#include <StartFrom.hh>

Inheritance diagram for protocols::ligand_docking::StartFrom:

[legend]

Public Member Functions
	StartFrom ()

	~StartFrom () override

	StartFrom (StartFrom const &that)

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	add_coords (core::Vector const &coords, std::string const &pdb_tag="default")
	Add the given coordinates as a valid starting position for the given pdb_tag. More...

void	add_coords_hash (core::Vector const &coords, std::string const &hash_value)
	Add the given coordinates as a valid starting position for the given structure hash. More...

void	chain (utility::vector1< std::string > const &chains)
	Set which chains the mover operates on. More...

void	chain (std::string const &chain)
	Add a chain to the mover targets. More...

std::string	chain ()
	Get which chains the mover operates on. More...

void	use_nbr (bool setting)
	Set if we should use the neighbor atom or the all-atom centroid to center the ligand. More...

bool	use_nbr ()
	Get whether we should use the neighbor atom or the all-atom centroid to center the ligand. More...

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

void	parse_startfrom_file (std::string const &filename)
	Parse the json-format startfrom file. More...

void	parse_pdb_file (std::string const &filename, std::string const &atom_name="", std::string const &tag="default")
	Parse a PDB file, grabbing the positions from the heavy atom coordinates. If atom_name is not empty, only grab coordinates from the specified atom name. 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 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
utility::vector1< std::string >	chains_
	The chain which to move. More...

bool	use_nbr_
	If true, try to center the chain based on the neighbor atom of the first residue Otherwise, use the all-atom centroid of the chain. More...

std::map< std::string, utility::vector1< core::Vector > >	starting_positions_
	The possible starting positions, indexed by tag (or "default") More...

std::map< std::string, utility::vector1< core::Vector > >	hash_starting_positions_
	The possible starting positions, indexed by hash. More...

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

◆ StartFrom() [1/2]

protocols::ligand_docking::StartFrom::StartFrom ( )

◆ ~StartFrom()

protocols::ligand_docking::StartFrom::~StartFrom ( )

overridedefault

◆ StartFrom() [2/2]

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

default

Member Function Documentation

◆ add_coords()

void protocols::ligand_docking::StartFrom::add_coords	(	core::Vector const &	coords,
		std::string const &	pdb_tag = `"default"`
	)

Add the given coordinates as a valid starting position for the given pdb_tag.

References protocols::simple_filters::coords(), and starting_positions_.

Referenced by parse_my_tag(), parse_pdb_file(), and parse_startfrom_file().

◆ add_coords_hash()

void protocols::ligand_docking::StartFrom::add_coords_hash	(	core::Vector const &	coords,
		std::string const &	hash_value
	)

Add the given coordinates as a valid starting position for the given structure hash.

Add the given coordinates as a valid starting position for the given hash value.

References protocols::simple_filters::coords(), hash_starting_positions_, and boost::tuples::hash_value().

Referenced by parse_startfrom_file().

◆ apply()

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

overridevirtual

Main Method.

Implements protocols::moves::Mover.

References protocols::vip::base_name(), chain(), chains_, protocols::jd2::current_input_tag(), protocols::abinitio::filename(), core::pose::get_sha1_hash_excluding_chain(), protocols::jd2::get_string_real_pairs_from_current_job(), core::pose::has_chain(), hash_starting_positions_, protocols::ligand_docking::move_ligand_neighbor_to_desired_position(), protocols::ligand_docking::move_ligand_to_desired_centroid(), core::scoring::rg, protocols::sparta::split(), starting_positions_, protocols::ligand_docking::TR(), and use_nbr_.

◆ chain() [1/3]

std::string protocols::ligand_docking::StartFrom::chain ( )

inline

Get which chains the mover operates on.

References chains_.

Referenced by apply(), and chain().

◆ chain() [2/3]

void protocols::ligand_docking::StartFrom::chain ( std::string const & chain )

inline

Add a chain to the mover targets.

References chain(), and chains_.

◆ chain() [3/3]

void protocols::ligand_docking::StartFrom::chain ( utility::vector1< std::string > const & chains )

inline

Set which chains the mover operates on.

References chains_.

◆ clone()

protocols::moves::MoverOP protocols::ligand_docking::StartFrom::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.

◆ fresh_instance()

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

overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

Referenced by provide_citation_info().

◆ mover_name()

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

static

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

◆ parse_my_tag()

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

overridevirtual

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

Reimplemented from protocols::moves::Mover.

References add_coords(), chains_, protocols::moves::Mover::name(), parse_pdb_file(), parse_startfrom_file(), protocols::ligand_docking::TR(), and use_nbr().

◆ parse_pdb_file()

void protocols::ligand_docking::StartFrom::parse_pdb_file	(	std::string const &	filename,
		std::string const &	atom_name = `""`,
		std::string const &	tag = `"default"`
	)

Parse a PDB file, grabbing the positions from the heavy atom coordinates. If atom_name is not empty, only grab coordinates from the specified atom name.

References protocols::cluster::calibur::aa, add_coords(), core::io::pdb::create_sfr_from_pdb_file_contents(), core::io::pose_from_sfr::create_working_data(), core::io::AtomInformation::element, protocols::abinitio::filename(), core::io::AtomInformation::name, protocols::moves::Mover::name(), protocols::ligand_docking::TR(), core::io::AtomInformation::x, core::io::AtomInformation::y, and core::io::AtomInformation::z.

Referenced by parse_my_tag().

◆ parse_startfrom_file()

void protocols::ligand_docking::StartFrom::parse_startfrom_file ( std::string const & filename )

Parse the json-format startfrom file.

References add_coords(), add_coords_hash(), protocols::simple_filters::coords(), protocols::abinitio::filename(), and core::conformation::membrane::in.

Referenced by parse_my_tag().

◆ provide_citation_info()

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

overridevirtual

Provide the citation.

Reimplemented from protocols::moves::Mover.

References get_name().

◆ provide_xml_schema()

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

static

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

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

◆ use_nbr() [1/2]

bool protocols::ligand_docking::StartFrom::use_nbr ( )

inline

Get whether we should use the neighbor atom or the all-atom centroid to center the ligand.

References use_nbr_.

Referenced by parse_my_tag().

◆ use_nbr() [2/2]

void protocols::ligand_docking::StartFrom::use_nbr ( bool setting )

inline

Set if we should use the neighbor atom or the all-atom centroid to center the ligand.

References use_nbr_.

Member Data Documentation

◆ chains_

utility::vector1<std::string> protocols::ligand_docking::StartFrom::chains_

private

The chain which to move.

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

◆ hash_starting_positions_

std::map< std::string, utility::vector1<core::Vector> > protocols::ligand_docking::StartFrom::hash_starting_positions_

private

The possible starting positions, indexed by hash.

Referenced by add_coords_hash(), and apply().

◆ starting_positions_

std::map< std::string, utility::vector1<core::Vector> > protocols::ligand_docking::StartFrom::starting_positions_

private

The possible starting positions, indexed by tag (or "default")

Referenced by add_coords(), and apply().

◆ use_nbr_

bool protocols::ligand_docking::StartFrom::use_nbr_

private

If true, try to center the chain based on the neighbor atom of the first residue Otherwise, use the all-atom centroid of the chain.

Referenced by apply(), and use_nbr().

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

src/protocols/ligand_docking/StartFrom.hh
src/protocols/ligand_docking/StartFrom.cc

Public Member Functions

Static Public Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

◆ StartFrom() [1/2]

◆ ~StartFrom()

◆ StartFrom() [2/2]

Member Function Documentation

◆ add_coords()

◆ add_coords_hash()

◆ apply()

◆ chain() [1/3]

◆ chain() [2/3]

◆ chain() [3/3]

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ mover_name()

◆ parse_my_tag()

◆ parse_pdb_file()

◆ parse_startfrom_file()

◆ provide_citation_info()

◆ provide_xml_schema()

◆ use_nbr() [1/2]

◆ use_nbr() [2/2]

Member Data Documentation

◆ chains_

◆ hash_starting_positions_

◆ starting_positions_

◆ use_nbr_