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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>

Inheritance diagram for protocols::docking::DockingInitialPerturbation:
Inheritance graph
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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, bool const autofoldtree=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 () override
 
void apply (core::pose::Pose &pose) override
 Make starting perturbations for rigid body moves. More...
 
void apply_body (core::pose::Pose &pose, core::Size jump_number)
 
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 or_randomize2 (bool randomize2)
 
void set_use_ellipsoidal_randomization (bool use_ellipsoidal_randomization)
 
void set_dock_pert (utility::vector1< core::Real > dock_pert)
 
void set_tilt (utility::vector1< core::Real > tilt)
 
void set_tilt1_center (std::string tilt_center)
 
void set_tilt2_center (std::string tilt_center)
 
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 &) override
 zhe for rosetta_scripts More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
std::string get_name () const override
 Each derived class must specify its name. The class name. 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...
 
virtual MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. 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 void register_options ()
 Associates relevant options with the DockingInitialPerturbation class. More...
 
static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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...
 
bool autofoldtree_
 adjust foldtree in Ellipsoidal docking? 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_
 
utility::vector1< core::Realtilt_
 
std::string tilt1_center_
 
std::string tilt2_center_
 
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 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

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_, and multiple_jumps_.

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_, and multiple_jumps_.

protocols::docking::DockingInitialPerturbation::DockingInitialPerturbation ( DockJumps const  movable_jumps,
bool const  slide = true,
bool const  autofoldtree = 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_, and multiple_jumps_.

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

Member Function Documentation

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

Make starting perturbations for rigid body moves.

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++
Author
Monica Berrondo June 14 2007

Implements protocols::moves::Mover.

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

Referenced by protocols::topology_broker::AsymFoldandDockClaimer::initialize_dofs().

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

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.

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

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

Implements protocols::moves::Mover.

References mover_name().

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 or_randomize2(), set_center(), set_dock_pert(), set_randomize1(), set_spin(), set_tilt(), set_tilt1_center(), set_tilt2_center(), set_uniform_trans(), set_use_ellipsoidal_randomization(), and protocols::docking::TR().

Referenced by init().

std::string protocols::docking::DockingInitialPerturbation::mover_name ( )
static
void protocols::docking::DockingInitialPerturbation::or_randomize2 ( bool  randomize2)
inline

References randomize2_.

Referenced by init_from_options().

void protocols::docking::DockingInitialPerturbation::parse_my_tag ( utility::tag::TagCOP  tag,
basic::datacache::DataMap &  data_map 
)
overridevirtual
void protocols::docking::DockingInitialPerturbation::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::docking::DockingInitialPerturbation::register_options ( )
static

Associates relevant options with the DockingInitialPerturbation class.

void protocols::docking::DockingInitialPerturbation::set_center ( bool  center)
inline
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 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_tilt ( utility::vector1< core::Real tilt)
inline

References tilt_.

Referenced by init_from_options().

void protocols::docking::DockingInitialPerturbation::set_tilt1_center ( std::string  tilt_center)
inline

References tilt1_center_.

Referenced by init_from_options().

void protocols::docking::DockingInitialPerturbation::set_tilt2_center ( std::string  tilt_center)
inline

References tilt2_center_.

Referenced by init_from_options().

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::autofoldtree_
private

adjust foldtree in Ellipsoidal docking?

Referenced by apply_body().

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().

std::string protocols::docking::DockingInitialPerturbation::tilt1_center_
private

Referenced by apply_body(), and set_tilt1_center().

std::string protocols::docking::DockingInitialPerturbation::tilt2_center_
private

Referenced by apply_body(), and set_tilt2_center().

utility::vector1< core::Real > protocols::docking::DockingInitialPerturbation::tilt_
private

Referenced by apply_body(), and set_tilt().

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: