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Rosetta 3.5
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Rosetta 3.5
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#include <ExtendedPoseMover.hh>
Public Member Functions | |
| ExtendedPoseMover (const string &sequence="", const string &residue_type_set_="centroid") | |
| void | apply (core::pose::Pose &pose) |
| Creates an extended, idealized pose from the sequence and residue type set specified in the constructor. More... | |
| string | get_name () const |
| Returns the name of this mover. More... | |
| bool | valid () const |
| Returns true if this instance is valid (i.e. contains a sequence). Since RosettaScripts mandates the existence of a no-argument constructor, we lose the ability to reason about the validity of a particular instance. More... | |
| const string & | sequence () const |
| Returns the sequence. More... | |
| const string & | residue_type_set () const |
| Returns the residue type set. More... | |
| void | sequence (const string &sequence) |
| Updates the sequence to be used in calls to apply() More... | |
| void | residue_type_set (const string &residue_type_set) |
| Updates the residue type set to be used in calls to apply() More... | |
| protocols::moves::MoverOP | clone () const |
| Creates a replica of this protocols::moves::Mover. More... | |
| protocols::moves::MoverOP | fresh_instance () const |
| Creates a new instance by calling the no-argument constructor. More... | |
| void | parse_my_tag (const utility::tag::TagPtr tag, protocols::moves::DataMap &data, const protocols::filters::Filters_map &filters, const protocols::moves::Movers_map &movers, const core::pose::Pose &pose) |
| protocols::moves::Mover-specific parsing required by RosettaScripts 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) | |
| Mover & | operator= (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 Strings & | info () |
| 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 Types | |
| typedef std::string | string |
Private Attributes | |
| string | sequence_ |
| string | residue_type_set_ |
Additional Inherited Members | |
| 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 |
| 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... | |
Definition at line 35 of file ExtendedPoseMover.hh.
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private |
Definition at line 36 of file ExtendedPoseMover.hh.
| protocols::simple_moves::ExtendedPoseMover::ExtendedPoseMover | ( | const string & | sequence = "", |
| const string & | residue_type_set_ = "centroid" |
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| ) |
Definition at line 44 of file ExtendedPoseMover.cc.
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virtual |
Creates an extended, idealized pose from the sequence and residue type set specified in the constructor.
Implements protocols::moves::Mover.
Definition at line 52 of file ExtendedPoseMover.cc.
References core::pose::Pose::clear(), core::pose::make_pose_from_sequence(), residue_type_set_, sequence_, protocols::loops::set_extended_torsions_and_idealize_loops(), and valid().
Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairing().
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Creates a replica of this protocols::moves::Mover.
Reimplemented from protocols::moves::Mover.
Definition at line 82 of file ExtendedPoseMover.cc.
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Creates a new instance by calling the no-argument constructor.
Reimplemented from protocols::moves::Mover.
Definition at line 86 of file ExtendedPoseMover.cc.
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Returns the name of this mover.
Implements protocols::moves::Mover.
Definition at line 62 of file ExtendedPoseMover.cc.
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virtual |
protocols::moves::Mover-specific parsing required by RosettaScripts
Reimplemented from protocols::moves::Mover.
Definition at line 90 of file ExtendedPoseMover.cc.
References residue_type_set(), and sequence().
| const std::string & protocols::simple_moves::ExtendedPoseMover::residue_type_set | ( | ) | const |
Returns the residue type set.
Definition at line 70 of file ExtendedPoseMover.cc.
References residue_type_set_.
Referenced by parse_my_tag(), and residue_type_set().
| void protocols::simple_moves::ExtendedPoseMover::residue_type_set | ( | const string & | residue_type_set) |
Updates the residue type set to be used in calls to apply()
Definition at line 78 of file ExtendedPoseMover.cc.
References residue_type_set(), and residue_type_set_.
| const std::string & protocols::simple_moves::ExtendedPoseMover::sequence | ( | ) | const |
Returns the sequence.
Definition at line 66 of file ExtendedPoseMover.cc.
References sequence_.
Referenced by parse_my_tag(), sequence(), and valid().
| void protocols::simple_moves::ExtendedPoseMover::sequence | ( | const string & | sequence) |
Updates the sequence to be used in calls to apply()
Definition at line 74 of file ExtendedPoseMover.cc.
References sequence(), and sequence_.
| bool protocols::simple_moves::ExtendedPoseMover::valid | ( | ) | const |
Returns true if this instance is valid (i.e. contains a sequence). Since RosettaScripts mandates the existence of a no-argument constructor, we lose the ability to reason about the validity of a particular instance.
Definition at line 48 of file ExtendedPoseMover.cc.
References sequence().
Referenced by apply().
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private |
Definition at line 84 of file ExtendedPoseMover.hh.
Referenced by apply(), and residue_type_set().
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private |
Definition at line 83 of file ExtendedPoseMover.hh.
Referenced by apply(), and sequence().
1.8.4