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protocols::docking::DockMCMCycle Class Reference

#include <DockMCMCycle.hh>

Inheritance diagram for protocols::docking::DockMCMCycle:
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Collaboration diagram for protocols::docking::DockMCMCycle:
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Public Member Functions

 DockMCMCycle ()
 Default constructor. More...
 
 DockMCMCycle (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn)
 Constructor with two arguments: The first argument is the jump number to dock over. The second is a scorefunction that will be used for docking and packing. More...
 
 DockMCMCycle (core::Size const rb_jump, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
 Constructor with arguments: The first argument is the jump number to dock over. The second is a scorefunction that will be used for docking, the third is a scorefunction that will be used for packing. More...
 
 DockMCMCycle (DockJumps const movable_jumps, core::scoring::ScoreFunctionOP scorefxn, core::scoring::ScoreFunctionOP scorefxn_pack)
 Constructor with arguments: The first argument is a DockJumps vector. The second is a scorefunction that will be used for docking, the third is a scorefunction that will be used for packing. More...
 
 ~DockMCMCycle ()
 
protocols::moves::MoverOP clone () const
 clone has to be overridden only if clone invocation is expected. More...
 
void set_default ()
 Sets the default values for all members. More...
 
void set_move_map (core::kinematics::MoveMapOP movemap)
 
void set_min_type (std::string min_type)
 
void set_task_factory (core::pack::task::TaskFactoryCOP tf)
 
moves::MonteCarloOP get_mc ()
 
virtual void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
void show (std::ostream &out=std::cout) const
 
void reset_cycle_index ()
 
void init_mc (core::pose::Pose &pose)
 
void set_scmin (bool setting)
 
void set_rtmin (bool setting)
 
void set_rot_magnitude (core::Real value)
 
DockJumps const & movable_jumps () const
 
- 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
 
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)
 
virtual void parse_my_tag (TagPtr const tag, DataMap &data, Filters_map const &filters, Movers_map const &movers, Pose const &pose)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
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
 this function informs 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
 this function informs 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
 this is like clone(), except it generates a new mover object freshly created with the default ctor. This function should be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage). More...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 

Private Types

typedef core::Real Real
 

Private Member Functions

void setup_protocol (core::pose::Pose &pose)
 main entrance to do monte carlo minimization More...
 

Private Attributes

core::scoring::ScoreFunctionOP scorefxn_
 
core::scoring::ScoreFunctionOP scorefxn_pack_
 
core::kinematics::MoveMapOP movemap_
 
moves::CycleMoverOP dock_mcm_cycle_
 
moves::MonteCarloOP mc_
 
DockJumps movable_jumps_
 
core::Real trans_magnitude_
 
core::Real rot_magnitude_
 
bool rtmin_
 
bool scmin_
 
core::pack::task::TaskFactoryOP tf_
 tf_ will be used internally by dockinghires. It will be initialized through the init_task_factory_ below More...
 
core::Size repack_period_
 task_factory_ is used by outside movers to set the internal taskfactory. Does not actually override internal TF! init_task_factory_ instead acts as a starting point and the docking mover masks over init_task_factory More...
 
bool norepack1_
 
bool norepack2_
 
core::Real min_tolerance_
 
bool nb_list_
 
std::string min_type_
 

Friends

std::ostream & operator<< (std::ostream &out, const DockMCMCycle &dp)
 

Additional Inherited Members

- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagPtr TagPtr
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
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. these options will end up in -help of your application if users of this mover call register_options. do this recursively! if you use movers within your mover, call their register_options in your register_options() method. 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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::docking::DockMCMCycle::DockMCMCycle ( )

Default constructor.

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

Referenced by clone().

protocols::docking::DockMCMCycle::DockMCMCycle ( core::Size const  rb_jump,
core::scoring::ScoreFunctionOP  scorefxn 
)

Constructor with two arguments: The first argument is the jump number to dock over. The second is a scorefunction that will be used for docking and packing.

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

protocols::docking::DockMCMCycle::DockMCMCycle ( core::Size const  rb_jump,
core::scoring::ScoreFunctionOP  scorefxn,
core::scoring::ScoreFunctionOP  scorefxn_pack 
)

Constructor with arguments: The first argument is the jump number to dock over. The second is a scorefunction that will be used for docking, the third is a scorefunction that will be used for packing.

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

protocols::docking::DockMCMCycle::DockMCMCycle ( DockJumps const  movable_jumps,
core::scoring::ScoreFunctionOP  scorefxn,
core::scoring::ScoreFunctionOP  scorefxn_pack 
)

Constructor with arguments: The first argument is a DockJumps vector. The second is a scorefunction that will be used for docking, the third is a scorefunction that will be used for packing.

References movable_jumps(), movable_jumps_, set_default(), and protocols::moves::Mover::type().

protocols::docking::DockMCMCycle::~DockMCMCycle ( )

Member Function Documentation

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

docking high resolution apply function

Detailed:
decides what to call according to options

Implements protocols::moves::Mover.

References dock_mcm_cycle_, init_mc(), and protocols::TR().

protocols::moves::MoverOP protocols::docking::DockMCMCycle::clone ( ) const
virtual

clone has to be overridden only if clone invocation is expected.

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 DockMCMCycle().

moves::MonteCarloOP protocols::docking::DockMCMCycle::get_mc ( )
inline

References mc_.

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

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

Implements protocols::moves::Mover.

void protocols::docking::DockMCMCycle::init_mc ( core::pose::Pose pose)

References mc_, setup_protocol(), show(), and protocols::TR().

Referenced by apply().

DockJumps const & protocols::docking::DockMCMCycle::movable_jumps ( ) const

References movable_jumps_.

Referenced by DockMCMCycle().

void protocols::docking::DockMCMCycle::reset_cycle_index ( )

References dock_mcm_cycle_.

void protocols::docking::DockMCMCycle::set_default ( )
void protocols::docking::DockMCMCycle::set_min_type ( std::string  min_type)
inline

References min_type_.

void protocols::docking::DockMCMCycle::set_move_map ( core::kinematics::MoveMapOP  movemap)

References movemap_.

void protocols::docking::DockMCMCycle::set_rot_magnitude ( core::Real  value)
inline

References rot_magnitude_.

void protocols::docking::DockMCMCycle::set_rtmin ( bool  setting)
inline

References rtmin_.

void protocols::docking::DockMCMCycle::set_scmin ( bool  setting)
inline

References scmin_.

void protocols::docking::DockMCMCycle::set_task_factory ( core::pack::task::TaskFactoryCOP  tf)

References tf_.

void protocols::docking::DockMCMCycle::setup_protocol ( core::pose::Pose pose)
private

main entrance to do monte carlo minimization

dock_mcm_protocol

Detailed:
single cycle of mcm minimization. Then it is rigid-body minimized to a stringent tolerance.
Remarks
References: docking_mcm_protocol from docking_minimize.cc
pose_docking_monte_carlo_minimize from pose_docking.cc
Authors
Monica Berrondo
Last Modified: August 19 2010

References protocols::moves::MoverContainer::add_mover(), dock_mcm_cycle_, mc_, min_tolerance_, min_type_, movemap_, nb_list_, core::pack::pack_rotamers(), protocols::rigid::partner_downstream, repack_period_, rot_magnitude_, rtmin_, scmin_, scorefxn_, scorefxn_pack_, tf_, and trans_magnitude_.

Referenced by init_mc().

void protocols::docking::DockMCMCycle::show ( std::ostream &  out = std::cout) const

Show the complete setup of the docking protocol

Referenced by init_mc().

Friends And Related Function Documentation

std::ostream& operator<< ( std::ostream &  out,
const DockMCMCycle dp 
)
friend

Member Data Documentation

moves::CycleMoverOP protocols::docking::DockMCMCycle::dock_mcm_cycle_
private
moves::MonteCarloOP protocols::docking::DockMCMCycle::mc_
private
core::Real protocols::docking::DockMCMCycle::min_tolerance_
private

Referenced by set_default(), and setup_protocol().

std::string protocols::docking::DockMCMCycle::min_type_
private
DockJumps protocols::docking::DockMCMCycle::movable_jumps_
private
core::kinematics::MoveMapOP protocols::docking::DockMCMCycle::movemap_
private
bool protocols::docking::DockMCMCycle::nb_list_
private

Referenced by set_default(), and setup_protocol().

bool protocols::docking::DockMCMCycle::norepack1_
private
bool protocols::docking::DockMCMCycle::norepack2_
private
core::Size protocols::docking::DockMCMCycle::repack_period_
private

task_factory_ is used by outside movers to set the internal taskfactory. Does not actually override internal TF! init_task_factory_ instead acts as a starting point and the docking mover masks over init_task_factory

Referenced by set_default(), and setup_protocol().

core::Real protocols::docking::DockMCMCycle::rot_magnitude_
private
bool protocols::docking::DockMCMCycle::rtmin_
private
bool protocols::docking::DockMCMCycle::scmin_
private
core::scoring::ScoreFunctionOP protocols::docking::DockMCMCycle::scorefxn_
private
core::scoring::ScoreFunctionOP protocols::docking::DockMCMCycle::scorefxn_pack_
private
core::pack::task::TaskFactoryOP protocols::docking::DockMCMCycle::tf_
private

tf_ will be used internally by dockinghires. It will be initialized through the init_task_factory_ below

Referenced by set_default(), set_task_factory(), and setup_protocol().

core::Real protocols::docking::DockMCMCycle::trans_magnitude_
private

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