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protocols::motifs::MotifDnaPacker Class Reference

#include <MotifDnaPacker.hh>

Inheritance diagram for protocols::motifs::MotifDnaPacker:
Inheritance graph
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Public Member Functions

 MotifDnaPacker ()
 lightweight default constructor More...
 
 MotifDnaPacker (core::scoring::ScoreFunctionOP, bool minimize=false, std::string filename_root="dnapacker")
 
 ~MotifDnaPacker () override
 destructor More...
 
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
 
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
 
void apply (core::pose::Pose &) override
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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
 
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...
 

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 Member Functions

void init_standard (core::pose::Pose &)
 
void init_options ()
 
void run_motifs (core::pose::Pose &pose, utility::vector1< core::Size > &design_positions, std::set< core::Size > &src_pos, std::map< core::Size, core::pack::rotamer_set::Rotamers > &rotamer_map, std::map< core::Size, std::set< std::string > > &types_map, std::list< std::string > &info_lines, core::pack::task::TaskFactoryOP taskfactory)
 
void expand_motifs (core::pose::Pose &pose, utility::vector1< core::Size > &design_positions, std::set< core::Size > &src_pos, std::map< core::Size, core::pack::rotamer_set::Rotamers > &rotamer_map, std::map< core::Size, std::set< std::string > > &types_map, std::list< std::string > &info_lines, core::pack::task::TaskFactoryOP taskfactory)
 
void aromatic_motifs (core::pose::Pose &pose, utility::vector1< core::Size > &design_positions, std::set< core::Size > &src_pos, std::map< core::Size, core::pack::rotamer_set::Rotamers > &rotamer_map, std::map< core::Size, std::set< std::string > > &types_map, std::list< std::string > &info_lines, core::pack::task::TaskFactoryOP taskfactory)
 
void motif_expansion_inner_loop (core::pose::Pose &pose, std::set< core::Size > current_pos, std::map< core::Size, core::pack::rotamer_set::Rotamers >::const_iterator it, std::set< std::string >::const_iterator it2, std::map< core::Size, core::pack::rotamer_set::Rotamers > &rotamer_map, std::list< std::string > &info_lines, core::pack::task::TaskFactoryOP taskfactory)
 

Private Attributes

protocols::dna::DnaInterfacePackerOP dna_packer_
 
protocols::motifs::MotifSearchOP motif_search_
 
core::scoring::ScoreFunctionOP scorefxn_
 
protocols::dna::PDBOutputOP pdboutput_
 
core::pose::PoseCOP starting_pose_
 
protocols::dna::DnaDesignDefOPs targeted_dna_
 
bool run_motifs_
 
bool expand_motifs_
 
bool aromatic_motifs_
 
bool minimize_dna_
 
core::Real special_rotweight_
 
core::Real num_repacks_
 
bool flex_dna_sugar_
 
std::string filename_root_
 
bool dna_design_
 

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::motifs::MotifDnaPacker::MotifDnaPacker ( )

lightweight default constructor

References init_options().

protocols::motifs::MotifDnaPacker::MotifDnaPacker ( core::scoring::ScoreFunctionOP  ,
bool  minimize = false,
std::string  filename_root = "dnapacker" 
)
protocols::motifs::MotifDnaPacker::~MotifDnaPacker ( )
overridedefault

destructor

Member Function Documentation

void protocols::motifs::MotifDnaPacker::apply ( core::pose::Pose pose)
overridevirtual
void protocols::motifs::MotifDnaPacker::aromatic_motifs ( core::pose::Pose pose,
utility::vector1< core::Size > &  design_positions,
std::set< core::Size > &  src_pos,
std::map< core::Size, core::pack::rotamer_set::Rotamers > &  rotamer_map,
std::map< core::Size, std::set< std::string > > &  types_map,
std::list< std::string > &  info_lines,
core::pack::task::TaskFactoryOP  taskfactory 
)
private
protocols::moves::MoverOP protocols::motifs::MotifDnaPacker::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

void protocols::motifs::MotifDnaPacker::expand_motifs ( core::pose::Pose pose,
utility::vector1< core::Size > &  design_positions,
std::set< core::Size > &  src_pos,
std::map< core::Size, core::pack::rotamer_set::Rotamers > &  rotamer_map,
std::map< core::Size, std::set< std::string > > &  types_map,
std::list< std::string > &  info_lines,
core::pack::task::TaskFactoryOP  taskfactory 
)
private

References core::sequence::end, and motif_expansion_inner_loop().

Referenced by apply().

protocols::moves::MoverOP protocols::motifs::MotifDnaPacker::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::motifs::MotifDnaPacker::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::motifs::MotifDnaPacker::init_options ( )
private
void protocols::motifs::MotifDnaPacker::init_standard ( core::pose::Pose pose)
private
void protocols::motifs::MotifDnaPacker::motif_expansion_inner_loop ( core::pose::Pose pose,
std::set< core::Size current_pos,
std::map< core::Size, core::pack::rotamer_set::Rotamers >::const_iterator  it,
std::set< std::string >::const_iterator  it2,
std::map< core::Size, core::pack::rotamer_set::Rotamers > &  rotamer_map,
std::list< std::string > &  info_lines,
core::pack::task::TaskFactoryOP  taskfactory 
)
private
std::string protocols::motifs::MotifDnaPacker::mover_name ( )
static
void protocols::motifs::MotifDnaPacker::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::motifs::MotifDnaPacker::run_motifs ( core::pose::Pose pose,
utility::vector1< core::Size > &  design_positions,
std::set< core::Size > &  src_pos,
std::map< core::Size, core::pack::rotamer_set::Rotamers > &  rotamer_map,
std::map< core::Size, std::set< std::string > > &  types_map,
std::list< std::string > &  info_lines,
core::pack::task::TaskFactoryOP  taskfactory 
)
private

Member Data Documentation

bool protocols::motifs::MotifDnaPacker::aromatic_motifs_
private
bool protocols::motifs::MotifDnaPacker::dna_design_
private

Referenced by apply(), and init_options().

protocols::dna::DnaInterfacePackerOP protocols::motifs::MotifDnaPacker::dna_packer_
private
bool protocols::motifs::MotifDnaPacker::expand_motifs_
private

Referenced by apply(), init_options(), and run_motifs().

std::string protocols::motifs::MotifDnaPacker::filename_root_
private
bool protocols::motifs::MotifDnaPacker::flex_dna_sugar_
private

Referenced by init_options().

bool protocols::motifs::MotifDnaPacker::minimize_dna_
private

Referenced by init_options().

protocols::motifs::MotifSearchOP protocols::motifs::MotifDnaPacker::motif_search_
private

Referenced by apply(), and run_motifs().

core::Real protocols::motifs::MotifDnaPacker::num_repacks_
private
protocols::dna::PDBOutputOP protocols::motifs::MotifDnaPacker::pdboutput_
private
bool protocols::motifs::MotifDnaPacker::run_motifs_
private

Referenced by apply(), and init_options().

core::scoring::ScoreFunctionOP protocols::motifs::MotifDnaPacker::scorefxn_
private
core::Real protocols::motifs::MotifDnaPacker::special_rotweight_
private
core::pose::PoseCOP protocols::motifs::MotifDnaPacker::starting_pose_
private
protocols::dna::DnaDesignDefOPs protocols::motifs::MotifDnaPacker::targeted_dna_
private

Referenced by apply(), and init_standard().


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