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protocols::docking::SlideIntoContact Class Reference

More general function for low-res or highres DockingSlideIntoContact. More...

#include <DockingInitialPerturbation.hh>

Inheritance diagram for protocols::docking::SlideIntoContact:
Inheritance graph
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Public Member Functions

 SlideIntoContact ()
 default constructor, default jump = 1, default scorefunction is lowres More...
 
 SlideIntoContact (core::Size const jump)
 constructor with arguments More...
 
 ~SlideIntoContact () override
 destructor More...
 
void apply (core::pose::Pose &pose) override
 apply More...
 
void show (std::ostream &output=std::cout) const override
 show More...
 
void slide_axis (core::Vector const &slide_axis)
 set slide axis in Mover More...
 
void vary_stepsize (bool yesno)
 vary the stepsize depending on the distance between the partners More...
 
void stepsize (core::Real stepsize)
 set the stepsize to walk between the partners More...
 
void move_apart_first (bool yesno)
 move partners apart first More...
 
void set_starting_rep (core::Real starting_rep)
 set starting repulsion More...
 
void scorefunction (std::string sfxn_name, std::string scoretype_for_sliding)
 scorefunction and scoreterm used for evaluating closeness of partners More...
 
std::string get_name () const override
 Get the name of this mover. More...
 
core::Size get_jump_num () const
 get the jump number between the partners More...
 
core::Real get_stepsize () const
 get the stepsize to walk between the partners More...
 
std::string get_sfxn_name () const
 get the scorefunction name that is used to evaluate closeness btw partners 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 MoverOP clone () const
 Return a clone of the Mover object. 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
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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 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 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...
 

Private Member Functions

void register_options ()
 Register Options with JD2. More...
 
void init_from_cmd ()
 Initialize Mover options from the comandline. More...
 

Private Attributes

core::Size jump_
 which jump to use for docking More...
 
core::Vector slide_axis_
 slide axis from the constructor More...
 
bool vary_stepsize_
 stepsize More...
 
core::Real stepsize_
 
bool move_apart_first_
 Move apart first. More...
 
core::scoring::ScoreFunctionOP scorefxn_
 scorefunction for sliding together More...
 
core::scoring::ScoreType scoretype_
 scoreterm for evaluating closeness of partners More...
 
core::Real threshold_
 Scoreterm threshold. More...
 
core::Real starting_rep_
 starting repulsion More...
 

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
 
- 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

More general function for low-res or highres DockingSlideIntoContact.

Both DockingSlideIntoContact and FaDockingSlideIntoContact have their issues and are not as general as they could be; they should be a single class, not two; since they are called quite often, I am rewriting the class for now and will replace it's use later on

Contrary to the name, slides things apart first, then together. OK for proteins, bad for ligands (because they may escape the pocket permanently).

Constructor & Destructor Documentation

protocols::docking::SlideIntoContact::SlideIntoContact ( )

default constructor, default jump = 1, default scorefunction is lowres

More general function for low-res or highres DockingSlideIntoContact.

Both DockingSlideIntoContact and FaDockingSlideIntoContact have their issues and are not as general as they could be; they should be a single class, not two; since they are called quite often, I am rewriting the class for now and will replace it's use later on

Contrary to the name, slides things apart first, then together. OK for proteins, bad for ligands (because they may escape the pocket permanently). default constructor, default jump = 1, default scorefunction is lowres

protocols::docking::SlideIntoContact::SlideIntoContact ( core::Size const  jump)

constructor with arguments

protocols::docking::SlideIntoContact::~SlideIntoContact ( )
overridedefault

destructor

Member Function Documentation

void protocols::docking::SlideIntoContact::apply ( core::pose::Pose pose)
overridevirtual
core::Size protocols::docking::SlideIntoContact::get_jump_num ( ) const

get the jump number between the partners

References jump_.

Referenced by show().

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

Get the name of this mover.

Implements protocols::moves::Mover.

std::string protocols::docking::SlideIntoContact::get_sfxn_name ( ) const

get the scorefunction name that is used to evaluate closeness btw partners

References scorefxn_.

core::Real protocols::docking::SlideIntoContact::get_stepsize ( ) const

get the stepsize to walk between the partners

References stepsize_.

void protocols::docking::SlideIntoContact::init_from_cmd ( )
private

Initialize Mover options from the comandline.

References threshold_.

Referenced by apply().

void protocols::docking::SlideIntoContact::move_apart_first ( bool  yesno)

move partners apart first

References move_apart_first_.

void protocols::docking::SlideIntoContact::register_options ( )
private

Register Options with JD2.

Referenced by apply().

void protocols::docking::SlideIntoContact::scorefunction ( std::string  sfxn_name,
std::string  scoretype_for_sliding 
)

scorefunction and scoreterm used for evaluating closeness of partners

References core::scoring::ScoreFunctionFactory::create_score_function(), core::scoring::score_type_from_name(), scorefxn_, and scoretype_.

void protocols::docking::SlideIntoContact::set_starting_rep ( core::Real  starting_rep)

set starting repulsion

References starting_rep_.

void protocols::docking::SlideIntoContact::show ( std::ostream &  output = std::cout) const
overridevirtual

show

Reimplemented from protocols::moves::Mover.

References get_jump_num().

void protocols::docking::SlideIntoContact::slide_axis ( core::Vector const &  slide_axis)

set slide axis in Mover

References slide_axis_.

void protocols::docking::SlideIntoContact::stepsize ( core::Real  stepsize)

set the stepsize to walk between the partners

References stepsize_.

void protocols::docking::SlideIntoContact::vary_stepsize ( bool  yesno)

vary the stepsize depending on the distance between the partners

References vary_stepsize_.

Member Data Documentation

core::Size protocols::docking::SlideIntoContact::jump_
private

which jump to use for docking

Referenced by apply(), and get_jump_num().

bool protocols::docking::SlideIntoContact::move_apart_first_
private

Move apart first.

Referenced by apply(), and move_apart_first().

core::scoring::ScoreFunctionOP protocols::docking::SlideIntoContact::scorefxn_
private

scorefunction for sliding together

Referenced by apply(), get_sfxn_name(), and scorefunction().

core::scoring::ScoreType protocols::docking::SlideIntoContact::scoretype_
private

scoreterm for evaluating closeness of partners

Referenced by apply(), and scorefunction().

core::Vector protocols::docking::SlideIntoContact::slide_axis_
private

slide axis from the constructor

Referenced by apply(), and slide_axis().

core::Real protocols::docking::SlideIntoContact::starting_rep_
private

starting repulsion

Referenced by apply(), and set_starting_rep().

core::Real protocols::docking::SlideIntoContact::stepsize_
private

Referenced by get_stepsize(), and stepsize().

core::Real protocols::docking::SlideIntoContact::threshold_
private

Scoreterm threshold.

Referenced by apply(), and init_from_cmd().

bool protocols::docking::SlideIntoContact::vary_stepsize_
private

stepsize

Referenced by apply(), and vary_stepsize().


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