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protocols::splice::SpliceOut Class Reference

#include <SpliceOut.hh>

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

Public Types

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
 

Public Member Functions

 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_fold_tree_nodes (core::pose::Pose const &pose)
 
virtual void set_source_from_to_res ()
 
virtual core::Size set_anchor_res ()
 
virtual void build_ideal_segment (core::pose::Pose &pose)
 
virtual void set_loop_length_change (protocols::protein_interface_design::movers::LoopLengthChange &llc)
 
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::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

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

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)
 

Private Attributes

core::Size saved_from_res_ = 0
 
core::Size saved_to_res_ = 0
 
std::string source_pdb_ = ""
 
core::Real rms_cutoff_ = 999999
 
core::Real rms_cutoff_loop_
 
bool randomize_cut_ = false
 true: place cut in a randomly chosen loop residue, if available. false: place cut at loop's end More...
 
bool cut_secondarystruc_ = false
 
core::pack::task::TaskFactoryOP task_factory_
 true: allows placing the cut within secondary structures More...
 
core::kinematics::FoldTreeOP saved_fold_tree_
 
bool thread_original_sequence_ = false
 
std::string dbase_file_name_ = ""
 
utility::pointer::shared_ptr
< basic::datacache::DataMapObj
< std::string > > 
mover_tag_
 
protocols::filters::FilterOP splice_filter_
 
std::map< std::string,
utility::vector1< std::string > > 
order_segments_
 
bool rb_sensitive_ = false
 
std::map< std::string,
std::string > 
database_segment_map_
 
bool CG_const_ = false
 
bool delete_hairpin_ = false
 
core::Size delete_hairpin_n_ = 0
 
core::Size delete_hairpin_c_ = 0
 
core::Size source_from_res_ = 0
 
core::Size source_to_res_ = 0
 
bool superimposed_ = false
 

Member Typedef Documentation

typedef utility::vector1< ResidueBBDofs >::const_iterator protocols::splice::SpliceOut::dbase_const_iterator

Constructor & Destructor Documentation

protocols::splice::SpliceOut::SpliceOut ( )
protocols::splice::SpliceOut::~SpliceOut ( )
overridedefault

Member Function Documentation

void protocols::splice::SpliceOut::abstract_parse_tag ( TagCOP const  tag)
virtual
void protocols::splice::SpliceOut::apply ( Pose )
overridevirtual

Main Method.

Implements protocols::moves::Mover.

Reimplemented in protocols::splice::SpliceOutAntibody.

References protocols::splice::SpliceManager::add_coordinate_constraints(), protocols::splice::SpliceManager::add_dihedral_constraints(), protocols::splice::SpliceManager::add_sequence_constraints(), protocols::splice::SpliceManager::adjust_stem_positions_by_template(), protocols::splice::SpliceManager::anchor_res(), build_ideal_segment(), call_mover, CG_const_, check_source_segment(), core::pose::Pose::conformation(), copy_dofs_from_source(), 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(), protocols::splice::SpliceManager::fold_tree(), core::pose::Pose::fold_tree(), fold_tree_nodes_, core::conformation::Residue::has_variant_type(), minimize_segment(), protocols::splice::SpliceManager::mm(), protocols::splice::SpliceManager::mover_name(), protocols::moves::MS_SUCCESS, core::kinematics::FoldTree::num_jump(), protocols::splice::parse_pdb_code(), place_cut_site_in_segment(), protocols::splice::SpliceManager::pose_from_res(), protocols::splice::SpliceManager::pose_to_res(), core::pose::Pose::remove_constraints(), protocols::splice::SpliceManager::repack_shell(), core::pose::Pose::residue(), protocols::splice::SpliceManager::residue_diff(), protocols::rosetta_scripts::residue_packer_states(), protocols::protein_interface_design::movers::AddChainBreak::resnum(), saved_fold_tree_, scorefxn(), protocols::splice::SpliceManager::scorefxn(), set_anchor_res(), protocols::splice::SpliceManager::set_BB_dofs(), set_fold_tree_nodes(), protocols::moves::Mover::set_last_move_status(), set_loop_length_change(), set_source_from_to_res(), source_from_res(), source_pdb_, protocols::splice::SpliceManager::source_pdb_name(), source_pose_, source_to_res(), splicemanager, SpliceOutFilter(), SpliceOutRMSDFilter(), submover_, superimpose_source_on_pose(), protocols::protein_interface_design::filters::Torsion::task_factory(), protocols::splice::SpliceManager::task_factory(), core::id::to_string(), protocols::splice::TR(), protocols::splice::TR_constraints(), protocols::splice::SpliceManager::update_pose_stem_positions(), and write_database_to_file().

Referenced by protocols::splice::SpliceOutAntibody::apply(), and SpliceOutFilter().

void protocols::splice::SpliceOut::build_ideal_segment ( core::pose::Pose pose)
virtual
void protocols::splice::SpliceOut::ccd_mover ( core::pose::Pose pose,
core::kinematics::MoveMapOP  mm 
)
void protocols::splice::SpliceOut::check_pose_pssm_match ( core::pose::PoseOP  pose,
utility::vector1< core::sequence::SequenceProfileOP profile_vector 
)
protected
void protocols::splice::SpliceOut::check_source_segment ( )
protocols::moves::MoverOP protocols::splice::SpliceOut::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::SpliceOutTail, and protocols::splice::SpliceOutAntibody.

void protocols::splice::SpliceOut::copy_dofs_from_source ( )
void protocols::splice::SpliceOut::cut_secondarystruc ( bool const  r)
inline

References cut_secondarystruc_.

bool protocols::splice::SpliceOut::cut_secondarystruc ( ) const
inline
std::string protocols::splice::SpliceOut::dbase_file_name ( ) const

References dbase_file_name_.

void protocols::splice::SpliceOut::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

References dbase_file_name_.

void protocols::splice::SpliceOut::delete_hairpin ( bool const  b)
inline
bool protocols::splice::SpliceOut::delete_hairpin ( ) const
inline
core::Size protocols::splice::SpliceOut::delete_hairpin_c ( ) const
inline
void protocols::splice::SpliceOut::delete_hairpin_c ( core::Size const  c)
inline
core::Size protocols::splice::SpliceOut::delete_hairpin_n ( ) const
inline
void protocols::splice::SpliceOut::delete_hairpin_n ( core::Size const  c)
inline
core::Size protocols::splice::SpliceOut::find_non_active_site_cut_site ( core::pose::Pose const &  pose)
protected

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.

References protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::dssp_reduced(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::conformation::Residue::name1(), core::conformation::Residue::name3(), protocols::splice::parse_pdb_code(), core::pose::Pose::pdb_info(), core::pose::Pose::residue(), protocols::splice::SpliceManager::segment_type(), protocols::splice::SpliceManager::splice_segments(), splicemanager, core::pose::Pose::total_residue(), protocols::splice::TR(), and protocols::splice::TR_pssm().

protocols::moves::MoverOP protocols::splice::SpliceOut::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::SpliceOutTail, and protocols::splice::SpliceOutAntibody.

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

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

Implements protocols::moves::Mover.

Reimplemented in protocols::splice::SpliceOutTail, and protocols::splice::SpliceOutAntibody.

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

void protocols::splice::SpliceOut::handle_mover_tag ( TagCOP const  tag,
basic::datacache::DataMap &  data 
)
void protocols::splice::SpliceOut::load_pdb_segments_from_pose_comments ( core::pose::Pose const &  p)

sequence profiles Splice changes the backbone of the current pose and the following methods deal with dynamically constructing a sequence profile for the current backbone choices.

References core::pose::get_all_comments(), protocols::splice::SpliceManager::pdb_segments(), splicemanager, protocols::splice::TR(), and protocols::hybridization::val.

void protocols::splice::SpliceOut::min_mover ( core::pose::Pose pose,
core::kinematics::MoveMapOP  mm 
)
void protocols::splice::SpliceOut::minimize_segment ( core::pose::Pose pose)
std::string protocols::splice::SpliceOut::mover_name ( )
static
std::string protocols::splice::SpliceOut::name_for_filter ( )
virtual
void protocols::splice::SpliceOut::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::SpliceOutAntibody.

References abstract_parse_tag(), core::pose::parse_resnum(), core::scoring::parse_score_function(), protocols::splice::SpliceManager::parse_segments(), parse_SpliceOut_tags(), protocols::splice::SpliceManager::parse_tags(), scorefxn(), source_from_res(), source_pose_, source_to_res(), splicemanager, and superimposed().

void protocols::splice::SpliceOut::parse_SpliceOut_tags ( TagCOP const  tag,
basic::datacache::DataMap &  data 
)
void protocols::splice::SpliceOut::place_cut_site_in_segment ( core::pose::Pose const &  pose)
virtual
void protocols::splice::SpliceOut::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::splice::SpliceOut::randomize_cut ( bool const  b)
inline
bool protocols::splice::SpliceOut::randomize_cut ( )
inline

References randomize_cut_.

Referenced by abstract_parse_tag().

bool protocols::splice::SpliceOut::rb_sensitive ( ) const
inline

References rb_sensitive_.

void protocols::splice::SpliceOut::rb_sensitive ( bool const  r)
inline

References rb_sensitive_.

void protocols::splice::SpliceOut::remove_hairpin ( core::pose::Pose pose) const
void protocols::splice::SpliceOut::retrieve_values ( )
protected
core::Real protocols::splice::SpliceOut::rms_cutoff ( ) const
inline

References rms_cutoff_.

Referenced by parse_SpliceOut_tags(), and SpliceOutRMSDFilter().

void protocols::splice::SpliceOut::rms_cutoff ( core::Real const  r)
inline

References rms_cutoff_.

core::Real protocols::splice::SpliceOut::rms_cutoff_loop ( ) const
inline
void protocols::splice::SpliceOut::rms_cutoff_loop ( core::Real const  r)
inline

References rms_cutoff_loop_.

void protocols::splice::SpliceOut::save_values ( )
protected

splice apply might change the from_res/to_res internals since they sometimes refer to the template file. If that happens, we want the values to revert to their original values before the end of the apply function (so retrieve_values) below must be called before return.

References protocols::splice::SpliceManager::pose_from_res(), protocols::splice::SpliceManager::pose_to_res(), saved_from_res_, saved_to_res_, and splicemanager.

void protocols::splice::SpliceOut::scorefxn ( core::scoring::ScoreFunctionOP  sf)

References scorefxn_.

core::scoring::ScoreFunctionOP protocols::splice::SpliceOut::scorefxn ( ) const
core::Size protocols::splice::SpliceOut::set_anchor_res ( )
virtual
void protocols::splice::SpliceOut::set_fold_tree_nodes ( core::pose::Pose const &  pose)
virtual
void protocols::splice::SpliceOut::set_loop_length_change ( protocols::protein_interface_design::movers::LoopLengthChange llc)
virtual
void protocols::splice::SpliceOut::set_source_from_to_res ( )
virtual
void protocols::splice::SpliceOut::source_from_res ( core::Size const  c)
inline
core::Size protocols::splice::SpliceOut::source_from_res ( )
inline
std::string protocols::splice::SpliceOut::source_pdb ( ) const
inline
void protocols::splice::SpliceOut::source_pdb ( std::string const &  s)
inline

References source_pdb_.

void protocols::splice::SpliceOut::source_to_res ( core::Size const  c)
inline
core::Size protocols::splice::SpliceOut::source_to_res ( )
inline
protocols::filters::FilterOP protocols::splice::SpliceOut::splice_filter ( ) const

the torsion dbase should have the following structure: each line represents a single loop. Each four values represent <phi> <psi> <omega> <3-let resid>; the last entry in a line represents <loop start>=""> <loop stop>=""> <cut site>=""> cut; where cut signifies that this is the loop designator

References splice_filter_.

Referenced by parse_SpliceOut_tags(), and SpliceOutFilter().

void protocols::splice::SpliceOut::splice_filter ( protocols::filters::FilterOP  f)

References splice_filter_.

int protocols::splice::SpliceOut::SpliceOutFilter ( core::pose::Pose pose)
int protocols::splice::SpliceOut::SpliceOutRMSDFilter ( core::pose::Pose pose)
void protocols::splice::SpliceOut::superimpose_source_on_pose ( core::pose::Pose const &  pose,
core::pose::Pose source_pose 
)
virtual
void protocols::splice::SpliceOut::superimposed ( bool const  b)
inline
bool protocols::splice::SpliceOut::superimposed ( )
inline
void protocols::splice::SpliceOut::tail_mover ( core::pose::Pose pose,
core::kinematics::MoveMapOP  mm 
)
bool protocols::splice::SpliceOut::thread_original_sequence ( ) const
inline
void protocols::splice::SpliceOut::thread_original_sequence ( bool const  s)
inline
void protocols::splice::SpliceOut::write_database_to_file ( core::pose::Pose const &  pose)
virtual

Member Data Documentation

void(SpliceOut::* protocols::splice::SpliceOut::call_mover)(core::pose::Pose &pose, core::kinematics::MoveMapOP mm)
protected
void(SpliceOut::* protocols::splice::SpliceOut::call_mover_tail_)(core::pose::Pose &pose, core::kinematics::MoveMapOP mm)
protected
bool protocols::splice::SpliceOut::CG_const_ = false
private

Referenced by apply(), and parse_SpliceOut_tags().

bool protocols::splice::SpliceOut::cut_secondarystruc_ = false
private

Referenced by cut_secondarystruc().

std::map< std::string, std::string> protocols::splice::SpliceOut::database_segment_map_
private
std::string protocols::splice::SpliceOut::dbase_file_name_ = ""
private

Referenced by dbase_file_name().

bool protocols::splice::SpliceOut::delete_hairpin_ = false
private

Referenced by delete_hairpin().

core::Size protocols::splice::SpliceOut::delete_hairpin_c_ = 0
private

Referenced by delete_hairpin_c().

core::Size protocols::splice::SpliceOut::delete_hairpin_n_ = 0
private

Referenced by delete_hairpin_n().

core::Real protocols::splice::SpliceOut::design_shell_ = 6.0
protected
utility::vector1<std::array<int, 3> > protocols::splice::SpliceOut::fold_tree_nodes_
protected
bool protocols::splice::SpliceOut::ignore_chain_break_ = false
protected
utility::pointer::shared_ptr< basic::datacache::DataMapObj< std::string > > protocols::splice::SpliceOut::mover_tag_
private
std::vector< std::string> protocols::splice::SpliceOut::mover_type_ = {"MinMover","LoopMover_Refine_CCD","TailSegmentMover"}
protected
std::map< std::string, utility::vector1< std::string > > protocols::splice::SpliceOut::order_segments_
private
std::map< std::string, std::string > protocols::splice::SpliceOut::pdb_to_H3_seq_map_
protected
std::map< std::string, std::string> protocols::splice::SpliceOut::protein_family_to_database_
protected
bool protocols::splice::SpliceOut::randomize_cut_ = false
private

true: place cut in a randomly chosen loop residue, if available. false: place cut at loop's end

Referenced by randomize_cut().

bool protocols::splice::SpliceOut::rb_sensitive_ = false
private

Referenced by rb_sensitive().

core::Real protocols::splice::SpliceOut::repack_shell_ = 8.0
protected
core::Real protocols::splice::SpliceOut::rms_cutoff_ = 999999
private

Referenced by rms_cutoff().

core::Real protocols::splice::SpliceOut::rms_cutoff_loop_
private

Referenced by rms_cutoff_loop().

core::kinematics::FoldTreeOP protocols::splice::SpliceOut::saved_fold_tree_
private

Referenced by apply().

core::Size protocols::splice::SpliceOut::saved_from_res_ = 0
private

Referenced by retrieve_values(), and save_values().

core::Size protocols::splice::SpliceOut::saved_to_res_ = 0
private

Referenced by retrieve_values(), and save_values().

core::scoring::ScoreFunctionOP protocols::splice::SpliceOut::scorefxn_
protected
core::Size protocols::splice::SpliceOut::source_from_res_ = 0
private

Referenced by source_from_res().

std::string protocols::splice::SpliceOut::source_pdb_ = ""
private
core::pose::PoseOP protocols::splice::SpliceOut::source_pose_
protected
core::Size protocols::splice::SpliceOut::source_to_res_ = 0
private

Referenced by source_to_res().

protocols::filters::FilterOP protocols::splice::SpliceOut::splice_filter_
private

Referenced by splice_filter().

SpliceManager protocols::splice::SpliceOut::splicemanager
protected

Referenced by protocols::splice::SpliceOutTail::abstract_parse_tag(), abstract_parse_tag(), protocols::splice::SpliceOutAntibody::adjust_n_ter_tail_length(), protocols::splice::SpliceInAntibody::adjust_n_ter_tail_length(), protocols::splice::SpliceInAntibody::adjust_template_jump(), protocols::splice::SpliceOutAntibody::apply(), protocols::splice::SpliceInAntibody::apply(), protocols::splice::SpliceIn::apply(), protocols::splice::SpliceInTail::apply(), apply(), protocols::splice::SpliceOutAntibody::assign_from_res_to_res(), protocols::splice::SpliceIn::assign_from_res_to_res(), protocols::splice::SpliceInTail::assign_from_res_to_res(), protocols::splice::SpliceInAntibody::assign_from_res_to_res(), protocols::splice::SpliceOutTail::build_ideal_segment(), protocols::splice::SpliceOutAntibody::build_ideal_segment(), protocols::splice::SpliceInTail::build_ideal_segment(), protocols::splice::SpliceIn::build_ideal_segment(), protocols::splice::SpliceInAntibody::build_ideal_segment(), build_ideal_segment(), ccd_mover(), check_pose_pssm_match(), copy_dofs_from_source(), protocols::splice::SpliceInAntibody::find_dbase_entry(), protocols::splice::SpliceIn::find_dbase_entry(), protocols::splice::SpliceInTail::find_dbase_entry(), find_non_active_site_cut_site(), load_pdb_segments_from_pose_comments(), min_mover(), protocols::splice::SpliceIn::minimize_segment(), minimize_segment(), protocols::splice::SpliceOutAntibody::name_for_filter(), protocols::splice::SpliceOutAntibody::parse_my_tag(), protocols::splice::SpliceInAntibody::parse_my_tag(), protocols::splice::SpliceIn::parse_my_tag(), protocols::splice::SpliceInTail::parse_my_tag(), parse_my_tag(), protocols::splice::SpliceOutTail::place_cut_site_in_segment(), protocols::splice::SpliceOutAntibody::place_cut_site_in_segment(), place_cut_site_in_segment(), protocols::splice::SpliceIn::read_torsion_database(), retrieve_values(), protocols::splice::SpliceIn::rtmin(), save_values(), protocols::splice::SpliceOutTail::set_anchor_res(), protocols::splice::SpliceInTail::set_anchor_res(), protocols::splice::SpliceOutAntibody::set_anchor_res(), protocols::splice::SpliceInAntibody::set_anchor_res(), protocols::splice::SpliceIn::set_anchor_res(), set_anchor_res(), protocols::splice::SpliceOutAntibody::set_fold_tree_nodes(), protocols::splice::SpliceInTail::set_fold_tree_nodes(), protocols::splice::SpliceOutTail::set_fold_tree_nodes(), protocols::splice::SpliceInAntibody::set_fold_tree_nodes(), protocols::splice::SpliceIn::set_fold_tree_nodes(), set_fold_tree_nodes(), protocols::splice::SpliceInTail::set_loop_length_change(), protocols::splice::SpliceOutTail::set_loop_length_change(), protocols::splice::SpliceOutAntibody::set_loop_length_change(), protocols::splice::SpliceInAntibody::set_loop_length_change(), protocols::splice::SpliceIn::set_loop_length_change(), set_loop_length_change(), protocols::splice::SpliceOutTail::set_source_from_to_res(), protocols::splice::SpliceOutAntibody::set_source_from_to_res(), set_source_from_to_res(), protocols::splice::SpliceIn::SpliceIn(), protocols::splice::SpliceInAntibody::SpliceInAntibody(), protocols::splice::SpliceInTail::SpliceInTail(), SpliceOut(), protocols::splice::SpliceOutAntibody::SpliceOutAntibody(), SpliceOutFilter(), SpliceOutRMSDFilter(), protocols::splice::SpliceOutTail::SpliceOutTail(), protocols::splice::SpliceOutAntibody::superimpose_source_on_pose(), protocols::splice::SpliceOutTail::superimpose_source_on_pose(), superimpose_source_on_pose(), tail_mover(), protocols::splice::SpliceOutAntibody::update_vl_vh_cut(), protocols::splice::SpliceInAntibody::update_vl_vh_cut(), protocols::splice::SpliceOutTail::write_database_to_file(), protocols::splice::SpliceOutAntibody::write_database_to_file(), and write_database_to_file().

protocols::moves::MoverOP protocols::splice::SpliceOut::submover_
protected
bool protocols::splice::SpliceOut::superimposed_ = false
private

Referenced by superimposed().

core::pack::task::TaskFactoryOP protocols::splice::SpliceOut::task_factory_
private

true: allows placing the cut within secondary structures

bool protocols::splice::SpliceOut::thread_original_sequence_ = false
private
core::Real protocols::splice::SpliceOut::tolerance_ = 0.23
protected
bool protocols::splice::SpliceOut::write_to_database_ = true
protected

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