#include <CartesianMD.hh>

Inheritance diagram for protocols::md::CartesianMD:

Public Member Functions
	CartesianMD ()

	CartesianMD (core::pose::Pose const &pose, core::scoring::ScoreFunctionCOP sfxn, core::kinematics::MoveMapCOP movemap=0)

	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)

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)

Multivec	get_current_eqxyz () const

void	update_restraint (pose::Pose &pose, CartesianMinimizerMap const &min_map)

void	cst_on_pose_simple (pose::Pose &pose) const

void	cst_on_pose_dynamic (pose::Pose &pose, Multivec const &ref_xyz, Multivec const &curr_eqxyz, Multivec &prv_eqxyz, CartesianMinimizerMap const &min_map) const

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::Pose >	dump_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 () const

void	set_dt (core::Real const value)

Size	n_dof () const

Real	cummulative_time () const

void	set_constraint (Real const sdev)

void	cst_on_pose (pose::Pose &pose)

void	set_nstep (core::Size const nstep)

void	set_temperature (core::Real const temp0)

void	set_reportstep (core::Size const nstep)

void	set_energy_reportstep (core::Size const nstep)

void	set_rsr_update_step (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 () const

core::Real	temp0 () const

void	set_store_trj (bool const value)

bool	store_trj () const

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

void	report_as_silent (std::string const filename, bool const scoreonly)

void	set_Kappa (core::Real const value)

void	set_Gamma (core::Real const value)

void	set_write_dynamic_rsr (std::string const filename)

Public Member Functions inherited from protocols::moves::Mover
	Mover ()

virtual	~Mover ()

virtual MoverSP	create ()

MoverCOP	get_self_ptr () const

MoverOP	get_self_ptr ()

MoverCAP	get_self_weak_ptr () const

MoverAP	get_self_weak_ptr ()

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)

Mover &	operator= (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...

virtual 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 Strings &	info ()
	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)

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 (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, CartesianMinimizerMap const &min_map, bool const report_trj)

Private Attributes
core::optimization::CartesianMinimizerMap	min_map_

timeval	inittime_

bool	use_rattle_

core::pose::Pose	native_

bool	native_given_

std::map< Size, Size >	native_resmap_

Additional Inherited Members
Public Types inherited from protocols::md::MDBase
typedef protocols::moves::Mover	parent

typedef utility::vector1< Real >	Multivec

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::string >	Strings

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_

Size	md_energy_report_stepsize_

Size	md_rsr_update_stepsize_

core::pose::Pose	pose0_

bool	report_scorecomp_

core::Size	context_update_step_

Size	ncyc_premin_

Size	ncyc_postmin_

bool	scheduled_

utility::vector1< MDscheduleData >	mdsch_

bool	constrained_

Real	cst_sdev_

Real	temp0_

Size	nstep_

Real	temperature_

Real	kinetic_energy_

Real	potential_energy_

Multivec	xyz_

Multivec	vel_

Multivec	acc_

bool	report_as_silent_

bool	trj_score_only_

std::string	silentname_

bool	store_trj_

utility::vector1< Multivec >	trj_

utility::vector1< Multivec >	trj_scratch_

Multivec	ref_xyz_

Multivec	prv_eqxyz_

Real	Kappa_

Real	Gamma_

bool	write_dynamic_rsr_

std::string	rsrfilename_

Constructor & Destructor Documentation

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

References core::init::init().

Referenced by fresh_instance().

protocols::md::CartesianMD::CartesianMD	(	core::pose::Pose const &	pose,
		core::scoring::ScoreFunctionCOP	sfxn,
		core::kinematics::MoveMapCOP	movemap = `0`
	)

References core::id::D, core::init::init(), and core::id::THETA.

protocols::md::CartesianMD::CartesianMD	(	core::pose::Pose const &	pose,
		core::scoring::ScoreFunction const &	sfxn
	)

References core::scoring::ScoreFunction::clone(), core::id::D, core::init::init(), core::kinematics::MoveMap::set(), core::kinematics::MoveMap::set_bb(), core::kinematics::MoveMap::set_jump(), and core::id::THETA.

protocols::md::CartesianMD::CartesianMD	(	core::pose::Pose const &	pose,
		core::scoring::ScoreFunction const &	sfxn,
		core::kinematics::MoveMap const &	movemap
	)

References core::kinematics::MoveMap::clone(), core::scoring::ScoreFunction::clone(), and core::init::init().

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

virtual

Member Function Documentation

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

virtual

Implements protocols::md::MDBase.

References core::pose::symmetry::is_symmetric(), core::pose::symmetry::make_symmetric_movemap(), core::optimization::MinimizerOptions::max_iter(), and core::optimization::CartesianMinimizerMap::setup().

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

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::cst_on_pose_dynamic	(	pose::Pose &	pose,
		Multivec const &	ref_xyz,
		Multivec const &	curr_eqxyz,
		Multivec &	prv_eqxyz,
		CartesianMinimizerMap const &	min_map
	)		const

References core::pose::Pose::add_constraint(), core::conformation::Residue::atom_name(), core::id::AtomID::atomno(), core::chemical::element::F, core::optimization::CartesianMinimizerMap::get_atom(), core::chemical::element::I, core::conformation::Residue::name(), core::pose::Pose::remove_constraints(), core::pose::Pose::residue(), and core::id::AtomID::rsd().

void protocols::md::CartesianMD::cst_on_pose_simple ( pose::Pose & pose ) const

References core::pose::Pose::add_constraint(), core::scoring::constraints::add_fa_constraints_from_cmdline_to_pose(), core::conformation::Residue::atom_index(), core::conformation::Residue::has(), core::conformation::Residue::name(), core::pose::Pose::remove_constraints(), core::pose::Pose::residue(), core::pose::Pose::total_residue(), protocols::kinmatch::xyz(), and core::pose::Pose::xyz().

void protocols::md::CartesianMD::do_initialize ( core::pose::Pose & pose )

private

References core::chemical::ResidueType::atom(), core::id::AtomID::atomno(), core::optimization::CartesianMinimizerMap::copy_dofs_from_pose(), core::chemical::Atom::element_type(), core::optimization::CartesianMinimizerMap::get_atom(), core::optimization::CartesianMinimizerMap::natoms(), core::optimization::CartesianMinimizerMap::ndofs(), core::pose::Pose::residue_type(), core::id::AtomID::rsd(), and core::optimization::CartesianMinimizerMap::setup().

void protocols::md::CartesianMD::do_MD	(	core::pose::Pose &	pose,
		core::Size const &	nstep,
		core::Real const &	temp0 = `300`,
		bool const &	initialize = `false`
	)

private

References core::optimization::CartesianMinimizerMap::copy_dofs_from_pose(), core::optimization::CartesianMinimizerMap::copy_dofs_to_pose(), protocols::md::GasConst(), protocols::md::Thermostat::get_temperature(), protocols::md::Rattle::ncst(), protocols::md::Thermostat::nstep_per_update(), protocols::md::Thermostat::rescale(), and core::optimization::CartesianMinimizerMap::setup().

void protocols::md::CartesianMD::do_minimize	(	pose::Pose &	pose,
		core::optimization::MinimizerOptions const &	options,
		bool const &	show_energy
	)

private

References core::optimization::CartesianMinimizer::run().

utility::vector1< pose::Pose > protocols::md::CartesianMD::dump_poses ( pose::Pose const & pose_ref ) const

References core::optimization::CartesianMinimizerMap::copy_dofs_to_pose(), and core::optimization::CartesianMinimizerMap::setup().

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

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().

Multivec protocols::md::CartesianMD::get_current_eqxyz ( ) const

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

References core::conformation::Residue::is_protein(), core::pose::Pose::pdb_info(), core::import_pose::pose_from_pdb(), core::pose::Pose::residue(), and core::pose::Pose::total_residue().

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

void protocols::md::CartesianMD::initialize_velocity ( core::Real const & temperature )

private

References protocols::md::Boltzmann(), protocols::md::Thermostat::get_temperature(), and core::scoring::rg.

virtual core::kinematics::MoveMapOP protocols::md::CartesianMD::movemap ( ) const

inlinevirtual

Implements protocols::md::MDBase.

References protocols::md::MDBase::movemap_.

void protocols::md::CartesianMD::parse_movemap	(	TagCOP	tag,
		basic::datacache::DataMap &	data,
		Pose const &	pose
	)

References protocols::rosetta_scripts::parse_movemap().

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,
		CartesianMinimizerMap const &	min_map,
		bool const	report_trj
	)

private

References core::scoring::CA_gdttm(), core::scoring::CA_rmsd(), core::pose::Pose::constraint_set(), core::optimization::CartesianMinimizerMap::copy_dofs_from_pose(), core::optimization::CartesianMinimizerMap::ndofs(), and protocols::kinmatch::xyz().

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

virtual

Implements protocols::md::MDBase.

void protocols::md::CartesianMD::update_restraint	(	pose::Pose &	pose,
		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

References core::optimization::CartesianMinimizerMap::copy_dofs_to_pose(), core::optimization::CartesianMultifunc::dfunc(), protocols::md::MaxAccel(), protocols::md::MaxVel(), protocols::md::MDForceFactor(), protocols::md::Rattle::run_rattle1(), and protocols::md::Rattle::run_rattle2().

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

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

src/protocols/md/CartesianMD.hh
src/protocols/md/CartesianMD.cc

Public Member Functions

Private Member Functions

Private Attributes

Additional Inherited Members

Constructor & Destructor Documentation

Member Function Documentation

Member Data Documentation