ResidueTypeBase::mode(), core::conformation::Residue::name3(), core::chemical::ResidueTypeFinder::name3(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), and core::conformation::Residue::type().

Referenced by make_packer_task_from_vector().

◆ fresh_instance()

protocols::moves::MoverOP protocols::ligand_docking::HighResDocker::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::HighResDocker::get_name ( ) const

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

◆ initialize_from_options()

void protocols::ligand_docking::HighResDocker::initialize_from_options ( )

protected

function to be called by constructors to assign values to allow_minimization_, allow_repacking, and all_residues

References all_residues_, allow_minimization_, allow_repacking_, and protocols::ligand_docking::TR().

Referenced by HighResDocker().

◆ make_packer_task()

core::pack::task::PackerTaskOP protocols::ligand_docking::HighResDocker::make_packer_task	(	core::pose::Pose const &	pose,
		bool	all_residues = `false`
	)		const

protected

References protocols::ligand_docking::ligand_options::InterfaceInfo::is_interface, make_packer_task_from_vector(), movemap_builder_, and core::pose::Pose::size().

Referenced by apply().

◆ make_packer_task_from_vector()

core::pack::task::PackerTaskOP protocols::ligand_docking::HighResDocker::make_packer_task_from_vector	(	core::pose::Pose const &	pose,
		ligand_options::Interface const &	allow_repack
	)		const

protected

References core::chemical::ResidueTypeBase::base_name(), protocols::vip::base_name(), core::pack::task::TaskFactory::create_packer_task(), enable_ligand_rotamer_packing(), core::chemical::ResidueTypeFinder::get_all_possible_residue_types(), core::chemical::ResidueType::is_ligand(), core::conformation::Residue::is_ligand(), core::chemical::ResidueTypeBase::mode(), core::chemical::ResidueTypeBase::name3(), core::chemical::ResidueTypeFinder::name3(), protocols::ligand_docking::ligand_options::InterfaceInfo::non_interface, core::pack::task::parse_resfile(), resfile_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), core::pose::Pose::residue_type_set_for_pose(), core::pose::Pose::size(), core::pose::Pose::total_residue(), protocols::ligand_docking::TR(), and protocols::moves::Mover::type().

Referenced by make_packer_task().

◆ mover_name()

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

static

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

◆ parse_my_tag()

void protocols::ligand_docking::HighResDocker::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	datamap
	)

overridevirtual

parse XML (specifically in the context of the parser/scripting scheme)

Reimplemented from protocols::moves::Mover.

References movemap_builder_, num_cycles_, repack_every_Nth_, resfile_, and score_fxn_.

◆ provide_citation_info()

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

static

References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().

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

◆ remove_ligand_dihedral_restraints()

void protocols::ligand_docking::HighResDocker::remove_ligand_dihedral_restraints	(	core::pose::Pose &	pose,
		MinimizeLigandOPs &	minimized_ligands
	)		const

protected

Referenced by apply().

◆ remove_ligand_tethers()

void protocols::ligand_docking::HighResDocker::remove_ligand_tethers	(	core::pose::Pose	pose,
		TetherLigandOPs	ligand_tethers
	)

protected

Referenced by apply().

◆ set_all_residues()

void protocols::ligand_docking::HighResDocker::set_all_residues ( bool input )

References all_residues_.

◆ set_allow_repacking()

void protocols::ligand_docking::HighResDocker::set_allow_repacking ( bool input )

References allow_repacking_.

◆ setup_ligands_to_minimize()

MinimizeLigandOPs protocols::ligand_docking::HighResDocker::setup_ligands_to_minimize	(	core::pose::Pose &	pose,
		char	chain = `0`
	)

protected

References movemap_builder_.

Referenced by apply().

◆ tether_ligands()

TetherLigandOPs protocols::ligand_docking::HighResDocker::tether_ligands	(	core::pose::Pose &	pose,
		char	chain = `0`
	)

protected

References movemap_builder_.

Referenced by apply().

Member Data Documentation

◆ all_residues_

bool protocols::ligand_docking::HighResDocker::all_residues_ = false

private

Referenced by apply(), initialize_from_options(), and set_all_residues().

◆ allow_minimization_

bool protocols::ligand_docking::HighResDocker::allow_minimization_ = true

private

Referenced by apply(), and initialize_from_options().

◆ allow_repacking_

bool protocols::ligand_docking::HighResDocker::allow_repacking_ = true

private

Referenced by apply(), initialize_from_options(), and set_allow_repacking().

◆ chains_

std::vector<std::string> protocols::ligand_docking::HighResDocker::chains_

private

◆ movemap_builder_

MoveMapBuilderOP protocols::ligand_docking::HighResDocker::movemap_builder_

private

Referenced by apply(), create_rigid_body_movers(), make_packer_task(), parse_my_tag(), setup_ligands_to_minimize(), and tether_ligands().

◆ num_cycles_

core::Size protocols::ligand_docking::HighResDocker::num_cycles_

private

Referenced by apply(), and parse_my_tag().

◆ repack_every_Nth_

core::Size protocols::ligand_docking::HighResDocker::repack_every_Nth_

private

Referenced by apply(), and parse_my_tag().

◆ resfile_

std::string protocols::ligand_docking::HighResDocker::resfile_

private

Referenced by HighResDocker(), make_packer_task_from_vector(), and parse_my_tag().

◆ score_fxn_

core::scoring::ScoreFunctionOP protocols::ligand_docking::HighResDocker::score_fxn_

private

Referenced by apply(), and parse_my_tag().

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

src/protocols/ligand_docking/HighResDocker.hh
src/protocols/ligand_docking/HighResDocker.cc

Public Member Functions

Static Public Member Functions

Protected Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ HighResDocker() [1/3]

◆ ~HighResDocker()

◆ HighResDocker() [2/3]

◆ HighResDocker() [3/3]

Member Function Documentation

◆ apply() [1/3]

◆ apply() [2/3]

◆ apply() [3/3]

◆ apply_rigid_body_moves()

◆ clone()

◆ create_rigid_body_movers()

◆ enable_ligand_rotamer_packing()

◆ fresh_instance()

◆ get_name()

◆ initialize_from_options()

◆ make_packer_task()

◆ make_packer_task_from_vector()

◆ mover_name()

◆ parse_my_tag()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ remove_ligand_dihedral_restraints()

◆ remove_ligand_tethers()

◆ set_all_residues()

◆ set_allow_repacking()

◆ setup_ligands_to_minimize()

◆ tether_ligands()

Member Data Documentation

◆ all_residues_

◆ allow_minimization_

◆ allow_repacking_

◆ chains_

◆ movemap_builder_

◆ num_cycles_

◆ repack_every_Nth_

◆ resfile_

◆ score_fxn_