Log a detailed account of everything that happens in a loop modeling simulation. More...

#include <TrajectoryLogger.hh>

Public Member Functions
	TrajectoryLogger (string const &prefix="")
	Construct an empty logger. More...

	TrajectoryLogger (LoopMover const *mover, string const &prefix="")
	Construct a logger from a loop mover. More...

	TrajectoryLogger (protocols::loops::LoopsCOP loops, core::scoring::ScoreFunctionCOP scorefxn, string const &prefix="")
	Construct a logger from a score function and a loops object. More...

void	init (LoopMover const *mover)
	Initialize the logger from a loop mover after it has been constructed. More...

void	init (protocols::loops::LoopsCOP loops, core::scoring::ScoreFunctionCOP scorefxn)
	Initialize the logger from a score function and a loops object after it has been constructed. More...

void	record_move (basic::Tracer &tr, Pose &pose, core::Size const i, core::Size const j, core::Size const k, bool const proposed, bool const accepted) const
	Record a single Monte Carlo move. More...

void	record_move (basic::Tracer &tr, Pose &pose, core::Size const iteration, bool const proposed, bool const accepted) const
	Record a single Monte Carlo move. More...

void	record_new_pose (basic::Tracer &tr, Pose &pose) const
	Record when a low-scoring pose is recovered. More...

void	record_new_score_function (basic::Tracer &tr, Pose &pose) const
	Record when a score function term is ramped (and scores change as a result). More...

void	record_new_temperature (basic::Tracer &tr, Real temperature) const
	Record when the temperature is ramped. More...

void	record_endpoint (basic::Tracer &tr, Pose &pose) const
	Record the end of a protocol. More...

string	get_prefix () const
	Get the prefix that will be used for the scores associated with the pose at the end of the trajectory. More...

void	set_prefix (string)
	Set the prefix that will be used for the scores associated with the pose at the end of the trajectory. More...

Pose const &	get_native_pose () const
	Get the reference structure for RMSD calculations. More...

void	set_native_pose (Pose const &)
	Set the reference structure for RMSD calculations. More...

void	unset_native_pose ()
	Disable RMSD calculations. More...

protocols::loops::LoopsCOP	get_loops () const
	Get the region of the protein where an backbone heavy-atom RMSD will be calculated for each step in the trajectory. More...

void	set_loops (protocols::loops::LoopsCOP)
	Set the region of the protein where an backbone heavy-atom RMSD will be calculated for each step in the trajectory. More...

core::scoring::ScoreFunctionCOP	get_score_function () const
	Get the score function used to score each step in the trajectory. More...

void	set_score_function (core::scoring::ScoreFunctionCOP)
	Set the score function used to score each step in the trajectory. More...

long	get_timer () const
	Return how long the trajectory has been running in seconds. More...

void	reset_timer ()
	Indicate that the trajectory is starting now. More...

Private Member Functions
Real	calc_score (Pose &pose) const
	Return the score of the given pose. More...

Real	calc_rmsd_to_native (Pose &pose) const
	Return the heavy-atom backbone RMSD between the given pose and the `-in:file:native` pose within the given loops. More...

Private Attributes
string	prefix_
	The prefix that will be used for the scores associated with the pose at the end of the trajectory. More...

Pose	native_pose_
	The reference structure for RMSD calculations. More...

bool	have_native_pose_ = false
	Indicate that RMSDs can be calculated because there is a native pose. More...

protocols::loops::LoopsCOP	loops_ = nullptr
	The region of the protein where an backbone heavy-atom RMSD will be calculated for each step in the trajectory. More...

core::scoring::ScoreFunctionCOP	scorefxn_ = nullptr
	The score function used to score each step in the trajectory. More...

long	start_time_ = 0
	The number of seconds since the epoch that had elapsed at the beginning of the trajectory. More...

Detailed Description

Log a detailed account of everything that happens in a loop modeling simulation.

Basic usage is to initialize the logger either with one of the constructors or the init() method, then to call the record methods (e.g. record_move()) whenever something of note happens. The record method were written with LoopProtocol and LoopBuilder in mind, so you may have to add some of your own record methods if you want to use this logger with another LoopMover subclass.

Constructor & Destructor Documentation

◆ TrajectoryLogger() [1/3]

protocols::loop_modeling::utilities::TrajectoryLogger::TrajectoryLogger ( string const & prefix = "" )

Construct an empty logger.

Use the init() method to give the setup the logger before any of the record methods are called.

References core::import_pose::PDB_file, and core::import_pose::pose_from_file().

◆ TrajectoryLogger() [2/3]

protocols::loop_modeling::utilities::TrajectoryLogger::TrajectoryLogger	(	LoopMover const *	mover,
		string const &	prefix = `""`
	)

Construct a logger from a loop mover.

The given loop mover must have both a loops and a score function at the time to constructor is called. If either condition is not met, an exception will be raised.

References init().

◆ TrajectoryLogger() [3/3]

protocols::loop_modeling::utilities::TrajectoryLogger::TrajectoryLogger	(	protocols::loops::LoopsCOP	loops,
		core::scoring::ScoreFunctionCOP	scorefxn,
		string const &	prefix = `""`
	)

Construct a logger from a score function and a loops object.

Member Function Documentation

◆ calc_rmsd_to_native()

Real protocols::loop_modeling::utilities::TrajectoryLogger::calc_rmsd_to_native ( Pose & pose ) const

private

Return the heavy-atom backbone RMSD between the given pose and the -in:file:native pose within the given loops.

References have_native_pose_, core::scoring::is_protein_backbone(), loops_, native_pose_, core::scoring::rmsd_no_super_subset(), and core::pose::Pose::size().

Referenced by record_endpoint(), record_move(), and record_new_pose().

◆ calc_score()

Real protocols::loop_modeling::utilities::TrajectoryLogger::calc_score ( Pose & pose ) const

private

Return the score of the given pose.

References scorefxn_.

Referenced by record_endpoint(), record_move(), record_new_pose(), and record_new_score_function().

◆ get_loops()

LoopsCOP protocols::loop_modeling::utilities::TrajectoryLogger::get_loops ( void ) const

Get the region of the protein where an backbone heavy-atom RMSD will be calculated for each step in the trajectory.

See also: loops_

References loops_.

◆ get_native_pose()

Pose const & protocols::loop_modeling::utilities::TrajectoryLogger::get_native_pose ( ) const

Get the reference structure for RMSD calculations.

See also: native_pose_

References native_pose_.

◆ get_prefix()

string protocols::loop_modeling::utilities::TrajectoryLogger::get_prefix ( ) const

Get the prefix that will be used for the scores associated with the pose at the end of the trajectory.

References prefix_.

◆ get_score_function()

ScoreFunctionCOP protocols::loop_modeling::utilities::TrajectoryLogger::get_score_function ( ) const

Get the score function used to score each step in the trajectory.

References scorefxn_.

◆ get_timer()

long protocols::loop_modeling::utilities::TrajectoryLogger::get_timer ( ) const

Return how long the trajectory has been running in seconds.

References start_time_.

Referenced by record_endpoint(), and record_move().

◆ init() [1/2]

void protocols::loop_modeling::utilities::TrajectoryLogger::init ( LoopMover const * mover )

Initialize the logger from a loop mover after it has been constructed.

References protocols::loop_modeling::LoopMover::get_tool(), protocols::loop_modeling::ToolboxKeys::LOOPS, and protocols::loop_modeling::ToolboxKeys::SCOREFXN.

Referenced by TrajectoryLogger().

◆ init() [2/2]

void protocols::loop_modeling::utilities::TrajectoryLogger::init	(	protocols::loops::LoopsCOP	loops,
		core::scoring::ScoreFunctionCOP	scorefxn
	)

Initialize the logger from a score function and a loops object after it has been constructed.

◆ record_endpoint()

void protocols::loop_modeling::utilities::TrajectoryLogger::record_endpoint	(	basic::Tracer &	tr,
		Pose &	pose
	)		const

Record the end of a protocol.

Print out some more expensive quality metrics and attach some scores to the pose itself.

References calc_rmsd_to_native(), calc_score(), core::scoring::chainbreak, protocols::simple_filters::BuriedUnsatHbondFilter::compute(), core::pose::Pose::energies(), get_timer(), have_native_pose_, core::pose::Pose::is_fullatom(), native_pose_, prefix_, protocols::hybridization::score, protocols::simple_filters::BuriedUnsatHbondFilter::set_report_bb_heavy_atom_unsats(), protocols::simple_filters::BuriedUnsatHbondFilter::set_report_sc_heavy_atom_unsats(), core::pose::setPoseExtraScore(), core::scoring::Energies::total_energies(), and core::chemical::tr().

◆ record_move() [1/2]

void protocols::loop_modeling::utilities::TrajectoryLogger::record_move	(	basic::Tracer &	tr,
		Pose &	pose,
		core::Size const	i,
		core::Size const	j,
		core::Size const	k,
		bool const	proposed,
		bool const	accepted
	)		const

Record a single Monte Carlo move.

This overload is meant for use in LoopProtocol, which uses three nested for-loops to ramp some score function terms and the temperature at different rates.

Parameters

tr	The output stream to record the move to.
pose	The pose on which the last move was made (used for calculating a score and an RMSD).
i	The current "score function" cycle.
j	The current "temperature" cycle.
k	The current "mover" cycle.
proposed	Whether or not a move was proposed (i.e. did the loop mover succeed in producing a new conformation).
accepted	Whether or not the last move was accepted (i.e. did it pass the Metropolis criterion).

References calc_rmsd_to_native(), calc_score(), get_timer(), have_native_pose_, and core::chemical::tr().

◆ record_move() [2/2]

void protocols::loop_modeling::utilities::TrajectoryLogger::record_move	(	basic::Tracer &	tr,
		Pose &	pose,
		core::Size const	iteration,
		bool const	proposed,
		bool const	accepted
	)		const

Record a single Monte Carlo move.

This overload is meant for use in LoopBuilder, which generates loop conformation is a single non-nested for-loop.

Parameters

tr	The output stream to record the move to.
pose	The pose on which the last move was made (used for calculating a score and an RMSD).
i	The current iteration.
proposed	Whether or not a move was proposed (i.e. did the loop mover succeed in producing a new conformation).
accepted	Whether or not the last move was accepted (i.e. did it pass the Metropolis criterion).

References calc_rmsd_to_native(), calc_score(), get_timer(), have_native_pose_, and core::chemical::tr().

◆ record_new_pose()

void protocols::loop_modeling::utilities::TrajectoryLogger::record_new_pose	(	basic::Tracer &	tr,
		Pose &	pose
	)		const

Record when a low-scoring pose is recovered.

References calc_rmsd_to_native(), calc_score(), have_native_pose_, and core::chemical::tr().

◆ record_new_score_function()

void protocols::loop_modeling::utilities::TrajectoryLogger::record_new_score_function	(	basic::Tracer &	tr,
		Pose &	pose
	)		const

Record when a score function term is ramped (and scores change as a result).

References calc_score(), core::scoring::chainbreak, core::scoring::fa_rep, core::scoring::rama, core::scoring::rama2b, scorefxn_, and core::chemical::tr().

◆ record_new_temperature()

void protocols::loop_modeling::utilities::TrajectoryLogger::record_new_temperature	(	basic::Tracer &	tr,
		Real	temperature
	)		const

Record when the temperature is ramped.

References core::chemical::tr().

◆ reset_timer()

void protocols::loop_modeling::utilities::TrajectoryLogger::reset_timer ( )

Indicate that the trajectory is starting now.

The timer is automatically started when the logger is constructed, you only need to call this method if the logger is constructed significantly before the trajectory in question begins.

References start_time_.

◆ set_loops()

void protocols::loop_modeling::utilities::TrajectoryLogger::set_loops ( protocols::loops::LoopsCOP )

Set the region of the protein where an backbone heavy-atom RMSD will be calculated for each step in the trajectory.

See also: loops_

References loops_.

◆ set_native_pose()

void protocols::loop_modeling::utilities::TrajectoryLogger::set_native_pose ( Pose const & pose )

Set the reference structure for RMSD calculations.

See also: native_pose_

References have_native_pose_, and native_pose_.

◆ set_prefix()

void protocols::loop_modeling::utilities::TrajectoryLogger::set_prefix ( string prefix )

Set the prefix that will be used for the scores associated with the pose at the end of the trajectory.

References prefix_.

◆ set_score_function()

void protocols::loop_modeling::utilities::TrajectoryLogger::set_score_function ( core::scoring::ScoreFunctionCOP scorefxn )

Set the score function used to score each step in the trajectory.

References scorefxn_.

◆ unset_native_pose()

void protocols::loop_modeling::utilities::TrajectoryLogger::unset_native_pose ( )

Disable RMSD calculations.

References have_native_pose_.

Member Data Documentation

◆ have_native_pose_

bool protocols::loop_modeling::utilities::TrajectoryLogger::have_native_pose_ = false

private

Indicate that RMSDs can be calculated because there is a native pose.

Referenced by calc_rmsd_to_native(), record_endpoint(), record_move(), record_new_pose(), set_native_pose(), and unset_native_pose().

◆ loops_

protocols::loops::LoopsCOP protocols::loop_modeling::utilities::TrajectoryLogger::loops_ = nullptr

private

The region of the protein where an backbone heavy-atom RMSD will be calculated for each step in the trajectory.

The RMSD is calculated relative to the -in:file:native structure. If that option was not specified, no RMSD will be calculated.

Referenced by calc_rmsd_to_native(), get_loops(), and set_loops().

◆ native_pose_

Pose protocols::loop_modeling::utilities::TrajectoryLogger::native_pose_

private

The reference structure for RMSD calculations.

This structure is typically initialized from -in:file:native in the constructor. Reading a pose in from a file is fairly expensive, and we want to calculate RMSDs after every iteration, so it's important that this initialization only happen once.

Referenced by calc_rmsd_to_native(), get_native_pose(), record_endpoint(), and set_native_pose().

◆ prefix_

string protocols::loop_modeling::utilities::TrajectoryLogger::prefix_

private

The prefix that will be used for the scores associated with the pose at the end of the trajectory.

Referenced by get_prefix(), record_endpoint(), and set_prefix().

◆ scorefxn_

core::scoring::ScoreFunctionCOP protocols::loop_modeling::utilities::TrajectoryLogger::scorefxn_ = nullptr

private

The score function used to score each step in the trajectory.

Referenced by calc_score(), get_score_function(), record_new_score_function(), and set_score_function().

◆ start_time_

long protocols::loop_modeling::utilities::TrajectoryLogger::start_time_ = 0

private

The number of seconds since the epoch that had elapsed at the beginning of the trajectory.

Referenced by get_timer(), and reset_timer().

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

src/protocols/loop_modeling/utilities/TrajectoryLogger.hh
src/protocols/loop_modeling/utilities/TrajectoryLogger.cc

Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ TrajectoryLogger() [1/3]

◆ TrajectoryLogger() [2/3]

◆ TrajectoryLogger() [3/3]

Member Function Documentation

◆ calc_rmsd_to_native()

◆ calc_score()

◆ get_loops()

◆ get_native_pose()

◆ get_prefix()

◆ get_score_function()

◆ get_timer()

◆ init() [1/2]

◆ init() [2/2]

◆ record_endpoint()

◆ record_move() [1/2]

◆ record_move() [2/2]

◆ record_new_pose()

◆ record_new_score_function()

◆ record_new_temperature()

◆ reset_timer()

◆ set_loops()

◆ set_native_pose()

◆ set_prefix()

◆ set_score_function()

◆ unset_native_pose()

Member Data Documentation

◆ have_native_pose_

◆ loops_

◆ native_pose_

◆ prefix_

◆ scorefxn_

◆ start_time_