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protocols::splice::Splice Class Reference

container for BBDofs, providing a convenient operator [], size, other methods and iterators that allow splice to treat ResidueBBDofs as a simple vector (even though it contains other elements as well) More...

#include <Splice.hh>

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

Public Types

typedef core::pose::Pose Pose
 
typedef utility::vector1
< ResidueBBDofs >
::const_iterator 
dbase_const_iterator
 
typedef
utility::pointer::shared_ptr
< basic::datacache::DataMapObj
< bool > > 
DataccacheBoolDataOP
 
- 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

 Splice ()
 
void apply (Pose &pose) override
 Main Method. 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...
 
 ~Splice () override
 
void from_res (core::Size const f)
 
core::Size from_res (core::pose::Pose const &pose) const
 
void to_res (core::Size const t)
 
core::Size to_res (core::pose::Pose const &pose) const
 
std::string source_pdb () const
 
void source_pdb (std::string const &s)
 
void ccd (bool const c)
 
void design_shell (core::Real const c)
 
void repack_shell (core::Real const c)
 
bool ccd () const
 
core::Real dihedral_const () const
 
core::Real coor_const () const
 
core::Real design_shell () const
 
core::Real repack_shell () const
 
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 res_move (core::Size const r)
 
core::Size res_move () const
 
void randomize_cut (bool const r)
 
bool randomize_cut () const
 
void set_cut_res (core::Size const r)
 
core::Size set_cut_res () const
 
void cut_secondarystruc (bool const r)
 
bool cut_secondarystruc () const
 
core::pack::task::TaskFactoryOP task_factory () const
 
void task_factory (core::pack::task::TaskFactoryOP tf)
 
core::pack::task::TaskFactoryOP design_task_factory () const
 
void design_task_factory (core::pack::task::TaskFactoryOP tf)
 
void set_segment_names_ordered (utility::vector1< std::string > SegNameOrder)
 
utility::vector1< std::string > get_segment_names_ordered () const
 
void set_dofs_pdb_name (std::string dofsPDBname)
 
std::string get_dofs_pdb_name () const
 
std::string torsion_database_fname () const
 
void torsion_database_fname (std::string const &d)
 
core::Size database_entry () const
 
void database_entry (core::Size const d)
 
void read_torsion_database ()
 
utility::vector1< ResidueBBDofstorsion_database () const
 
void torsion_database (utility::vector1< ResidueBBDofs > const &d)
 
std::string template_file () const
 
void template_file (std::string const &s)
 
void poly_ala (bool const p)
 
bool poly_ala () const
 
void equal_length (bool const e)
 
bool equal_length () const
 
void fold_tree (core::pose::Pose &pose, core::Size const start, core::Size const stop, core::Size const cut) const
 set the fold tree around start/stop/cut sites. presently makes a simple fold tree, but at one point may be a more complicated function to include two poses More...
 
void tail_fold_tree (core::pose::Pose &pose, core::Size const vl_vh_cut, core::Size chain_break, std::string segment_name) const
 Setup fold tree for segments at the termini of the protein, gdl, Apr2014. More...
 
void set_fold_tree (core::pose::Pose &pose, core::Size const vl_vh_cut)
 a general fold tree to use for all antibodies, gideon, Apr2014 More...
 
bool design () const
 
void design (bool const d)
 
void delta_lengths (utility::vector1< int > const &dl)
 
utility::vector1< int > delta_lengths ()
 
bool dbase_iterate () const
 
void dbase_iterate (bool const d)
 
utility::vector1< core::Size >
::const_iterator 
dbase_begin () const
 
utility::vector1< core::Size >
::const_iterator 
dbase_end () const
 
core::Size find_dbase_entry (core::pose::Pose const &pose)
 controls which dbase entry will be used. Three options: 1. specific one according to user instruction; 2. randomized out of a subset of the dbase with fitting sequence lengths (if user specified 0); 3. iterating over dbase subset More...
 
core::Size locked_res () const
 
void locked_res (core::Size const r)
 
void locked_res_id (char const c)
 
char locked_res_id () const
 
std::string checkpointing_file () const
 
void checkpointing_file (std::string const &cf)
 
bool rtmin () const
 
void rtmin (bool const d)
 
bool allow_all_aa () const
 
void allow_all_aa (bool const d)
 
bool thread_original_sequence () const
 
void thread_original_sequence (bool const s)
 
void load_from_checkpoint ()
 
void save_to_checkpoint () const
 
std::string loop_dbase_file_name () const
 
void loop_dbase_file_name (std::string const &f)
 
void loop_pdb_source (std::string const &l)
 
std::string loop_pdb_source () const
 
protocols::filters::FilterOP splice_filter () const
 
void splice_filter (protocols::filters::FilterOP f)
 
void database_pdb_entry (std::string const &s)
 
std::string database_pdb_entry () const
 
void read_splice_segments (std::string const &segment_type, std::string const &segment_name, std::string const &file_name)
 
core::sequence::SequenceProfileOP generate_sequence_profile (core::pose::Pose &pose)
 
void load_pdb_segments_from_pose_comments (core::pose::Pose const &p)
 
void modify_pdb_segments_with_current_segment (std::string const &pdb_name)
 
void add_sequence_constraints (core::pose::Pose &pose)
 
void add_dihedral_constraints (core::pose::Pose &pose, core::pose::Pose const &source_pose, core::Size nearest_to_from, core::Size nearest_to_to)
 add dihedral constraint to grafted loop according to source pdb dihedral angles More...
 
void add_coordinate_constraints (core::pose::Pose &pose, core::pose::Pose const &source_pose, core::Size nearest_to_from, core::Size nearest_to_to, core::Size anchor, std::string atom_type="CA", core::pack::task::PackerTaskOP task=nullptr)
 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...
 
void profile_weight_away_from_interface (core::Real const p)
 
core::Real profile_weight_away_from_interface () const
 
bool restrict_to_repacking_chain2 () const
 
void restrict_to_repacking_chain2 (bool const r)
 
core::Size get_current_seg ()
 
bool add_sequence_constraints_only () const
 
void add_sequence_constraints_only (bool const a)
 
bool rb_sensitive () const
 
void rb_sensitive (bool const r)
 
void rb_adjust_template (core::pose::Pose const &pose)
 
void protein_family (std::string const &s)
 
core::Size chain_num () const
 
void chain_num (core::Size const c)
 
bool skip_alignment () const
 
void skip_alignment (bool const b)
 
bool superimposed () const
 
void superimposed (bool const b)
 
core::Size source_pdb_from_res () const
 
void source_pdb_from_res (core::Size const s)
 
core::Size source_pdb_to_res () const
 
void source_pdb_to_res (core::Size const s)
 
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
 
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
 
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 save_values (core::pose::Pose const &pose)
 
void retrieve_values ()
 
std::string parse_pdb_code (std::string pdb_file_name)
 This is helper function that cuts out a file name, removing the extension and the path. More...
 
void copy_stretch (core::pose::Pose &target, core::pose::Pose const &source, core::Size const from_res, core::Size const to_res)
 copy a stretch of aligned phi-psi dofs from source to target. No repacking no nothing. The core function, copy_segment, copies residues from the source to the target without aligning the residues, thereby delivering all of their dofs More...
 
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 superimpose_source_on_pose (core::pose::Pose const &, core::pose::Pose &)
 
void chainbreak_check (core::pose::Pose const &pose, core::Real const tolerance, bool fail_retry_if_found, bool crash_if_found)
 
void correct_bb_O_placements (core::pose::Pose Pose, core::Size cut_site)
 

Private Attributes

utility::vector1< std::string > segment_names_ordered_
 
std::string dofs_pdb_name
 
core::pose::ResidueIndexDescriptionCOP from_res_
 
core::pose::ResidueIndexDescriptionCOP to_res_
 
core::Size saved_from_res_
 
core::Size saved_to_res_
 
std::string source_pdb_
 
bool ccd_
 
core::Real dihedral_const_
 
core::Real coor_const_
 
core::Real design_shell_
 
core::Real repack_shell_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::Real rms_cutoff_
 
core::Real rms_cutoff_loop_
 
core::Size res_move_
 
bool randomize_cut_
 
bool cut_secondarystruc_
 
core::Size set_cut_res_
 
core::pack::task::TaskFactoryOP task_factory_
 
core::pack::task::TaskFactoryOP design_task_factory_
 
std::string torsion_database_fname_
 
core::Size database_entry_
 
std::string database_pdb_entry_
 
utility::vector1< ResidueBBDofstorsion_database_
 
utility::vector1< ResidueBBDofstail_torsion_database_
 
std::string template_file_
 
bool poly_ala_
 
bool equal_length_
 
core::pose::PoseCOP template_pose_
 
core::pose::PoseCOP start_pose_
 
core::pose::PoseOP source_pose_
 
core::kinematics::FoldTreeOP saved_fold_tree_
 
bool design_
 
utility::vector1< int > delta_lengths_
 
bool dbase_iterate_
 
bool allow_all_aa_
 
bool thread_original_sequence_
 
bool rtmin_
 
bool first_pass_
 
utility::vector1< core::Sizedbase_subset_
 
utility::vector1< core::Size >
::const_iterator 
current_dbase_entry_
 
DataccacheBoolDataOP end_dbase_subset_
 
utility::pointer::shared_ptr
< basic::datacache::DataMapObj
< utility::vector1< core::Size > > > 
locked_res_
 
char locked_res_id_
 
std::string checkpointing_file_
 
std::string loop_dbase_file_name_
 
std::string loop_pdb_source_
 
utility::pointer::shared_ptr
< basic::datacache::DataMapObj
< std::string > > 
mover_tag_
 
protocols::filters::FilterOP splice_filter_
 
std::string Pdb4LetName_
 
std::string protein_family_
 
std::map< std::string,
utility::vector1< std::string > > 
order_segments_
 
core::Size chain_num_
 
bool use_sequence_profiles_
 
std::string segment_type_
 
core::Size current_segment_pos
 
std::map< std::string,
SpliceSegmentOP
splice_segments_
 
std::map< std::string,
std::string > 
pdb_segments_
 
core::Real profile_weight_away_from_interface_
 
bool restrict_to_repacking_chain2_
 
bool add_sequence_constraints_only_
 
bool set_fold_tree_only_
 
bool rb_sensitive_
 
std::map< std::string,
std::string > 
protein_family_to_database_
 
bool skip_alignment_
 
std::map< std::string,
std::string > 
database_segment_map_
 
core::Size vl_vh_cut
 
std::string tail_segment_
 
bool min_seg_
 
bool CG_const_
 
bool debug_
 
std::string mover_name_
 
std::map< std::string,
std::string > 
pdb_to_H3_seq_map_
 
bool superimposed_
 
core::Size source_pdb_from_res_
 
core::Size source_pdb_to_res_
 
bool ignore_chain_break_
 
core::Real tolerance_
 
bool delete_hairpin_
 
core::Size delete_hairpin_n_
 
core::Size delete_hairpin_c_
 
core::Size allowed_cuts_
 
bool enzdes_
 
std::map< std::string,
BBMatchingOP
bb_comp_db_
 

Additional Inherited Members

- 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...
 

Detailed Description

container for BBDofs, providing a convenient operator [], size, other methods and iterators that allow splice to treat ResidueBBDofs as a simple vector (even though it contains other elements as well)

Member Typedef Documentation

typedef utility::pointer::shared_ptr< basic::datacache::DataMapObj< bool > > protocols::splice::Splice::DataccacheBoolDataOP
typedef utility::vector1< ResidueBBDofs >::const_iterator protocols::splice::Splice::dbase_const_iterator

Constructor & Destructor Documentation

protocols::splice::Splice::Splice ( )
protocols::splice::Splice::~Splice ( )
overridedefault

Member Function Documentation

void protocols::splice::Splice::add_coordinate_constraints ( core::pose::Pose pose,
core::pose::Pose const &  source_pose,
core::Size  nearest_to_from,
core::Size  nearest_to_to,
core::Size  anchor,
std::string  atom_type = "CA",
core::pack::task::PackerTaskOP  task = nullptr 
)
void protocols::splice::Splice::add_dihedral_constraints ( core::pose::Pose pose,
core::pose::Pose const &  source_pose,
core::Size  nearest_to_from,
core::Size  nearest_to_to 
)
void protocols::splice::Splice::add_sequence_constraints ( core::pose::Pose pose)
bool protocols::splice::Splice::add_sequence_constraints_only ( ) const
inline

References add_sequence_constraints_only_.

Referenced by apply(), and parse_my_tag().

void protocols::splice::Splice::add_sequence_constraints_only ( bool const  a)
inline
bool protocols::splice::Splice::allow_all_aa ( ) const
inline

References allow_all_aa_.

Referenced by apply(), and parse_my_tag().

void protocols::splice::Splice::allow_all_aa ( bool const  d)
inline

References allow_all_aa_.

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

Main Method.

Implements protocols::moves::Mover.

References core::chemical::aa_from_name(), core::pose::add_comment(), add_coordinate_constraints(), add_dihedral_constraints(), add_sequence_constraints(), add_sequence_constraints_only(), allow_all_aa(), protocols::protein_interface_design::movers::AddChainBreak::apply(), protocols::minimization_packing::RotamerTrialsMinMover::apply(), protocols::minimization_packing::PackRotamersMover::apply(), core::conformation::Residue::atom_index(), core::conformation::Residue::build_atom_ideal(), protocols::splice::calculate_rmsd(), ccd(), ccd_, CG_const_, protocols::simple_moves::CutChainMover::chain_cut(), core::conformation::Conformation::chain_end(), chain_num_, chainbreak_check(), protocols::protein_interface_design::movers::AddChainBreak::change_foldtree(), protocols::splice::ResidueBBDofs::clear(), clone(), core::pose::Pose::conformation(), copy_stretch(), cut_secondarystruc(), debug_, design(), design_shell(), design_task_factory(), core::conformation::Conformation::detect_disulfides(), core::chemical::DISULFIDE, dofs_pdb_name, protocols::simple_filters::dssp(), core::scoring::dssp::Dssp::dssp_reduced(), core::pose::Pose::dump_pdb(), protocols::moves::FAIL_DO_NOT_RETRY, protocols::moves::FAIL_RETRY, protocols::protein_interface_design::movers::AddChainBreak::find_automatically(), find_dbase_entry(), protocols::rosetta_scripts::find_nearest_disulfide(), protocols::rosetta_scripts::find_nearest_res(), find_non_active_site_cut_site(), fold_tree(), core::pose::Pose::fold_tree(), from_res(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::conformation::Residue::has_variant_type(), ignore_chain_break_, protocols::splice::load_pdb_segments_from_pose_comments(), locked_res(), locked_res_id(), loop_dbase_file_name_, loop_pdb_source_, protocols::mean_field::min(), protocols::splice::min_seg(), min_seg_, modify_pdb_segments_with_current_segment(), mover_name_, mover_tag_, protocols::moves::MS_SUCCESS, core::conformation::Residue::name1(), core::conformation::Residue::name3(), core::conformation::Conformation::num_chains(), core::kinematics::FoldTree::num_jump(), protocols::splice::BBDofs::omega(), core::scoring::omega, core::pose::Pose::omega(), core::chemical::oneletter_code_from_aa(), parse_pdb_code(), Pdb4LetName_, pdb_segments_, protocols::splice::BBDofs::phi(), core::pose::Pose::phi(), poly_ala(), protein_family_, protocols::splice::BBDofs::psi(), core::pose::Pose::psi(), randomize_cut(), rb_adjust_template(), core::pose::Pose::remove_constraints(), remove_hairpin(), repack_shell(), core::pose::Pose::replace_residue(), res_move(), protocols::splice::BBDofs::resid(), core::conformation::Conformation::residue(), core::pose::Pose::residue(), protocols::rosetta_scripts::residue_packer_states(), protocols::splice::BBDofs::resn(), protocols::protein_interface_design::movers::AddChainBreak::resnum(), restrict_to_repacking_chain2(), retrieve_values(), core::scoring::rg, rms_cutoff(), rms_cutoff_loop(), rtmin(), save_values(), saved_fold_tree_, scorefxn(), segment_type_, set_fold_tree(), set_fold_tree_only_, protocols::moves::Mover::set_last_move_status(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), core::conformation::Residue::set_xyz(), skip_alignment(), source_pdb_, source_pdb_from_res(), source_pdb_to_res(), source_pose_, splice_filter(), core::pose::Pose::split_by_chain(), superimpose_source_on_pose(), superimposed(), tail_fold_tree(), tail_segment_, tail_torsion_database_, protocols::protein_interface_design::filters::Torsion::task_factory(), task_factory(), protocols::splice::TailSegmentMover::temp_initial(), template_file_, template_pose_, thread_original_sequence(), to_res(), core::id::to_string(), tolerance_, torsion_database_, torsion_database_fname_, core::pose::Pose::total_residue(), protocols::splice::TR(), protocols::splice::TR_ccd(), protocols::splice::TR_constraints(), core::pose::Pose::update_residue_neighbors(), use_sequence_profiles_, vl_vh_cut, and core::conformation::Residue::xyz().

void protocols::splice::Splice::ccd ( bool const  c)
inline

References core::pack::dunbrack::c, and ccd_.

bool protocols::splice::Splice::ccd ( ) const
inline

References ccd_.

Referenced by apply(), and parse_my_tag().

core::Size protocols::splice::Splice::chain_num ( ) const
inline

References chain_num_.

Referenced by copy_stretch(), fold_tree(), and Splice().

void protocols::splice::Splice::chain_num ( core::Size const  c)
inline
void protocols::splice::Splice::chainbreak_check ( core::pose::Pose const &  pose,
core::Real const  tolerance,
bool  fail_retry_if_found,
bool  crash_if_found 
)
private
std::string protocols::splice::Splice::checkpointing_file ( ) const

References checkpointing_file_.

Referenced by parse_my_tag().

void protocols::splice::Splice::checkpointing_file ( std::string const &  cf)

References checkpointing_file_.

protocols::moves::MoverOP protocols::splice::Splice::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.

Referenced by apply().

core::Real protocols::splice::Splice::coor_const ( ) const
inline

References coor_const_.

void protocols::splice::Splice::copy_stretch ( core::pose::Pose target,
core::pose::Pose const &  source,
core::Size const  from_res,
core::Size const  to_res 
)
private

copy a stretch of aligned phi-psi dofs from source to target. No repacking no nothing. The core function, copy_segment, copies residues from the source to the target without aligning the residues, thereby delivering all of their dofs

References core::conformation::Conformation::chain_end(), chain_num(), chain_num_, core::pose::Pose::conformation(), core::pose::Pose::copy_segment(), debug_, core::pose::Pose::dump_pdb(), protocols::rosetta_scripts::find_nearest_res(), core::pose::Pose::fold_tree(), protocols::protein_interface_design::movers::LoopLengthChange::loop_start(), mover_name_, segment_type_, and protocols::splice::TR().

Referenced by apply().

void protocols::splice::Splice::correct_bb_O_placements ( core::pose::Pose  Pose,
core::Size  cut_site 
)
private
void protocols::splice::Splice::cut_secondarystruc ( bool const  r)
inline

References cut_secondarystruc_.

bool protocols::splice::Splice::cut_secondarystruc ( ) const
inline

References cut_secondarystruc_.

Referenced by apply(), and parse_my_tag().

core::Size protocols::splice::Splice::database_entry ( ) const
inline

References database_entry_.

Referenced by find_dbase_entry(), and parse_my_tag().

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

References database_entry_.

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

References database_pdb_entry_.

std::string protocols::splice::Splice::database_pdb_entry ( ) const
inline

References database_pdb_entry_.

Referenced by parse_my_tag().

utility::vector1< core::Size >::const_iterator protocols::splice::Splice::dbase_begin ( ) const

References dbase_subset_.

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

References dbase_subset_.

Referenced by find_dbase_entry().

bool protocols::splice::Splice::dbase_iterate ( ) const
inline

References dbase_iterate_.

Referenced by find_dbase_entry(), and parse_my_tag().

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

References dbase_iterate_.

void protocols::splice::Splice::delete_hairpin ( bool const  b)
inline
bool protocols::splice::Splice::delete_hairpin ( ) const
inline

References delete_hairpin_.

Referenced by parse_my_tag(), remove_hairpin(), and Splice().

core::Size protocols::splice::Splice::delete_hairpin_c ( ) const
inline

References delete_hairpin_c_.

Referenced by parse_my_tag(), remove_hairpin(), and Splice().

void protocols::splice::Splice::delete_hairpin_c ( core::Size const  c)
inline
core::Size protocols::splice::Splice::delete_hairpin_n ( ) const
inline

References delete_hairpin_n_.

Referenced by parse_my_tag(), remove_hairpin(), and Splice().

void protocols::splice::Splice::delete_hairpin_n ( core::Size const  c)
inline
void protocols::splice::Splice::delta_lengths ( utility::vector1< int > const &  dl)
inline

References delta_lengths_.

utility::vector1< int > protocols::splice::Splice::delta_lengths ( )
inline

References delta_lengths_.

bool protocols::splice::Splice::design ( ) const
inline

References design_.

Referenced by apply(), and parse_my_tag().

void protocols::splice::Splice::design ( bool const  d)
inline

References design_.

void protocols::splice::Splice::design_shell ( core::Real const  c)
inline
core::Real protocols::splice::Splice::design_shell ( ) const
inline

References design_shell_.

Referenced by apply(), and parse_my_tag().

core::pack::task::TaskFactoryOP protocols::splice::Splice::design_task_factory ( ) const

References design_task_factory_.

Referenced by apply(), and parse_my_tag().

void protocols::splice::Splice::design_task_factory ( core::pack::task::TaskFactoryOP  tf)

References design_task_factory_.

core::Real protocols::splice::Splice::dihedral_const ( ) const
inline

References dihedral_const_.

void protocols::splice::Splice::equal_length ( bool const  e)
inline

References equal_length_.

bool protocols::splice::Splice::equal_length ( ) const
inline

References equal_length_.

Referenced by find_dbase_entry(), and parse_my_tag().

core::Size protocols::splice::Splice::find_dbase_entry ( core::pose::Pose const &  pose)
core::Size protocols::splice::Splice::find_non_active_site_cut_site ( core::pose::Pose const &  pose)
private

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(), parse_pdb_code(), core::pose::Pose::pdb_info(), protein_family_, core::pose::Pose::residue(), segment_type_, splice_segments_, core::pose::Pose::total_residue(), protocols::splice::TR(), and protocols::splice::TR_pssm().

Referenced by apply().

void protocols::splice::Splice::fold_tree ( core::pose::Pose pose,
core::Size const  start,
core::Size const  stop,
core::Size const  cut 
) const
protocols::moves::MoverOP protocols::splice::Splice::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.

void protocols::splice::Splice::from_res ( core::Size const  f)
core::Size protocols::splice::Splice::from_res ( core::pose::Pose const &  pose) const

References from_res_.

core::sequence::SequenceProfileOP protocols::splice::Splice::generate_sequence_profile ( core::pose::Pose pose)
core::Size protocols::splice::Splice::get_current_seg ( )
inline

References current_segment_pos.

std::string protocols::splice::Splice::get_dofs_pdb_name ( ) const
inline

References dofs_pdb_name.

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

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

Implements protocols::moves::Mover.

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

utility::vector1< std::string > protocols::splice::Splice::get_segment_names_ordered ( ) const
inline
void protocols::splice::Splice::load_from_checkpoint ( )

The checkpointing file has the following structure: the first line contains an ordered list of the dbase_subset_ for splice to iterate over the loop database. The second line contains the last element tested (the loop-entry number in the database; not the iterator to it!) and the third line contains the best element tested (again, the loop number from the database, not the iterator!). To recover from a checkpoint the following reads the dbase_subset_ then, if this is a first_pass_ the best entry becomes current, and if it is not a first_pass then the current entry is current.

References checkpointing_file_, current_dbase_entry_, dbase_subset_, and protocols::splice::TR().

Referenced by find_dbase_entry().

void protocols::splice::Splice::load_pdb_segments_from_pose_comments ( core::pose::Pose const &  p)
core::Size protocols::splice::Splice::locked_res ( ) const

References locked_res_.

Referenced by apply(), find_dbase_entry(), and fold_tree().

void protocols::splice::Splice::locked_res ( core::Size const  r)

References locked_res_.

void protocols::splice::Splice::locked_res_id ( char const  c)
char protocols::splice::Splice::locked_res_id ( ) const

References locked_res_id_.

Referenced by apply().

std::string protocols::splice::Splice::loop_dbase_file_name ( ) const

References loop_dbase_file_name_.

Referenced by parse_my_tag().

void protocols::splice::Splice::loop_dbase_file_name ( std::string const &  f)

References loop_dbase_file_name_.

void protocols::splice::Splice::loop_pdb_source ( std::string const &  l)

References loop_pdb_source_.

std::string protocols::splice::Splice::loop_pdb_source ( ) const

References loop_pdb_source_.

Referenced by parse_my_tag().

void protocols::splice::Splice::modify_pdb_segments_with_current_segment ( std::string const &  pdb_name)

References pdb_segments_, and segment_type_.

Referenced by apply().

std::string protocols::splice::Splice::mover_name ( )
static

Referenced by parse_my_tag(), and provide_xml_schema().

void protocols::splice::Splice::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.

References add_sequence_constraints_only(), allow_all_aa(), allowed_cuts_, bb_comp_db_, ccd(), CG_const_, chain_num_, checkpointing_file(), checkpointing_file_, cut_secondarystruc(), database_entry(), database_pdb_entry(), database_pdb_entry_, database_segment_map_, dbase_iterate(), debug_, delete_hairpin(), delete_hairpin_c(), delete_hairpin_n(), delta_lengths_, design(), design_shell(), design_task_factory(), end_dbase_subset_, enzdes_, equal_length(), protocols::rosetta_scripts::find_nearest_disulfide(), from_res_, ignore_chain_break_, protocols::rosetta_scripts::legacy_saved_pose_or_input(), locked_res_, loop_dbase_file_name(), loop_dbase_file_name_, loop_pdb_source(), min_seg_, mover_name(), mover_name_, mover_tag_, order_segments_, protocols::rosetta_scripts::parse_filter(), core::pose::parse_resnum(), core::scoring::parse_score_function(), core::pack::task::parse_task_operations(), pdb_to_H3_seq_map_, poly_ala(), core::import_pose::pose_from_file(), profile_weight_away_from_interface(), protein_family(), protein_family_, protein_family_to_database_, randomize_cut(), rb_sensitive(), protocols::splice::read_H3_seq(), read_torsion_database(), repack_shell(), res_move(), restrict_to_repacking_chain2(), rms_cutoff(), rms_cutoff_loop(), rtmin(), scorefxn(), segment_names_ordered_, segment_type_, set_fold_tree_only_, skip_alignment(), source_pdb(), source_pdb_, source_pdb_from_res(), source_pdb_to_res(), source_pose_, splice_filter(), splice_segments_, start_pose_, superimposed(), tail_segment_, task_factory(), template_file(), template_file_, template_pose_, thread_original_sequence(), to_res_, tolerance_, torsion_database_, torsion_database_fname(), torsion_database_fname_, protocols::splice::TR(), and use_sequence_profiles_.

std::string protocols::splice::Splice::parse_pdb_code ( std::string  pdb_file_name)
private

This is helper function that cuts out a file name, removing the extension and the path.

Referenced by apply(), find_non_active_site_cut_site(), and generate_sequence_profile().

void protocols::splice::Splice::poly_ala ( bool const  p)
inline

References poly_ala_.

bool protocols::splice::Splice::poly_ala ( ) const
inline

References poly_ala_.

Referenced by apply(), and parse_my_tag().

void protocols::splice::Splice::profile_weight_away_from_interface ( core::Real const  p)
core::Real protocols::splice::Splice::profile_weight_away_from_interface ( ) const
void protocols::splice::Splice::protein_family ( std::string const &  s)
inline

References protein_family_.

Referenced by parse_my_tag().

void protocols::splice::Splice::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::splice::Splice::randomize_cut ( bool const  r)
inline

References randomize_cut_.

bool protocols::splice::Splice::randomize_cut ( ) const
inline

References randomize_cut_.

Referenced by apply(), and parse_my_tag().

void protocols::splice::Splice::rb_adjust_template ( core::pose::Pose const &  pose)
bool protocols::splice::Splice::rb_sensitive ( ) const
inline

References rb_sensitive_.

Referenced by parse_my_tag(), and rb_adjust_template().

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

References rb_sensitive_.

void protocols::splice::Splice::read_splice_segments ( std::string const &  segment_type,
std::string const &  segment_name,
std::string const &  file_name 
)

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 segment_type_, splice_segments_, protocols::splice::TR(), and use_sequence_profiles_.

void protocols::splice::Splice::read_torsion_database ( )

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 protocols::splice::ResidueBBDofs::clear(), debug_, core::scoring::omega, tail_torsion_database_, torsion_database_, torsion_database_fname_, and protocols::splice::TR().

Referenced by parse_my_tag(), and set_fold_tree().

void protocols::splice::Splice::remove_hairpin ( core::pose::Pose pose) const
void protocols::splice::Splice::repack_shell ( core::Real const  c)
inline
core::Real protocols::splice::Splice::repack_shell ( ) const
inline

References repack_shell_.

Referenced by apply(), and parse_my_tag().

void protocols::splice::Splice::res_move ( core::Size const  r)
inline

References res_move_.

core::Size protocols::splice::Splice::res_move ( ) const
inline

References res_move_.

Referenced by apply(), and parse_my_tag().

bool protocols::splice::Splice::restrict_to_repacking_chain2 ( ) const
inline

References restrict_to_repacking_chain2_.

Referenced by apply(), and parse_my_tag().

void protocols::splice::Splice::restrict_to_repacking_chain2 ( bool const  r)
inline
void protocols::splice::Splice::retrieve_values ( )
private
core::Real protocols::splice::Splice::rms_cutoff ( ) const
inline

References rms_cutoff_.

Referenced by apply(), and parse_my_tag().

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

References rms_cutoff_.

core::Real protocols::splice::Splice::rms_cutoff_loop ( ) const
inline

References rms_cutoff_loop_.

Referenced by apply(), and parse_my_tag().

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

References rms_cutoff_loop_.

bool protocols::splice::Splice::rtmin ( ) const
inline

References rtmin_.

Referenced by apply(), and parse_my_tag().

void protocols::splice::Splice::rtmin ( bool const  d)
inline

References rtmin_.

void protocols::splice::Splice::save_to_checkpoint ( ) const
void protocols::splice::Splice::save_values ( core::pose::Pose const &  pose)
private

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 from_res(), saved_from_res_, saved_to_res_, and to_res().

Referenced by apply().

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

References scorefxn_.

core::scoring::ScoreFunctionOP protocols::splice::Splice::scorefxn ( ) const
void protocols::splice::Splice::set_cut_res ( core::Size const  r)
inline

References set_cut_res_.

core::Size protocols::splice::Splice::set_cut_res ( ) const
inline

References set_cut_res_.

void protocols::splice::Splice::set_dofs_pdb_name ( std::string  dofsPDBname)
inline

References dofs_pdb_name.

void protocols::splice::Splice::set_fold_tree ( core::pose::Pose pose,
core::Size const  vl_vh_cut 
)
void protocols::splice::Splice::set_segment_names_ordered ( utility::vector1< std::string >  SegNameOrder)
inline
bool protocols::splice::Splice::skip_alignment ( ) const
inline

References skip_alignment_.

Referenced by apply(), find_dbase_entry(), and parse_my_tag().

void protocols::splice::Splice::skip_alignment ( bool const  b)
inline
std::string protocols::splice::Splice::source_pdb ( ) const
inline
void protocols::splice::Splice::source_pdb ( std::string const &  s)
inline

References source_pdb_.

core::Size protocols::splice::Splice::source_pdb_from_res ( ) const
inline
void protocols::splice::Splice::source_pdb_from_res ( core::Size const  s)
inline

References source_pdb_from_res_.

core::Size protocols::splice::Splice::source_pdb_to_res ( ) const
inline
void protocols::splice::Splice::source_pdb_to_res ( core::Size const  s)
inline

References source_pdb_to_res_.

protocols::filters::FilterOP protocols::splice::Splice::splice_filter ( ) const

References splice_filter_.

Referenced by apply(), and parse_my_tag().

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

References splice_filter_.

void protocols::splice::Splice::superimpose_source_on_pose ( core::pose::Pose const &  pose,
core::pose::Pose source_pose 
)
private
bool protocols::splice::Splice::superimposed ( ) const
inline
void protocols::splice::Splice::superimposed ( bool const  b)
inline
void protocols::splice::Splice::tail_fold_tree ( core::pose::Pose pose,
core::Size const  vl_vh_cut,
core::Size  chain_break,
std::string  segment_name 
) const
core::pack::task::TaskFactoryOP protocols::splice::Splice::task_factory ( ) const

References task_factory_.

Referenced by apply(), and parse_my_tag().

void protocols::splice::Splice::task_factory ( core::pack::task::TaskFactoryOP  tf)

References task_factory_.

std::string protocols::splice::Splice::template_file ( ) const
inline

References template_file_.

Referenced by parse_my_tag().

void protocols::splice::Splice::template_file ( std::string const &  s)
inline

References template_file_.

bool protocols::splice::Splice::thread_original_sequence ( ) const
inline

References thread_original_sequence_.

Referenced by apply(), and parse_my_tag().

void protocols::splice::Splice::thread_original_sequence ( bool const  s)
inline
void protocols::splice::Splice::to_res ( core::Size const  t)
core::Size protocols::splice::Splice::to_res ( core::pose::Pose const &  pose) const

References to_res_.

utility::vector1< ResidueBBDofs > protocols::splice::Splice::torsion_database ( ) const
inline

References torsion_database_.

void protocols::splice::Splice::torsion_database ( utility::vector1< ResidueBBDofs > const &  d)
inline

References torsion_database_.

std::string protocols::splice::Splice::torsion_database_fname ( ) const
inline

References torsion_database_fname_.

Referenced by parse_my_tag().

void protocols::splice::Splice::torsion_database_fname ( std::string const &  d)
inline

Member Data Documentation

bool protocols::splice::Splice::add_sequence_constraints_only_
private
bool protocols::splice::Splice::allow_all_aa_
private

Referenced by allow_all_aa().

core::Size protocols::splice::Splice::allowed_cuts_
private

Referenced by chainbreak_check(), and parse_my_tag().

std::map< std::string, BBMatchingOP > protocols::splice::Splice::bb_comp_db_
private

Referenced by find_dbase_entry(), and parse_my_tag().

bool protocols::splice::Splice::ccd_
private
bool protocols::splice::Splice::CG_const_
private

Referenced by apply(), and parse_my_tag().

core::Size protocols::splice::Splice::chain_num_
private
std::string protocols::splice::Splice::checkpointing_file_
private
core::Real protocols::splice::Splice::coor_const_
private

Referenced by coor_const().

utility::vector1< core::Size >::const_iterator protocols::splice::Splice::current_dbase_entry_
private
core::Size protocols::splice::Splice::current_segment_pos
private

Referenced by get_current_seg().

bool protocols::splice::Splice::cut_secondarystruc_
private

Referenced by cut_secondarystruc().

core::Size protocols::splice::Splice::database_entry_
private

Referenced by database_entry().

std::string protocols::splice::Splice::database_pdb_entry_
private
std::map< std::string, std::string> protocols::splice::Splice::database_segment_map_
private

Referenced by parse_my_tag(), and set_fold_tree().

bool protocols::splice::Splice::dbase_iterate_
private

Referenced by dbase_iterate().

utility::vector1< core::Size > protocols::splice::Splice::dbase_subset_
private
bool protocols::splice::Splice::debug_
private
bool protocols::splice::Splice::delete_hairpin_
private

Referenced by delete_hairpin().

core::Size protocols::splice::Splice::delete_hairpin_c_
private

Referenced by delete_hairpin_c().

core::Size protocols::splice::Splice::delete_hairpin_n_
private

Referenced by delete_hairpin_n().

utility::vector1< int > protocols::splice::Splice::delta_lengths_
private
bool protocols::splice::Splice::design_
private

Referenced by design().

core::Real protocols::splice::Splice::design_shell_
private

Referenced by design_shell(), and Splice().

core::pack::task::TaskFactoryOP protocols::splice::Splice::design_task_factory_
private

Referenced by design_task_factory().

core::Real protocols::splice::Splice::dihedral_const_
private

Referenced by dihedral_const().

std::string protocols::splice::Splice::dofs_pdb_name
private
DataccacheBoolDataOP protocols::splice::Splice::end_dbase_subset_
private
bool protocols::splice::Splice::enzdes_
private

Referenced by parse_my_tag().

bool protocols::splice::Splice::equal_length_
private

Referenced by equal_length().

bool protocols::splice::Splice::first_pass_
private
core::pose::ResidueIndexDescriptionCOP protocols::splice::Splice::from_res_
private

Referenced by from_res(), and parse_my_tag().

bool protocols::splice::Splice::ignore_chain_break_
private

Referenced by apply(), and parse_my_tag().

utility::pointer::shared_ptr< basic::datacache::DataMapObj < utility::vector1< core::Size > > > protocols::splice::Splice::locked_res_
private

Referenced by locked_res(), and parse_my_tag().

char protocols::splice::Splice::locked_res_id_
private

Referenced by locked_res_id().

std::string protocols::splice::Splice::loop_dbase_file_name_
private
std::string protocols::splice::Splice::loop_pdb_source_
private

Referenced by apply(), and loop_pdb_source().

bool protocols::splice::Splice::min_seg_
private

Referenced by apply(), and parse_my_tag().

std::string protocols::splice::Splice::mover_name_
private
utility::pointer::shared_ptr< basic::datacache::DataMapObj< std::string > > protocols::splice::Splice::mover_tag_
private

Referenced by apply(), and parse_my_tag().

std::map< std::string, utility::vector1< std::string > > protocols::splice::Splice::order_segments_
private

Referenced by parse_my_tag(), and Splice().

std::string protocols::splice::Splice::Pdb4LetName_
private
std::map< std::string, std::string > protocols::splice::Splice::pdb_segments_
private
std::map< std::string, std::string > protocols::splice::Splice::pdb_to_H3_seq_map_
private
bool protocols::splice::Splice::poly_ala_
private

Referenced by poly_ala().

core::Real protocols::splice::Splice::profile_weight_away_from_interface_
private
std::string protocols::splice::Splice::protein_family_
private
std::map< std::string, std::string> protocols::splice::Splice::protein_family_to_database_
private

Referenced by parse_my_tag(), and Splice().

bool protocols::splice::Splice::randomize_cut_
private

Referenced by randomize_cut().

bool protocols::splice::Splice::rb_sensitive_
private

Referenced by rb_sensitive(), and Splice().

core::Real protocols::splice::Splice::repack_shell_
private

Referenced by repack_shell(), and Splice().

core::Size protocols::splice::Splice::res_move_
private

Referenced by res_move().

bool protocols::splice::Splice::restrict_to_repacking_chain2_
private
core::Real protocols::splice::Splice::rms_cutoff_
private

Referenced by rms_cutoff().

core::Real protocols::splice::Splice::rms_cutoff_loop_
private

Referenced by rms_cutoff_loop().

bool protocols::splice::Splice::rtmin_
private

Referenced by rtmin().

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

Referenced by apply().

core::Size protocols::splice::Splice::saved_from_res_
private

Referenced by retrieve_values(), and save_values().

core::Size protocols::splice::Splice::saved_to_res_
private

Referenced by retrieve_values(), and save_values().

core::scoring::ScoreFunctionOP protocols::splice::Splice::scorefxn_
private

Referenced by scorefxn().

utility::vector1< std::string > protocols::splice::Splice::segment_names_ordered_
private
std::string protocols::splice::Splice::segment_type_
private
core::Size protocols::splice::Splice::set_cut_res_
private

Referenced by set_cut_res().

bool protocols::splice::Splice::set_fold_tree_only_
private

Referenced by apply(), parse_my_tag(), and Splice().

bool protocols::splice::Splice::skip_alignment_
private

Referenced by skip_alignment(), and Splice().

std::string protocols::splice::Splice::source_pdb_
private
core::Size protocols::splice::Splice::source_pdb_from_res_
private

Referenced by source_pdb_from_res().

core::Size protocols::splice::Splice::source_pdb_to_res_
private

Referenced by source_pdb_to_res().

core::pose::PoseOP protocols::splice::Splice::source_pose_
private
protocols::filters::FilterOP protocols::splice::Splice::splice_filter_
private

Referenced by splice_filter().

std::map< std::string, SpliceSegmentOP > protocols::splice::Splice::splice_segments_
private
core::pose::PoseCOP protocols::splice::Splice::start_pose_
private

Referenced by parse_my_tag().

bool protocols::splice::Splice::superimposed_
private

Referenced by superimposed().

std::string protocols::splice::Splice::tail_segment_
private
utility::vector1< ResidueBBDofs > protocols::splice::Splice::tail_torsion_database_
private

Referenced by apply(), and read_torsion_database().

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

Referenced by task_factory().

std::string protocols::splice::Splice::template_file_
private

Referenced by apply(), parse_my_tag(), and template_file().

core::pose::PoseCOP protocols::splice::Splice::template_pose_
private
bool protocols::splice::Splice::thread_original_sequence_
private
core::pose::ResidueIndexDescriptionCOP protocols::splice::Splice::to_res_
private

Referenced by parse_my_tag(), and to_res().

core::Real protocols::splice::Splice::tolerance_
private

Referenced by apply(), parse_my_tag(), and Splice().

utility::vector1< ResidueBBDofs > protocols::splice::Splice::torsion_database_
private
std::string protocols::splice::Splice::torsion_database_fname_
private
bool protocols::splice::Splice::use_sequence_profiles_
private
core::Size protocols::splice::Splice::vl_vh_cut
private

Referenced by apply().


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