Rosetta Protocols  2014.35
Public Member Functions | Private Member Functions | Private Attributes | List of all members
protocols::md::CartesianMD Class Reference

#include <CartesianMD.hh>

Public Member Functions

 CartesianMD ()
 
 CartesianMD (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP sfxn, core::kinematics::MoveMapCOP movemap)
 
void init ()
 
virtual ~CartesianMD ()
 
virtual protocols::moves::MoverOP fresh_instance () const
 Generates a new Mover object freshly created with the default ctor. More...
 
virtual protocols::moves::MoverOP clone () const
 Return a clone of the Mover object. More...
 
virtual void apply (core::pose::Pose &pose)
 
virtual std::string get_name () const
 Each derived class must specify its name. The class name. More...
 
virtual void set_movemap (core::pose::Pose const &, core::kinematics::MoveMapCOP movemap)
 
virtual core::kinematics::MoveMapOP movemap () const
 
void use_rattle (bool const value)
 
virtual void parse_my_tag (TagCOP, basic::datacache::DataMap &, Filters_map const &, protocols::moves::Movers_map const &, Pose const &)
 Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
 
void parse_opts (TagCOP tag, basic::datacache::DataMap &data, Pose const &pose)
 
void parse_movemap (TagCOP tag, basic::datacache::DataMap &data, Pose const &pose)
 
utility::vector1< pose::Posedump_poses (pose::Pose const &pose_ref) const
 
- Public Member Functions inherited from protocols::md::MDBase
 MDBase ()
 
 ~MDBase ()
 
void set_defaults ()
 
core::scoring::ScoreFunctionOP scorefxn ()
 
core::scoring::ScoreFunctionCOP scorefxn () const
 
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)
 
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...
 
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...
 

Private Member Functions

void get_native_info (pose::Pose const &pose)
 
void do_initialize (core::pose::Pose &pose, core::Real const &temp0)
 
void Berendsen_Integrator (core::pose::Pose &pose, core::optimization::CartesianMinimizerMap &min_map)
 
void VelocityVerlet_Integrator (core::pose::Pose &pose, core::optimization::CartesianMinimizerMap &min_map, md::Rattle &rattle)
 
void do_minimize (pose::Pose &pose, core::optimization::MinimizerOptions const &options, bool const &show_energy)
 
void do_MD (core::pose::Pose &pose, core::Size const &nstep, core::Real const &temp0=300, bool const &initialize=false)
 
void initialize_velocity (core::Real const &temperature)
 
void report_MD (core::pose::Pose &pose)
 

Private Attributes

core::optimization::CartesianMinimizerMap min_map_
 
timeval inittime_
 
bool use_rattle_
 
core::pose::Pose native_
 
bool native_given_
 
std::map< Size, Sizenative_resmap_
 

Additional Inherited Members

- Public Types inherited from protocols::md::MDBase
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
 
- 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...
 
- Protected Attributes inherited from protocols::md::MDBase
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_
 

Constructor & Destructor Documentation

protocols::md::CartesianMD::CartesianMD ( )

References protocols::init::init().

Referenced by fresh_instance().

protocols::md::CartesianMD::CartesianMD ( core::pose::Pose const &  pose,
core::scoring::ScoreFunctionCOP  sfxn,
core::kinematics::MoveMapCOP  movemap 
)
protocols::md::CartesianMD::~CartesianMD ( )
virtual

Member Function Documentation

void protocols::md::CartesianMD::apply ( core::pose::Pose pose)
virtual
void protocols::md::CartesianMD::Berendsen_Integrator ( core::pose::Pose pose,
core::optimization::CartesianMinimizerMap min_map 
)
private
protocols::moves::MoverOP protocols::md::CartesianMD::clone ( ) const
virtual

Return a clone of the Mover object.

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.

void protocols::md::CartesianMD::do_initialize ( core::pose::Pose pose,
core::Real const &  temp0 
)
private
void protocols::md::CartesianMD::do_MD ( core::pose::Pose pose,
core::Size const &  nstep,
core::Real const &  temp0 = 300,
bool const &  initialize = false 
)
private
void protocols::md::CartesianMD::do_minimize ( pose::Pose pose,
core::optimization::MinimizerOptions const &  options,
bool const &  show_energy 
)
private
utility::vector1< pose::Pose > protocols::md::CartesianMD::dump_poses ( pose::Pose const &  pose_ref) const
virtual protocols::moves::MoverOP protocols::md::CartesianMD::fresh_instance ( ) const
inlinevirtual

Generates a new Mover object freshly created with the default ctor.

fresh_instance is meant to return a new object of this class, created with the default constructor. 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. This is used by the August 08 job distributor.

Reimplemented from protocols::moves::Mover.

References CartesianMD().

std::string protocols::md::CartesianMD::get_name ( ) const
virtual

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

Implements protocols::md::MDBase.

void protocols::md::CartesianMD::get_native_info ( pose::Pose const &  pose)
private
void protocols::md::CartesianMD::init ( void  )

References in::file::md_schfile, option, and user.

void protocols::md::CartesianMD::initialize_velocity ( core::Real const &  temperature)
private
virtual core::kinematics::MoveMapOP protocols::md::CartesianMD::movemap ( ) const
inlinevirtual
void protocols::md::CartesianMD::parse_movemap ( TagCOP  tag,
basic::datacache::DataMap data,
Pose const &  pose 
)
void protocols::md::CartesianMD::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap data,
Filters_map const &  filters,
protocols::moves::Movers_map const &  movers,
Pose const &  pose 
)
virtual

Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.

Some movers need not be parsed, so we shouldn't stop executions. This, however, calls attention to the lack of this method, which could be due to something as silly as a wrong parameters definition.

Reimplemented from protocols::moves::Mover.

References protocols::rosetta_scripts::parse_movemap().

void protocols::md::CartesianMD::parse_opts ( TagCOP  tag,
basic::datacache::DataMap data,
Pose const &  pose 
)
void protocols::md::CartesianMD::report_MD ( core::pose::Pose pose)
private
void protocols::md::CartesianMD::set_movemap ( core::pose::Pose const &  ,
core::kinematics::MoveMapCOP  movemap 
)
virtual

Implements protocols::md::MDBase.

void protocols::md::CartesianMD::use_rattle ( bool const  value)
inline
void protocols::md::CartesianMD::VelocityVerlet_Integrator ( core::pose::Pose pose,
core::optimization::CartesianMinimizerMap min_map,
md::Rattle rattle 
)
private

Member Data Documentation

timeval protocols::md::CartesianMD::inittime_
private
core::optimization::CartesianMinimizerMap protocols::md::CartesianMD::min_map_
private
core::pose::Pose protocols::md::CartesianMD::native_
private
bool protocols::md::CartesianMD::native_given_
private
std::map< Size, Size > protocols::md::CartesianMD::native_resmap_
private
bool protocols::md::CartesianMD::use_rattle_
private

Referenced by use_rattle().


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