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protocols::membrane::AddMembraneMover Class Reference

Initialize the RosettaMP framework by adding representations of the membrane. More...

#include <AddMembraneMover.hh>

Inheritance diagram for protocols::membrane::AddMembraneMover:
Inheritance graph
[legend]

Public Member Functions

 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...
 
protocols::moves::MoverOP clone () const override
 Create a Clone of this mover. 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 &data) override
 Pase Rosetta Scripts Options for this Mover. More...
 
std::string get_name () const override
 Mover Methods ///. 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)
 
virtual core::Size add_membrane_virtual (core::pose::Pose &pose)
 Create and append a membrane virtual residue to the pose. 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 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

virtual core::Size initialize_membrane_residue (core::pose::Pose &pose, core::Size membrane_rsd)
 Initialize Membrane Residue given pose. More...
 
virtual utility::vector1
< core::SSize
check_pdb_for_mem (core::pose::Pose &pose)
 Helper Method - Check for Membrane residue already in the PDB. More...
 
void register_options ()
 Register options from JD2. More...
 
void init_from_cmd ()
 Initialize Mover options from the comandline. More...
 
std::string read_spanfile_from_db ()
 Read path to the spanfile from an input sql database. More...
 

Private Attributes

bool restore_lazaridis_IMM1_behavior_
 
std::string lipid_composition_
 
core::Real temperature_
 
bool user_override_pore_
 
std::string spanfile_
 
core::conformation::membrane::SpanningTopologyOP topology_
 
utility::vector1< SpanInfospan_infos_
 
core::Size anchor_rsd_
 
core::Size membrane_rsd_
 
core::Vector center_
 
core::Vector normal_
 
bool user_defined_membrane_pos_
 
core::Real thickness_
 
core::Real steepness_
 
core::Real membrane_core_
 
std::string database_table_
 
utility::sql_database::sessionOP db_session_
 

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

Initialize the RosettaMP framework by adding representations of the membrane.

Constructor & Destructor Documentation

protocols::membrane::AddMembraneMover::AddMembraneMover ( )

Create a default RosettaMP membrane setup.

Constructors ///.

Create a default RosettaMP membrane setup

References init_from_cmd(), and register_options().

Referenced by clone(), and fresh_instance().

protocols::membrane::AddMembraneMover::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.

References init_from_cmd(), and register_options().

protocols::membrane::AddMembraneMover::AddMembraneMover ( core::Size  membrane_rsd,
std::string  lipid_composition = "DLPC",
core::Real  temperature = 37.0 
)

Create a RosettaMP setup from an existing membrane residue.

References init_from_cmd(), and register_options().

protocols::membrane::AddMembraneMover::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.

References init_from_cmd(), and register_options().

protocols::membrane::AddMembraneMover::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.

Create a RosettaMP setup from an existing residue at a specific anchor point.

References init_from_cmd(), and register_options().

protocols::membrane::AddMembraneMover::AddMembraneMover ( AddMembraneMover const &  src)
default

Create a deep copy of the data in this mover.

protocols::membrane::AddMembraneMover::~AddMembraneMover ( )
overridedefault

Destructor.

Member Function Documentation

core::Size protocols::membrane::AddMembraneMover::add_membrane_virtual ( core::pose::Pose pose)
virtual

Create and append a membrane virtual residue to the pose.

Functions that can be overloaded for sub-classes of this mover ///.

Helper Method - Add a membrane virtual residue

Reimplemented in protocols::membrane::symmetry::SymmetricAddMembraneMover.

References anchor_rsd_, core::pose::Pose::append_residue_by_jump(), core::pose::Pose::fold_tree(), core::pose::Pose::pdb_info(), core::pose::Pose::residue_type_set_for_pose(), core::kinematics::FoldTree::show(), core::pose::Pose::size(), and protocols::TR().

Referenced by initialize_membrane_residue().

void protocols::membrane::AddMembraneMover::apply ( core::pose::Pose pose)
overridevirtual
void protocols::membrane::AddMembraneMover::attributes_for_parse_center_normal_from_tag ( utility::tag::AttributeList &  attributes)
static
utility::vector1< core::SSize > protocols::membrane::AddMembraneMover::check_pdb_for_mem ( core::pose::Pose pose)
privatevirtual
protocols::moves::MoverOP protocols::membrane::AddMembraneMover::clone ( ) const
overridevirtual

Create a Clone of this mover.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::membrane::symmetry::SymmetricAddMembraneMover.

References AddMembraneMover().

protocols::moves::MoverOP protocols::membrane::AddMembraneMover::fresh_instance ( ) const
overridevirtual

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

Reimplemented in protocols::membrane::symmetry::SymmetricAddMembraneMover.

References AddMembraneMover().

std::string protocols::membrane::AddMembraneMover::get_name ( ) const
overridevirtual

Mover Methods ///.

Implements protocols::moves::Mover.

Reimplemented in protocols::membrane::symmetry::SymmetricAddMembraneMover.

References mover_name().

std::string protocols::membrane::AddMembraneMover::get_spanfile ( ) const

Path to file with transmembrane span data.

Read & write access to data ///.

Path to file with transmembrane span data

References spanfile_.

Referenced by protocols::membrane::symmetry::SymmetricAddMembraneMover::init_from_cmd().

void protocols::membrane::AddMembraneMover::init_from_cmd ( )
private
core::Size protocols::membrane::AddMembraneMover::initialize_membrane_residue ( core::pose::Pose pose,
core::Size  membrane_pos 
)
privatevirtual
std::string protocols::membrane::AddMembraneMover::mover_name ( )
static
void protocols::membrane::AddMembraneMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual
void protocols::membrane::AddMembraneMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
std::string protocols::membrane::AddMembraneMover::read_spanfile_from_db ( )
private

Read path to the spanfile from an input sql database.

Read a spanfile from a relational database provided as input to RosettaScripts.

References database_table_, db_session_, protocols::pack_daemon::error_message, and spanfile().

void protocols::membrane::AddMembraneMover::register_options ( )
private
void protocols::membrane::AddMembraneMover::restore_lazaridis_IMM1_behavior ( bool  restore)
void protocols::membrane::AddMembraneMover::spanfile ( std::string  spanfile)

Member Data Documentation

core::Size protocols::membrane::AddMembraneMover::anchor_rsd_
private
core::Vector protocols::membrane::AddMembraneMover::center_
private

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

std::string protocols::membrane::AddMembraneMover::database_table_
private
utility::sql_database::sessionOP protocols::membrane::AddMembraneMover::db_session_
private
std::string protocols::membrane::AddMembraneMover::lipid_composition_
private

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

core::Real protocols::membrane::AddMembraneMover::membrane_core_
private

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

core::Size protocols::membrane::AddMembraneMover::membrane_rsd_
private
core::Vector protocols::membrane::AddMembraneMover::normal_
private

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

bool protocols::membrane::AddMembraneMover::restore_lazaridis_IMM1_behavior_
private
utility::vector1< SpanInfo > protocols::membrane::AddMembraneMover::span_infos_
private

Referenced by apply(), and parse_my_tag().

std::string protocols::membrane::AddMembraneMover::spanfile_
private
core::Real protocols::membrane::AddMembraneMover::steepness_
private

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

core::Real protocols::membrane::AddMembraneMover::temperature_
private

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

core::Real protocols::membrane::AddMembraneMover::thickness_
private

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

core::conformation::membrane::SpanningTopologyOP protocols::membrane::AddMembraneMover::topology_
private

Referenced by apply().

bool protocols::membrane::AddMembraneMover::user_defined_membrane_pos_
private
bool protocols::membrane::AddMembraneMover::user_override_pore_
private

Referenced by apply(), and init_from_cmd().


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