Rosetta  2020.37
 All Classes Namespaces Files Functions Variables Typedefs Enumerations Enumerator Friends Macros Pages
Public Types | Public Member Functions | Static Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::switches::GraftSwitchMover Class Reference

A protocols::moves::Mover that grafts a sequence onto the terminal helix of a helical-bundle monomer. Utilizes SimpleThreadingMover alongside. More...

#include <GraftSwitchMover.hh>

Inheritance diagram for protocols::switches::GraftSwitchMover:
Inheritance graph
[legend]

Public Types

typedef
core::pack::task::PackerTaskCOP 
PackerTaskCOP
 
typedef
core::pack::task::TaskFactoryCOP 
TaskFactoryCOP
 
typedef
core::pack::task::TaskFactoryOP 
TaskFactoryOP
 
typedef
core::scoring::ScoreFunctionCOP 
ScoreFunctionCOP
 
typedef
core::scoring::ScoreFunctionOP 
ScoreFunctionOP
 
- 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

 GraftSwitchMover ()
 default constructor More...
 
 ~GraftSwitchMover () override
 
 GraftSwitchMover (GraftSwitchMover const &other)
 
void apply (Pose &pose) override
 Grafts, minimizes, and scores functional sequences grafted onto LOCKR type de novo protien switches. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
void parse_my_tag (TagCOP, basic::datacache::DataMap &) override
 parse XML (specifically in the context of the parser/scripting scheme) More...
 
virtual void parse_score_function (TagCOP, basic::datacache::DataMap const &)
 parse "scorefxn" XML option (can be employed virtually by derived Packing movers) More...
 
virtual void parse_task_operations (TagCOP, basic::datacache::DataMap const &)
 parse "task_operations" XML option (can be employed virtually by derived Packing movers) 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 task_factory (TaskFactoryCOP tf)
 Sets the TaskFactory to <tf> More...
 
void score_function (ScoreFunctionCOP sf)
 Sets the ScoreFunction to <sf> More...
 
core::pose::PoseOP get_additional_output () override
 Mechanism by which a mover may return multiple output poses from a single input pose. More...
 
void add_sequence (std::string seq)
 
void set_start_graft (core::Size start)
 
void set_end_graft (core::Size end)
 
void set_important_residues (utility::vector1< core::Size > residue_list)
 
void set_pack_neighbors (bool input)
 
void set_pack_min (bool input)
 
std::list< utility::vector1
< core::Size > > 
get_output_list ()
 
- 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...
 
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 void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static std::string mover_name ()
 
- 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 get_c_terminal_helix (core::pose::PoseOP const &pose)
 finds the residue number that starts the C-terminal helix More...
 
core::Size get_n_terminal_helix (core::pose::PoseOP const &pose)
 finds the residue number that starts the C-terminal helix More...
 
bool init_burial_filter (core::pose::Pose const &pose, core::Size index, core::Size thread_position)
 inital filter to determine if the key residues that need to be caged, are. More...
 
std::list< utility::vector1
< core::Size > > 
all_threading_start_combinations ()
 returns all tuples of size n representing starting positions for each sequences More...
 

Private Attributes

ScoreFunctionCOP scorefxn_
 
TaskFactoryCOP task_factory_
 
core::Size start_graft_
 
core::Size end_graft_
 
bool n_terminus_
 
bool pack_neighbors_
 
bool graft_loop_
 
bool find_helix_
 
bool seq_in_any_order_
 
bool pack_min_
 
utility::vector1< std::string > sequences_
 
utility::vector1
< utility::vector1< core::Size > > 
important_residues_
 
std::set< core::Sizethreadable_residues_
 
core::Real burial_cutoff_
 
std::list< utility::vector1
< core::Size > > 
output_list_
 
core::pose::PoseOP orig_pose_
 
core::select::residue_selector::ResidueSelectorOP threadable_residues_selector_
 

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

A protocols::moves::Mover that grafts a sequence onto the terminal helix of a helical-bundle monomer. Utilizes SimpleThreadingMover alongside.

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::switches::GraftSwitchMover::GraftSwitchMover ( )

default constructor

protocols::switches::GraftSwitchMover::~GraftSwitchMover ( )
overridedefault
protocols::switches::GraftSwitchMover::GraftSwitchMover ( GraftSwitchMover const &  other)

Member Function Documentation

void protocols::switches::GraftSwitchMover::add_sequence ( std::string  seq)
inline

References sequences_.

std::list< utility::vector1< core::Size > > protocols::switches::GraftSwitchMover::all_threading_start_combinations ( )
private

returns all tuples of size n representing starting positions for each sequences

Creates a list of vectors (using a list for speed in deletion phase) where each vector is of length=number of sequences. Each number in the vector corresponds to a starting position for threading that will fit the corresponding sequence.

References protocols::mean_field::add(), seq_in_any_order_, sequences_, and threadable_residues_.

Referenced by apply().

void protocols::switches::GraftSwitchMover::apply ( Pose pose)
overridevirtual
protocols::moves::MoverOP protocols::switches::GraftSwitchMover::clone ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

protocols::moves::MoverOP protocols::switches::GraftSwitchMover::fresh_instance ( ) const
overridevirtual

required in the context of the parser/scripting scheme

Reimplemented from protocols::moves::Mover.

core::pose::PoseOP protocols::switches::GraftSwitchMover::get_additional_output ( )
overridevirtual

Mechanism by which a mover may return multiple output poses from a single input pose.

fpd

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

Mechanism by which a mover may return multiple output poses from a single input pose. After apply is called, calling this function will return subsequent output poses. NULL is returned if the mover has no more output poses remaining. The base class implementation returns NULL always; multi-output movers must override this. RosettaScripts uses this interface to produce a 'branched' protocol.

Reimplemented from protocols::moves::Mover.

References core::select::fill_neighbor_residues(), protocols::mean_field::min(), orig_pose_, output_list_, pack_min_, pack_neighbors_, PACKER_ITER, scorefxn_, sequences_, and task_factory_.

core::Size protocols::switches::GraftSwitchMover::get_c_terminal_helix ( core::pose::PoseOP const &  pose)
private

finds the residue number that starts the C-terminal helix

returns a single residue number as an integer

References core::scoring::dssp::Dssp::get_dssp_secstruct(), and graft_loop_.

Referenced by apply().

core::Size protocols::switches::GraftSwitchMover::get_n_terminal_helix ( core::pose::PoseOP const &  pose)
private

finds the residue number that starts the C-terminal helix

returns a single residue number as an integer

References core::scoring::dssp::Dssp::get_dssp_secstruct(), and graft_loop_.

Referenced by apply().

std::string protocols::switches::GraftSwitchMover::get_name ( ) const
overridevirtual

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

Implements protocols::moves::Mover.

References mover_name().

std::list< utility::vector1<core::Size> > protocols::switches::GraftSwitchMover::get_output_list ( )
inline

References output_list_.

bool protocols::switches::GraftSwitchMover::init_burial_filter ( core::pose::Pose const &  pose,
core::Size  index,
core::Size  thread_position 
)
private

inital filter to determine if the key residues that need to be caged, are.

uses NeighborsByDistanceCalculator as metric for burial

References burial_cutoff_, protocols::ligand_docking::ga_ligand_dock::count_neighbors(), core::pose::metrics::StructureDependentCalculator::get(), important_residues_, and core::pose::Pose::size().

Referenced by apply().

std::string protocols::switches::GraftSwitchMover::mover_name ( )
static
void protocols::switches::GraftSwitchMover::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  datamap 
)
overridevirtual
void protocols::switches::GraftSwitchMover::parse_score_function ( TagCOP  tag,
basic::datacache::DataMap const &  datamap 
)
virtual

parse "scorefxn" XML option (can be employed virtually by derived Packing movers)

References core::scoring::parse_score_function(), and score_function().

Referenced by parse_my_tag().

void protocols::switches::GraftSwitchMover::parse_task_operations ( TagCOP  tag,
basic::datacache::DataMap const &  datamap 
)
virtual

parse "task_operations" XML option (can be employed virtually by derived Packing movers)

References core::pack::task::parse_task_operations(), and task_factory().

Referenced by parse_my_tag().

void protocols::switches::GraftSwitchMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::switches::GraftSwitchMover::score_function ( ScoreFunctionCOP  sf)

Sets the ScoreFunction to <sf>

example(s): graftmover.score_function(scorefxn)

References scorefxn_.

Referenced by parse_score_function().

void protocols::switches::GraftSwitchMover::set_end_graft ( core::Size  end)
inline

References core::sequence::end, and end_graft_.

void protocols::switches::GraftSwitchMover::set_important_residues ( utility::vector1< core::Size residue_list)
inline

References important_residues_.

void protocols::switches::GraftSwitchMover::set_pack_min ( bool  input)
inline

References pack_min_.

void protocols::switches::GraftSwitchMover::set_pack_neighbors ( bool  input)
inline

References pack_neighbors_.

void protocols::switches::GraftSwitchMover::set_start_graft ( core::Size  start)
inline
void protocols::switches::GraftSwitchMover::task_factory ( TaskFactoryCOP  tf)

Sets the TaskFactory to <tf>

example(s): graftmover.task_factory(task_design)

References task_factory_.

Referenced by parse_task_operations().

Member Data Documentation

core::Real protocols::switches::GraftSwitchMover::burial_cutoff_
private
core::Size protocols::switches::GraftSwitchMover::end_graft_
private
bool protocols::switches::GraftSwitchMover::find_helix_
private
bool protocols::switches::GraftSwitchMover::graft_loop_
private
utility::vector1< utility::vector1< core::Size > > protocols::switches::GraftSwitchMover::important_residues_
private
bool protocols::switches::GraftSwitchMover::n_terminus_
private
core::pose::PoseOP protocols::switches::GraftSwitchMover::orig_pose_
private

Referenced by apply(), and get_additional_output().

std::list< utility::vector1<core::Size> > protocols::switches::GraftSwitchMover::output_list_
private
bool protocols::switches::GraftSwitchMover::pack_min_
private
bool protocols::switches::GraftSwitchMover::pack_neighbors_
private
ScoreFunctionCOP protocols::switches::GraftSwitchMover::scorefxn_
private
bool protocols::switches::GraftSwitchMover::seq_in_any_order_
private
utility::vector1< std::string > protocols::switches::GraftSwitchMover::sequences_
private
core::Size protocols::switches::GraftSwitchMover::start_graft_
private
TaskFactoryCOP protocols::switches::GraftSwitchMover::task_factory_
private
std::set< core::Size > protocols::switches::GraftSwitchMover::threadable_residues_
private
core::select::residue_selector::ResidueSelectorOP protocols::switches::GraftSwitchMover::threadable_residues_selector_
private

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