More general function for low-res or highres DockingSlideIntoContact. More...
#include <DockingInitialPerturbation.hh>
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 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... | |
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
◆ SlideIntoContact() [1/2]
| 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
◆ SlideIntoContact() [2/2]
| protocols::docking::SlideIntoContact::SlideIntoContact | ( | core::Size const | jump | ) |
constructor with arguments
◆ ~SlideIntoContact()
|
overridedefault |
destructor
Member Function Documentation
◆ apply()
|
overridevirtual |
apply
Implements protocols::moves::Mover.
References core::scoring::ScoreFunctionFactory::create_score_function(), core::pose::Pose::energies(), init_from_cmd(), jump_, move_apart_first_, core::scoring::name_from_score_type(), register_options(), core::scoring::score_type_from_name(), scorefxn_, scoretype_, protocols::moves::Mover::set_current_tag(), slide_axis_, starting_rep_, threshold_, core::scoring::Energies::total_energies(), protocols::docking::TR(), and vary_stepsize_.
◆ get_jump_num()
| core::Size protocols::docking::SlideIntoContact::get_jump_num | ( | ) | const |
◆ get_name()
|
overridevirtual |
Get the name of this mover.
Implements protocols::moves::Mover.
◆ get_sfxn_name()
| std::string protocols::docking::SlideIntoContact::get_sfxn_name | ( | ) | const |
get the scorefunction name that is used to evaluate closeness btw partners
References scorefxn_.
◆ get_stepsize()
| core::Real protocols::docking::SlideIntoContact::get_stepsize | ( | ) | const |
get the stepsize to walk between the partners
References stepsize_.
◆ init_from_cmd()
|
private |
◆ move_apart_first()
| void protocols::docking::SlideIntoContact::move_apart_first | ( | bool | yesno | ) |
move partners apart first
References move_apart_first_.
◆ register_options()
|
private |
Register Options with JD2.
Referenced by apply().
◆ scorefunction()
| 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_.
◆ set_starting_rep()
| void protocols::docking::SlideIntoContact::set_starting_rep | ( | core::Real | starting_rep | ) |
set starting repulsion
References starting_rep_.
◆ show()
|
overridevirtual |
◆ slide_axis()
| void protocols::docking::SlideIntoContact::slide_axis | ( | core::Vector const & | slide_axis | ) |
set slide axis in Mover
References slide_axis_.
◆ stepsize()
| void protocols::docking::SlideIntoContact::stepsize | ( | core::Real | stepsize | ) |
set the stepsize to walk between the partners
References stepsize_.
◆ vary_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
◆ jump_
|
private |
which jump to use for docking
Referenced by apply(), and get_jump_num().
◆ move_apart_first_
|
private |
Move apart first.
Referenced by apply(), and move_apart_first().
◆ scorefxn_
|
private |
scorefunction for sliding together
Referenced by apply(), get_sfxn_name(), and scorefunction().
◆ scoretype_
|
private |
scoreterm for evaluating closeness of partners
Referenced by apply(), and scorefunction().
◆ slide_axis_
|
private |
slide axis from the constructor
Referenced by apply(), and slide_axis().
◆ starting_rep_
|
private |
starting repulsion
Referenced by apply(), and set_starting_rep().
◆ stepsize_
|
private |
Referenced by get_stepsize(), and stepsize().
◆ threshold_
|
private |
Scoreterm threshold.
Referenced by apply(), and init_from_cmd().
◆ vary_stepsize_
|
private |
stepsize
Referenced by apply(), and vary_stepsize().
The documentation for this class was generated from the following files:
- src/protocols/docking/DockingInitialPerturbation.hh
- src/protocols/docking/DockingInitialPerturbation.cc
