Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker Class Reference

#include <PolarHydrogenPacker.hh>

Inheritance diagram for protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker:
Inheritance graph

Public Member Functions

 PolarHydrogenPacker ()
 ~PolarHydrogenPacker () override
void apply (core::pose::Pose &pose) override
 Apply the corresponding move to <pose>. More...
std::string get_name () const override
 Return the name of the Mover. More...
void set_allow_virtual_o2prime_hydrogens (bool const setting)
- 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 MoverOP clone () const
 Return a clone of the Mover object. 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...
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
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_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. 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...

Private Member Functions

void init ()
void check_hbond_score (core::Vector const &H_xyz, core::Vector const &D_xyz, core::Real &best_score, core::Vector &best_hydrogen_xyz)
void get_best_hxyz (core::conformation::Residue const &residue, utility::vector1< core::Vector > const &ideal_hydrogen_xyz_positions, core::Size const abase, core::Size const abase2, core::Vector const &donor_xyz, core::Real &best_score, core::Vector &best_hydrogen_xyz)
utility::vector1< core::Vectorget_ideal_hxyz_positions (core::conformation::Residue const &residue, core::conformation::Residue const &ideal_res, core::Size const j, core::kinematics::Stub const &current_input_stub, core::kinematics::Stub const &ideal_input_stub)
void virtualize_poor_scoring_o2prime_hydrogens (core::pose::Pose &pose, core::Size const i, core::Size const j, core::Real const best_score)
void get_possible_hbond_acceptors (core::pose::Pose const &pose, core::Size const moving_res, core::Size const atomno)

Private Attributes

core::scoring::hbonds::HBondOptionsOP hbond_options_
core::scoring::hbonds::HBondDatabaseCOP hbond_database_
< utility::vector1
< core::Vector > > 
< core::scoring::hbonds::HBEvalTuple
bool allow_virtual_o2prime_hydrogens_
bool disallow_vary_geometry_proton_chi_

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
- 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 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::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::PolarHydrogenPacker ( )

References init().

protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::~PolarHydrogenPacker ( )

Member Function Documentation

void protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::apply ( core::pose::Pose pose)
void protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::check_hbond_score ( core::Vector const &  H_xyz,
core::Vector const &  D_xyz,
core::Real best_score,
core::Vector best_hydrogen_xyz 
void protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_best_hxyz ( core::conformation::Residue const &  residue,
utility::vector1< core::Vector > const &  ideal_hydrogen_xyz_positions,
core::Size const  abase,
core::Size const  abase2,
core::Vector const &  donor_xyz,
core::Real best_score,
core::Vector best_hydrogen_xyz 
utility::vector1< Vector > protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_ideal_hxyz_positions ( core::conformation::Residue const &  residue,
core::conformation::Residue const &  ideal_res,
core::Size const  j,
core::kinematics::Stub const &  current_input_stub,
core::kinematics::Stub const &  ideal_input_stub 
std::string protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_name ( ) const

Return the name of the Mover.

Implements protocols::moves::Mover.

void protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::get_possible_hbond_acceptors ( core::pose::Pose const &  pose,
core::Size const  moving_res,
core::Size const  atomno 
void protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::init ( void  )

References hbond_database_, and hbond_options_.

Referenced by PolarHydrogenPacker().

void protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::set_allow_virtual_o2prime_hydrogens ( bool const  setting)
void protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::virtualize_poor_scoring_o2prime_hydrogens ( core::pose::Pose pose,
core::Size const  i,
core::Size const  j,
core::Real const  best_score 

Member Data Documentation

bool protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::allow_virtual_o2prime_hydrogens_
bool protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::disallow_vary_geometry_proton_chi_

Referenced by apply(), and get_ideal_hxyz_positions().

utility::vector1< core::scoring::hbonds::HBEvalTuple > protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::hb_eval_tuples_
core::scoring::hbonds::HBondDatabaseCOP protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::hbond_database_

Referenced by check_hbond_score(), and init().

core::scoring::hbonds::HBondOptionsOP protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::hbond_options_

Referenced by check_hbond_score(), and init().

utility::vector1< utility::vector1< core::Vector > > protocols::stepwise::modeler::polar_hydrogens::PolarHydrogenPacker::possible_hbond_acceptors_

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