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protocols::protein_interface_design::movers::Splice Class Reference

designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines. More...

#include <Splice.hh>

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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::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::string > Strings
 

Public Member Functions

 Splice ()
 
void apply (Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
protocols::moves::MoverOP fresh_instance () const
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
virtual ~Splice ()
 
void from_res (core::Size const f)
 
core::Size from_res () const
 
void to_res (core::Size const t)
 
core::Size to_res () const
 
std::string source_pdb () const
 
void source_pdb (std::string const s)
 
void ccd (bool const c)
 
bool ccd () const
 
void scorefxn (core::scoring::ScoreFunctionOP sf)
 
core::scoring::ScoreFunctionOP scorefxn () const
 
core::Real rms_cutoff () const
 
void rms_cutoff (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 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)
 
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...
 
bool design () const
 
void design (bool const d)
 
void delta_lengths (utility::vector1< int > const dl)
 
utility::vector1< intdelta_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)
 
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 ()
 
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 profile_weight_away_from_interface (core::Real const p)
 
core::Real profile_weight_away_from_interface () const
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
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...
 
void set_current_tag (std::string const &new_tag)
 
virtual void set_input_pose (PoseCOP pose)
 setter for poses contained for rms More...
 
virtual void set_native_pose (PoseCOP pose)
 setter for native poses contained for rms -— we should get rid of this method? it is widely used, but a bit unsafe More...
 
PoseCOP get_input_pose () const
 
PoseCOP get_native_pose () const
 
virtual void 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...
 
void type (const std::string &type_in)
 
std::string get_type () const
 
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...
 
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 reinitialize_for_each_job () const
 this function informs 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
 this function informs 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Member Functions

void save_values ()
 
void retrieve_values ()
 

Private Attributes

core::Size from_res_
 
core::Size to_res_
 
core::Size saved_from_res_
 
core::Size saved_to_res_
 
std::string source_pdb_
 
bool ccd_
 
core::scoring::ScoreFunctionOP scorefxn_
 
core::Real rms_cutoff_
 
core::Size res_move_
 
bool randomize_cut_
 
bool cut_secondarystruc_
 
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_
 
std::string template_file_
 
bool poly_ala_
 
bool equal_length_
 dflt true; thread ala residues in each position other than Gly/Pro or conserved in the source pdb. If false, keeps the input sequence (except Gly/Pro, which are replaced) More...
 
core::pose::PoseOP template_pose_
 
core::pose::PoseOP start_pose_
 
core::kinematics::FoldTreeOP saved_fold_tree_
 
bool design_
 
utility::vector1< intdelta_lengths_
 
bool dbase_iterate_
 
bool first_pass_
 
utility::vector1< core::Sizedbase_subset_
 
utility::vector1< core::Size >
::const_iterator 
current_dbase_entry_
 
utility::pointer::owning_ptr
< protocols::moves::DataMapObj
< bool > > 
end_dbase_subset_
 
utility::pointer::owning_ptr
< protocols::moves::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::owning_ptr
< protocols::moves::DataMapObj
< std::string > > 
mover_tag_
 
protocols::filters::FilterOP splice_filter_
 dflt NULL; to communicate the current Splice mover's loop origin to the GenericMC More...
 
bool use_sequence_profiles_
 sequence profiles More...
 
std::string segment_type_
 
std::map< std::string,
SpliceSegmentOP
splice_segments_
 
std::map< std::string,
std::string > 
pdb_segments_
 
core::Real profile_weight_away_from_interface_
 

Additional Inherited Members

- 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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. More...
 
- 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

designs alanine residues in place of the residue identities at the interface. Retains interface glycines and prolines.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::protein_interface_design::movers::Splice::Splice ( )
protocols::protein_interface_design::movers::Splice::~Splice ( )
virtual

Member Function Documentation

void protocols::protein_interface_design::movers::Splice::add_sequence_constraints ( core::pose::Pose pose)
void protocols::protein_interface_design::movers::Splice::apply ( Pose pose)
virtual

Implements protocols::moves::Mover.

References core::chemical::aa_from_name(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::apply(), protocols::simple_moves::PackRotamersMover::apply(), protocols::protein_interface_design::movers::ResidueBBDofs::clear(), core::io::serialization::clone(), core::pose::Pose::conformation(), protocols::protein_interface_design::movers::copy_stretch(), protocols::toolbox::task_operations::DesignAroundOperation::design_shell(), core::conformation::Conformation::detect_disulfides(), core::chemical::DISULFIDE, core::scoring::dssp::Dssp::dssp_reduced(), protocols::moves::FAIL_DO_NOT_RETRY, protocols::moves::FAIL_RETRY, protocols::rosetta_scripts::find_nearest_res(), core::pose::Pose::fold_tree(), core::scoring::dssp::Dssp::get_dssp_secstruct(), core::conformation::Residue::has_variant_type(), protocols::toolbox::task_operations::DesignAroundOperation::include_residue(), protocols::protein_interface_design::movers::LoopLengthChange::loop_start(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::move_map(), protocols::moves::MS_SUCCESS, core::conformation::Residue::name1(), core::conformation::Residue::name3(), core::conformation::Conformation::num_chains(), protocols::protein_interface_design::movers::BBDofs::omega(), core::scoring::omega, core::pose::Pose::omega(), core::chemical::oneletter_code_from_aa(), protocols::protein_interface_design::movers::BBDofs::phi(), protocols::swa::phi(), core::pose::Pose::phi(), core::import_pose::pose_from_pdb(), protocols::protein_interface_design::movers::BBDofs::psi(), protocols::swa::psi(), core::pose::Pose::psi(), protocols::protein_interface_design::movers::BBDofs::resid(), core::pose::Pose::residue(), protocols::rosetta_scripts::residue_packer_states(), protocols::protein_interface_design::movers::BBDofs::resn(), protocols::protein_interface_design::movers::AddChainBreak::resnum(), core::scoring::rms, core::kinematics::MoveMap::set_chi(), core::pose::Pose::set_omega(), core::pose::Pose::set_phi(), core::pose::Pose::set_psi(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::set_task_factory(), protocols::toolbox::task_operations::ThreadSequenceOperation::target_sequence(), protocols::protein_interface_design::filters::Torsion::task_factory(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::temp_final(), protocols::loops::loop_mover::refine::LoopMover_Refine_CCD::temp_initial(), core::pose::Pose::total_residue(), and core::conformation::Residue::xyz().

void protocols::protein_interface_design::movers::Splice::ccd ( bool const  c)
inline

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

bool protocols::protein_interface_design::movers::Splice::ccd ( ) const
inline

References ccd_.

std::string protocols::protein_interface_design::movers::Splice::checkpointing_file ( ) const
void protocols::protein_interface_design::movers::Splice::checkpointing_file ( std::string const  cf)
protocols::moves::MoverOP protocols::protein_interface_design::movers::Splice::clone ( ) const
virtual

clone has to be overridden only if clone invocation is expected.

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.

void protocols::protein_interface_design::movers::Splice::cut_secondarystruc ( bool const  r)
inline

References cut_secondarystruc_.

bool protocols::protein_interface_design::movers::Splice::cut_secondarystruc ( ) const
inline

References cut_secondarystruc_.

core::Size protocols::protein_interface_design::movers::Splice::database_entry ( ) const
inline

References database_entry_.

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

References database_entry_.

void protocols::protein_interface_design::movers::Splice::database_pdb_entry ( std::string const  s)
inline

References database_pdb_entry_.

std::string protocols::protein_interface_design::movers::Splice::database_pdb_entry ( ) const
inline

References database_pdb_entry_.

utility::vector1< core::Size >::const_iterator protocols::protein_interface_design::movers::Splice::dbase_begin ( ) const
utility::vector1< core::Size >::const_iterator protocols::protein_interface_design::movers::Splice::dbase_end ( ) const
bool protocols::protein_interface_design::movers::Splice::dbase_iterate ( ) const
inline

References dbase_iterate_.

void protocols::protein_interface_design::movers::Splice::dbase_iterate ( bool const  d)
inline

References dbase_iterate_.

void protocols::protein_interface_design::movers::Splice::delta_lengths ( utility::vector1< int > const  dl)
inline

References delta_lengths_.

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

References delta_lengths_.

bool protocols::protein_interface_design::movers::Splice::design ( ) const
inline

References design_.

void protocols::protein_interface_design::movers::Splice::design ( bool const  d)
inline

References design_.

core::pack::task::TaskFactoryOP protocols::protein_interface_design::movers::Splice::design_task_factory ( ) const
void protocols::protein_interface_design::movers::Splice::design_task_factory ( core::pack::task::TaskFactoryOP  tf)
void protocols::protein_interface_design::movers::Splice::equal_length ( bool const  e)
inline

References equal_length_.

bool protocols::protein_interface_design::movers::Splice::equal_length ( ) const
inline

References equal_length_.

core::Size protocols::protein_interface_design::movers::Splice::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

References protocols::rosetta_scripts::find_nearest_res(), protocols::protein_interface_design::movers::RG(), protocols::protein_interface_design::movers::ResidueBBDofs::size(), protocols::protein_interface_design::movers::ResidueBBDofs::start_loop(), and protocols::protein_interface_design::movers::ResidueBBDofs::stop_loop().

void protocols::protein_interface_design::movers::Splice::fold_tree ( core::pose::Pose pose,
core::Size const  start,
core::Size const  stop,
core::Size const  cut 
) const
protocols::moves::MoverOP protocols::protein_interface_design::movers::Splice::fresh_instance ( ) const
inlinevirtual

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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::protein_interface_design::movers::Splice::from_res ( core::Size const  f)
inline

References from_res_.

core::Size protocols::protein_interface_design::movers::Splice::from_res ( ) const
inline

References from_res_.

core::sequence::SequenceProfileOP protocols::protein_interface_design::movers::Splice::generate_sequence_profile ( )
std::string protocols::protein_interface_design::movers::Splice::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

References protocols::protein_interface_design::movers::SpliceCreator::mover_name().

void protocols::protein_interface_design::movers::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.

void protocols::protein_interface_design::movers::Splice::load_pdb_segments_from_pose_comments ( core::pose::Pose const &  p)
core::Size protocols::protein_interface_design::movers::Splice::locked_res ( ) const
void protocols::protein_interface_design::movers::Splice::locked_res ( core::Size const  r)
void protocols::protein_interface_design::movers::Splice::locked_res_id ( char const  c)
char protocols::protein_interface_design::movers::Splice::locked_res_id ( ) const
std::string protocols::protein_interface_design::movers::Splice::loop_dbase_file_name ( ) const
void protocols::protein_interface_design::movers::Splice::loop_dbase_file_name ( std::string const  f)
void protocols::protein_interface_design::movers::Splice::loop_pdb_source ( std::string const  l)
std::string protocols::protein_interface_design::movers::Splice::loop_pdb_source ( ) const
void protocols::protein_interface_design::movers::Splice::modify_pdb_segments_with_current_segment ( std::string const  pdb_name)
void protocols::protein_interface_design::movers::Splice::parse_my_tag ( utility::tag::TagPtr const  tag,
protocols::moves::DataMap data,
protocols::filters::Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
core::pose::Pose const &  pose 
)
virtual

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 stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References protocols::moves::DataMap::add(), protocols::moves::DataMap::get(), protocols::moves::get_set_from_datamap(), protocols::moves::DataMap::has(), core::conformation::Residue::name1(), protocols::rosetta_scripts::parse_filter(), core::pose::parse_resnum(), protocols::rosetta_scripts::parse_score_function(), protocols::rosetta_scripts::parse_task_operations(), core::import_pose::pose_from_pdb(), and core::pose::Pose::residue().

void protocols::protein_interface_design::movers::Splice::poly_ala ( bool const  p)
inline

References poly_ala_.

bool protocols::protein_interface_design::movers::Splice::poly_ala ( ) const
inline

References poly_ala_.

void protocols::protein_interface_design::movers::Splice::profile_weight_away_from_interface ( core::Real const  p)
core::Real protocols::protein_interface_design::movers::Splice::profile_weight_away_from_interface ( ) const
void protocols::protein_interface_design::movers::Splice::randomize_cut ( bool const  r)
inline

References randomize_cut_.

bool protocols::protein_interface_design::movers::Splice::randomize_cut ( ) const
inline

References randomize_cut_.

void protocols::protein_interface_design::movers::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.

void protocols::protein_interface_design::movers::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::protein_interface_design::movers::ResidueBBDofs::clear(), protocols::protein_interface_design::movers::ResidueBBDofs::cut_site(), core::scoring::omega, protocols::swa::phi(), protocols::swa::psi(), protocols::protein_interface_design::movers::ResidueBBDofs::push_back(), protocols::protein_interface_design::movers::ResidueBBDofs::source_pdb(), protocols::protein_interface_design::movers::ResidueBBDofs::start_loop(), and protocols::protein_interface_design::movers::ResidueBBDofs::stop_loop().

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

References res_move_.

core::Size protocols::protein_interface_design::movers::Splice::res_move ( ) const
inline

References res_move_.

void protocols::protein_interface_design::movers::Splice::retrieve_values ( )
private
core::Real protocols::protein_interface_design::movers::Splice::rms_cutoff ( ) const
inline

References rms_cutoff_.

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

References rms_cutoff_.

void protocols::protein_interface_design::movers::Splice::save_to_checkpoint ( ) const
void protocols::protein_interface_design::movers::Splice::save_values ( )
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.

void protocols::protein_interface_design::movers::Splice::scorefxn ( core::scoring::ScoreFunctionOP  sf)
core::scoring::ScoreFunctionOP protocols::protein_interface_design::movers::Splice::scorefxn ( ) const
std::string protocols::protein_interface_design::movers::Splice::source_pdb ( ) const
inline

References source_pdb_.

void protocols::protein_interface_design::movers::Splice::source_pdb ( std::string const  s)
inline

References source_pdb_.

protocols::filters::FilterOP protocols::protein_interface_design::movers::Splice::splice_filter ( ) const
void protocols::protein_interface_design::movers::Splice::splice_filter ( protocols::filters::FilterOP  f)
core::pack::task::TaskFactoryOP protocols::protein_interface_design::movers::Splice::task_factory ( ) const
void protocols::protein_interface_design::movers::Splice::task_factory ( core::pack::task::TaskFactoryOP  tf)
std::string protocols::protein_interface_design::movers::Splice::template_file ( ) const
inline

References template_file_.

void protocols::protein_interface_design::movers::Splice::template_file ( std::string const  s)
inline

References template_file_.

void protocols::protein_interface_design::movers::Splice::to_res ( core::Size const  t)
inline
core::Size protocols::protein_interface_design::movers::Splice::to_res ( ) const
inline

References to_res_.

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

References torsion_database_.

void protocols::protein_interface_design::movers::Splice::torsion_database ( utility::vector1< ResidueBBDofs > const  d)
inline

References torsion_database_.

std::string protocols::protein_interface_design::movers::Splice::torsion_database_fname ( ) const
inline
void protocols::protein_interface_design::movers::Splice::torsion_database_fname ( std::string const  d)
inline

Member Data Documentation

bool protocols::protein_interface_design::movers::Splice::ccd_
private

Referenced by ccd().

std::string protocols::protein_interface_design::movers::Splice::checkpointing_file_
private
utility::vector1< core::Size >::const_iterator protocols::protein_interface_design::movers::Splice::current_dbase_entry_
private
bool protocols::protein_interface_design::movers::Splice::cut_secondarystruc_
private

Referenced by cut_secondarystruc().

core::Size protocols::protein_interface_design::movers::Splice::database_entry_
private

Referenced by database_entry().

std::string protocols::protein_interface_design::movers::Splice::database_pdb_entry_
private

Referenced by database_pdb_entry().

bool protocols::protein_interface_design::movers::Splice::dbase_iterate_
private

Referenced by dbase_iterate().

utility::vector1< core::Size > protocols::protein_interface_design::movers::Splice::dbase_subset_
private

Referenced by Splice().

utility::vector1< int > protocols::protein_interface_design::movers::Splice::delta_lengths_
private

Referenced by delta_lengths(), and Splice().

bool protocols::protein_interface_design::movers::Splice::design_
private

Referenced by design().

core::pack::task::TaskFactoryOP protocols::protein_interface_design::movers::Splice::design_task_factory_
private
utility::pointer::owning_ptr< protocols::moves::DataMapObj< bool > > protocols::protein_interface_design::movers::Splice::end_dbase_subset_
private

Referenced by Splice().

bool protocols::protein_interface_design::movers::Splice::equal_length_
private

dflt true; thread ala residues in each position other than Gly/Pro or conserved in the source pdb. If false, keeps the input sequence (except Gly/Pro, which are replaced)

Referenced by equal_length().

bool protocols::protein_interface_design::movers::Splice::first_pass_
private
core::Size protocols::protein_interface_design::movers::Splice::from_res_
private

Referenced by from_res().

utility::pointer::owning_ptr< protocols::moves::DataMapObj < utility::vector1< core::Size > > > protocols::protein_interface_design::movers::Splice::locked_res_
private
char protocols::protein_interface_design::movers::Splice::locked_res_id_
private
std::string protocols::protein_interface_design::movers::Splice::loop_dbase_file_name_
private
std::string protocols::protein_interface_design::movers::Splice::loop_pdb_source_
private
utility::pointer::owning_ptr< protocols::moves::DataMapObj< std::string > > protocols::protein_interface_design::movers::Splice::mover_tag_
private
std::map< std::string, std::string > protocols::protein_interface_design::movers::Splice::pdb_segments_
private

Referenced by Splice().

bool protocols::protein_interface_design::movers::Splice::poly_ala_
private

Referenced by poly_ala().

core::Real protocols::protein_interface_design::movers::Splice::profile_weight_away_from_interface_
private
bool protocols::protein_interface_design::movers::Splice::randomize_cut_
private

Referenced by randomize_cut().

core::Size protocols::protein_interface_design::movers::Splice::res_move_
private

Referenced by res_move().

core::Real protocols::protein_interface_design::movers::Splice::rms_cutoff_
private

Referenced by rms_cutoff().

core::kinematics::FoldTreeOP protocols::protein_interface_design::movers::Splice::saved_fold_tree_
private
core::Size protocols::protein_interface_design::movers::Splice::saved_from_res_
private
core::Size protocols::protein_interface_design::movers::Splice::saved_to_res_
private
core::scoring::ScoreFunctionOP protocols::protein_interface_design::movers::Splice::scorefxn_
private
std::string protocols::protein_interface_design::movers::Splice::segment_type_
private
std::string protocols::protein_interface_design::movers::Splice::source_pdb_
private

Referenced by source_pdb().

protocols::filters::FilterOP protocols::protein_interface_design::movers::Splice::splice_filter_
private

dflt NULL; to communicate the current Splice mover's loop origin to the GenericMC

std::map< std::string, SpliceSegmentOP > protocols::protein_interface_design::movers::Splice::splice_segments_
private

Referenced by Splice().

core::pose::PoseOP protocols::protein_interface_design::movers::Splice::start_pose_
private
core::pack::task::TaskFactoryOP protocols::protein_interface_design::movers::Splice::task_factory_
private
std::string protocols::protein_interface_design::movers::Splice::template_file_
private

Referenced by template_file().

core::pose::PoseOP protocols::protein_interface_design::movers::Splice::template_pose_
private
core::Size protocols::protein_interface_design::movers::Splice::to_res_
private

Referenced by to_res().

utility::vector1< ResidueBBDofs > protocols::protein_interface_design::movers::Splice::torsion_database_
private

Referenced by Splice(), and torsion_database().

std::string protocols::protein_interface_design::movers::Splice::torsion_database_fname_
private

Referenced by torsion_database_fname().

bool protocols::protein_interface_design::movers::Splice::use_sequence_profiles_
private

sequence profiles


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