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

#include <AddMembraneMover.hh>

Inheritance diagram for protocols::membrane::AddMembraneMover:

[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 Strings &	info ()
	non-const accessor More...

virtual Strings const &	info () const
	const accessor More...

virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. 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< SpanInfo >	span_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_

core::conformation::membrane::MP_GEOMETRY_TRANSITION	mp_geometry_

bool	has_pore_ = false

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

◆ AddMembraneMover() [1/6]

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().

◆ AddMembraneMover() [2/6]

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().

◆ AddMembraneMover() [3/6]

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().

◆ AddMembraneMover() [4/6]

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().

◆ AddMembraneMover() [5/6]

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().

◆ AddMembraneMover() [6/6]

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

default

Create a deep copy of the data in this mover.

◆ ~AddMembraneMover()

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

overridedefault

Destructor.

Member Function Documentation

◆ add_membrane_virtual()

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::conformation::ResidueFactory::create_residue(), 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().

◆ apply()

void protocols::membrane::AddMembraneMover::apply ( core::pose::Pose & pose )

overridevirtual

Initialize the RosettaMP elements with this pose.

Mover-Specific Methods & Rosetta Scripts Support ///.

Initialize the RosettaMP elements with this pose

Implements protocols::moves::Mover.

References anchor_rsd_, center_, protocols::loops::chainID, core::pose::Pose::conformation(), protocols::membrane::create_membrane_foldtree_from_anchors(), core::sequence::end, core::pose::Pose::fold_tree(), protocols::membrane::get_anchor_points_for_tmcom(), protocols::membrane::get_chain_and_z(), core::pose::get_pdb2pose_numbering_as_stdmap(), protocols::membrane::get_secstruct(), has_pore_, initialize_membrane_residue(), protocols::membrane::is_membrane_fixed(), lipid_composition_, membrane_core_, core::conformation::Conformation::membrane_info(), membrane_rsd_, mp_geometry_, normal_, core::kinematics::FoldTree::num_jump(), restore_lazaridis_IMM1_behavior_, core::conformation::Conformation::set_membrane_info(), core::kinematics::FoldTree::show(), core::pose::Pose::size(), span_infos_, spanfile_, protocols::loops::start, steepness_, temperature_, thickness_, topology_, protocols::TR(), user_defined_membrane_pos_, and user_override_pore_.

◆ attributes_for_parse_center_normal_from_tag()

void protocols::membrane::AddMembraneMover::attributes_for_parse_center_normal_from_tag ( utility::tag::AttributeList & attributes )

static

Referenced by provide_xml_schema(), protocols::membrane::SetMembranePositionMover::provide_xml_schema(), protocols::membrane::symmetry::SymmetricAddMembraneMover::provide_xml_schema(), and protocols::membrane::TransformIntoMembraneMover::provide_xml_schema().

◆ check_pdb_for_mem()

utility::vector1< core::SSize > protocols::membrane::AddMembraneMover::check_pdb_for_mem ( core::pose::Pose & pose )

privatevirtual

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

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

References core::conformation::Residue::has_property(), core::conformation::Residue::name3(), core::pose::Pose::residue(), core::pose::Pose::size(), and protocols::TR().

Referenced by initialize_membrane_residue().

◆ clone()

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().

◆ fresh_instance()

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().

◆ get_name()

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

overridevirtual

Mover Methods ///.

Implements protocols::moves::Mover.

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

References mover_name().

◆ get_spanfile()

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().

◆ init_from_cmd()

void protocols::membrane::AddMembraneMover::init_from_cmd ( )

private

Initialize Mover options from the comandline.

References core::conformation::membrane::BICELLE, center_, core::conformation::membrane::DOUBLE_VESICLE, protocols::buns::geometry, lipid_composition_, membrane_core_, membrane_rsd_, mp_geometry_, normal_, protocols::membrane::read_center_normal_from_cmd(), restore_lazaridis_IMM1_behavior_, core::conformation::membrane::SLAB, spanfile_, steepness_, temperature_, core::conformation::membrane::thickness, thickness_, protocols::TR(), user_override_pore_, and core::conformation::membrane::VESICLE.

Referenced by AddMembraneMover().

◆ initialize_membrane_residue()

core::Size protocols::membrane::AddMembraneMover::initialize_membrane_residue	(	core::pose::Pose &	pose,
		core::Size	membrane_pos
	)

privatevirtual

Initialize Membrane Residue given pose.

Helper methods for setup ///.

Initialize Membrane Residue given pose

References add_membrane_virtual(), check_pdb_for_mem(), core::pose::Pose::conformation(), core::conformation::Residue::has_property(), membrane_rsd_, core::conformation::Conformation::residue(), core::pose::Pose::size(), protocols::TR(), and user_defined_membrane_pos_.

Referenced by apply().

◆ mover_name()

std::string protocols::membrane::AddMembraneMover::mover_name ( )

static

Referenced by get_name(), protocols::membrane::AddMembraneMoverCreator::keyname(), and provide_xml_schema().

◆ parse_my_tag()

void protocols::membrane::AddMembraneMover::parse_my_tag	(	utility::tag::TagCOP	tag,
		basic::datacache::DataMap &	data
	)

overridevirtual

Pase Rosetta Scripts Options for this Mover.

Reimplemented from protocols::moves::Mover.

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

References anchor_rsd_, core::conformation::membrane::BICELLE, center_, database_table_, db_session_, core::conformation::membrane::DOUBLE_VESICLE, core::sequence::end, core::conformation::membrane::in, lipid_composition_, membrane_core_, membrane_rsd_, mp_geometry_, normal_, core::conformation::membrane::out, core::pose::parse_resnum(), protocols::membrane::read_center_normal_from_tag(), restore_lazaridis_IMM1_behavior_, core::conformation::membrane::SLAB, span_infos_, spanfile_, protocols::loops::start, steepness_, temperature_, thickness_, protocols::TR(), and core::conformation::membrane::VESICLE.

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

◆ provide_xml_schema()

void protocols::membrane::AddMembraneMover::provide_xml_schema ( utility::tag::XMLSchemaDefinition & xsd )

static

References attributes_for_parse_center_normal_from_tag(), mover_name(), and protocols::moves::xsd_type_definition_w_attributes_and_repeatable_subelements().

Referenced by protocols::membrane::AddMembraneMoverCreator::provide_xml_schema().

◆ read_spanfile_from_db()

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().

◆ register_options()

void protocols::membrane::AddMembraneMover::register_options ( )

private

Register options from JD2.

References core::conformation::membrane::center, protocols::buns::geometry, core::conformation::membrane::normal, and core::conformation::membrane::thickness.

Referenced by AddMembraneMover().

◆ restore_lazaridis_IMM1_behavior()

void protocols::membrane::AddMembraneMover::restore_lazaridis_IMM1_behavior ( bool restore )

References restore_lazaridis_IMM1_behavior_.

◆ spanfile()

void protocols::membrane::AddMembraneMover::spanfile ( std::string spanfile )

Set path to spanfile.

References spanfile_.

Referenced by protocols::membrane::symmetry::SymmetricAddMembraneMover::init_from_cmd(), and read_spanfile_from_db().

Member Data Documentation

◆ anchor_rsd_

core::Size protocols::membrane::AddMembraneMover::anchor_rsd_

private

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

◆ center_

core::Vector protocols::membrane::AddMembraneMover::center_

private

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

◆ database_table_

std::string protocols::membrane::AddMembraneMover::database_table_

private

Referenced by parse_my_tag(), and read_spanfile_from_db().

◆ db_session_

utility::sql_database::sessionOP protocols::membrane::AddMembraneMover::db_session_

private

Referenced by parse_my_tag(), and read_spanfile_from_db().

◆ has_pore_

bool protocols::membrane::AddMembraneMover::has_pore_ = false

private

Referenced by apply().

◆ lipid_composition_

std::string protocols::membrane::AddMembraneMover::lipid_composition_

private

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

◆ membrane_core_

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

private

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

◆ membrane_rsd_

core::Size protocols::membrane::AddMembraneMover::membrane_rsd_

private

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

◆ mp_geometry_

core::conformation::membrane::MP_GEOMETRY_TRANSITION protocols::membrane::AddMembraneMover::mp_geometry_

private

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

◆ normal_

core::Vector protocols::membrane::AddMembraneMover::normal_

private

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

◆ restore_lazaridis_IMM1_behavior_

bool protocols::membrane::AddMembraneMover::restore_lazaridis_IMM1_behavior_

private

Referenced by apply(), init_from_cmd(), parse_my_tag(), and restore_lazaridis_IMM1_behavior().

◆ span_infos_

utility::vector1< SpanInfo > protocols::membrane::AddMembraneMover::span_infos_

private

Referenced by apply(), and parse_my_tag().

◆ spanfile_

std::string protocols::membrane::AddMembraneMover::spanfile_

private

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

◆ steepness_

core::Real protocols::membrane::AddMembraneMover::steepness_

private

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

◆ temperature_

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

private

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

◆ thickness_

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

private

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

◆ topology_

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

private

Referenced by apply().

◆ user_defined_membrane_pos_

bool protocols::membrane::AddMembraneMover::user_defined_membrane_pos_

private

Referenced by apply(), and initialize_membrane_residue().

◆ user_override_pore_

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:

src/protocols/membrane/AddMembraneMover.hh
src/protocols/membrane/AddMembraneMover.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Detailed Description

Constructor & Destructor Documentation

◆ AddMembraneMover() [1/6]

◆ AddMembraneMover() [2/6]

◆ AddMembraneMover() [3/6]

◆ AddMembraneMover() [4/6]

◆ AddMembraneMover() [5/6]

◆ AddMembraneMover() [6/6]

◆ ~AddMembraneMover()

Member Function Documentation

◆ add_membrane_virtual()

◆ apply()

◆ attributes_for_parse_center_normal_from_tag()

◆ check_pdb_for_mem()

◆ clone()

◆ fresh_instance()

◆ get_name()

◆ get_spanfile()

◆ init_from_cmd()

◆ initialize_membrane_residue()

◆ mover_name()

◆ parse_my_tag()

◆ provide_xml_schema()

◆ read_spanfile_from_db()

◆ register_options()

◆ restore_lazaridis_IMM1_behavior()

◆ spanfile()

Member Data Documentation

◆ anchor_rsd_

◆ center_

◆ database_table_

◆ db_session_

◆ has_pore_

◆ lipid_composition_

◆ membrane_core_

◆ membrane_rsd_

◆ mp_geometry_

◆ normal_

◆ restore_lazaridis_IMM1_behavior_

◆ span_infos_

◆ spanfile_

◆ steepness_

◆ temperature_

◆ thickness_

◆ topology_

◆ user_defined_membrane_pos_

◆ user_override_pore_