Rosetta  2021.16
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Static Public Member Functions | Protected Member Functions | Private Attributes | List of all members
protocols::ligand_docking::HighResDocker Class Reference

#include <HighResDocker.hh>

Inheritance diagram for protocols::ligand_docking::HighResDocker:
Inheritance graph

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 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 Stringsinfo ()
 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
< 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 ( )
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 )
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 

Referenced by apply().

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

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

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

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

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_.

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

Provide the citation.

Reimplemented from protocols::moves::Mover.

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

Referenced by apply().

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

Referenced by apply().

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

References movemap_builder_.

Referenced by apply().

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

References movemap_builder_.

Referenced by apply().

Member Data Documentation

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

Referenced by apply(), and parse_my_tag().

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

Referenced by apply(), and parse_my_tag().

std::string protocols::ligand_docking::HighResDocker::resfile_
core::scoring::ScoreFunctionOP protocols::ligand_docking::HighResDocker::score_fxn_

Referenced by apply(), and parse_my_tag().

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