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protocols::ligand_docking::StartFrom Class Reference

#include <StartFrom.hh>

Inheritance diagram for protocols::ligand_docking::StartFrom:
Inheritance graph
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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...
 
bool mover_provides_citation_info () const override
 Does this mover provide information about how to cite it? More...
 
utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () 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 Stringsinfo ()
 non-const accessor More...
 
virtual Strings const & info () const
 const accessor More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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

protocols::ligand_docking::StartFrom::StartFrom ( )
protocols::ligand_docking::StartFrom::~StartFrom ( )
overridedefault
protocols::ligand_docking::StartFrom::StartFrom ( StartFrom const &  that)
default

Member Function Documentation

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 starting_positions_.

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

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 hash_starting_positions_, and boost::tuples::hash_value().

Referenced by parse_startfrom_file().

void protocols::ligand_docking::StartFrom::apply ( core::pose::Pose )
overridevirtual
void protocols::ligand_docking::StartFrom::chain ( utility::vector1< std::string > const &  chains)
inline

Set which chains the mover operates on.

References chains_.

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

Add a chain to the mover targets.

References chains_.

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

Get which chains the mover operates on.

References chains_.

Referenced by apply().

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.

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.

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().

std::string protocols::ligand_docking::StartFrom::mover_name ( )
static
bool protocols::ligand_docking::StartFrom::mover_provides_citation_info ( ) const
overridevirtual

Does this mover provide information about how to cite it?

Returns true.

Reimplemented from protocols::moves::Mover.

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().

void protocols::ligand_docking::StartFrom::parse_pdb_file ( std::string const &  filename,
std::string const &  atom_name = "",
std::string const &  tag = "default" 
)
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(), and core::conformation::membrane::in.

Referenced by parse_my_tag().

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::ligand_docking::StartFrom::provide_citation_info ( ) const
overridevirtual

Provide the citation.

Returns
A vector of citation collections. This allows the mover to provide citations for itself and for any modules that it invokes.

Reimplemented from protocols::moves::Mover.

References get_name().

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

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().

Member Data Documentation

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

The chain which to move.

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

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().

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().

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: