protocols::md::CartesianMD Class Reference

#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=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< 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 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 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...

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::Size >	native_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

CartesianMD() [1/4]

protocols::md::CartesianMD::CartesianMD

(

)

References core::init::init().

CartesianMD() [2/4]

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

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

CartesianMD() [3/4]

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

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

CartesianMD() [4/4]

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

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

~CartesianMD()

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

overridedefault

Member Function Documentation

apply()

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

overridevirtual

Main Method.

Implements protocols::md::MDBase.

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

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

Berendsen_Integrator()

void protocols::md::CartesianMD::Berendsen_Integrator ( core::pose::Pose &  pose, core::optimization::CartesianMinimizerMap &  min_map  )

private

clone()

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.

cst_on_pose_dynamic()

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

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(), core::id::AtomID::rsd(), and protocols::md::TR().

cst_on_pose_simple()

void protocols::md::CartesianMD::cst_on_pose_simple

(

core::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::size(), protocols::md::TR(), core::pose::Pose::xyz(), and protocols::kinmatch::xyz().

do_initialize()

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

private

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

do_MD()

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(), core::pose::mass(), protocols::md::Rattle::ncst(), protocols::md::Thermostat::nstep_per_update(), protocols::md::Thermostat::rescale(), core::optimization::CartesianMinimizerMap::setup(), protocols::md::TR(), and protocols::kinmatch::xyz().

do_minimize()

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

private

References core::optimization::CartesianMinimizer::run(), and protocols::md::TR().

dump_poses()

utility::vector1< pose::Pose > protocols::md::CartesianMD::dump_poses

(

core::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().

fresh_instance()

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.

get_current_eqxyz()

Multivec protocols::md::CartesianMD::get_current_eqxyz

(

)

const

get_name()

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

overridevirtual

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

Implements protocols::md::MDBase.

get_native_info()

void protocols::md::CartesianMD::get_native_info ( core::pose::Pose const &  pose )

private

References core::chemical::FULL_ATOM_t, core::conformation::Residue::is_protein(), core::import_pose::PDB_file, core::pose::Pose::pdb_info(), core::import_pose::pose_from_file(), core::pose::Pose::residue(), core::pose::Pose::residue_type_set_for_pose(), and core::pose::Pose::size().

initialize_velocity()

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

private

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

mover_name()

std::string protocols::md::CartesianMD::mover_name ( )

static

Referenced by protocols::md::CartesianMDCreator::keyname().

parse_movemap()

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

References protocols::rosetta_scripts::parse_movemap_factory_legacy().

parse_my_tag()

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.

parse_opts()

void protocols::md::CartesianMD::parse_opts	(	TagCOP	tag,
		basic::datacache::DataMap &	data
	)

provide_xml_schema()

void protocols::md::CartesianMD::provide_xml_schema ( utility::tag::XMLSchemaDefinition &  xsd )

static

References protocols::moves::xsd_type_definition_w_attributes().

Referenced by protocols::md::CartesianMDCreator::provide_xml_schema().

report_MD()

void protocols::md::CartesianMD::report_MD ( core::pose::Pose &  pose, core::optimization::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(), protocols::hybridization::score, and protocols::md::TR().

update_restraint()

void protocols::md::CartesianMD::update_restraint	(	core::pose::Pose &	pose,
		core::optimization::CartesianMinimizerMap const &	min_map
	)

References protocols::md::TR().

use_rattle()

void protocols::md::CartesianMD::use_rattle

(

bool const

value

)

References protocols::md::TR().

VelocityVerlet_Integrator()

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(), core::pose::mass(), protocols::md::MDForceFactor(), protocols::md::Rattle::run_rattle1(), protocols::md::Rattle::run_rattle2(), and protocols::kinmatch::xyz().

Member Data Documentation

inittime_

timeval protocols::md::CartesianMD::inittime_

private

min_map_

core::optimization::CartesianMinimizerMap protocols::md::CartesianMD::min_map_

private

movemap_factory_

core::select::movemap::MoveMapFactoryCOP protocols::md::CartesianMD::movemap_factory_

private

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

native_

core::pose::Pose protocols::md::CartesianMD::native_

private

native_given_

bool protocols::md::CartesianMD::native_given_ = false

private

native_resmap_

std::map< core::Size, core::Size > protocols::md::CartesianMD::native_resmap_

private

use_rattle_

bool protocols::md::CartesianMD::use_rattle_ = true

private

---

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

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