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protocols::cyclic_peptide::PeptideCyclizeMover Class Reference

#include <PeptideCyclizeMover.hh>

Inheritance diagram for protocols::cyclic_peptide::PeptideCyclizeMover:
Inheritance graph
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Public Member Functions

 PeptideCyclizeMover ()
 Constructor for PeptideCyclizeMover. More...
 
 ~PeptideCyclizeMover () override
 destructor of the mover More...
 
void apply (Pose &) override
 Actually apply the mover to the pose. More...
 
moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
void parse_my_tag (utility::tag::TagCOP, basic::datacache::DataMap &) override
 Returns the name of this mover ("PeptideCyclizeMover"). More...
 
virtual void set_bond (core::Size, std::string, core::Size, std::string, bool, bool)
 
virtual void set_distance (core::Size, std::string, core::Size, std::string, std::string)
 
virtual void set_angle (core::Size, std::string, core::Size, std::string, core::Size, std::string, std::string)
 
virtual void set_torsion (core::Size, std::string, core::Size, std::string, core::Size, std::string, core::Size, std::string, std::string)
 
virtual void set_selector (core::select::residue_selector::ResidueSelectorCOP)
 
virtual void set_default ()
 
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 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

void get_all (core::select::residue_selector::ResidueSubset, core::pose::Pose const &)
 
void get_values ()
 getters More...
 

Private Attributes

core::Size counter_
 
utility::vector1< core::Sizeres1_
 
utility::vector1< std::string > atom1_
 
utility::vector1< core::Sizeres2_
 
utility::vector1< std::string > atom2_
 
utility::vector1< booladd_termini_
 
utility::vector1< boolrebuild_fold_tree_
 
bool bond_assigned_
 
utility::vector1< core::Sizeres1_dist_
 
utility::vector1< std::string > atom1_dist_
 
utility::vector1< core::Sizeres2_dist_
 
utility::vector1< std::string > atom2_dist_
 
utility::vector1< std::string > cst_func_dist_
 
bool distance_assigned_
 
utility::vector1< core::Sizeres1_angle_
 
utility::vector1< std::string > atom1_angle_
 
utility::vector1< std::string > atom1_angle2_
 
utility::vector1< core::Sizeres2_angle_
 
utility::vector1< std::string > atom2_angle_
 
utility::vector1< std::string > atom2_angle2_
 
utility::vector1< core::Sizeres_center_
 
utility::vector1< core::Sizeres_center2_
 
utility::vector1< std::string > atom_center_
 
utility::vector1< std::string > atom_center2_
 
utility::vector1< std::string > cst_func_angle_
 
utility::vector1< std::string > cst_func_angle2_
 
bool angle_assigned_
 
utility::vector1< core::Sizeres1_torsion_
 
utility::vector1< std::string > atom1_torsion_
 
utility::vector1< core::Sizeres2_torsion_
 
utility::vector1< std::string > atom2_torsion_
 
utility::vector1< core::Sizeres3_torsion_
 
utility::vector1< std::string > atom3_torsion_
 
utility::vector1< core::Sizeres4_torsion_
 
utility::vector1< std::string > atom4_torsion_
 
utility::vector1< std::string > cst_func_torsion_
 
bool torsion_assigned_
 
core::Real angle1_
 
core::Real angle2_
 
core::Real distance_
 
std::string distance_func_
 
std::string angle1_func_
 
std::string angle2_func_
 
core::select::residue_selector::ResidueSelectorCOP selector_
 

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...
 

Constructor & Destructor Documentation

protocols::cyclic_peptide::PeptideCyclizeMover::PeptideCyclizeMover ( )
protocols::cyclic_peptide::PeptideCyclizeMover::~PeptideCyclizeMover ( )
overridedefault

destructor of the mover

Member Function Documentation

void protocols::cyclic_peptide::PeptideCyclizeMover::apply ( Pose pose)
overridevirtual
moves::MoverOP protocols::cyclic_peptide::PeptideCyclizeMover::clone ( ) const
overridevirtual

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.

moves::MoverOP protocols::cyclic_peptide::PeptideCyclizeMover::fresh_instance ( ) const
overridevirtual

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.

void protocols::cyclic_peptide::PeptideCyclizeMover::get_all ( core::select::residue_selector::ResidueSubset  subset,
core::pose::Pose const &  pose 
)
private
std::string protocols::cyclic_peptide::PeptideCyclizeMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

void protocols::cyclic_peptide::PeptideCyclizeMover::get_values ( )
private
std::string protocols::cyclic_peptide::PeptideCyclizeMover::mover_name ( )
static
void protocols::cyclic_peptide::PeptideCyclizeMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

Returns the name of this mover ("PeptideCyclizeMover").

parse XML (specifically in the context of the parser/scripting scheme)

Reimplemented from protocols::moves::Mover.

References counter_, protocols::moves::Mover::name(), core::select::residue_selector::parse_residue_selector(), set_angle(), set_bond(), set_distance(), set_selector(), and set_torsion().

void protocols::cyclic_peptide::PeptideCyclizeMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::cyclic_peptide::PeptideCyclizeMover::set_angle ( core::Size  res_center,
std::string  atom_center,
core::Size  res1,
std::string  atom1,
core::Size  res2,
std::string  atom2,
std::string  cst_func 
)
virtual
void protocols::cyclic_peptide::PeptideCyclizeMover::set_bond ( core::Size  res1,
std::string  atom1,
core::Size  res2,
std::string  atom2,
bool  add_termini,
bool  rebuild_fold_tree 
)
virtual
void protocols::cyclic_peptide::PeptideCyclizeMover::set_default ( )
virtual
void protocols::cyclic_peptide::PeptideCyclizeMover::set_distance ( core::Size  res1,
std::string  atom1,
core::Size  res2,
std::string  atom2,
std::string  cst_func 
)
virtual
void protocols::cyclic_peptide::PeptideCyclizeMover::set_selector ( core::select::residue_selector::ResidueSelectorCOP  selector_in)
virtual

References selector_.

Referenced by parse_my_tag().

void protocols::cyclic_peptide::PeptideCyclizeMover::set_torsion ( core::Size  res1,
std::string  atom1,
core::Size  res2,
std::string  atom2,
core::Size  res3,
std::string  atom3,
core::Size  res4,
std::string  atom4,
std::string  cst_func 
)
virtual

Member Data Documentation

utility::vector1<bool> protocols::cyclic_peptide::PeptideCyclizeMover::add_termini_
private

Referenced by apply(), get_all(), and set_bond().

core::Real protocols::cyclic_peptide::PeptideCyclizeMover::angle1_
private

Referenced by get_all(), and get_values().

std::string protocols::cyclic_peptide::PeptideCyclizeMover::angle1_func_
private

Referenced by get_all().

core::Real protocols::cyclic_peptide::PeptideCyclizeMover::angle2_
private

Referenced by get_all(), and get_values().

std::string protocols::cyclic_peptide::PeptideCyclizeMover::angle2_func_
private

Referenced by get_all().

bool protocols::cyclic_peptide::PeptideCyclizeMover::angle_assigned_
private
utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::atom1_
private

Referenced by apply(), get_all(), and set_bond().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::atom1_angle2_
private

Referenced by apply(), and get_all().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::atom1_angle_
private

Referenced by apply(), get_all(), and set_angle().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::atom1_dist_
private

Referenced by apply(), get_all(), and set_distance().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::atom1_torsion_
private

Referenced by apply(), get_all(), and set_torsion().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::atom2_
private

Referenced by apply(), get_all(), and set_bond().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::atom2_angle2_
private

Referenced by apply(), and get_all().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::atom2_angle_
private

Referenced by apply(), get_all(), and set_angle().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::atom2_dist_
private

Referenced by apply(), get_all(), and set_distance().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::atom2_torsion_
private

Referenced by apply(), get_all(), and set_torsion().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::atom3_torsion_
private

Referenced by apply(), get_all(), and set_torsion().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::atom4_torsion_
private

Referenced by apply(), get_all(), and set_torsion().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::atom_center2_
private

Referenced by apply(), and get_all().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::atom_center_
private

Referenced by apply(), get_all(), and set_angle().

bool protocols::cyclic_peptide::PeptideCyclizeMover::bond_assigned_
private
core::Size protocols::cyclic_peptide::PeptideCyclizeMover::counter_
private

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

utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::cst_func_angle2_
private

Referenced by apply(), and get_all().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::cst_func_angle_
private

Referenced by apply(), get_all(), and set_angle().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::cst_func_dist_
private

Referenced by apply(), get_all(), and set_distance().

utility::vector1<std::string> protocols::cyclic_peptide::PeptideCyclizeMover::cst_func_torsion_
private

Referenced by apply(), get_all(), and set_torsion().

core::Real protocols::cyclic_peptide::PeptideCyclizeMover::distance_
private

Referenced by get_all(), and get_values().

bool protocols::cyclic_peptide::PeptideCyclizeMover::distance_assigned_
private
std::string protocols::cyclic_peptide::PeptideCyclizeMover::distance_func_
private
utility::vector1<bool> protocols::cyclic_peptide::PeptideCyclizeMover::rebuild_fold_tree_
private

Referenced by apply(), get_all(), and set_bond().

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideCyclizeMover::res1_
private

Referenced by apply(), get_all(), and set_bond().

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideCyclizeMover::res1_angle_
private

Referenced by apply(), get_all(), and set_angle().

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideCyclizeMover::res1_dist_
private

Referenced by apply(), get_all(), and set_distance().

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideCyclizeMover::res1_torsion_
private

Referenced by apply(), get_all(), and set_torsion().

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideCyclizeMover::res2_
private

Referenced by apply(), get_all(), and set_bond().

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideCyclizeMover::res2_angle_
private

Referenced by apply(), get_all(), and set_angle().

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideCyclizeMover::res2_dist_
private

Referenced by apply(), get_all(), and set_distance().

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideCyclizeMover::res2_torsion_
private

Referenced by apply(), get_all(), and set_torsion().

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideCyclizeMover::res3_torsion_
private

Referenced by apply(), get_all(), and set_torsion().

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideCyclizeMover::res4_torsion_
private

Referenced by apply(), get_all(), and set_torsion().

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideCyclizeMover::res_center2_
private

Referenced by apply(), and get_all().

utility::vector1<core::Size> protocols::cyclic_peptide::PeptideCyclizeMover::res_center_
private

Referenced by apply(), get_all(), and set_angle().

core::select::residue_selector::ResidueSelectorCOP protocols::cyclic_peptide::PeptideCyclizeMover::selector_
private

Referenced by apply(), and set_selector().

bool protocols::cyclic_peptide::PeptideCyclizeMover::torsion_assigned_
private

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