Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::cyclic_peptide::PeptideStubMover Class Reference

#include <PeptideStubMover.hh>

Public Member Functions

 PeptideStubMover ()
 
virtual ~PeptideStubMover ()
 
void init ()
 
virtual void apply (Pose &)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
virtual void parse_my_tag (TagCOP, basic::datacache::DataMap &, Filters_map const &, moves::Movers_map const &, Pose const &)
 parse XML (specifically in the context of the parser/scripting scheme) More...
 
- 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
 
void set_type (std::string const &setting)
 
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
 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Private Member Functions

virtual void rebuild_atoms (core::pose::Pose &pose, core::Size const residue_index) const
 Rebuilds all atoms that are dependent on bonds between residue_index and any other residues (including atoms on the other residues). More...
 
virtual void update_pdb_numbering (core::pose::Pose &pose) const
 Updates the PDB numbering (PDB number/chain ID) as residues are added. More...
 

Private Attributes

bool reset_
 
bool update_pdb_numbering_
 As residues are added, should the PDB numbering be updated? Default true. More...
 
utility::vector1< StubModestub_mode_
 
utility::vector1< std::stringstub_rsd_names_
 
utility::vector1< boolstub_rsd_jumping_
 
utility::vector1< std::stringstub_rsd_connecting_atom_
 
utility::vector1< core::Sizestub_rsd_repeat_
 
utility::vector1< core::Sizestub_insert_pos_
 
utility::vector1< core::Sizestub_anchor_rsd_
 
utility::vector1< std::stringstub_anchor_rsd_connecting_atom_
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- 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 inherited from protocols::moves::Mover
void set_last_move_status (MoverStatus status)
 nonvirtual setter for MoverStatus last_status_. Protected means that only the mover itself will be able to change its own status. The job distributor (august 08 vintage) is aware of status set with this function and will do what the MoverStatus says. More...
 

Constructor & Destructor Documentation

protocols::cyclic_peptide::PeptideStubMover::PeptideStubMover ( )
protocols::cyclic_peptide::PeptideStubMover::~PeptideStubMover ( )
virtual

Member Function Documentation

void protocols::cyclic_peptide::PeptideStubMover::apply ( Pose pose)
virtual

Implements protocols::moves::Mover.

References core::pose::add_variant_type_to_pose_residue(), core::pose::Pose::annotated_sequence(), protocols::cyclic_peptide::append, core::pose::Pose::append_polymer_residue_after_seqpos(), core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), core::chemical::ResidueType::atom_index(), core::chemical::ResidueConnection::atomno(), core::pose::Pose::clear(), core::conformation::Residue::connect_map(), core::conformation::Residue::connected_residue_at_resconn(), core::chemical::ResConnID::connid(), core::conformation::ResidueFactory::create_residue(), CUTPOINT_LOWER, CUTPOINT_UPPER, core::pose::Pose::dump_pdb(), core::chemical::FA_STANDARD, core::pose::Pose::fold_tree(), core::chemical::ChemicalManager::get_instance(), core::conformation::Residue::has_variant_type(), core::chemical::ResidueType::has_variant_type(), protocols::cyclic_peptide::insert, core::pose::Pose::insert_residue_by_bond(), core::kinematics::FoldTree::is_cutpoint(), core::kinematics::FoldTree::is_jump_point(), core::conformation::Residue::is_protein(), core::chemical::ResidueType::lower_connect_id(), LOWER_TERMINUS_VARIANT, core::chemical::ResidueType::n_residue_connections(), protocols::cyclic_peptide::prepend, core::pose::Pose::prepend_polymer_residue_before_seqpos(), rebuild_atoms(), core::pose::remove_variant_type_from_pose_residue(), reset_, core::pose::Pose::residue(), core::chemical::ResidueType::residue_connection(), core::chemical::ResidueType::residue_connection_id_for_atom(), core::pose::Pose::residue_type(), core::chemical::ChemicalManager::residue_type_set(), runtime_assert_string_msg, core::kinematics::FoldTree::show(), stub_anchor_rsd_, stub_anchor_rsd_connecting_atom_, stub_insert_pos_, stub_mode_, stub_rsd_connecting_atom_, stub_rsd_jumping_, stub_rsd_names_, stub_rsd_repeat_, core::pose::Pose::total_residue(), protocols::TR, update_pdb_numbering(), update_pdb_numbering_, core::pose::Pose::update_residue_neighbors(), core::chemical::ResidueType::upper_connect_id(), and UPPER_TERMINUS_VARIANT.

moves::MoverOP protocols::cyclic_peptide::PeptideStubMover::clone ( ) const
virtual

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.

References PeptideStubMover().

moves::MoverOP protocols::cyclic_peptide::PeptideStubMover::fresh_instance ( ) const
virtual

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.

References PeptideStubMover().

std::string protocols::cyclic_peptide::PeptideStubMover::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::cyclic_peptide::PeptideStubMover::init ( void  )

References reset_, and update_pdb_numbering_.

Referenced by PeptideStubMover().

void protocols::cyclic_peptide::PeptideStubMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap ,
Filters_map const &  ,
moves::Movers_map const &  ,
Pose const &   
)
virtual
void protocols::cyclic_peptide::PeptideStubMover::rebuild_atoms ( core::pose::Pose pose,
core::Size const  residue_index 
) const
privatevirtual
void protocols::cyclic_peptide::PeptideStubMover::update_pdb_numbering ( core::pose::Pose pose) const
privatevirtual

Updates the PDB numbering (PDB number/chain ID) as residues are added.

References core::pose::Pose::chain(), utility::pointer::owning_ptr< T >::get(), core::pose::Pose::n_residue(), and core::pose::Pose::pdb_info().

Referenced by apply().

Member Data Documentation

bool protocols::cyclic_peptide::PeptideStubMover::reset_
private

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

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideStubMover::stub_anchor_rsd_
private

Referenced by apply(), and parse_my_tag().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideStubMover::stub_anchor_rsd_connecting_atom_
private

Referenced by apply(), and parse_my_tag().

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideStubMover::stub_insert_pos_
private

Referenced by apply(), and parse_my_tag().

utility::vector1<StubMode> protocols::cyclic_peptide::PeptideStubMover::stub_mode_
private

Referenced by apply(), and parse_my_tag().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideStubMover::stub_rsd_connecting_atom_
private

Referenced by apply(), and parse_my_tag().

utility::vector1<bool> protocols::cyclic_peptide::PeptideStubMover::stub_rsd_jumping_
private

Referenced by apply(), and parse_my_tag().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideStubMover::stub_rsd_names_
private

Referenced by apply(), and parse_my_tag().

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideStubMover::stub_rsd_repeat_
private

Referenced by apply(), and parse_my_tag().

bool protocols::cyclic_peptide::PeptideStubMover::update_pdb_numbering_
private

As residues are added, should the PDB numbering be updated? Default true.

Referenced by apply(), and init().


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