Public Member Functions | Static Public Member Functions | List of all members
protocols::splice::SpliceOutTail Class Reference

#include <SpliceOutTail.hh>

Inheritance diagram for protocols::splice::SpliceOutTail:
Inheritance graph

Public Member Functions

 SpliceOutTail ()
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
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...
 ~SpliceOutTail () override
void set_source_from_to_res () override
core::Size set_anchor_res () override
void set_loop_length_change (protocols::protein_interface_design::movers::LoopLengthChange &llc) override
void set_fold_tree_nodes (core::pose::Pose const &pose) override
void place_cut_site_in_segment (core::pose::Pose const &pose) override
 choose cutsite randomly within loop residues on the loop (no 2ary structure) More...
void abstract_parse_tag (TagCOP const tag) override
void write_database_to_file (core::pose::Pose const &pose) override
void superimpose_source_on_pose (core::pose::Pose const &pose, core::pose::Pose &source_pose) override
 add dihedral constraint to grafted loop according to source pdb dihedral angles More...
void build_ideal_segment (core::pose::Pose &pose) override
std::string name_for_filter () override
- Public Member Functions inherited from protocols::splice::SpliceOut
 SpliceOut ()
void apply (Pose &pose) override
 Main Method. More...
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &) override
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 ~SpliceOut () override
std::string source_pdb () const
void source_pdb (std::string const &s)
void scorefxn (core::scoring::ScoreFunctionOP sf)
core::scoring::ScoreFunctionOP scorefxn () const
core::Real rms_cutoff () const
void rms_cutoff (core::Real const r)
core::Real rms_cutoff_loop () const
void rms_cutoff_loop (core::Real const r)
void cut_secondarystruc (bool const r)
bool cut_secondarystruc () const
bool thread_original_sequence () const
void thread_original_sequence (bool const s)
std::string dbase_file_name () const
void dbase_file_name (std::string const &f)
 apply coordinate constraints on the segment being inserted. "to" and "from" are residue number of the pose(!), anchor residue number is also on the pose More...
protocols::filters::FilterOP splice_filter () const
void splice_filter (protocols::filters::FilterOP f)
void ccd_mover (core::pose::Pose &pose, core::kinematics::MoveMapOP mm)
void min_mover (core::pose::Pose &pose, core::kinematics::MoveMapOP mm)
void tail_mover (core::pose::Pose &pose, core::kinematics::MoveMapOP mm)
int SpliceOutFilter (core::pose::Pose *pose)
int SpliceOutRMSDFilter (core::pose::Pose *pose)
void load_pdb_segments_from_pose_comments (core::pose::Pose const &p)
bool rb_sensitive () const
void rb_sensitive (bool const r)
void delete_hairpin (bool const b)
bool delete_hairpin () const
core::Size delete_hairpin_n () const
void delete_hairpin_n (core::Size const c)
core::Size delete_hairpin_c () const
void delete_hairpin_c (core::Size const c)
void remove_hairpin (core::pose::Pose &pose) const
void check_source_segment ()
void copy_dofs_from_source ()
void superimposed (bool const b)
bool superimposed ()
void source_from_res (core::Size const c)
core::Size source_from_res ()
void source_to_res (core::Size const c)
core::Size source_to_res ()
void handle_mover_tag (TagCOP const tag, basic::datacache::DataMap &data)
void parse_SpliceOut_tags (TagCOP const tag, basic::datacache::DataMap &data)
void randomize_cut (bool const b)
bool randomize_cut ()
void minimize_segment (core::pose::Pose &pose)
- 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 void provide_citation_info (basic::citation_manager::CitationCollectionList &) const
 Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Static Public Member Functions

static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
static std::string mover_name ()
- Static Public Member Functions inherited from protocols::splice::SpliceOut
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
static std::string mover_name ()
- 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...

Additional Inherited Members

- Public Types inherited from protocols::splice::SpliceOut
typedef core::pose::Pose Pose
typedef utility::vector1< ResidueBBDofs >::const_iterator dbase_const_iterator
- 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::splice::SpliceOut
void save_values ()
void retrieve_values ()
core::Size find_non_active_site_cut_site (core::pose::Pose const &pose)
 Since we want to minimally perturb the active site confirmation (whether it be binding or catalytic) the cut site should be placed farthest away. For each protein family we will probably need special definitions unless we find a more general way. For antibodies I go from the conserved Trp res at the base of CDR1 and then continue going to the C-ter until I find the distal loops. More...
void check_pose_pssm_match (core::pose::PoseOP pose, utility::vector1< core::sequence::SequenceProfileOP > profile_vector)
- 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...
- Protected Attributes inherited from protocols::splice::SpliceOut
protocols::moves::MoverOP submover_
core::Real design_shell_ = 6.0
core::Real repack_shell_ = 8.0
core::scoring::ScoreFunctionOP scorefxn_
core::pose::PoseOP source_pose_
std::map< std::string, std::string > protein_family_to_database_
std::map< std::string, std::string > pdb_to_H3_seq_map_
bool ignore_chain_break_ = false
core::Real tolerance_ = 0.23
std::vector< std::string > mover_type_ = {"MinMover","LoopMover_Refine_CCD","TailSegmentMover"}
utility::vector1< std::array< int, 3 > > fold_tree_nodes_
bool write_to_database_ = true
SpliceManager splicemanager
void(SpliceOut::* call_mover )(core::pose::Pose &pose, core::kinematics::MoveMapOP mm)
void(SpliceOut::* call_mover_tail_ )(core::pose::Pose &pose, core::kinematics::MoveMapOP mm)

Constructor & Destructor Documentation

◆ SpliceOutTail()

protocols::splice::SpliceOutTail::SpliceOutTail ( )

◆ ~SpliceOutTail()

protocols::splice::SpliceOutTail::~SpliceOutTail ( )

Member Function Documentation

◆ abstract_parse_tag()

void protocols::splice::SpliceOutTail::abstract_parse_tag ( TagCOP const  tag)

◆ build_ideal_segment()

void protocols::splice::SpliceOutTail::build_ideal_segment ( core::pose::Pose pose)

◆ clone()

protocols::moves::MoverOP protocols::splice::SpliceOutTail::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::splice::SpliceOut.

◆ fresh_instance()

protocols::moves::MoverOP protocols::splice::SpliceOutTail::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::splice::SpliceOut.

◆ get_name()

std::string protocols::splice::SpliceOutTail::get_name ( ) const

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

Reimplemented from protocols::splice::SpliceOut.

References protocols::splice::SpliceOutTailCreator::mover_name().

◆ mover_name()

std::string protocols::splice::SpliceOutTail::mover_name ( )

Referenced by provide_xml_schema().

◆ name_for_filter()

std::string protocols::splice::SpliceOutTail::name_for_filter ( )

◆ place_cut_site_in_segment()

void protocols::splice::SpliceOutTail::place_cut_site_in_segment ( core::pose::Pose const &  pose)

◆ provide_xml_schema()

void protocols::splice::SpliceOutTail::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ set_anchor_res()

core::Size protocols::splice::SpliceOutTail::set_anchor_res ( )

◆ set_fold_tree_nodes()

void protocols::splice::SpliceOutTail::set_fold_tree_nodes ( core::pose::Pose const &  pose)

◆ set_loop_length_change()

void protocols::splice::SpliceOutTail::set_loop_length_change ( protocols::protein_interface_design::movers::LoopLengthChange llc)

◆ set_source_from_to_res()

void protocols::splice::SpliceOutTail::set_source_from_to_res ( )

◆ superimpose_source_on_pose()

void protocols::splice::SpliceOutTail::superimpose_source_on_pose ( core::pose::Pose const &  pose,
core::pose::Pose source_pose 

◆ write_database_to_file()

void protocols::splice::SpliceOutTail::write_database_to_file ( core::pose::Pose const &  pose)

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