Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::flexpep_docking::FlexPepDockingAbInitio Class Reference

#include <FlexPepDockingAbInitio.hh>

Inheritance diagram for protocols::flexpep_docking::FlexPepDockingAbInitio:
Inheritance graph

Public Member Functions

 FlexPepDockingAbInitio (FlexPepDockingFlags const &flags_in, core::scoring::ScoreFunctionOP scorefxn_in, core::kinematics::MoveMapOP movemap_in, core::Size const rb_jump_in=1)
 constructor for low resolution flexpible peptide docking More...
 ~FlexPepDockingAbInitio () override
void apply (core::pose::Pose &pose) override
 Main Method. 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 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 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 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 setup_for_apply (core::pose::Pose &pose)
 initial setup for apply More...
void to_centroid (core::pose::Pose &pose) const
void to_allatom (core::pose::Pose &pose, core::pose::Pose &referencePose) const
void torsions_monte_carlo (core::pose::Pose &pose, const int cycles, core::Real &acceptance_rate)
void loopclosure_monte_carlo (core::pose::Pose &pose)
void rigidbody_monte_carlo (core::pose::Pose &pose, const int cycles, const float trans_magnitude, const float rot_magnitude, core::Real &acceptance_rate)
void convertPSERtoASP (core::pose::Pose &pose, std::set< int > &pSer_positions)
void convertPSERtoGLU (core::pose::Pose &pose, std::set< int > &pSer_positions)
void restorePSER (core::pose::Pose &pose, std::set< int > const &pSer_positions)

Private Attributes

FlexPepDockingFlags flags_
core::scoring::ScoreFunctionOP scorefxn_
core::kinematics::MoveMapOP movemap_
core::Size rb_jump_
 the jump number across which to do rigid_body transformations More...
moves::MonteCarloOP mc_
 whether or not to initialize the viewer (for opengl) More...
protocols::minimization_packing::MinMoverOP minimizer_
protocols::relax::loop::LoopRelaxMoverOP loop_relax_mover_
core::fragment::ConstantLengthFragSetOP fragset3mer_
core::fragment::ConstantLengthFragSetOP fragset9mer_
core::fragment::ConstantLengthFragSetOP fragset5mer_

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...

Constructor & Destructor Documentation

◆ FlexPepDockingAbInitio()

FlexPepDockingAbInitio::FlexPepDockingAbInitio ( FlexPepDockingFlags const &  flags_in,
core::scoring::ScoreFunctionOP  scorefxn_in,
core::kinematics::MoveMapOP  movemap_in,
core::Size const  rb_jump_in = 1 

constructor for low resolution flexpible peptide docking

References fragset3mer_, fragset5mer_, fragset9mer_, loop_relax_mover_, protocols::loops::read_loop_fragments(), and scorefxn_.

◆ ~FlexPepDockingAbInitio()

FlexPepDockingAbInitio::~FlexPepDockingAbInitio ( )

Member Function Documentation

◆ apply()

void FlexPepDockingAbInitio::apply ( core::pose::Pose )

◆ convertPSERtoASP()

void FlexPepDockingAbInitio::convertPSERtoASP ( core::pose::Pose pose,
std::set< int > &  pSer_positions 

◆ convertPSERtoGLU()

void FlexPepDockingAbInitio::convertPSERtoGLU ( core::pose::Pose pose,
std::set< int > &  pSer_positions 

◆ get_name()

std::string FlexPepDockingAbInitio::get_name ( ) const

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

Implements protocols::moves::Mover.

◆ loopclosure_monte_carlo()

void FlexPepDockingAbInitio::loopclosure_monte_carlo ( core::pose::Pose pose)

◆ restorePSER()

void FlexPepDockingAbInitio::restorePSER ( core::pose::Pose pose,
std::set< int > const &  pSer_positions 

◆ rigidbody_monte_carlo()

void FlexPepDockingAbInitio::rigidbody_monte_carlo ( core::pose::Pose pose,
const int  cycles,
const float  trans_magnitude,
const float  rot_magnitude,
core::Real acceptance_rate 

References protocols::moves::accept_reject, mc_, and rb_jump_.

Referenced by apply().

◆ setup_for_apply()

void FlexPepDockingAbInitio::setup_for_apply ( core::pose::Pose pose)

initial setup for apply

References mc_, minimizer_, movemap_, and scorefxn_.

Referenced by apply().

◆ to_allatom()

void FlexPepDockingAbInitio::to_allatom ( core::pose::Pose pose,
core::pose::Pose referencePose 
) const

◆ to_centroid()

void FlexPepDockingAbInitio::to_centroid ( core::pose::Pose pose) const

◆ torsions_monte_carlo()

void FlexPepDockingAbInitio::torsions_monte_carlo ( core::pose::Pose pose,
const int  cycles,
core::Real acceptance_rate 

Member Data Documentation

◆ flags_

FlexPepDockingFlags protocols::flexpep_docking::FlexPepDockingAbInitio::flags_

◆ fragset3mer_

core::fragment::ConstantLengthFragSetOP protocols::flexpep_docking::FlexPepDockingAbInitio::fragset3mer_

◆ fragset5mer_

core::fragment::ConstantLengthFragSetOP protocols::flexpep_docking::FlexPepDockingAbInitio::fragset5mer_

◆ fragset9mer_

core::fragment::ConstantLengthFragSetOP protocols::flexpep_docking::FlexPepDockingAbInitio::fragset9mer_

◆ loop_relax_mover_

protocols::relax::loop::LoopRelaxMoverOP protocols::flexpep_docking::FlexPepDockingAbInitio::loop_relax_mover_

◆ mc_

moves::MonteCarloOP protocols::flexpep_docking::FlexPepDockingAbInitio::mc_

whether or not to initialize the viewer (for opengl)

Referenced by apply(), rigidbody_monte_carlo(), setup_for_apply(), and torsions_monte_carlo().

◆ minimizer_

protocols::minimization_packing::MinMoverOP protocols::flexpep_docking::FlexPepDockingAbInitio::minimizer_

Referenced by apply(), and setup_for_apply().

◆ movemap_

core::kinematics::MoveMapOP protocols::flexpep_docking::FlexPepDockingAbInitio::movemap_

◆ rb_jump_

core::Size protocols::flexpep_docking::FlexPepDockingAbInitio::rb_jump_

the jump number across which to do rigid_body transformations

Referenced by rigidbody_monte_carlo().

◆ scorefxn_

core::scoring::ScoreFunctionOP protocols::flexpep_docking::FlexPepDockingAbInitio::scorefxn_

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