Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::membrane::AddMembraneMover Class Reference

Add Membrane components to the pose, sets up MembraneInfo object includes: spanning topology, lips info, embeddings, and a membrane virtual residue describing the membrane position. More...

#include <AddMembraneMover.hh>

Public Member Functions

 AddMembraneMover ()
 Constructors ///. More...
 
 AddMembraneMover (Vector emb_center, Vector emb_normal, std::string spanfile, bool view_in_pymol=false)
 Custom Constructor - mainly for PyRosetta. More...
 
 AddMembraneMover (Vector emb_center, Vector emb_normal, std::string spanfile, std::string lipsfile, bool view_in_pymol=false)
 Custorm Constructur with lips info - mainly for PyRosetta. More...
 
 AddMembraneMover (AddMembraneMover const &src)
 Copy Constructor. More...
 
virtual ~AddMembraneMover ()
 Destructor. More...
 
virtual protocols::moves::MoverOP clone () const
 Rosetta Scripts Methods ///. More...
 
virtual protocols::moves::MoverOP fresh_instance () const
 Create a Fresh Instance of this Mover. More...
 
void parse_my_tag (utility::tag::TagCOP tag, basic::datacache::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
 Pase Rosetta Scripts Options for this Mover. More...
 
virtual std::string get_name () const
 Mover Methods ///. More...
 
virtual void apply (Pose &pose)
 Add Membrane Components to Pose. More...
 
- Public Member Functions inherited from protocols::moves::Mover
 Mover ()
 
virtual ~Mover ()
 
virtual MoverSP create ()
 
virtual void apply (core::io::serialization::PipeMap &pmap)
 
virtual void parse_state (SerializableState const &state)
 
virtual void parse_def (utility::lua::LuaObject const &def, utility::lua::LuaObject const &score_fxns, utility::lua::LuaObject const &tasks, MoverCacheSP cache)
 
virtual void save_state (SerializableState &state)
 
 Mover (std::string const &type_name)
 sets the type for a mover; name_ has been removed (2010/05/14) More...
 
 Mover (Mover const &other)
 
Moveroperator= (Mover const &other)
 assignment operator More...
 
virtual core::Real last_proposal_density_ratio ()
 
std::string const & type () const
 
void set_type (std::string const &setting)
 
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...
 
void set_current_tag (std::string const &new_tag)
 
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
 
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...
 
void type (const std::string &type_in)
 
std::string get_type () const
 
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...
 
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 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Private Member Functions

void register_options ()
 Setup Methods ///. More...
 
void init_from_cmd ()
 Initialize Mover options from the comandline. More...
 
core::Size setup_anchoring_virtual (Pose &pose)
 Helper method - Setup anchored virtual residue - origin. More...
 
core::Size setup_membrane_virtual (Pose &pose)
 Helper Method - Setup Membrane Virtual. More...
 

Private Attributes

bool fullatom_
 
bool include_lips_
 
bool view_in_pymol_
 
bool anchored_foldtree_
 
Vector center_
 
Vector normal_
 
std::string spanfile_
 
std::string lipsfile_
 

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
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 
- 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...
 
- 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

Add Membrane components to the pose, sets up MembraneInfo object includes: spanning topology, lips info, embeddings, and a membrane virtual residue describing the membrane position.

Constructor & Destructor Documentation

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

Constructors ///.

Default Constructor

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.

References init_from_cmd(), and register_options().

Referenced by clone(), and fresh_instance().

protocols::membrane::AddMembraneMover::AddMembraneMover ( Vector  emb_center,
Vector  emb_normal,
std::string  spanfile,
bool  view_in_pymol = false 
)

Custom Constructor - mainly for PyRosetta.

Custom Constructor - for PyRosetta.

Creates a membrane pose setting the membrane center at emb_center and normal at emb_normal and will load in spanning regions from list of spanfiles provided

Creates a membrane pose setting the membrane center at emb_center and normal at emb_normal and will load in spanning regions from list of spanfile provided

References init_from_cmd(), and register_options().

protocols::membrane::AddMembraneMover::AddMembraneMover ( Vector  emb_center,
Vector  emb_normal,
std::string  spanfile,
std::string  lips_acc,
bool  view_in_pymol = false 
)

Custorm Constructur with lips info - mainly for PyRosetta.

Custorm Constructur with lips info - for PyRosetta.

Creates a membrane pose setting the membrane center at emb_center and normal at emb_normal and will load in spanning regions from list of spanfiles provided. Will also load in lips info from lips_acc info provided

Creates a membrane pose setting the membrane center at emb_center and normal at emb_normal and will load in spanning regions from list of spanfile provided. Will also load in lips info from lips_acc info provided

References init_from_cmd(), and register_options().

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

Copy Constructor.

Create a deep copy of this mover

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

Destructor.

Member Function Documentation

void protocols::membrane::AddMembraneMover::apply ( Pose pose)
virtual

Add Membrane Components to Pose.

Add membrane components to pose which includes spanning topology, lips info, embeddings, and a membrane virtual residue describing the membrane position

Implements protocols::moves::Mover.

References core::pose::Pose::conformation(), include_lips_, lipsfile_, core::conformation::Conformation::set_membrane_info(), setup_membrane_virtual(), spanfile_, core::pose::Pose::total_residue(), protocols::TR, and view_in_pymol_.

protocols::moves::MoverOP protocols::membrane::AddMembraneMover::clone ( ) const
virtual

Rosetta Scripts Methods ///.

Create a Clone of this mover

Reimplemented from protocols::moves::Mover.

References AddMembraneMover().

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

Create a Fresh Instance of this Mover.

Reimplemented from protocols::moves::Mover.

References AddMembraneMover().

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

Mover Methods ///.

Get the name of this Mover (AddMembraneMover)

Implements protocols::moves::Mover.

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

Initialize Mover options from the comandline.

Initialize mover settings from the commandline mainly in the membrane_new, setup group: center, normal, spanfiles and lipsfiles paths

Initialize mover settings from the commandline mainly in the membrane_new, setup group: center, normal, spanfile and lipsfiles paths

References anchored_foldtree_, center_, fullatom_, include_lips_, lipsfile_, normal_, option, spanfile_, user, view_in_pymol_, numeric::xyzVector< class >::x(), numeric::xyzVector< class >::y(), and numeric::xyzVector< class >::z().

Referenced by AddMembraneMover().

void protocols::membrane::AddMembraneMover::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap ,
protocols::filters::Filters_map const &  ,
protocols::moves::Movers_map const &  ,
core::pose::Pose const &   
)
virtual
void protocols::membrane::AddMembraneMover::register_options ( )
private

Setup Methods ///.

Register Options from Command Line

Register mover-relevant options with JD2 - includes membrane_new, seutp options: center, normal, spanfiles and lipsfiles

Register Options from Command Line

Register mover-relevant options with JD2 - includes membrane_new, seutp options: center, normal, spanfile and lipsfiles

References utility::options::OptionCollection::add_relevant(), and option.

Referenced by AddMembraneMover().

core::Size protocols::membrane::AddMembraneMover::setup_anchoring_virtual ( Pose pose)
private

Helper method - Setup anchored virtual residue - origin.

Create a new virtual residue of type VRT to root the membrane and protein in the system. This scenario is analagous to docking, except both partners are moveable

References core::pose::Pose::append_residue_by_jump(), core::chemical::CENTROID, core::conformation::ResidueFactory::create_residue(), core::chemical::FA_STANDARD, core::pose::Pose::fold_tree(), fullatom_, core::chemical::ChemicalManager::get_instance(), nres, core::kinematics::FoldTree::reorder(), residue_type_set, core::kinematics::FoldTree::root(), core::pose::Pose::total_residue(), and protocols::TR.

core::Size protocols::membrane::AddMembraneMover::setup_membrane_virtual ( Pose pose)
private

Helper Method - Setup Membrane Virtual.

Create a new virtual residue of type MEM from the pose typeset (fullatom or centroid). Add this virtual residue by appending to the last residue of the pose. Then set this position as the root of the fold tree.

Create a new virtual residue of type MEM from the pose typeset (fullatom or centroid). Add this virtual residue by appending to the last residue of the pose. Then set this position as the root of the fold tree.

do not call this method before anchoring the pose with a virtual. Moves will not occur in a reasonable way if so. 7/2/14

References core::pose::Pose::append_residue_by_jump(), core::chemical::CENTROID, core::conformation::ResidueFactory::create_residue(), core::chemical::FA_STANDARD, fullatom_, core::chemical::ChemicalManager::get_instance(), membrane, residue_type_set, core::pose::Pose::total_residue(), and protocols::TR.

Referenced by apply().

Member Data Documentation

bool protocols::membrane::AddMembraneMover::anchored_foldtree_
private

Referenced by init_from_cmd().

Vector protocols::membrane::AddMembraneMover::center_
private

Referenced by init_from_cmd(), and parse_my_tag().

bool protocols::membrane::AddMembraneMover::fullatom_
private
bool protocols::membrane::AddMembraneMover::include_lips_
private

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

std::string protocols::membrane::AddMembraneMover::lipsfile_
private

Referenced by apply(), and init_from_cmd().

Vector protocols::membrane::AddMembraneMover::normal_
private

Referenced by init_from_cmd(), and parse_my_tag().

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

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

bool protocols::membrane::AddMembraneMover::view_in_pymol_
private

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


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