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protocols::membrane::symmetry::SymmetricAddMembraneMover Class Reference

#include <SymmetricAddMembraneMover.hh>

Inheritance diagram for protocols::membrane::symmetry::SymmetricAddMembraneMover:
Inheritance graph
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Public Member Functions

 SymmetricAddMembraneMover ()
 Constructors ///. More...
 
 SymmetricAddMembraneMover (std::string spanfile)
 Custom Constructor for SymmetricAddMembraneMover. More...
 
 SymmetricAddMembraneMover (core::conformation::membrane::SpanningTopologyOP topology)
 Custom Constructor for SymmetricAddMembraneMover. More...
 
 SymmetricAddMembraneMover (SymmetricAddMembraneMover const &src)
 Copy Constructor for SymmetricAddMembraneMover. More...
 
 ~SymmetricAddMembraneMover () override
 Destructor. More...
 
protocols::moves::MoverOP clone () const override
 Rosetta Scripts Methods ///. More...
 
protocols::moves::MoverOP fresh_instance () const override
 Create a Fresh Instance of this Mover. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &dm) override
 Pase Rosetta Scripts Options for this Mover. More...
 
core::Size add_membrane_virtual (core::pose::Pose &pose) override
 Mover Methods ///. More...
 
std::string get_name () const override
 Mover Methods ///. More...
 
utility::vector1< core::SSizecheck_pdb_for_mem (core::pose::Pose &pose) override
 Helper Method - Check for Membrane residue already in the PDB. More...
 
- Public Member Functions inherited from protocols::membrane::AddMembraneMover
 AddMembraneMover ()
 Create a default RosettaMP membrane setup. More...
 
 AddMembraneMover (std::string spanfile, core::Size membrane_rsd=0, std::string lipid_composition="DLPC", core::Real temperature=37.0)
 Create a RosettaMP setup from a user specified spanfile. More...
 
 AddMembraneMover (core::Size membrane_rsd, std::string lipid_composition="DLPC", core::Real temperature=37.0)
 Create a RosettaMP setup from an existing membrane residue. More...
 
 AddMembraneMover (core::conformation::membrane::SpanningTopologyOP topology, core::Size anchor_rsd=1, core::Size membrane_rsd=0)
 Create a RosettaMP setup from a user specified SpanningTopology. More...
 
 AddMembraneMover (core::Size anchor_rsd, bool anchor_format, bool second_anchor_format, core::Size membrane_rsd=0)
 Create a RosettaMP setup by setting the root of the fold tree to anchor_rsd and designating MEM as membrane_rsd. The two booleans are dummy variables intended to differentiate. More...
 
 AddMembraneMover (AddMembraneMover const &src)
 Create a deep copy of the data in this mover. More...
 
 ~AddMembraneMover () override
 Destructor. More...
 
void apply (core::pose::Pose &pose) override
 Initialize the RosettaMP elements with this pose. More...
 
std::string get_spanfile () const
 Path to file with transmembrane span data. More...
 
void spanfile (std::string spanfile)
 Set path to spanfile. More...
 
void restore_lazaridis_IMM1_behavior (bool restore)
 
- 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::membrane::AddMembraneMover
static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
static void attributes_for_parse_center_normal_from_tag (utility::tag::AttributeList &attributes)
 
- 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 register_options ()
 Setup Methods ///. More...
 
void init_from_cmd ()
 Initialize Mover options from the comandline. More...
 

Private Attributes

utility::vector1
< core::conformation::membrane::SpanOP
spans_from_xml_
 

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::membrane::symmetry::SymmetricAddMembraneMover::SymmetricAddMembraneMover ( )

Constructors ///.

Default constructor of SymmetricAddMembraneMover

Create a membrane pose, setting the membrane center at center=(0, 0, 0), normal=(0, 0, 1) and loads in spans and lips from the command line interface. Calls the default constructor of AddMembraneMover

References init_from_cmd(), and register_options().

protocols::membrane::symmetry::SymmetricAddMembraneMover::SymmetricAddMembraneMover ( std::string  spanfile)

Custom Constructor for SymmetricAddMembraneMover.

Creates a membrane pose, setting the membrane center at center=(0, 0, 0), normal=(0, 0, 1). Uses the user provided spanfile in this constructor to load the spanning topology. Calls the analagous parent constructor in AddMembraneMover

References init_from_cmd(), and register_options().

protocols::membrane::symmetry::SymmetricAddMembraneMover::SymmetricAddMembraneMover ( core::conformation::membrane::SpanningTopologyOP  topology)

Custom Constructor for SymmetricAddMembraneMover.

Creates a membrane pose, setting the membrane center at center=(0, 0, 0), normal=(0, 0, 1). Uses the user provided SpanningTopology to be set in MembraneInfo. Calls the analagous parent constructor in AddMembraneMover

References init_from_cmd(), and register_options().

protocols::membrane::symmetry::SymmetricAddMembraneMover::SymmetricAddMembraneMover ( SymmetricAddMembraneMover const &  src)
default

Copy Constructor for SymmetricAddMembraneMover.

Create a deep copy of SymmetricAddMembraneMover

protocols::membrane::symmetry::SymmetricAddMembraneMover::~SymmetricAddMembraneMover ( )
overridedefault

Destructor.

Member Function Documentation

core::Size protocols::membrane::symmetry::SymmetricAddMembraneMover::add_membrane_virtual ( core::pose::Pose pose)
overridevirtual

Mover Methods ///.

Add a membrane virtual residue to the pose by inserting by jump.

Get the name of this Mover (SymmetricAddMembraneMover) Add a membrane virtual residue to the pose by inserting by jump

Adds a virtual residue to the pose by selecting the VRT_0_Base as the anchoring residue and nres_complex+1 as tne new sequence position Not equivalent to an append_by_jump!

Adds a virtual residue to the pose by selecting the VRT_0_Base as the anchoring residue and nres_complex+1 as tne new sequence position Not equivalent to an append_by_jump!

Reimplemented from protocols::membrane::AddMembraneMover.

References core::pose::Pose::conformation(), core::pose::Pose::fold_tree(), core::conformation::Conformation::insert_residue_by_jump(), core::pose::symmetry::is_symmetric(), core::kinematics::FoldTree::reorder(), core::pose::Pose::residue_type_set_for_pose(), core::pose::Pose::size(), and protocols::TR().

utility::vector1< core::SSize > protocols::membrane::symmetry::SymmetricAddMembraneMover::check_pdb_for_mem ( core::pose::Pose pose)
overridevirtual

Helper Method - Check for Membrane residue already in the PDB.

If there is an MEM residue in the PDB at the end of the pose with property MEMBRANE, return a vector of all of those residues.

Reimplemented from protocols::membrane::AddMembraneMover.

protocols::moves::MoverOP protocols::membrane::symmetry::SymmetricAddMembraneMover::clone ( ) const
overridevirtual

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::membrane::AddMembraneMover.

protocols::moves::MoverOP protocols::membrane::symmetry::SymmetricAddMembraneMover::fresh_instance ( ) const
overridevirtual

Create a Fresh Instance of this Mover.

Reimplemented from protocols::membrane::AddMembraneMover.

std::string protocols::membrane::symmetry::SymmetricAddMembraneMover::get_name ( ) const
overridevirtual

Mover Methods ///.

Reimplemented from protocols::membrane::AddMembraneMover.

References mover_name().

void protocols::membrane::symmetry::SymmetricAddMembraneMover::init_from_cmd ( )
private

Initialize Mover options from the comandline.

Initialize mover settings from the commandline mainly in the mp, setup group: spans_from_structure, spanfile and lipsfiles paths

References protocols::membrane::AddMembraneMover::get_spanfile(), protocols::membrane::AddMembraneMover::spanfile(), and protocols::TR().

Referenced by SymmetricAddMembraneMover().

std::string protocols::membrane::symmetry::SymmetricAddMembraneMover::mover_name ( )
static
void protocols::membrane::symmetry::SymmetricAddMembraneMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  dm 
)
overridevirtual

Pase Rosetta Scripts Options for this Mover.

Reimplemented from protocols::membrane::AddMembraneMover.

References protocols::membrane::AddMembraneMover::parse_my_tag().

void protocols::membrane::symmetry::SymmetricAddMembraneMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::membrane::symmetry::SymmetricAddMembraneMover::register_options ( )
private

Setup Methods ///.

Create a new copy of this mover.

Register Options from Command Line

Register mover-relevant options with JD2 - includes mp seutp options: spanfiles, lipsfile, and spans_from_structure.

Return the Name of this mover (as seen by Rscripts) Mover name for Rosetta Scripts Mover Methods /// Get the name of this Mover (SymmetricAddMembraneMover) Setup Methods /// Register Options from Command Line

Register mover-relevant options with JD2 - includes mp seutp options: spanfiles, lipsfile, and spans_from_structure.

Referenced by SymmetricAddMembraneMover().

Member Data Documentation

utility::vector1< core::conformation::membrane::SpanOP > protocols::membrane::symmetry::SymmetricAddMembraneMover::spans_from_xml_
private

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