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protocols::ligand_docking::HighResDocker Class Reference

#include <HighResDocker.hh>

Inheritance diagram for protocols::ligand_docking::HighResDocker:
Inheritance graph
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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...
 
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...
 
utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const override
 Provide a list of authors and their e-mail addresses, as strings. 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...
 

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)
 
- 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_
 

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

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

References resfile_.

protocols::ligand_docking::HighResDocker::~HighResDocker ( )
overridedefault
protocols::ligand_docking::HighResDocker::HighResDocker ( HighResDocker const &  that)
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 = "" 
)

Member Function Documentation

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

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.

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

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().

core::pack::task::PackerTaskOP protocols::ligand_docking::HighResDocker::make_packer_task ( core::pose::Pose const &  pose,
bool  all_residues = false 
) const
protected
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
std::string protocols::ligand_docking::HighResDocker::mover_name ( )
static
bool protocols::ligand_docking::HighResDocker::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::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_.

utility::vector1< basic::citation_manager::UnpublishedModuleInfoCOP > protocols::ligand_docking::HighResDocker::provide_authorship_info_for_unpublished ( ) const
overridevirtual

Provide a list of authors and their e-mail addresses, as strings.

Returns
A list of pairs of (author, e-mail address). This mover IS published, so it returns nothing for itself, but can return information for preselection filters and movers.

Reimplemented from protocols::moves::Mover.

utility::vector1< basic::citation_manager::CitationCollectionCOP > protocols::ligand_docking::HighResDocker::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.

Also provides citations for movers called by the HighResDocker.

Reimplemented from protocols::moves::Mover.

void protocols::ligand_docking::HighResDocker::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::ligand_docking::HighResDocker::remove_ligand_dihedral_restraints ( core::pose::Pose pose,
MinimizeLigandOPs minimized_ligands 
) const
protected

Referenced by apply().

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

Referenced by apply().

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

References movemap_builder_.

Referenced by apply().

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

References movemap_builder_.

Referenced by apply().

Member Data Documentation

std::vector<std::string> protocols::ligand_docking::HighResDocker::chains_
private
MoveMapBuilderOP protocols::ligand_docking::HighResDocker::movemap_builder_
private
core::Size protocols::ligand_docking::HighResDocker::num_cycles_
private

Referenced by apply(), and parse_my_tag().

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

Referenced by apply(), and parse_my_tag().

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