#include <ExtendedPoseMover.hh>
Public Member Functions | |
| ExtendedPoseMover (string const &sequence="", string const &residue_type_set_="centroid") | |
| void | apply (core::pose::Pose &pose) override |
| Creates an extended, idealized pose from the sequence and residue type set specified in the constructor. More... | |
| bool | valid () const |
| Returns the name of this mover. 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 override |
| Creates a replica of this protocols::moves::Mover. More... | |
| protocols::moves::MoverOP | fresh_instance () const override |
| Creates a new instance by calling the no-argument constructor. More... | |
| void | parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override |
| protocols::moves::Mover-specific parsing required by RosettaScripts More... | |
| string | chain () const |
| void | chain (string const &setting) |
| 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 Strings & | info () |
| non-const accessor More... | |
| virtual Strings const & | info () const |
| const accessor More... | |
| virtual void | provide_citation_info (basic::citation_manager::CitationCollectionList &) const |
| Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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 Types | |
| typedef std::string | string |
Private Attributes | |
| string | sequence_ |
| string | residue_type_set_ |
| string | chain_ |
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 std::list< std::string > | Strings |
| 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... | |
Member Typedef Documentation
◆ string
|
private |
Constructor & Destructor Documentation
◆ ExtendedPoseMover()
| protocols::pose_creation::ExtendedPoseMover::ExtendedPoseMover | ( | std::string const & | sequence = "", |
| std::string const & | residue_type_set = "centroid" |
||
| ) |
Member Function Documentation
◆ apply()
|
overridevirtual |
Creates an extended, idealized pose from the sequence and residue type set specified in the constructor.
Implements protocols::moves::Mover.
References chain(), core::pose::Pose::clear(), protocols::moves::Mover::info(), core::pose::make_pose_from_sequence(), core::pose::Pose::pdb_info(), residue_type_set_, sequence_, protocols::loops::set_extended_torsions_and_idealize_loops(), and valid().
Referenced by protocols::hybridization::FoldTreeHybridize::add_strand_pairing().
◆ chain() [1/2]
|
inline |
References chain_.
Referenced by apply(), and parse_my_tag().
◆ chain() [2/2]
|
inline |
References chain_.
◆ clone()
|
overridevirtual |
Creates a replica of this protocols::moves::Mover.
Reimplemented from protocols::moves::Mover.
◆ fresh_instance()
|
overridevirtual |
Creates a new instance by calling the no-argument constructor.
Reimplemented from protocols::moves::Mover.
◆ get_name()
|
overridevirtual |
Each derived class must specify its name. The class name.
Implements protocols::moves::Mover.
References mover_name().
◆ mover_name()
|
static |
Referenced by get_name(), protocols::pose_creation::ExtendedPoseMoverCreator::keyname(), and provide_xml_schema().
◆ parse_my_tag()
|
overridevirtual |
protocols::moves::Mover-specific parsing required by RosettaScripts
Reimplemented from protocols::moves::Mover.
References chain(), protocols::abinitio::filename(), core::sequence::read_fasta_file(), residue_type_set(), and sequence().
◆ provide_xml_schema()
|
static |
References mover_name(), and protocols::moves::xsd_type_definition_w_attributes().
Referenced by protocols::pose_creation::ExtendedPoseMoverCreator::provide_xml_schema().
◆ residue_type_set() [1/2]
| const std::string & protocols::pose_creation::ExtendedPoseMover::residue_type_set | ( | ) | const |
Returns the residue type set.
References residue_type_set_.
Referenced by parse_my_tag(), and residue_type_set().
◆ residue_type_set() [2/2]
| void protocols::pose_creation::ExtendedPoseMover::residue_type_set | ( | const string & | residue_type_set | ) |
Updates the residue type set to be used in calls to apply()
References residue_type_set(), and residue_type_set_.
◆ sequence() [1/2]
| const std::string & protocols::pose_creation::ExtendedPoseMover::sequence | ( | ) | const |
◆ sequence() [2/2]
| void protocols::pose_creation::ExtendedPoseMover::sequence | ( | const string & | sequence | ) |
Updates the sequence to be used in calls to apply()
References sequence(), and sequence_.
◆ valid()
| bool protocols::pose_creation::ExtendedPoseMover::valid | ( | ) | const |
Returns the name of this mover.
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.
References sequence().
Referenced by apply().
Member Data Documentation
◆ chain_
◆ residue_type_set_
|
private |
Referenced by apply(), and residue_type_set().
◆ sequence_
|
private |
Referenced by apply(), and sequence().
The documentation for this class was generated from the following files:
- src/protocols/pose_creation/ExtendedPoseMover.hh
- src/protocols/pose_creation/ExtendedPoseMover.cc
