protocols::simple_moves::sidechain_moves::SidechainMCMover Class Reference

class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions More...

#include <SidechainMCMover.hh>

Inheritance diagram for protocols::simple_moves::sidechain_moves::SidechainMCMover:

Collaboration diagram for protocols::simple_moves::sidechain_moves::SidechainMCMover:

List of all members.

Public Member Functions
	SidechainMCMover ()
	default constructor
	SidechainMCMover (core::pack::dunbrack::RotamerLibrary const &rotamer_library)
	constructor with user provided rotamer library
	~SidechainMCMover ()
void	show_counters (std::ostream &out)
void	setup (core::scoring::ScoreFunctionCOP sfxn)
protocols::moves::MoverOP	clone () const
	clone has to be overridden only if clone invocation is expected.
protocols::moves::MoverOP	fresh_instance () const
	this is like clone(), except it generates a new mover object freshly created with the default ctor. This function _should_ be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).
void	parse_my_tag (utility::tag::TagPtr const tag, protocols::moves::DataMap &, protocols::filters::Filters_map const &, protocols::moves::Movers_map const &, core::pose::Pose const &)
	Called by MoverFactory when constructing new Movers. Takes care of the specific mover's parsing.
void	apply (core::pose::Pose &pose)
	apply a sidechain move to a Pose object
virtual std::string	get_name () const
	Each derived class must specify its name. The class name.
void	set_ntrials (core::Size ntrial)
core::Size	ntrials ()
void	set_temperature (core::Real temp)
core::Real	temperature ()
void	set_inherit_scorefxn_temperature (bool inherit_scorefxn_temperature)
bool	inherit_scorefxn_temperature () const
void	set_scorefunction (core::scoring::ScoreFunction const &sfxn)
	Set score function.
core::scoring::ScoreFunction &	scorefunction ()
virtual void	initialize_simulation (core::pose::Pose &pose, protocols::canonical_sampling::MetropolisHastingsMover const &metropolis_hastings_mover, core::Size cycle)
	callback executed before any Monte Carlo trials
virtual core::Real	last_proposal_density_ratio ()
	get the ratio of proposal densities for the last move
virtual bool	is_multi_trial ()
	determine whether the move performs multiple trials on a single apply
virtual core::Real	last_inner_score_temperature_delta ()
	get change in internal score/temperature for last apply method of multiple trial movers
virtual protocols::canonical_sampling::MetropolisHastingsMoverAP	metropolis_hastings_mover ()
	get the MetropolisHastingsMover for multiple trial movers
virtual void	set_metropolis_hastings_mover (protocols::canonical_sampling::MetropolisHastingsMoverAP metropolis_hastings_mover)
	set the MetropolisHastingsMover for multiple trial movers

---

Detailed Description

class for non-discrete side chain sampling using Dunbrack rotamer probabilities/distributions

---

Constructor & Destructor Documentation

protocols::simple_moves::sidechain_moves::SidechainMCMover::SidechainMCMover

(

)

default constructor

protocols::simple_moves::sidechain_moves::SidechainMCMover::SidechainMCMover

(

core::pack::dunbrack::RotamerLibrary const &

rotamer_library

)

constructor with user provided rotamer library

protocols::simple_moves::sidechain_moves::SidechainMCMover::~SidechainMCMover

(

)

---

Member Function Documentation

void protocols::simple_moves::sidechain_moves::SidechainMCMover::apply

(

core::pose::Pose &

pose

)

[virtual]

apply a sidechain move to a Pose object

Detailed:

Reimplemented from protocols::simple_moves::sidechain_moves::SidechainMover.

References core::pose::Pose::dump_pdb(), protocols::simple_moves::sidechain_moves::SidechainMover::init_task(), protocols::simple_moves::sidechain_moves::SidechainMover::last_proposal_density_ratio(), protocols::simple_moves::sidechain_moves::SidechainMover::make_move(), core::conformation::Residue::name1(), protocols::simple_moves::sidechain_moves::SidechainMover::packed_residues(), core::pose::Pose::replace_residue(), core::pose::Pose::residue(), Rg(), set_temperature(), core::pose::Pose::total_residue(), protocols::simple_moves::TR(), and protocols::moves::Mover::type().

protocols::moves::MoverOP protocols::simple_moves::sidechain_moves::SidechainMCMover::clone

(

)

const [virtual]

clone has to be overridden only if clone invocation is expected.

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::simple_moves::sidechain_moves::SidechainMover.

protocols::moves::MoverOP protocols::simple_moves::sidechain_moves::SidechainMCMover::fresh_instance

(

)

const [virtual]

this is like clone(), except it generates a new mover object freshly created with the default ctor. This function _should_ be pure virtual but that would disrupt the code base; MAKE SURE YOU DEFINE IT if you want to have your mover be a protocol handed to the job distributor (august 08 vintage).

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.

std::string protocols::simple_moves::sidechain_moves::SidechainMCMover::get_name

(

)

const [virtual]

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

Reimplemented from protocols::simple_moves::sidechain_moves::SidechainMover.

bool protocols::simple_moves::sidechain_moves::SidechainMCMover::inherit_scorefxn_temperature

(

)

const [inline]

Referenced by parse_my_tag(), and set_inherit_scorefxn_temperature().

void protocols::simple_moves::sidechain_moves::SidechainMCMover::initialize_simulation	(	core::pose::Pose &	pose,
		protocols::canonical_sampling::MetropolisHastingsMover const &	metropolis_hastings_mover,
		core::Size	cycle
	)		[virtual]

callback executed before any Monte Carlo trials

Reimplemented from protocols::simple_moves::sidechain_moves::SidechainMover.

References set_scorefunction(), and set_temperature().

virtual bool protocols::simple_moves::sidechain_moves::SidechainMCMover::is_multi_trial

(

)

[inline, virtual]

determine whether the move performs multiple trials on a single apply

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

virtual core::Real protocols::simple_moves::sidechain_moves::SidechainMCMover::last_inner_score_temperature_delta

(

)

[inline, virtual]

get change in internal score/temperature for last apply method of multiple trial movers

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

virtual core::Real protocols::simple_moves::sidechain_moves::SidechainMCMover::last_proposal_density_ratio

(

)

[inline, virtual]

get the ratio of proposal densities for the last move

Reimplemented from protocols::simple_moves::sidechain_moves::SidechainMover.

virtual protocols::canonical_sampling::MetropolisHastingsMoverAP protocols::simple_moves::sidechain_moves::SidechainMCMover::metropolis_hastings_mover

(

)

[inline, virtual]

get the MetropolisHastingsMover for multiple trial movers

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

Referenced by set_metropolis_hastings_mover().

core::Size protocols::simple_moves::sidechain_moves::SidechainMCMover::ntrials

(

)

[inline]

void protocols::simple_moves::sidechain_moves::SidechainMCMover::parse_my_tag	(	utility::tag::TagPtr const	tag,
		protocols::moves::DataMap &	data,
		protocols::filters::Filters_map const &	filters,
		protocols::moves::Movers_map const &	movers,
		core::pose::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::simple_moves::sidechain_moves::SidechainMover.

References core::pack::task::TaskFactory::create_packer_task(), core::sequence::end, protocols::moves::DataMap::get(), protocols::moves::DataMap::has(), inherit_scorefxn_temperature(), protocols::simple_moves::sidechain_moves::SidechainMover::preserve_detailed_balance(), protocols::simple_moves::sidechain_moves::SidechainMover::prob_random_pert_current(), protocols::simple_moves::sidechain_moves::SidechainMover::prob_uniform(), protocols::simple_moves::sidechain_moves::SidechainMover::prob_withinrot(), set_inherit_scorefxn_temperature(), protocols::simple_moves::sidechain_moves::SidechainMover::set_preserve_detailed_balance(), protocols::simple_moves::sidechain_moves::SidechainMover::set_prob_random_pert_current(), protocols::simple_moves::sidechain_moves::SidechainMover::set_prob_uniform(), protocols::simple_moves::sidechain_moves::SidechainMover::set_prob_withinrot(), protocols::simple_moves::sidechain_moves::SidechainMover::set_task(), protocols::simple_moves::sidechain_moves::SidechainMover::set_task_factory(), setup(), and protocols::simple_moves::TR().

core::scoring::ScoreFunction& protocols::simple_moves::sidechain_moves::SidechainMCMover::scorefunction

(

)

[inline]

void protocols::simple_moves::sidechain_moves::SidechainMCMover::set_inherit_scorefxn_temperature

(

bool

inherit_scorefxn_temperature

)

[inline]

References inherit_scorefxn_temperature().

Referenced by parse_my_tag().

virtual void protocols::simple_moves::sidechain_moves::SidechainMCMover::set_metropolis_hastings_mover

(

protocols::canonical_sampling::MetropolisHastingsMoverAP

metropolis_hastings_mover

)

[inline, virtual]

set the MetropolisHastingsMover for multiple trial movers

Reimplemented from protocols::canonical_sampling::ThermodynamicMover.

References metropolis_hastings_mover().

void protocols::simple_moves::sidechain_moves::SidechainMCMover::set_ntrials

(

core::Size

ntrial

)

[inline]

void protocols::features::DatabaseJobInputter::set_scorefunction

(

core::scoring::ScoreFunction const &

sfxn

)

[inline]

Set score function.

Referenced by initialize_simulation(), and setup().

void protocols::simple_moves::rational_mc::RationalMonteCarlo::set_temperature

(

core::Real

temp

)

[inline]

Referenced by apply(), and initialize_simulation().

void protocols::simple_moves::sidechain_moves::SidechainMCMover::setup

(

core::scoring::ScoreFunctionCOP

sfxn

)

References set_scorefunction().

Referenced by parse_my_tag().

void protocols::simple_moves::sidechain_moves::SidechainMCMover::show_counters

(

std::ostream &

out

)

core::Real protocols::simple_moves::sidechain_moves::SidechainMCMover::temperature

(

)

[inline]

---

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

• src/protocols/simple_moves/sidechain_moves/SidechainMCMover.hh
• src/protocols/features/DatabaseJobInputter.cc
• src/protocols/simple_moves/rational_mc/RationalMonteCarlo.cc
• src/protocols/simple_moves/sidechain_moves/SidechainMCMover.cc