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protocols::splice::SpliceIn Class Reference

#include <SpliceIn.hh>

Inheritance diagram for protocols::splice::SpliceIn:
Inheritance graph
[legend]

Public Member Functions

 SpliceIn ()
 
void apply (Pose &pose) override
 Main Method. More...
 
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...
 
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...
 
 ~SpliceIn () override
 
virtual core::Size find_dbase_entry (core::pose::Pose const &pose)
 
virtual void assign_from_res_to_res (core::pose::Pose const &pose)
 
core::Size database_entry () const
 
void database_entry (core::Size const d)
 
void load_from_checkpoint ()
 
utility::vector1< core::Size >
::const_iterator 
dbase_begin () const
 
utility::vector1< core::Size >
::const_iterator 
dbase_end () const
 
bool dbase_iterate () const
 
void dbase_iterate (bool const d)
 
bool min_seg () const
 
void min_seg (bool const d)
 
virtual void minimize_segment (core::pose::Pose &pose)
 
virtual void read_torsion_database ()
 
void database_pdb_entry (std::string const &s)
 
std::string database_pdb_entry () const
 
void scorefxn (core::scoring::ScoreFunctionOP sf)
 
core::scoring::ScoreFunctionOP scorefxn () const
 
void set_loop_length_change (protocols::protein_interface_design::movers::LoopLengthChange &llc) override
 
void set_fold_tree_nodes (core::pose::Pose const &pose) override
 
core::Size set_anchor_res () override
 
void build_ideal_segment (core::pose::Pose &pose) override
 
void rtmin (core::pose::Pose &pose, core::pack::task::TaskFactoryOP tf)
 
void pack (core::pose::Pose &pose, core::pack::task::TaskFactoryOP tf)
 
- Public Member Functions inherited from protocols::splice::SpliceOut
 SpliceOut ()
 
void apply (Pose &pose) override
 Main Method. More...
 
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...
 
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)
 
virtual void superimpose_source_on_pose (core::pose::Pose const &pose, core::pose::Pose &source_pose)
 add dihedral constraint to grafted loop according to source pdb dihedral angles More...
 
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 ()
 
virtual void place_cut_site_in_segment (core::pose::Pose const &pose)
 choose cutsite randomly within loop residues on the loop (no 2ary structure) More...
 
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)
 
virtual void set_source_from_to_res ()
 
virtual void write_database_to_file (core::pose::Pose const &pose)
 
void parse_SpliceOut_tags (TagCOP const tag, basic::datacache::DataMap &data)
 
virtual void abstract_parse_tag (TagCOP const tag)
 
void randomize_cut (bool const b)
 
bool randomize_cut ()
 
void minimize_segment (core::pose::Pose &pose)
 
virtual std::string name_for_filter ()
 
- 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_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 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...
 

Protected Attributes

utility::vector1< core::Sizedbase_subset_
 
utility::vector1< core::Size >
::const_iterator 
current_dbase_entry_
 
bool dbase_iterate_
 
DataccacheBoolDataOP end_dbase_subset_
 
std::string checkpointing_file_
 
bool min_seg_
 
utility::vector1< ResidueBBDofstorsion_database_
 
bool first_pass_
 
core::Size database_entry_
 
std::string database_pdb_entry_
 
utility::vector1< ResidueBBDofstail_torsion_database_
 
utility::vector1< int > delta_lengths_
 
core::Size allowed_cuts_
 
- 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)
 

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...
 

Constructor & Destructor Documentation

protocols::splice::SpliceIn::SpliceIn ( )
protocols::splice::SpliceIn::~SpliceIn ( )
overridedefault

Member Function Documentation

void protocols::splice::SpliceIn::apply ( Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

Reimplemented in protocols::splice::SpliceInTail, and protocols::splice::SpliceInAntibody.

References core::pose::add_comment(), protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::splice::SpliceManager::add_dihedral_constraints(), protocols::splice::SpliceManager::add_sequence_constraints(), protocols::splice::SpliceManager::anchor_res(), assign_from_res_to_res(), build_ideal_segment(), protocols::splice::SpliceManager::chainbreak_check(), protocols::splice::SpliceManager::cut_site(), protocols::splice::SpliceManager::debug(), protocols::splice::SpliceManager::design_shell(), core::chemical::DISULFIDE, protocols::splice::SpliceManager::dofs(), core::pose::Pose::dump_pdb(), find_dbase_entry(), protocols::splice::fix_chain_break_residue(), protocols::splice::SpliceManager::fold_tree(), core::pose::Pose::fold_tree(), protocols::splice::SpliceOut::fold_tree_nodes_, core::conformation::Residue::has_variant_type(), protocols::splice::load_pdb_segments_from_pose_comments(), minimize_segment(), protocols::splice::SpliceManager::mm(), protocols::splice::SpliceManager::modify_pdb_segments_with_current_segment(), protocols::splice::SpliceManager::mover_name(), protocols::moves::MS_SUCCESS, pack(), protocols::splice::SpliceManager::pdb_segments(), protocols::splice::SpliceManager::pose_from_res(), protocols::splice::SpliceManager::pose_to_res(), protocols::splice::SpliceManager::repack_shell(), core::pose::Pose::residue(), protocols::splice::SpliceManager::residue_diff(), protocols::protein_interface_design::movers::AddChainBreak::resnum(), rtmin(), scorefxn(), protocols::splice::SpliceManager::scorefxn(), protocols::splice::SpliceManager::segment_type(), set_anchor_res(), protocols::splice::SpliceManager::set_BB_dofs(), set_fold_tree_nodes(), protocols::moves::Mover::set_last_move_status(), set_loop_length_change(), protocols::splice::SpliceManager::source_pdb_name(), protocols::splice::SpliceOut::splicemanager, protocols::splice::SpliceManager::task_factory(), core::id::to_string(), protocols::splice::SpliceOut::tolerance_, torsion_database_, and protocols::splice::TR().

Referenced by protocols::splice::SpliceInAntibody::apply().

void protocols::splice::SpliceIn::assign_from_res_to_res ( core::pose::Pose const &  pose)
virtual
void protocols::splice::SpliceIn::build_ideal_segment ( core::pose::Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::splice::SpliceIn::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.

Reimplemented in protocols::splice::SpliceInTail, and protocols::splice::SpliceInAntibody.

core::Size protocols::splice::SpliceIn::database_entry ( ) const
inline
void protocols::splice::SpliceIn::database_entry ( core::Size const  d)
inline

References database_entry_.

void protocols::splice::SpliceIn::database_pdb_entry ( std::string const &  s)
inline

References database_pdb_entry_.

std::string protocols::splice::SpliceIn::database_pdb_entry ( ) const
inline
utility::vector1<core::Size>::const_iterator protocols::splice::SpliceIn::dbase_begin ( ) const
inline

References dbase_subset_.

utility::vector1<core::Size>::const_iterator protocols::splice::SpliceIn::dbase_end ( ) const
inline

References dbase_subset_.

Referenced by find_dbase_entry().

bool protocols::splice::SpliceIn::dbase_iterate ( ) const
inline
void protocols::splice::SpliceIn::dbase_iterate ( bool const  d)
inline

References dbase_iterate_.

core::Size protocols::splice::SpliceIn::find_dbase_entry ( core::pose::Pose const &  pose)
virtual
protocols::moves::MoverOP protocols::splice::SpliceIn::fresh_instance ( ) const
inlineoverridevirtual

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.

Reimplemented in protocols::splice::SpliceInTail, and protocols::splice::SpliceInAntibody.

std::string protocols::splice::SpliceIn::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

Reimplemented in protocols::splice::SpliceInTail, and protocols::splice::SpliceInAntibody.

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

void protocols::splice::SpliceIn::load_from_checkpoint ( )
bool protocols::splice::SpliceIn::min_seg ( ) const
inline
void protocols::splice::SpliceIn::min_seg ( bool const  d)
inline

References min_seg_.

void protocols::splice::SpliceIn::minimize_segment ( core::pose::Pose pose)
virtual
std::string protocols::splice::SpliceIn::mover_name ( )
static

Referenced by provide_xml_schema().

void protocols::splice::SpliceIn::pack ( core::pose::Pose pose,
core::pack::task::TaskFactoryOP  tf 
)
void protocols::splice::SpliceIn::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::splice::SpliceInTail, and protocols::splice::SpliceInAntibody.

References protocols::splice::SpliceManager::allowed_cuts(), database_entry(), database_pdb_entry(), database_pdb_entry_, protocols::splice::SpliceManager::dbase_file_name(), dbase_iterate(), delta_lengths_, min_seg(), core::scoring::parse_score_function(), protocols::splice::SpliceManager::parse_segments(), protocols::splice::SpliceManager::parse_tags(), read_torsion_database(), scorefxn(), protocols::splice::SpliceOut::splicemanager, protocols::splice::SpliceOut::tolerance_, torsion_database_, and protocols::splice::TR().

void protocols::splice::SpliceIn::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::splice::SpliceIn::read_torsion_database ( )
virtual
void protocols::splice::SpliceIn::rtmin ( core::pose::Pose pose,
core::pack::task::TaskFactoryOP  tf 
)
void protocols::splice::SpliceIn::scorefxn ( core::scoring::ScoreFunctionOP  sf)
inline
core::scoring::ScoreFunctionOP protocols::splice::SpliceIn::scorefxn ( ) const
inline
core::Size protocols::splice::SpliceIn::set_anchor_res ( )
overridevirtual
void protocols::splice::SpliceIn::set_fold_tree_nodes ( core::pose::Pose const &  pose)
overridevirtual
void protocols::splice::SpliceIn::set_loop_length_change ( protocols::protein_interface_design::movers::LoopLengthChange llc)
overridevirtual

Member Data Documentation

core::Size protocols::splice::SpliceIn::allowed_cuts_
protected
std::string protocols::splice::SpliceIn::checkpointing_file_
protected

Referenced by load_from_checkpoint().

utility::vector1< core::Size >::const_iterator protocols::splice::SpliceIn::current_dbase_entry_
protected
core::Size protocols::splice::SpliceIn::database_entry_
protected
std::string protocols::splice::SpliceIn::database_pdb_entry_
protected
bool protocols::splice::SpliceIn::dbase_iterate_
protected
utility::vector1< core::Size > protocols::splice::SpliceIn::dbase_subset_
protected
utility::vector1< int > protocols::splice::SpliceIn::delta_lengths_
protected
DataccacheBoolDataOP protocols::splice::SpliceIn::end_dbase_subset_
protected
bool protocols::splice::SpliceIn::first_pass_
protected
bool protocols::splice::SpliceIn::min_seg_
protected
utility::vector1< ResidueBBDofs > protocols::splice::SpliceIn::tail_torsion_database_
protected
utility::vector1< ResidueBBDofs > protocols::splice::SpliceIn::torsion_database_
protected

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