DumpTrajectoryEnergy, a util_method that allows one to dump rosetta trajectories through the use of the dump_trajectory ScoreType. More...

#include <DumpTrajectoryEnergy.hh>

Inheritance diagram for core::energy_methods::DumpTrajectoryEnergy:

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Public Types
typedef core::scoring::methods::WholeStructureEnergy	parent1

typedef core::scoring::annealing::ResidueArrayAnnealableEnergy	parent2

Public Types inherited from core::scoring::methods::WholeStructureEnergy
typedef EnergyMethod	parent

Public Types inherited from core::scoring::methods::EnergyMethod
typedef utility::VirtualBase	parent

Public Member Functions
	DumpTrajectoryEnergy (core::scoring::methods::EnergyMethodOptions const &options)
	Options constructor. More...

	DumpTrajectoryEnergy (DumpTrajectoryEnergy const &src)
	Copy constructor. More...

	~DumpTrajectoryEnergy () override
	Default destructor. More...

core::scoring::methods::EnergyMethodOP	clone () const override
	Clone: create a copy of this object, and return an owning pointer to the copy. More...

void	indicate_required_context_graphs (utility::vector1< bool > &context_graphs_required) const override
	DumpTrajectoryEnergy is context-independent and thus indicates that no context graphs need to be maintained by class Energies. More...

core::Size	version () const override
	DumpTrajectoryEnergy is version 2 right now. More...

void	setup_for_scoring (core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn) const override
	This is where the state_ moves to SCORING. More...

void	finalize_total_energy (core::pose::Pose &pose, core::scoring::ScoreFunction const &sfxn, core::scoring::EnergyMap &total_energy) const override
	Dump out a pose whenever we evaluate the energy. More...

void	setup_for_minimizing (pose::Pose &, core::scoring::ScoreFunction const &, kinematics::MinimizerMapBase const &) const override
	This is where the state_ moves to MINIMIZING. More...

void	finalize_after_minimizing (core::pose::Pose &pose) const override
	Reset the state to IDLE. More...

void	setup_for_derivatives (pose::Pose &pose, core::scoring::ScoreFunction const &sfxn) const override
	This is where the minimizer frames are dumped. More...

void	set_up_residuearrayannealableenergy_for_packing (core::pose::Pose &pose, core::pack::rotamer_set::RotamerSets const &rotamersets, core::scoring::ScoreFunction const &sfxn) override
	This is where the state_ moves to PACKING. More...

void	clean_up_residuearrayannealableenergy_after_packing (core::pose::Pose &pose) override
	Switch state back to IDLE. More...

core::Real	calculate_energy (utility::vector1< core::conformation::ResidueCOP > const &resvect, utility::vector1< core::Size > const &rotamer_ids, core::Size const substitution_position=0) const override
	Should be possible to dump the packer from here. Not implemented yet though. More...

Public Member Functions inherited from core::scoring::methods::WholeStructureEnergy
	WholeStructureEnergy (EnergyMethodCreatorOP)
	Constructor with EnergyMethodCreator to list the ScoreTypes computed by this WholeStructureEnergy. More...

	~WholeStructureEnergy () override

EnergyMethodType	method_type () const override
	Return one of the 7 kinds of energy methods that exist: e.g. context-dependent-one-body vs whole-structure. More...

virtual Distance	atomic_interaction_cutoff () const
	how far apart must two heavy atoms be to have a zero interaction energy? More...

Public Member Functions inherited from core::scoring::methods::EnergyMethod
	EnergyMethod (EnergyMethodCreatorOP creator)
	Constructor with EnergyMethodCreator, which lists the score types that this energy method is responsible for. More...

virtual void	setup_for_packing (pose::Pose &, utility::vector1< bool > const &, utility::vector1< bool > const &) const
	if an energy method needs to cache data in the Energies object, before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More...

virtual void	setup_for_packing_with_rotsets (pose::Pose &pose, pack_basic::RotamerSetsBaseOP const &rotsets, ScoreFunction const &sfxn) const
	if an energy method needs to cache data in the Energies object, before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing. More...

virtual void	prepare_rotamers_for_packing (pose::Pose const &, conformation::RotamerSetBase &) const
	If an energy method needs to cache data in a packing::RotamerSet object before rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing. More...

virtual void	update_residue_for_packing (pose::Pose &, Size resid) const
	If the pose changes in the middle of a packing (as happens in rotamer trials) and if an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing. More...

virtual bool	requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring (pose::Pose const &pose) const
	Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false. More...

virtual void	setup_for_scoring_for_residue (conformation::Residue const &rsd, pose::Pose const &pose, ScoreFunction const &sfxn, basic::datacache::BasicDataCache &residue_data_cache) const
	Do any setup work before scoring, caching any slow-to-compute data that will be used during energy evaluation inside of the input Residue object's data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.) More...

virtual void	finalize_after_derivatives (pose::Pose &, ScoreFunction const &) const
	called at the end of derivatives evaluation More...

virtual bool	minimize_in_whole_structure_context (pose::Pose const &) const
	Should this EnergyMethod have score and derivative evaluation evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that's serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction's traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return "true" cannot be included in RTMin. More...

virtual bool	defines_high_order_terms (pose::Pose const &) const
	Should this EnergyMethod have score and derivative evaluation evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta's get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns "false". More...

virtual void	eval_atom_derivative (id::AtomID const &id, pose::Pose const &pose, kinematics::DomainMap const &domain_map, ScoreFunction const &sfxn, EnergyMap const &emap, Vector &F1, Vector &F2) const
	Evaluate the XYZ derivative for an atom in the pose. Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom's XYZ derivative. More...

ScoreTypes const &	score_types () const
	Returns the score types that this energy method computes. More...

virtual void	show_additional_info (std::ostream &, pose::Pose &, bool) const
	show additional information of the energy method 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...

Public Member Functions inherited from core::scoring::annealing::ResidueArrayAnnealableEnergy
	ResidueArrayAnnealableEnergy ()
	Constructor. More...

	ResidueArrayAnnealableEnergy (ResidueArrayAnnealableEnergy const &src)
	Copy constructor. More...

virtual	~ResidueArrayAnnealableEnergy ()
	Destructor. More...

virtual void	commit_considered_substitution ()
	What to do when a substitution that was considered is accepted. More...

Private Types
enum	DumpState { IDLE, SCORING, MINIMIZING, PACKING }

Private Member Functions
void	try_move_to_idle () const
	Ensure that the previous activity has finished before starting a new one. More...

void	start_new_activity (DumpState new_state) const
	Perform initial setup related to an activity. More...

void	dump_pose (core::pose::Pose const &pose, bool const force=false) const
	Write out a pose, if it's appropriate to do so. More...

Private Attributes
DumpState	state_
	The activity we are currently dumping. More...

std::string	dump_filename_
	The filename where frames are being dumped to. More...

Size	dumped_frames_
	Number of dumped frames so far. More...

std::string	dump_prefix_
	Prefix for dump files. More...

bool	dump_as_gz_
	If true, output is g-zipped. More...

core::Size	dump_on_every_nth_call_
	How many function calls must elapse before we dump a pose? More...

core::Size	call_count_
	How many times has this function been called? More...

Additional Inherited Members
Protected Member Functions inherited from core::scoring::methods::EnergyMethod
void	set_score_types (EnergyMethodCreatorOP creator)
	Override the entirety of the score types list if they were initialized incorrectly in a parent's constructor. More...

Detailed Description

DumpTrajectoryEnergy, a util_method that allows one to dump rosetta trajectories through the use of the dump_trajectory ScoreType.

Member Typedef Documentation

typedef core::scoring::methods::WholeStructureEnergy core::energy_methods::DumpTrajectoryEnergy::parent1

typedef core::scoring::annealing::ResidueArrayAnnealableEnergy core::energy_methods::DumpTrajectoryEnergy::parent2

Member Enumeration Documentation

enum core::energy_methods::DumpTrajectoryEnergy::DumpState

private

Enumerator
IDLE
SCORING
MINIMIZING
PACKING

Constructor & Destructor Documentation

core::energy_methods::DumpTrajectoryEnergy::DumpTrajectoryEnergy ( core::scoring::methods::EnergyMethodOptions const & options )

Options constructor.

core::energy_methods::DumpTrajectoryEnergy::DumpTrajectoryEnergy ( DumpTrajectoryEnergy const & src )

Copy constructor.

Must move to IDLE before we duplicate.

References call_count_, dump_as_gz_, dump_filename_, dump_on_every_nth_call_, dump_prefix_, dumped_frames_, IDLE, state_, and try_move_to_idle().

core::energy_methods::DumpTrajectoryEnergy::~DumpTrajectoryEnergy ( )

override

Default destructor.

Member Function Documentation

core::Real core::energy_methods::DumpTrajectoryEnergy::calculate_energy	(	utility::vector1< core::conformation::ResidueCOP > const &	resvect,
		utility::vector1< core::Size > const &	rotamer_ids,
		core::Size const	substitution_position = `0`
	)		const

overridevirtual

Should be possible to dump the packer from here. Not implemented yet though.

Implements core::scoring::annealing::ResidueArrayAnnealableEnergy.

References core::pose::Pose::append_residue_by_bond(), core::pose::Pose::append_residue_by_jump(), call_count_, dump_on_every_nth_call_, and dump_pose().

void core::energy_methods::DumpTrajectoryEnergy::clean_up_residuearrayannealableenergy_after_packing ( core::pose::Pose & pose )

overridevirtual

Switch state back to IDLE.

Reimplemented from core::scoring::annealing::ResidueArrayAnnealableEnergy.

References call_count_, dump_on_every_nth_call_, dump_pose(), IDLE, PACKING, and state_.

core::scoring::methods::EnergyMethodOP core::energy_methods::DumpTrajectoryEnergy::clone ( ) const

overridevirtual

Clone: create a copy of this object, and return an owning pointer to the copy.

Implements core::scoring::methods::EnergyMethod.

void core::energy_methods::DumpTrajectoryEnergy::dump_pose	(	core::pose::Pose const &	pose,
		bool const	force = `false`
	)		const

private

Write out a pose, if it's appropriate to do so.

If force is true, the pose is always written out. If force is false (the default), then we check the call count and the stride, and only write if we're at the appropriate interval.

References core::io::pdb::add_to_multimodel_pdb(), call_count_, dump_filename_, dump_on_every_nth_call_, dumped_frames_, IDLE, and state_.

Referenced by calculate_energy(), clean_up_residuearrayannealableenergy_after_packing(), finalize_after_minimizing(), finalize_total_energy(), and setup_for_derivatives().

void core::energy_methods::DumpTrajectoryEnergy::finalize_after_minimizing ( core::pose::Pose & pose ) const

overridevirtual

Reset the state to IDLE.

Reimplemented from core::scoring::methods::EnergyMethod.

References call_count_, dump_on_every_nth_call_, dump_pose(), IDLE, MINIMIZING, and state_.

void core::energy_methods::DumpTrajectoryEnergy::finalize_total_energy	(	core::pose::Pose &	pose,
		core::scoring::ScoreFunction const &	sfxn,
		core::scoring::EnergyMap &	total_energy
	)		const

overridevirtual

Dump out a pose whenever we evaluate the energy.

Reimplemented from core::scoring::methods::EnergyMethod.

References dump_pose(), SCORING, and state_.

void core::energy_methods::DumpTrajectoryEnergy::indicate_required_context_graphs ( utility::vector1< bool > & context_graphs_required ) const

overridevirtual

DumpTrajectoryEnergy is context-independent and thus indicates that no context graphs need to be maintained by class Energies.

Implements core::scoring::methods::EnergyMethod.

void core::energy_methods::DumpTrajectoryEnergy::set_up_residuearrayannealableenergy_for_packing	(	core::pose::Pose &	pose,
		core::pack::rotamer_set::RotamerSets const &	rotamersets,
		core::scoring::ScoreFunction const &	sfxn
	)

overridevirtual

This is where the state_ moves to PACKING.

Reimplemented from core::scoring::annealing::ResidueArrayAnnealableEnergy.

References PACKING, and start_new_activity().

void core::energy_methods::DumpTrajectoryEnergy::setup_for_derivatives	(	pose::Pose &	pose,
		core::scoring::ScoreFunction const &	sfxn
	)		const

overridevirtual

This is where the minimizer frames are dumped.

Assumption: All minimizers must evaluate derivatives repeatedly while minimizing. Although these won't be equally spaced, dumping them is the best we can do without modifying the minimizers.

Reimplemented from core::scoring::methods::EnergyMethod.

References dump_pose().

void core::energy_methods::DumpTrajectoryEnergy::setup_for_minimizing	(	pose::Pose &	,
		core::scoring::ScoreFunction const &	,
		kinematics::MinimizerMapBase const &
	)		const