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protocols::denovo_design::movers::AlignResiduesMover Class Reference

Aligns one residue onto another. More...

#include <AlignResiduesMover.hh>

Inheritance diagram for protocols::denovo_design::movers::AlignResiduesMover:
Inheritance graph
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Public Types

typedef utility::vector1
< core::select::residue_selector::ResidueSelectorCOP
ResidueSelectorCOPs
 
typedef utility::vector1
< core::select::residue_selector::ResidueVector
ResidueVectors
 
- 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
 

Public Member Functions

 AlignResiduesMover ()
 
 ~AlignResiduesMover () override
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void show (std::ostream &output=std::cout) const override
 Outputs details about the Mover, including current settings. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &data) override
 parse XML tag (to use this Mover in Rosetta Scripts) 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...
 
void set_id (std::string const &id)
 
void add_template_selector (core::select::residue_selector::ResidueSelector const &selector)
 
void add_target_selector (core::select::residue_selector::ResidueSelector const &selector)
 
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 bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. 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 Member Functions

core::Size align_residues (core::pose::Pose &pose, core::Size const align_count, core::select::residue_selector::ResidueVector const &template_subset, core::select::residue_selector::ResidueVector const &target_subset) const
 aligns residues from template and target subsets More...
 
void align_residues (core::pose::Pose &pose, core::Size const align_count, core::Size const template_resid, core::Size const target_resid) const
 
void align_residues (core::pose::Pose &pose, core::Size const jump_idx, core::Size const template_resid, core::Size const target_resid, core::Size const res_with_torsions) const
 aligns two residues so their backbones are completely superimposed More...
 
void copy_residue (core::pose::Pose &pose, core::Size const resid_has_info, core::Size const resid_wants_info) const
 
void add_metadata (components::StructureData &sd, core::Size const align_count, std::string const &template_segment, std::string const &target_segment, core::Size const target_resid) const
 
ResidueVectors compute_target_residues (core::pose::Pose const &pose) const
 
ResidueVectors compute_template_residues (core::pose::Pose const &pose) const
 
void delete_residues (core::pose::Pose &pose, core::select::residue_selector::ResidueVector const &resids) const
 

Private Attributes

std::string id_
 
ResidueSelectorCOPs template_selectors_
 
ResidueSelectorCOPs target_selectors_
 

Additional Inherited Members

- 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

Aligns one residue onto another.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::denovo_design::movers::AlignResiduesMover::AlignResiduesMover ( )
protocols::denovo_design::movers::AlignResiduesMover::~AlignResiduesMover ( )
overridedefault

Member Function Documentation

void protocols::denovo_design::movers::AlignResiduesMover::add_metadata ( components::StructureData sd,
core::Size const  align_count,
std::string const &  template_segment,
std::string const &  target_segment,
core::Size const  target_resid 
) const
private
void protocols::denovo_design::movers::AlignResiduesMover::add_target_selector ( core::select::residue_selector::ResidueSelector const &  selector)
void protocols::denovo_design::movers::AlignResiduesMover::add_template_selector ( core::select::residue_selector::ResidueSelector const &  selector)
core::Size protocols::denovo_design::movers::AlignResiduesMover::align_residues ( core::pose::Pose pose,
core::Size const  align_count,
core::select::residue_selector::ResidueVector const &  template_subset,
core::select::residue_selector::ResidueVector const &  target_subset 
) const
private

aligns residues from template and target subsets

Returns
template resid that was aligned

References mover_name(), and core::scoring::rg.

Referenced by align_residues(), and apply().

void protocols::denovo_design::movers::AlignResiduesMover::align_residues ( core::pose::Pose pose,
core::Size const  align_count,
core::Size const  template_resid,
core::Size const  target_resid 
) const
private
void protocols::denovo_design::movers::AlignResiduesMover::align_residues ( core::pose::Pose pose,
core::Size const  jump_idx,
core::Size const  template_resid,
core::Size const  target_resid,
core::Size const  res_with_torsions 
) const
private
void protocols::denovo_design::movers::AlignResiduesMover::apply ( core::pose::Pose )
overridevirtual
protocols::moves::MoverOP protocols::denovo_design::movers::AlignResiduesMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

AlignResiduesMover::ResidueVectors protocols::denovo_design::movers::AlignResiduesMover::compute_target_residues ( core::pose::Pose const &  pose) const
private
AlignResiduesMover::ResidueVectors protocols::denovo_design::movers::AlignResiduesMover::compute_template_residues ( core::pose::Pose const &  pose) const
private
void protocols::denovo_design::movers::AlignResiduesMover::copy_residue ( core::pose::Pose pose,
core::Size const  resid_has_info,
core::Size const  resid_wants_info 
) const
private
void protocols::denovo_design::movers::AlignResiduesMover::delete_residues ( core::pose::Pose pose,
core::select::residue_selector::ResidueVector const &  resids 
) const
private
protocols::moves::MoverOP protocols::denovo_design::movers::AlignResiduesMover::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

std::string protocols::denovo_design::movers::AlignResiduesMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::string protocols::denovo_design::movers::AlignResiduesMover::mover_name ( )
static
void protocols::denovo_design::movers::AlignResiduesMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

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

Reimplemented from protocols::moves::Mover.

References id_, protocols::denovo_design::movers::parse_residue_selectors(), target_selectors_, and template_selectors_.

void protocols::denovo_design::movers::AlignResiduesMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::denovo_design::movers::AlignResiduesMover::set_id ( std::string const &  id)

References id_.

void protocols::denovo_design::movers::AlignResiduesMover::show ( std::ostream &  output = std::cout) const
overridevirtual

Outputs details about the Mover, including current settings.

Ideally, a child Mover should call Mover.show() and add additional information particular to that Mover.

Reimplemented from protocols::moves::Mover.

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

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

Member Data Documentation

std::string protocols::denovo_design::movers::AlignResiduesMover::id_
private

Referenced by add_metadata(), parse_my_tag(), and set_id().

ResidueSelectorCOPs protocols::denovo_design::movers::AlignResiduesMover::target_selectors_
private
ResidueSelectorCOPs protocols::denovo_design::movers::AlignResiduesMover::template_selectors_
private

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