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protocols::md::CartesianMD Class Reference

#include <CartesianMD.hh>

Inheritance diagram for protocols::md::CartesianMD:
Inheritance graph
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Public Member Functions

 CartesianMD ()
 
 CartesianMD (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP sfxn, core::kinematics::MoveMapCOP movemap=nullptr)
 
 CartesianMD (core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn)
 
 CartesianMD (core::pose::Pose const &pose, core::scoring::ScoreFunction const &sfxn, core::kinematics::MoveMap const &movemap)
 
 ~CartesianMD () override
 
protocols::moves::MoverOP fresh_instance () const override
 Generates a new Mover object freshly created with the default ctor. More...
 
protocols::moves::MoverOP clone () const override
 Return a clone of the Mover object. More...
 
void apply (core::pose::Pose &pose) override
 Main Method. More...
 
void use_rattle (bool const value)
 
core::optimization::Multivec get_current_eqxyz () const
 
void update_restraint (core::pose::Pose &pose, core::optimization::CartesianMinimizerMap const &min_map)
 
void cst_on_pose_simple (core::pose::Pose &pose) const
 
void cst_on_pose_dynamic (core::pose::Pose &pose, core::optimization::Multivec const &ref_xyz, core::optimization::Multivec const &curr_eqxyz, core::optimization::Multivec &prv_eqxyz, core::optimization::CartesianMinimizerMap const &min_map) const
 
void parse_my_tag (TagCOP, basic::datacache::DataMap &) override
 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)
 
void parse_movemap (TagCOP tag, basic::datacache::DataMap &data)
 
std::string get_name () const override
 Each derived class must specify its name. The class name. More...
 
utility::vector1
< core::pose::Pose
dump_poses (core::pose::Pose const &pose_ref) const
 
- Public Member Functions inherited from protocols::md::MDBase
 MDBase ()
 
 ~MDBase () override
 
void set_defaults ()
 
virtual void set_movemap (core::pose::Pose const &pose, core::kinematics::MoveMapCOP movemap)
 
core::Real dt () const
 
core::Size n_dof () const
 
core::Size n_dof_temp () const
 
core::optimization::Multivec mass () const
 
core::Real mass (core::Size iatm) const
 
core::Real cummulative_time () const
 
core::Size nstep () const
 
core::Real temp0 () const
 
core::kinematics::MoveMapOP movemap () const
 
core::scoring::ScoreFunctionOP scorefxn () const
 
core::scoring::ScoreFunctionOP scorefxn_obj () const
 
std::string selectmode () const
 
core::pose::Pose pose_minobj () const
 
core::Real Emin_obj () const
 
core::Real time_minobj () const
 
core::Size md_report_stepsize () const
 
core::Size md_energy_report_stepsize () const
 
core::Size md_rsr_update_stepsize () const
 
core::pose::Pose pose0 () const
 
core::Size context_update_step () const
 
core::Size ncyc_premin () const
 
core::Size ncyc_postmin () const
 
bool scheduled () const
 
utility::vector1< MDscheduleDatamdsch () const
 
MDscheduleData mdsch (core::Size istep) const
 
bool uniform_coord_constrained () const
 
core::Real cst_sdev () const
 
core::Real temperature () const
 
core::Real kinetic_energy () const
 
core::Real potential_energy () const
 
core::optimization::Multivec xyz () const
 
core::optimization::Multivec vel () const
 
core::optimization::Multivec acc () const
 
core::Realxyz (core::Size idof)
 
core::Realvel (core::Size idof)
 
core::Realacc (core::Size idof)
 
core::optimization::Multivec
const & 
ref_xyz () const
 
core::optimization::Multivec
const & 
prv_eqxyz () const
 
core::Real Kappa () const
 
core::Real Gamma () const
 
bool report_scorecomp () const
 
bool report_as_silent () const
 
bool trj_score_only () const
 
std::string silentname () const
 
bool store_trj () const
 
utility::vector1
< core::optimization::Multivec
trj () const
 
core::optimization::Multivec trj (core::Size itrj) const
 
utility::vector1
< core::optimization::Multivec
trj_scratch () const
 
bool write_dynamic_rsr () const
 
std::string rsrfilename () const
 
void set_dt (core::Real setting)
 
void set_n_dof (core::Size setting)
 
void set_n_dof_temp (core::Size setting)
 
void set_mass (core::Size iatm, core::Real setting)
 
void set_cummulative_time (core::Real setting)
 
void set_temp0 (core::Real setting)
 
void set_nstep (core::Size setting)
 
void set_scorefxn (core::scoring::ScoreFunctionCOP setting)
 
void set_scorefxn_obj (core::scoring::ScoreFunctionCOP setting)
 
void set_scorefxn (core::scoring::ScoreFunction const &setting)
 
void set_scorefxn_obj (core::scoring::ScoreFunction const &setting)
 
void set_selectmode (std::string setting)
 
void set_pose_minobj (core::pose::Pose setting)
 
void set_Emin_obj (core::Real setting)
 
void set_time_minobj (core::Real setting)
 
void set_md_report_stepsize (core::Size setting)
 
void set_md_energy_report_stepsize (core::Size setting)
 
void set_md_rsr_update_stepsize (core::Size setting)
 
void set_pose0 (core::pose::Pose setting)
 
void set_context_update_step (core::Size setting)
 
void set_ncyc_premin (core::Size setting)
 
void set_ncyc_postmin (core::Size setting)
 
void set_scheduled (bool setting)
 
void set_mdsch (utility::vector1< MDscheduleData > setting)
 
void set_uniform_coord_constrained (bool setting)
 
void set_cst_sdev (core::Real setting)
 
void set_temperature (core::Real setting)
 
void set_kinetic_energy (core::Real setting)
 
void set_potential_energy (core::Real setting)
 
void set_xyz (core::optimization::Multivec setting)
 
void set_vel (core::optimization::Multivec setting)
 
void set_acc (core::optimization::Multivec setting)
 
void set_ref_xyz (core::optimization::Multivec setting)
 
void set_prv_eqxyz (core::optimization::Multivec setting)
 
void set_Kappa (core::Real setting)
 
void set_Gamma (core::Real setting)
 
void set_report_scorecomp (bool setting)
 
void set_report_as_silent (bool setting)
 
void set_trj_score_only (bool setting)
 
void set_silentname (std::string setting)
 
void set_store_trj (bool setting)
 
void set_trj (utility::vector1< core::optimization::Multivec > setting)
 
void set_trj_scratch (utility::vector1< core::optimization::Multivec > setting)
 
void set_write_dynamic_rsr (bool setting)
 
void set_rsrfilename (std::string setting)
 
void init ()
 
void set_constraint (core::Real const sdev)
 
void add_trj (core::optimization::Multivec xyz)
 
void add_trj_scratch (core::optimization::Multivec xyz)
 
void renew_trj_scratch ()
 
void resize_natm_variables ()
 
void parse_schfile (std::string const schfile)
 
void report_silent (core::pose::Pose &pose, core::Real rmsd=-1.0, core::Real gdttm=-1.0, core::Real gdtha=-1.0)
 
void set_write_dynamic_rsr (std::string const filename)
 
- 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 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...
 
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
 
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 bool mover_provides_citation_info () const
 Does this mover provide information about how to cite it? More...
 
virtual utility::vector1
< basic::citation_manager::CitationCollectionCOP > 
provide_citation_info () const
 Provide the citation. More...
 
virtual bool mover_is_unpublished () const
 Does this mover indicate that it is unpublished (and, by extension, that the author should be included in publications resulting from it)? More...
 
virtual utility::vector1
< basic::citation_manager::UnpublishedModuleInfoCOP > 
provide_authorship_info_for_unpublished () const
 Provide a list of authors and their e-mail addresses, as strings. More...
 

Static Public Member Functions

static std::string mover_name ()
 
static void provide_xml_schema (utility::tag::XMLSchemaDefinition &xsd)
 
- 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...
 

Private Member Functions

void get_native_info (core::pose::Pose const &pose)
 
void do_initialize (core::pose::Pose &pose)
 
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, bool const update_score=false)
 
void do_minimize (core::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, core::optimization::CartesianMinimizerMap const &min_map, bool const report_trj)
 

Private Attributes

core::select::movemap::MoveMapFactoryCOP movemap_factory_
 MoveMapFactory, for XML-based parsing Will override any manually set MoveMaps. More...
 
core::optimization::CartesianMinimizerMap min_map_
 
timeval inittime_
 
bool use_rattle_ = true
 
core::pose::Pose native_
 
bool native_given_ = false
 
std::map< core::Size, core::Sizenative_resmap_
 

Additional Inherited Members

- Public Types inherited from protocols::md::MDBase
typedef protocols::moves::Mover parent
 
- 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
 
- 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

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

References core::init::init().

protocols::md::CartesianMD::CartesianMD ( core::pose::Pose const &  pose,
core::scoring::ScoreFunctionCOP  sfxn,
core::kinematics::MoveMapCOP  movemap = nullptr 
)
protocols::md::CartesianMD::CartesianMD ( core::pose::Pose const &  pose,
core::scoring::ScoreFunction const &  sfxn 
)
protocols::md::CartesianMD::CartesianMD ( core::pose::Pose const &  pose,
core::scoring::ScoreFunction const &  sfxn,
core::kinematics::MoveMap const &  movemap 
)
protocols::md::CartesianMD::~CartesianMD ( )
overridedefault

Member Function Documentation

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

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::cst_on_pose_dynamic ( core::pose::Pose pose,
core::optimization::Multivec const &  ref_xyz,
core::optimization::Multivec const &  curr_eqxyz,
core::optimization::Multivec prv_eqxyz,
core::optimization::CartesianMinimizerMap const &  min_map 
) const
void protocols::md::CartesianMD::cst_on_pose_simple ( core::pose::Pose pose) const
void protocols::md::CartesianMD::do_initialize ( core::pose::Pose pose)
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 ( core::pose::Pose pose,
core::optimization::MinimizerOptions const &  options,
bool const &  show_energy 
)
private
utility::vector1< pose::Pose > protocols::md::CartesianMD::dump_poses ( core::pose::Pose const &  pose_ref) const
protocols::moves::MoverOP protocols::md::CartesianMD::fresh_instance ( ) const
inlineoverridevirtual

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.

Multivec protocols::md::CartesianMD::get_current_eqxyz ( ) const
std::string protocols::md::CartesianMD::get_name ( ) const
overridevirtual

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

Implements protocols::md::MDBase.

void protocols::md::CartesianMD::get_native_info ( core::pose::Pose const &  pose)
private
void protocols::md::CartesianMD::initialize_velocity ( core::Real const &  temperature)
private
std::string protocols::md::CartesianMD::mover_name ( )
static
void protocols::md::CartesianMD::parse_movemap ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
void protocols::md::CartesianMD::parse_my_tag ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
overridevirtual

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 force people to reimplement this method. However, we should be chatty about the fact that someone is using a RosettaScripts interface to a mover which didn't define parse_my_tag()

Reimplemented from protocols::moves::Mover.

void protocols::md::CartesianMD::parse_opts ( TagCOP  tag,
basic::datacache::DataMap &  data 
)
void protocols::md::CartesianMD::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd)
static
void protocols::md::CartesianMD::report_MD ( core::pose::Pose pose,
core::optimization::CartesianMinimizerMap const &  min_map,
bool const  report_trj 
)
private
void protocols::md::CartesianMD::update_restraint ( core::pose::Pose pose,
core::optimization::CartesianMinimizerMap const &  min_map 
)
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,
bool const  update_score = false 
)
private

Member Data Documentation

timeval protocols::md::CartesianMD::inittime_
private
core::optimization::CartesianMinimizerMap protocols::md::CartesianMD::min_map_
private
core::select::movemap::MoveMapFactoryCOP protocols::md::CartesianMD::movemap_factory_
private

MoveMapFactory, for XML-based parsing Will override any manually set MoveMaps.

core::pose::Pose protocols::md::CartesianMD::native_
private
bool protocols::md::CartesianMD::native_given_ = false
private
std::map< core::Size, core::Size > protocols::md::CartesianMD::native_resmap_
private
bool protocols::md::CartesianMD::use_rattle_ = true
private

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