Rosetta Protocols  2014.35
Public Member Functions | Static Public Member Functions | Private Attributes | List of all members
protocols::docking::DockingInitialPerturbation Class Reference

this mover carries out the initial perturbation phase of the RosettaDock algorithm based on user-inputted command line options More...

#include <DockingInitialPerturbation.hh>

Public Member Functions

 DockingInitialPerturbation ()
 Default constructor. More...
 
 DockingInitialPerturbation (core::Size const rb_jump, bool const slide=true)
 Constructor with two arguments. The first is the jump number to dock over, the second is a boolean (true will use slide into contact, false will not). More...
 
 DockingInitialPerturbation (DockJumps const movable_jumps, bool const slide=true)
 Constructor with two arguments. The first is the DockJumps, the second is a boolean (true will use slide into contact, false will not). More...
 
 ~DockingInitialPerturbation ()
 
virtual void apply (core::pose::Pose &pose)
 Make starting perturbations for rigid body moves. More...
 
void apply_body (core::pose::Pose &pose, core::Size jump_number)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void init ()
 Calls set_dault, register_from_options and init_from_options. More...
 
void set_default ()
 Sets members to default values. More...
 
void init_from_options ()
 Assigns user specified values to primitive members using command line options. More...
 
void set_randomize1 (bool randomize1)
 set functions More...
 
void set_randomize2 (bool randomize2)
 
void set_use_ellipsoidal_randomization (bool use_ellipsoidal_randomization)
 
void set_dock_pert (utility::vector1< core::Real > dock_pert)
 
void set_uniform_trans (core::Real uniform_trans)
 
void set_spin (bool spin)
 
void set_center (bool center)
 
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 &)
 zhe for rosetta_scripts More...
 
virtual protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. 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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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...
 

Static Public Member Functions

static void register_options ()
 Associates relevant options with the DockingInitialPerturbation class. More...
 
- 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 Attributes

bool slide_
 do slide into context? More...
 
DockJumps movable_jumps_
 
bool randomize1_
 
bool randomize2_
 
bool use_ellipsoidal_randomization_
 
bool spin_
 
bool if_dock_pert_
 
bool if_uniform_trans_
 
bool multiple_jumps_
 
bool center_at_interface_
 
utility::vector1< core::Realdock_pert_
 
core::Real uniform_trans_
 
core::Vector slide_axis_
 
core::Vector spin_center_
 
protocols::docking::RigidBodyInfoOP rigid_body_info_
 

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
 
- 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

this mover carries out the initial perturbation phase of the RosettaDock algorithm based on user-inputted command line options

Constructor & Destructor Documentation

protocols::docking::DockingInitialPerturbation::DockingInitialPerturbation ( )

Default constructor.

References init(), movable_jumps_, multiple_jumps_, and protocols::moves::Mover::type().

Referenced by clone().

protocols::docking::DockingInitialPerturbation::DockingInitialPerturbation ( core::Size const  rb_jump,
bool const  slide = true 
)

Constructor with two arguments. The first is the jump number to dock over, the second is a boolean (true will use slide into contact, false will not).

References init(), movable_jumps_, multiple_jumps_, and protocols::moves::Mover::type().

protocols::docking::DockingInitialPerturbation::DockingInitialPerturbation ( DockJumps const  movable_jumps,
bool const  slide = true 
)

Constructor with two arguments. The first is the DockJumps, the second is a boolean (true will use slide into contact, false will not).

References init(), movable_jumps_, multiple_jumps_, and protocols::moves::Mover::type().

protocols::docking::DockingInitialPerturbation::~DockingInitialPerturbation ( )

Member Function Documentation

void protocols::docking::DockingInitialPerturbation::apply ( core::pose::Pose pose)
virtual

Make starting perturbations for rigid body moves.

initial_perturbation

Detailed: There are several ways to perturb the structure before beginning
the search; they are controlled through command-line flags At the end, partners are slid into contact and scored (including mc_reset). Also, they are tested for passing the FAB filter.
References: see dock_structure or pose_docking from rosetta++
Authors
Monica Berrondo June 14 2007
Last Modified: October 17 2007

Implements protocols::moves::Mover.

References apply_body(), movable_jumps_, rigid_body_info_, runtime_assert, protocols::TR, and utility_exit_with_message.

Referenced by protocols::docking::DockingProtocol::apply(), protocols::ub_e2c::ubi_e2c_modeler::init_k48r_perturbation(), protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs(), and protocols::ub_e2c::ubi_e2c_modeler::monoub_first_perturbation().

void protocols::docking::DockingInitialPerturbation::apply_body ( core::pose::Pose pose,
core::Size  jump_number 
)
protocols::moves::MoverOP protocols::docking::DockingInitialPerturbation::clone ( ) const
virtual

Return a clone of the Mover object.

clone is meant to return an OP'ed deep copy of this object. This really should be a pure virtual in the base class, but adding pure virtuals to Mover would massively disrupt the code. This default implementation crashes at runtime instead of compiletime if you try to call it. If this code is causing you problems, your Mover needs to override this function.

Reimplemented from protocols::moves::Mover.

References DockingInitialPerturbation().

std::string protocols::docking::DockingInitialPerturbation::get_name ( ) const
virtual

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

Implements protocols::moves::Mover.

void protocols::docking::DockingInitialPerturbation::init ( void  )

Calls set_dault, register_from_options and init_from_options.

References init_from_options(), and set_default().

Referenced by DockingInitialPerturbation().

void protocols::docking::DockingInitialPerturbation::init_from_options ( )

Assigns user specified values to primitive members using command line options.

References option, set_center(), set_dock_pert(), set_randomize1(), set_randomize2(), set_spin(), set_uniform_trans(), set_use_ellipsoidal_randomization(), protocols::TR, and user.

Referenced by init().

void protocols::docking::DockingInitialPerturbation::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap data_map,
protocols::filters::Filters_map const &  ,
protocols::moves::Movers_map const &  ,
core::pose::Pose const &   
)
virtual
void protocols::docking::DockingInitialPerturbation::register_options ( )
static

Associates relevant options with the DockingInitialPerturbation class.

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

void protocols::docking::DockingInitialPerturbation::set_center ( bool  center)
inline

References center_at_interface_.

Referenced by init_from_options(), and parse_my_tag().

void protocols::docking::DockingInitialPerturbation::set_default ( )
void protocols::docking::DockingInitialPerturbation::set_dock_pert ( utility::vector1< core::Real dock_pert)
inline

References dock_pert_, and if_dock_pert_.

Referenced by init_from_options(), and parse_my_tag().

void protocols::docking::DockingInitialPerturbation::set_randomize1 ( bool  randomize1)
inline

set functions

References randomize1_.

Referenced by init_from_options(), and parse_my_tag().

void protocols::docking::DockingInitialPerturbation::set_randomize2 ( bool  randomize2)
inline

References randomize2_.

Referenced by init_from_options(), and parse_my_tag().

void protocols::docking::DockingInitialPerturbation::set_spin ( bool  spin)
inline

References spin_.

Referenced by init_from_options(), and parse_my_tag().

void protocols::docking::DockingInitialPerturbation::set_uniform_trans ( core::Real  uniform_trans)
inline
void protocols::docking::DockingInitialPerturbation::set_use_ellipsoidal_randomization ( bool  use_ellipsoidal_randomization)
inline

Member Data Documentation

bool protocols::docking::DockingInitialPerturbation::center_at_interface_
private

Referenced by apply_body(), set_center(), and set_default().

utility::vector1< core::Real > protocols::docking::DockingInitialPerturbation::dock_pert_
private
bool protocols::docking::DockingInitialPerturbation::if_dock_pert_
private
bool protocols::docking::DockingInitialPerturbation::if_uniform_trans_
private
DockJumps protocols::docking::DockingInitialPerturbation::movable_jumps_
private
bool protocols::docking::DockingInitialPerturbation::multiple_jumps_
private
bool protocols::docking::DockingInitialPerturbation::randomize1_
private
bool protocols::docking::DockingInitialPerturbation::randomize2_
private
protocols::docking::RigidBodyInfoOP protocols::docking::DockingInitialPerturbation::rigid_body_info_
private

Referenced by apply(), and parse_my_tag().

bool protocols::docking::DockingInitialPerturbation::slide_
private

do slide into context?

Referenced by apply_body(), and parse_my_tag().

core::Vector protocols::docking::DockingInitialPerturbation::slide_axis_
private

Referenced by apply_body(), and set_default().

bool protocols::docking::DockingInitialPerturbation::spin_
private

Referenced by apply_body(), set_default(), and set_spin().

core::Vector protocols::docking::DockingInitialPerturbation::spin_center_
private

Referenced by apply_body(), and set_default().

core::Real protocols::docking::DockingInitialPerturbation::uniform_trans_
private

Referenced by apply_body(), and set_uniform_trans().

bool protocols::docking::DockingInitialPerturbation::use_ellipsoidal_randomization_
private

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