protocols::md::MDBase Class Reference

#include <MDBase.hh>

Inheritance diagram for protocols::md::MDBase:

Public Types
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

Public Member Functions
	MDBase ()
	~MDBase () override
void	apply (core::pose::Pose &pose) override=0
	Main Method. More...
std::string	get_name () const override=0
	Each derived class must specify its name. The class name. More...
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< MDscheduleData >	mdsch () 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::Real &	xyz (core::Size idof)
core::Real &	vel (core::Size idof)
core::Real &	acc (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 MoverOP	clone () const
	Return a clone of the Mover object. 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...
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
virtual void	parse_my_tag (TagCOP tag, basic::datacache::DataMap &data)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing. More...
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 Strings &	info ()
	non-const accessor More...
virtual Strings const &	info () const
	const accessor More...
virtual void	provide_citation_info (basic::citation_manager::CitationCollectionList &) const
	Provide citations to the passed CitationCollectionList Subclasses should add the info for themselves and any other classes they use. More...

Private Attributes
core::kinematics::MoveMapOP	movemap_
core::scoring::ScoreFunctionOP	scorefxn_
std::string	selectmode_
core::scoring::ScoreFunctionOP	scorefxn_obj_
core::pose::Pose	pose_minobj_
core::Real	Emin_obj_
core::Real	time_minobj_
core::Size	n_dof_
core::Size	n_dof_temp_
core::Real	dt_
core::optimization::Multivec	mass_
core::Real	cummulative_time_
core::Size	md_report_stepsize_
core::Size	md_energy_report_stepsize_
core::Size	md_rsr_update_stepsize_
core::pose::Pose	pose0_
bool	report_scorecomp_
core::Size	context_update_step_
core::Size	ncyc_premin_
core::Size	ncyc_postmin_
bool	scheduled_
utility::vector1< MDscheduleData >	mdsch_
bool	uniform_coord_constrained_
core::Real	cst_sdev_
core::Real	temp0_
core::Size	nstep_
core::Real	temperature_
core::Real	kinetic_energy_
core::Real	potential_energy_
core::optimization::Multivec	xyz_
core::optimization::Multivec	vel_
core::optimization::Multivec	acc_
bool	report_as_silent_
bool	trj_score_only_
std::string	silentname_
bool	store_trj_
utility::vector1 < core::optimization::Multivec >	trj_
utility::vector1 < core::optimization::Multivec >	trj_scratch_
core::optimization::Multivec	ref_xyz_
core::optimization::Multivec	prv_eqxyz_
core::Real	Kappa_
core::Real	Gamma_
bool	write_dynamic_rsr_
std::string	rsrfilename_

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

typedef protocols::moves::Mover protocols::md::MDBase::parent

Constructor & Destructor Documentation

protocols::md::MDBase::MDBase

(

)

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

overridedefault

Member Function Documentation

core::optimization::Multivec protocols::md::MDBase::acc ( ) const

inline

References acc_.

core::Real& protocols::md::MDBase::acc ( core::Size  idof )

inline

References acc_.

void protocols::md::MDBase::add_trj ( core::optimization::Multivec  xyz )

inline

References trj_.

void protocols::md::MDBase::add_trj_scratch ( core::optimization::Multivec  xyz )

inline

References trj_scratch_.

void protocols::md::MDBase::apply ( core::pose::Pose &  )

overridepure virtual

Main Method.

Implements protocols::moves::Mover.

Implemented in protocols::md::CartesianMD.

core::Size protocols::md::MDBase::context_update_step ( ) const

inline

References context_update_step_.

core::Real protocols::md::MDBase::cst_sdev ( ) const

inline

References cst_sdev_.

core::Real protocols::md::MDBase::cummulative_time ( ) const

inline

References cummulative_time_.

Referenced by report_silent().

core::Real protocols::md::MDBase::dt ( ) const

inline

References dt_.

core::Real protocols::md::MDBase::Emin_obj ( ) const

inline

References Emin_obj_.

core::Real protocols::md::MDBase::Gamma ( ) const

inline

References Gamma_.

std::string protocols::md::MDBase::get_name ( ) const

overridepure virtual

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

Implements protocols::moves::Mover.

Implemented in protocols::md::CartesianMD.

void protocols::md::MDBase::init

(

void

)

References context_update_step_, dt_, Gamma_, Kappa_, md_energy_report_stepsize_, md_report_stepsize_, md_rsr_update_stepsize_, ncyc_postmin_, ncyc_premin_, nstep_, parse_schfile(), ref_xyz_, report_as_silent_, report_scorecomp_, rsrfilename_, scheduled_, selectmode_, silentname_, store_trj_, temp0_, trj_, trj_score_only_, trj_scratch_, uniform_coord_constrained_, and write_dynamic_rsr_.

core::Real protocols::md::MDBase::Kappa ( ) const

inline

References Kappa_.

core::Real protocols::md::MDBase::kinetic_energy ( ) const

inline

References kinetic_energy_.

core::optimization::Multivec protocols::md::MDBase::mass ( ) const

inline

References mass_.

core::Real protocols::md::MDBase::mass ( core::Size  iatm ) const

inline

References mass_.

core::Size protocols::md::MDBase::md_energy_report_stepsize ( ) const

inline

References md_energy_report_stepsize_.

core::Size protocols::md::MDBase::md_report_stepsize ( ) const

inline

References md_report_stepsize_.

core::Size protocols::md::MDBase::md_rsr_update_stepsize ( ) const

inline

References md_rsr_update_stepsize_.

utility::vector1< MDscheduleData > protocols::md::MDBase::mdsch ( ) const

inline

References mdsch_.

MDscheduleData protocols::md::MDBase::mdsch ( core::Size  istep ) const

inline

References mdsch_.

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

inline

References movemap_.

core::Size protocols::md::MDBase::n_dof ( ) const

inline

References n_dof_.

Referenced by resize_natm_variables().

core::Size protocols::md::MDBase::n_dof_temp ( ) const

inline

References n_dof_temp_.

core::Size protocols::md::MDBase::ncyc_postmin ( ) const

inline

References ncyc_postmin_.

core::Size protocols::md::MDBase::ncyc_premin ( ) const

inline

References ncyc_premin_.

core::Size protocols::md::MDBase::nstep ( ) const

inline

References nstep_.

void protocols::md::MDBase::parse_schfile

(

std::string const

schfile

)

References mdsch_, protocols::md::MDscheduleData::nstep, protocols::sparta::split(), protocols::md::MDscheduleData::temp0, protocols::md::TR(), and protocols::md::MDscheduleData::type.

Referenced by init().

core::pose::Pose protocols::md::MDBase::pose0 ( ) const

inline

References pose0_.

core::pose::Pose protocols::md::MDBase::pose_minobj ( ) const

inline

References pose_minobj_.

core::Real protocols::md::MDBase::potential_energy ( ) const

inline

References potential_energy_.

core::optimization::Multivec const& protocols::md::MDBase::prv_eqxyz ( ) const

inline

References prv_eqxyz_.

core::optimization::Multivec const& protocols::md::MDBase::ref_xyz ( ) const

inline

References ref_xyz_.

void protocols::md::MDBase::renew_trj_scratch ( )

inline

References trj_scratch_.

bool protocols::md::MDBase::report_as_silent ( ) const

inline

References report_as_silent_.

bool protocols::md::MDBase::report_scorecomp ( ) const

inline

References report_scorecomp_.

void protocols::md::MDBase::report_silent	(	core::pose::Pose &	pose,
		core::Real	rmsd = -1.0,
		core::Real	gdttm = -1.0,
		core::Real	gdtha = -1.0
	)

References cummulative_time(), scorefxn_, silentname_, trj_score_only_, and core::io::silent::SilentFileData::write_silent_struct().

void protocols::md::MDBase::resize_natm_variables

(

)

References acc_, mass_, n_dof(), vel_, and xyz_.

std::string protocols::md::MDBase::rsrfilename ( ) const

inline

References rsrfilename_.

bool protocols::md::MDBase::scheduled ( ) const

inline

References scheduled_.

core::scoring::ScoreFunctionOP protocols::md::MDBase::scorefxn ( ) const

inline

References scorefxn_.

core::scoring::ScoreFunctionOP protocols::md::MDBase::scorefxn_obj ( ) const

inline

References scorefxn_obj_.

std::string protocols::md::MDBase::selectmode ( ) const

inline

References selectmode_.

void protocols::md::MDBase::set_acc ( core::optimization::Multivec  setting )

inline

References acc_.

void protocols::md::MDBase::set_constraint

(

core::Real const

sdev

)

References core::scoring::coordinate_constraint, cst_sdev_, scorefxn_, and uniform_coord_constrained_.

Referenced by protocols::mpi_refinement::WorkUnit_MD::run().

void protocols::md::MDBase::set_context_update_step ( core::Size  setting )

inline

References context_update_step_.

void protocols::md::MDBase::set_cst_sdev ( core::Real  setting )

inline

References cst_sdev_.

void protocols::md::MDBase::set_cummulative_time ( core::Real  setting )

inline

References cummulative_time_.

void protocols::md::MDBase::set_defaults ( )

inline

References dt_.

void protocols::md::MDBase::set_dt ( core::Real  setting )

inline

References dt_.

void protocols::md::MDBase::set_Emin_obj ( core::Real  setting )

inline

References Emin_obj_.

void protocols::md::MDBase::set_Gamma ( core::Real  setting )

inline

References Gamma_.

void protocols::md::MDBase::set_Kappa ( core::Real  setting )

inline

References Kappa_.

void protocols::md::MDBase::set_kinetic_energy ( core::Real  setting )

inline

References kinetic_energy_.

void protocols::md::MDBase::set_mass ( core::Size  iatm, core::Real  setting  )

inline

References mass_.

void protocols::md::MDBase::set_md_energy_report_stepsize ( core::Size  setting )

inline

References md_energy_report_stepsize_.

void protocols::md::MDBase::set_md_report_stepsize ( core::Size  setting )

inline

References md_report_stepsize_.

Referenced by protocols::mpi_refinement::WorkUnit_MD::run().

void protocols::md::MDBase::set_md_rsr_update_stepsize ( core::Size  setting )

inline

References md_rsr_update_stepsize_.

void protocols::md::MDBase::set_mdsch ( utility::vector1< MDscheduleData >  setting )

inline

References mdsch_.

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

virtual

References movemap_.

void protocols::md::MDBase::set_n_dof ( core::Size  setting )

inline

References n_dof_.

void protocols::md::MDBase::set_n_dof_temp ( core::Size  setting )

inline

References n_dof_temp_.

void protocols::md::MDBase::set_ncyc_postmin ( core::Size  setting )

inline

References ncyc_postmin_.

void protocols::md::MDBase::set_ncyc_premin ( core::Size  setting )

inline

References ncyc_premin_.

void protocols::md::MDBase::set_nstep ( core::Size  setting )

inline

References nstep_.

Referenced by protocols::relax::FastRelax::do_md(), and protocols::mpi_refinement::WorkUnit_MD::run().

void protocols::md::MDBase::set_pose0 ( core::pose::Pose  setting )

inline

References pose0_.

void protocols::md::MDBase::set_pose_minobj ( core::pose::Pose  setting )

inline

References pose_minobj_.

void protocols::md::MDBase::set_potential_energy ( core::Real  setting )

inline

References potential_energy_.

void protocols::md::MDBase::set_prv_eqxyz ( core::optimization::Multivec  setting )

inline

References prv_eqxyz_.

void protocols::md::MDBase::set_ref_xyz ( core::optimization::Multivec  setting )

inline

References ref_xyz_.

void protocols::md::MDBase::set_report_as_silent ( bool  setting )

inline

References report_as_silent_.

void protocols::md::MDBase::set_report_scorecomp ( bool  setting )

inline

References report_scorecomp_.

void protocols::md::MDBase::set_rsrfilename ( std::string  setting )

inline

References rsrfilename_.

void protocols::md::MDBase::set_scheduled ( bool  setting )

inline

References scheduled_.

void protocols::md::MDBase::set_scorefxn ( core::scoring::ScoreFunctionCOP  setting )

inline

References scorefxn_.

void protocols::md::MDBase::set_scorefxn ( core::scoring::ScoreFunction const &  setting )

inline

References core::scoring::ScoreFunction::clone(), and scorefxn_.

void protocols::md::MDBase::set_scorefxn_obj ( core::scoring::ScoreFunctionCOP  setting )

inline

References scorefxn_obj_.

void protocols::md::MDBase::set_scorefxn_obj ( core::scoring::ScoreFunction const &  setting )

inline

References core::scoring::ScoreFunction::clone(), and scorefxn_obj_.

void protocols::md::MDBase::set_selectmode ( std::string  setting )

inline

References selectmode_.

void protocols::md::MDBase::set_silentname ( std::string  setting )

inline

References silentname_.

void protocols::md::MDBase::set_store_trj ( bool  setting )

inline

References store_trj_.

Referenced by protocols::mpi_refinement::WorkUnit_MD::run().

void protocols::md::MDBase::set_temp0 ( core::Real  setting )

inline

References temp0_.

Referenced by protocols::relax::FastRelax::do_md().

void protocols::md::MDBase::set_temperature ( core::Real  setting )

inline

References temperature_.

Referenced by protocols::mpi_refinement::WorkUnit_MD::run().

void protocols::md::MDBase::set_time_minobj ( core::Real  setting )

inline

References time_minobj_.

void protocols::md::MDBase::set_trj ( utility::vector1< core::optimization::Multivec >  setting )

inline

References trj_.

void protocols::md::MDBase::set_trj_score_only ( bool  setting )

inline

References trj_score_only_.

void protocols::md::MDBase::set_trj_scratch ( utility::vector1< core::optimization::Multivec >  setting )

inline

References trj_scratch_.

void protocols::md::MDBase::set_uniform_coord_constrained ( bool  setting )

inline

References uniform_coord_constrained_.

void protocols::md::MDBase::set_vel ( core::optimization::Multivec  setting )

inline

References vel_.

void protocols::md::MDBase::set_write_dynamic_rsr ( bool  setting )

inline

References write_dynamic_rsr_.

void protocols::md::MDBase::set_write_dynamic_rsr ( std::string const  filename )

inline

References protocols::abinitio::filename(), rsrfilename_, and write_dynamic_rsr_.

void protocols::md::MDBase::set_xyz ( core::optimization::Multivec  setting )

inline

References xyz_.

std::string protocols::md::MDBase::silentname ( ) const

inline

References silentname_.

bool protocols::md::MDBase::store_trj ( ) const

inline

References store_trj_.

core::Real protocols::md::MDBase::temp0 ( ) const

inline

References temp0_.

core::Real protocols::md::MDBase::temperature ( ) const

inline

References temperature_.

core::Real protocols::md::MDBase::time_minobj ( ) const

inline

References time_minobj_.

utility::vector1< core::optimization::Multivec > protocols::md::MDBase::trj ( ) const

inline

References trj_.

core::optimization::Multivec protocols::md::MDBase::trj ( core::Size  itrj ) const

inline

References trj_.

bool protocols::md::MDBase::trj_score_only ( ) const

inline

References trj_score_only_.

utility::vector1< core::optimization::Multivec > protocols::md::MDBase::trj_scratch ( ) const

inline

References trj_scratch_.

bool protocols::md::MDBase::uniform_coord_constrained ( ) const

inline

References uniform_coord_constrained_.

core::optimization::Multivec protocols::md::MDBase::vel ( ) const

inline

References vel_.

core::Real& protocols::md::MDBase::vel ( core::Size  idof )

inline

References vel_.

bool protocols::md::MDBase::write_dynamic_rsr ( ) const

inline

References write_dynamic_rsr_.

core::optimization::Multivec protocols::md::MDBase::xyz ( ) const

inline

References xyz_.

core::Real& protocols::md::MDBase::xyz ( core::Size  idof )

inline

References xyz_.

Member Data Documentation

core::optimization::Multivec protocols::md::MDBase::acc_

private

Referenced by acc(), resize_natm_variables(), and set_acc().

core::Size protocols::md::MDBase::context_update_step_

private

Referenced by context_update_step(), init(), and set_context_update_step().

core::Real protocols::md::MDBase::cst_sdev_

private

Referenced by cst_sdev(), set_constraint(), and set_cst_sdev().

core::Real protocols::md::MDBase::cummulative_time_

private

Referenced by cummulative_time(), and set_cummulative_time().

core::Real protocols::md::MDBase::dt_

private

Referenced by dt(), init(), set_defaults(), and set_dt().

core::Real protocols::md::MDBase::Emin_obj_

private

Referenced by Emin_obj(), and set_Emin_obj().

core::Real protocols::md::MDBase::Gamma_

private

Referenced by Gamma(), init(), and set_Gamma().

core::Real protocols::md::MDBase::Kappa_

private

Referenced by init(), Kappa(), and set_Kappa().

core::Real protocols::md::MDBase::kinetic_energy_

private

Referenced by kinetic_energy(), and set_kinetic_energy().

core::optimization::Multivec protocols::md::MDBase::mass_

private

Referenced by mass(), resize_natm_variables(), and set_mass().

core::Size protocols::md::MDBase::md_energy_report_stepsize_

private

Referenced by init(), md_energy_report_stepsize(), and set_md_energy_report_stepsize().

core::Size protocols::md::MDBase::md_report_stepsize_

private

Referenced by init(), md_report_stepsize(), and set_md_report_stepsize().

core::Size protocols::md::MDBase::md_rsr_update_stepsize_

private

Referenced by init(), md_rsr_update_stepsize(), and set_md_rsr_update_stepsize().

utility::vector1< MDscheduleData > protocols::md::MDBase::mdsch_

private

Referenced by mdsch(), parse_schfile(), and set_mdsch().

core::kinematics::MoveMapOP protocols::md::MDBase::movemap_

private

Referenced by movemap(), and set_movemap().

core::Size protocols::md::MDBase::n_dof_

private

Referenced by n_dof(), and set_n_dof().

core::Size protocols::md::MDBase::n_dof_temp_

private

Referenced by n_dof_temp(), and set_n_dof_temp().

core::Size protocols::md::MDBase::ncyc_postmin_

private

Referenced by init(), ncyc_postmin(), and set_ncyc_postmin().

core::Size protocols::md::MDBase::ncyc_premin_

private

Referenced by init(), ncyc_premin(), and set_ncyc_premin().

core::Size protocols::md::MDBase::nstep_

private

Referenced by init(), nstep(), and set_nstep().

core::pose::Pose protocols::md::MDBase::pose0_

private

Referenced by pose0(), and set_pose0().

core::pose::Pose protocols::md::MDBase::pose_minobj_

private

Referenced by pose_minobj(), and set_pose_minobj().

core::Real protocols::md::MDBase::potential_energy_

private

Referenced by potential_energy(), and set_potential_energy().

core::optimization::Multivec protocols::md::MDBase::prv_eqxyz_

private

Referenced by prv_eqxyz(), and set_prv_eqxyz().

core::optimization::Multivec protocols::md::MDBase::ref_xyz_

private

Referenced by init(), ref_xyz(), and set_ref_xyz().

bool protocols::md::MDBase::report_as_silent_

private

Referenced by init(), report_as_silent(), and set_report_as_silent().

bool protocols::md::MDBase::report_scorecomp_

private

Referenced by init(), report_scorecomp(), and set_report_scorecomp().

std::string protocols::md::MDBase::rsrfilename_

private

Referenced by init(), rsrfilename(), set_rsrfilename(), and set_write_dynamic_rsr().

bool protocols::md::MDBase::scheduled_

private

Referenced by init(), scheduled(), and set_scheduled().

core::scoring::ScoreFunctionOP protocols::md::MDBase::scorefxn_

private

Referenced by report_silent(), scorefxn(), set_constraint(), and set_scorefxn().

core::scoring::ScoreFunctionOP protocols::md::MDBase::scorefxn_obj_

private

Referenced by scorefxn_obj(), and set_scorefxn_obj().

std::string protocols::md::MDBase::selectmode_

private

Referenced by init(), selectmode(), and set_selectmode().

std::string protocols::md::MDBase::silentname_

private

Referenced by init(), report_silent(), set_silentname(), and silentname().

bool protocols::md::MDBase::store_trj_

private

Referenced by init(), set_store_trj(), and store_trj().

core::Real protocols::md::MDBase::temp0_

private

Referenced by init(), set_temp0(), and temp0().

core::Real protocols::md::MDBase::temperature_

private

Referenced by set_temperature(), and temperature().

core::Real protocols::md::MDBase::time_minobj_

private

Referenced by set_time_minobj(), and time_minobj().

utility::vector1< core::optimization::Multivec > protocols::md::MDBase::trj_

private

Referenced by add_trj(), init(), set_trj(), and trj().

bool protocols::md::MDBase::trj_score_only_

private

Referenced by init(), report_silent(), set_trj_score_only(), and trj_score_only().

utility::vector1< core::optimization::Multivec > protocols::md::MDBase::trj_scratch_

private

Referenced by add_trj_scratch(), init(), renew_trj_scratch(), set_trj_scratch(), and trj_scratch().

bool protocols::md::MDBase::uniform_coord_constrained_

private

Referenced by init(), set_constraint(), set_uniform_coord_constrained(), and uniform_coord_constrained().

core::optimization::Multivec protocols::md::MDBase::vel_

private

Referenced by resize_natm_variables(), set_vel(), and vel().

bool protocols::md::MDBase::write_dynamic_rsr_

private

Referenced by init(), set_write_dynamic_rsr(), and write_dynamic_rsr().

core::optimization::Multivec protocols::md::MDBase::xyz_

private

Referenced by resize_natm_variables(), set_xyz(), and xyz().

---

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

• src/protocols/md/MDBase.hh
• src/protocols/md/MDBase.cc