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protocols::md::MDBase Class Referenceabstract

#include <MDBase.hh>

Inheritance diagram for protocols::md::MDBase:
Inheritance graph
[legend]

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< 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 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 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...
 

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< MDscheduleDatamdsch_
 
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

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  )
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
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
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)
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 
)
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)
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
void protocols::md::MDBase::set_md_report_stepsize ( core::Size  setting)
inline
void protocols::md::MDBase::set_md_rsr_update_stepsize ( core::Size  setting)
inline
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
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
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
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
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
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
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
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
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
core::Real protocols::md::MDBase::cst_sdev_
private
core::Real protocols::md::MDBase::cummulative_time_
private
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
core::optimization::Multivec protocols::md::MDBase::mass_
private
core::Size protocols::md::MDBase::md_energy_report_stepsize_
private
core::Size protocols::md::MDBase::md_report_stepsize_
private
core::Size protocols::md::MDBase::md_rsr_update_stepsize_
private
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
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
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
bool protocols::md::MDBase::report_scorecomp_
private
std::string protocols::md::MDBase::rsrfilename_
private
bool protocols::md::MDBase::scheduled_
private

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

core::scoring::ScoreFunctionOP protocols::md::MDBase::scorefxn_
private
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
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
utility::vector1< core::optimization::Multivec > protocols::md::MDBase::trj_scratch_
private
bool protocols::md::MDBase::uniform_coord_constrained_
private
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
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: