Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover Class Reference

adds virtual residues to either side of a given Pose More...

#include <AddFlankingVirtualResiduesMover.hh>

Inheritance diagram for protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover:
Inheritance graph

Public Member Functions

 AddFlankingVirtualResiduesMover ()
 Constructors ///. More...
 AddFlankingVirtualResiduesMover (AddFlankingVirtualResiduesMover const &src)
 Copy constructor (not needed unless you need deep copies) More...
 ~AddFlankingVirtualResiduesMover () override
 Destructor (important for properly forward-declaring smart-pointer members) More...
void apply (core::pose::Pose &pose) override
 Mover Methods ///. More...
void add_flanking_virtual_residues (core::pose::Pose &pose)
void show (std::ostream &output=std::cout) const override
 Show the contents of the Mover. More...
core::Size get_N_term_length () const
core::Size get_C_term_length () const
core::select::residue_selector::ResidueSelectorCOP get_vital_selector () const
core::Size get_chain_to_modify () const
bool get_remove_pre_pose () const
void set_N_term_length (core::Size)
void set_C_term_length (core::Size)
void set_vital_selector (core::select::residue_selector::ResidueSelectorCOP)
void set_chain_to_modify (core::Size)
void set_remove_pre_pose (bool)
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 Rosetta Scripts Support ///. More...
protocols::moves::MoverOP fresh_instance () const override
 required in the context of the parser/scripting scheme More...
protocols::moves::MoverOP clone () const override
 required in the context of the parser/scripting scheme More...
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 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 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 Attributes

core::Size N_term_length_ = 0
core::Size C_term_length_ = 0
core::Size chain_to_modify_ = 1
core::select::residue_selector::ResidueSelectorCOP vital_selector_
bool remove_pre_pose_ = false

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...

Detailed Description

adds virtual residues to either side of a given Pose

Constructor & Destructor Documentation

◆ AddFlankingVirtualResiduesMover() [1/2]

protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::AddFlankingVirtualResiduesMover ( )

Constructors ///.

Default constructor

Referenced by clone().

◆ AddFlankingVirtualResiduesMover() [2/2]

protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::AddFlankingVirtualResiduesMover ( AddFlankingVirtualResiduesMover const &  src)

Copy constructor (not needed unless you need deep copies)

Copy constructor.

References C_term_length_, get_C_term_length(), get_N_term_length(), get_vital_selector(), N_term_length_, and vital_selector_.

◆ ~AddFlankingVirtualResiduesMover()

protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::~AddFlankingVirtualResiduesMover ( )

Destructor (important for properly forward-declaring smart-pointer members)

Member Function Documentation

◆ add_flanking_virtual_residues()

void protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::add_flanking_virtual_residues ( core::pose::Pose pose)

◆ apply()

void protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::apply ( core::pose::Pose pose)

Mover Methods ///.

Apply the mover

Implements protocols::moves::Mover.

References add_flanking_virtual_residues().

◆ clone()

protocols::moves::MoverOP protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::clone ( ) const

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

References AddFlankingVirtualResiduesMover().

◆ fresh_instance()

protocols::moves::MoverOP protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::fresh_instance ( ) const

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

◆ get_C_term_length()

core::Size protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::get_C_term_length ( ) const

◆ get_chain_to_modify()

core::Size protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::get_chain_to_modify ( ) const

References chain_to_modify_.

◆ get_N_term_length()

core::Size protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::get_N_term_length ( ) const

◆ get_name()

std::string protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::get_name ( ) const

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

Implements protocols::moves::Mover.

References mover_name().

◆ get_remove_pre_pose()

bool protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::get_remove_pre_pose ( ) const

References remove_pre_pose_.

◆ get_vital_selector()

core::select::residue_selector::ResidueSelectorCOP protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::get_vital_selector ( ) const

◆ mover_name()

std::string protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::mover_name ( )

◆ parse_my_tag()

void protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap datamap 

Rosetta Scripts Support ///.

parse XML tag (to use this Mover in Rosetta Scripts)

Reimplemented from protocols::moves::Mover.

References C_term_length_, chain_to_modify_, core::select::residue_selector::get_residue_selector(), N_term_length_, remove_pre_pose_, and vital_selector_.

◆ provide_xml_schema()

void protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)

◆ set_C_term_length()

void protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::set_C_term_length ( core::Size  C_length)

References C_term_length_.

◆ set_chain_to_modify()

void protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::set_chain_to_modify ( core::Size  chain)

References chain_to_modify_.

◆ set_N_term_length()

void protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::set_N_term_length ( core::Size  N_length)

References N_term_length_.

◆ set_remove_pre_pose()

void protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::set_remove_pre_pose ( bool  in)

◆ set_vital_selector()

void protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::set_vital_selector ( core::select::residue_selector::ResidueSelectorCOP  selector)

References vital_selector_.

◆ show()

void protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::show ( std::ostream &  output = std::cout) const

Show the contents of the Mover.

Reimplemented from protocols::moves::Mover.

References protocols::moves::Mover::show().

Referenced by protocols::pose_sewing::movers::operator<<().

Member Data Documentation

◆ C_term_length_

core::Size protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::C_term_length_ = 0

◆ chain_to_modify_

core::Size protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::chain_to_modify_ = 1

◆ N_term_length_

core::Size protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::N_term_length_ = 0

◆ remove_pre_pose_

bool protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::remove_pre_pose_ = false

◆ vital_selector_

core::select::residue_selector::ResidueSelectorCOP protocols::pose_sewing::movers::AddFlankingVirtualResiduesMover::vital_selector_

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