Rosetta Protocols  2014.35
Public Types | Public Member Functions | Protected Attributes | List of all members
protocols::md::MDBase Class Referenceabstract

#include <MDBase.hh>

Public Types

typedef protocols::moves::Mover parent
 
typedef utility::vector1< RealMultivec
 
- Public Types inherited from protocols::moves::Mover
typedef utility::tag::TagCOP TagCOP
 
typedef core::pose::Pose Pose
 
typedef core::pose::PoseCOP PoseCOP
 
typedef
protocols::filters::Filters_map 
Filters_map
 
typedef std::list< std::stringStrings
 

Public Member Functions

 MDBase ()
 
 ~MDBase ()
 
virtual void apply (core::pose::Pose &pose)=0
 
virtual std::string get_name () const =0
 Each derived class must specify its name. The class name. More...
 
void set_defaults ()
 
core::scoring::ScoreFunctionOP scorefxn ()
 
core::scoring::ScoreFunctionCOP scorefxn () const
 
virtual void set_movemap (core::pose::Pose const &pose, core::kinematics::MoveMapCOP movemap)=0
 
virtual core::kinematics::MoveMapOP movemap () const =0
 
Real dt ()
 
Size n_dof ()
 
Real cummulative_time ()
 
void set_nstep (core::Size const nstep)
 
void set_temperature (core::Real const temp0)
 
void set_reportstep (core::Size const nstep)
 
void set_scorefxn_obj (core::scoring::ScoreFunctionCOP sfxn)
 
void set_selectmode (std::string const selectmode_in)
 
void set_context_update_step (Size const value)
 
void set_premin (Size const value)
 
void set_report_scorecomp (bool const value)
 
void parse_schfile (std::string const schfile)
 
core::Size nstep ()
 
core::Real temp0 ()
 
void set_constraint (Real const sdev)
 
void cst_on_pose (pose::Pose &pose)
 
void set_store_trj (bool const value)
 
bool store_trj () 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
 
void set_type (std::string const &setting)
 
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 MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual void parse_my_tag (TagCOP tag, basic::datacache::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
 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...
 
void set_current_job (protocols::jobdist::BasicJobCOP job)
 
jobdist::BasicJobCOP get_current_job () const
 
virtual void show (std::ostream &output=std::cout) const
 Outputs details about the Mover, including current settings. More...
 

Protected Attributes

core::kinematics::MoveMapOP movemap_
 
core::scoring::ScoreFunctionOP scorefxn_
 
std::string selectmode_
 
core::scoring::ScoreFunctionOP scorefxn_obj_
 
core::pose::Pose pose_minobj_
 
Real Emin_obj_
 
Real time_minobj_
 
Size n_dof_
 
Size n_dof_temp_
 
Real dt_
 
Multivec mass_
 
Real cummulative_time_
 
Size md_report_stepsize_
 
core::pose::Pose pose0_
 
bool report_scorecomp_
 
core::Size context_update_step_
 
Size ncyc_premin_
 
Size ncyc_postmin_
 
bool scheduled_
 
utility::vector1< MDscheduleDatamdsch_
 
bool constrained_
 
Real cst_sdev_
 
Real temp0_
 
Size nstep_
 
Real temperature_
 
Real kinetic_energy_
 
Real potential_energy_
 
Multivec xyz_
 
Multivec vel_
 
Multivec acc_
 
bool store_trj_
 
utility::vector1< Multivectrj_
 

Additional Inherited Members

- 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...
 

Member Typedef Documentation

Constructor & Destructor Documentation

protocols::md::MDBase::MDBase ( )
inline
protocols::md::MDBase::~MDBase ( )
inline

Member Function Documentation

virtual void protocols::md::MDBase::apply ( core::pose::Pose pose)
pure virtual
void protocols::md::MDBase::cst_on_pose ( pose::Pose pose)
Real protocols::md::MDBase::cummulative_time ( )
inline
Real protocols::md::MDBase::dt ( )
inline
virtual std::string protocols::md::MDBase::get_name ( ) const
pure virtual

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

Implements protocols::moves::Mover.

Implemented in protocols::md::CartesianMD.

virtual core::kinematics::MoveMapOP protocols::md::MDBase::movemap ( ) const
pure virtual

Implemented in protocols::md::CartesianMD.

Size protocols::md::MDBase::n_dof ( )
inline
core::Size protocols::md::MDBase::nstep ( )
inline
void protocols::md::MDBase::parse_schfile ( std::string const  schfile)
core::scoring::ScoreFunctionOP protocols::md::MDBase::scorefxn ( )
inline
core::scoring::ScoreFunctionCOP protocols::md::MDBase::scorefxn ( ) const
inline
void protocols::md::MDBase::set_constraint ( Real const  sdev)
void protocols::md::MDBase::set_context_update_step ( Size const  value)
inline
void protocols::md::MDBase::set_defaults ( )
inline
virtual void protocols::md::MDBase::set_movemap ( core::pose::Pose const &  pose,
core::kinematics::MoveMapCOP  movemap 
)
pure virtual

Implemented in protocols::md::CartesianMD.

void protocols::md::MDBase::set_nstep ( core::Size const  nstep)
inline
void protocols::md::MDBase::set_premin ( Size const  value)
inline
void protocols::md::MDBase::set_report_scorecomp ( bool const  value)
inline
void protocols::md::MDBase::set_reportstep ( core::Size const  nstep)
inline
void protocols::md::MDBase::set_scorefxn_obj ( core::scoring::ScoreFunctionCOP  sfxn)
inline
void protocols::md::MDBase::set_selectmode ( std::string const  selectmode_in)
inline
void protocols::md::MDBase::set_store_trj ( bool const  value)
inline
void protocols::md::MDBase::set_temperature ( core::Real const  temp0)
inline
bool protocols::md::MDBase::store_trj ( ) const
inline
core::Real protocols::md::MDBase::temp0 ( )
inline

Member Data Documentation

Multivec protocols::md::MDBase::acc_
protected
bool protocols::md::MDBase::constrained_
protected

Referenced by cst_on_pose(), and set_constraint().

core::Size protocols::md::MDBase::context_update_step_
protected
Real protocols::md::MDBase::cst_sdev_
protected

Referenced by cst_on_pose(), and set_constraint().

Real protocols::md::MDBase::cummulative_time_
protected
Real protocols::md::MDBase::dt_
protected
Real protocols::md::MDBase::Emin_obj_
protected
Real protocols::md::MDBase::kinetic_energy_
protected
Multivec protocols::md::MDBase::mass_
protected
Size protocols::md::MDBase::md_report_stepsize_
protected
utility::vector1< MDscheduleData > protocols::md::MDBase::mdsch_
protected

Referenced by parse_schfile().

core::kinematics::MoveMapOP protocols::md::MDBase::movemap_
protected
Size protocols::md::MDBase::n_dof_
protected
Size protocols::md::MDBase::n_dof_temp_
protected
Size protocols::md::MDBase::ncyc_postmin_
protected
Size protocols::md::MDBase::ncyc_premin_
protected
Size protocols::md::MDBase::nstep_
protected
core::pose::Pose protocols::md::MDBase::pose0_
protected
core::pose::Pose protocols::md::MDBase::pose_minobj_
protected
Real protocols::md::MDBase::potential_energy_
protected
bool protocols::md::MDBase::report_scorecomp_
protected
bool protocols::md::MDBase::scheduled_
protected
core::scoring::ScoreFunctionOP protocols::md::MDBase::scorefxn_
protected

Referenced by set_constraint().

core::scoring::ScoreFunctionOP protocols::md::MDBase::scorefxn_obj_
protected
std::string protocols::md::MDBase::selectmode_
protected
bool protocols::md::MDBase::store_trj_
protected
Real protocols::md::MDBase::temp0_
protected
Real protocols::md::MDBase::temperature_
protected
Real protocols::md::MDBase::time_minobj_
protected
utility::vector1< Multivec > protocols::md::MDBase::trj_
protected
Multivec protocols::md::MDBase::vel_
protected
Multivec protocols::md::MDBase::xyz_
protected

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