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 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 ( )

Member Function Documentation

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

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 
void protocols::md::CartesianMD::do_MD ( core::pose::Pose pose,
core::Size const &  nstep,
core::Real const &  temp0 = 300,
bool const &  initialize = false 
void protocols::md::CartesianMD::do_minimize ( pose::Pose pose,
core::optimization::MinimizerOptions const &  options,
bool const &  show_energy 
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

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

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)
void protocols::md::CartesianMD::init ( void  )

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

void protocols::md::CartesianMD::initialize_velocity ( core::Real const &  temperature)
virtual core::kinematics::MoveMapOP protocols::md::CartesianMD::movemap ( ) const
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 

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)
void protocols::md::CartesianMD::set_movemap ( core::pose::Pose const &  ,
core::kinematics::MoveMapCOP  movemap 

Implements protocols::md::MDBase.

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

Member Data Documentation

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

Referenced by use_rattle().

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