The meat-and-potatoes for the helical_bundle_predict application, used to predict structures of helical bundles made from canonical or noncanonical building-blocks. More...

#include <HelicalBundlePredictApplication.hh>

Inheritance diagram for protocols::helical_bundle_predict::HelicalBundlePredictApplication:

[legend]

Public Member Functions
	HelicalBundlePredictApplication ()=delete
	Delete the default constructor, and require an options constructor. More...

	HelicalBundlePredictApplication (HelicalBundlePredictApplicationOptionsCOP options_in)
	Options constructor. More...

	HelicalBundlePredictApplication (HelicalBundlePredictApplicationOptionsCOP options_in, HBP_MoveGeneratorOP centroid_move_generator_in, core::scoring::ScoreFunctionOP centroid_sfxn_in, core::scoring::ScoreFunctionOP fullatom_sfxn_in)
	Options + move generator constructor. More...

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

	~HelicalBundlePredictApplication () override
	Destructor. More...

HelicalBundlePredictApplicationOP	clone () const
	Clone operator: copy this object and return a smart pointer to the copy. More...

void	run ()
	Actually run the application and produce output. More...

void	set_native (core::pose::PoseCOP native)
	Set the native pose. More...

core::Real	align_to_native_pose (core::pose::Pose &pose) const
	Given a pose, align it to the native pose. More...

HBP_MoveGeneratorOP	create_final_fullatom_refinement_move_generator () const
	Create the move generator used for the final fullatom refinement step. More...

void	set_nstruct (core::Size const nstruct_in)
	Set the number of repeats to try. More...

void	set_output_format (core::import_pose::FileType const type)
	Set the output format. (Automatically sets extension.) More...

void	set_silent_output ()
	Indicate that we're using silent output. This overrides set_ouput_format(), and sets the extension automatically. More...

void	set_output_prefix_and_suffix (std::string const &prefix, std::string const &suffix)
	Set the prefix and suffix for output. More...

Static Public Member Functions
static HBP_MoveGeneratorOP	create_centroid_move_generator ()
	Create a new move generator. Static, so this can be called from other classes (e.g. HelicalBundlePredictApplication_MPI.) More...

static core::scoring::ScoreFunctionOP	create_centroid_scorefunction ()
	Create the scorefunction used during centroid mode. More...

static core::scoring::ScoreFunctionOP	create_fullatom_scorefunction ()
	Create the scorefunction used during fullatom mode. More...

Private Member Functions
void	load_native_pose_from_disk ()
	Read the native pose in from disk, based on the native_file_ set in the options_ object. More...

void	set_up_centroid_move_generator ()
	Given the helix assignment file's contents, set up the HBP_HelixCoilMoveGenerator used in centroid mode.. More...

core::pose::PoseOP	make_pose_from_fasta_contents () const
	Construct a pose from the contents of a FASTA file. The conformation is set to linear at this point. More...

core::pose::PoseOP	make_pose_from_sequence_file_contents () const
	Construct a pose from the contents of a sequence file. The conformation is set to linear at this point. More...

void	do_a_simulated_annealing_round (core::pose::PoseOP &pose, core::Size num_steps, HBP_MoveGeneratorCOP move_generator, HBP_TemperatureScheduleGeneratorCOP temperature_generator, core::scoring::ScoreFunction const &sfxn) const
	Do a single simulated annealing round (a Monte Carlo trajectory with temperature ramping from high to low, once). More...

void	do_simulated_annealing (core::pose::PoseOP &pose, core::Size const num_rounds, core::Size const num_steps_per_round, HBP_MoveGeneratorOP move_generator, HBP_TemperatureScheduleGeneratorOP temperature_generator, core::scoring::ScoreFunction const &sfxn) const
	Entry point into the simulated annealing. More...

void	do_final_fullatom_refinement (core::pose::PoseOP &pose) const
	Carry out the final full-atom refinement steps. More...

bool	apply_metropolis_criterion (core::Real const &old_energy, core::Real const &new_energy, core::Real const &temperature) const
	Given the old energy, the new energy, and the temperature, apply the Metropolis criterion. More...

void	check_ignore_residues_reasonable (utility::vector1< core::Size > const &ignore_residues, core::pose::PoseCOP const &pose) const
	Check that the list of residues to ignore in calculating RMSD is reasonable. More...

Private Attributes
HelicalBundlePredictApplicationOptionsCOP	options_
	Options for the application. More...

core::pose::PoseCOP	native_pose_
	The native pose. Loaded from disk when run() is called unless provided separately. More...

core::pose::PoseOP	pose_
	The pose that we're working on. More...

HBP_MoveGeneratorOP	centroid_move_generator_
	Move generator for centroid-mode Monte Carlo. More...

HBP_TemperatureScheduleGeneratorOP	centroid_temperature_generator_
	Temperature schedule generator for centroid-mode Monte Carlo. More...

core::scoring::ScoreFunctionOP	centroid_sfxn_
	The scorefunction to use in centroid mode. More...

core::scoring::ScoreFunctionOP	fullatom_sfxn_
	The scoring function to use for fullatom refinement steps. More...

HBP_MoveGeneratorOP	final_fullatom_refinement_move_generator_
	Move generator for the full-atom refinement move at the end. More...

core::Size	nstruct_
	Number of repeats to attempt. More...

std::string	outfile_prefix_ = "result_"
	The output prefix. More...

std::string	outfile_suffix_ = ""
	The output suffix. More...

std::string	outfile_extension_ = "pdb"
	The output extension. More...

core::import_pose::FileType	output_filetype_ = core::import_pose::PDB_file
	The output format. More...

bool	silent_output_ = false
	Are we doing silent output? More...

Detailed Description

The meat-and-potatoes for the helical_bundle_predict application, used to predict structures of helical bundles made from canonical or noncanonical building-blocks.

Constructor & Destructor Documentation

◆ HelicalBundlePredictApplication() [1/4]

protocols::helical_bundle_predict::HelicalBundlePredictApplication::HelicalBundlePredictApplication ( )

delete

Delete the default constructor, and require an options constructor.

◆ HelicalBundlePredictApplication() [2/4]

protocols::helical_bundle_predict::HelicalBundlePredictApplication::HelicalBundlePredictApplication ( HelicalBundlePredictApplicationOptionsCOP options_in )

Options constructor.

Stores input options directly; doesn't clone.

Note: Triggers read from disk to set up move generator!

References options_, and set_up_centroid_move_generator().

◆ HelicalBundlePredictApplication() [3/4]

protocols::helical_bundle_predict::HelicalBundlePredictApplication::HelicalBundlePredictApplication	(	HelicalBundlePredictApplicationOptionsCOP	options_in,
		HBP_MoveGeneratorOP	centroid_move_generator_in,
		core::scoring::ScoreFunctionOP	centroid_sfxn_in,
		core::scoring::ScoreFunctionOP	fullatom_sfxn_in
	)

Options + move generator constructor.

Stores input options directly; doesn't clone.

Note: Avoids read from disk by using a move generator that was already set up. The input move generator and the input scorefunctions are used directly (not cloned).

References centroid_move_generator_, centroid_sfxn_, and fullatom_sfxn_.

◆ HelicalBundlePredictApplication() [4/4]

protocols::helical_bundle_predict::HelicalBundlePredictApplication::HelicalBundlePredictApplication ( HelicalBundlePredictApplication const & src )

Copy constructor.

References centroid_move_generator_, centroid_sfxn_, and fullatom_sfxn_.

◆ ~HelicalBundlePredictApplication()

protocols::helical_bundle_predict::HelicalBundlePredictApplication::~HelicalBundlePredictApplication ( )

override

Destructor.

Member Function Documentation

◆ align_to_native_pose()

core::Real protocols::helical_bundle_predict::HelicalBundlePredictApplication::align_to_native_pose ( core::pose::Pose & pose ) const

Given a pose, align it to the native pose.

Throws an error if there's a mismatch between the pose lengths or mainchain atom counts.

Returns: RMSD to native.

References core::chemical::ResidueType::atom_is_hydrogen(), core::id::AtomID::BOGUS_ATOM_ID(), core::pose::initialize_atomid_map(), core::chemical::ResidueTypeBase::is_polymer(), core::chemical::ResidueType::mainchain_atoms(), core::chemical::ResidueTypeBase::name3(), native_pose_, options_, core::pose::Pose::residue_type(), core::scoring::superimpose_pose(), core::id::to_string(), core::pose::Pose::total_residue(), and protocols::TR().

Referenced by run().

◆ apply_metropolis_criterion()

bool protocols::helical_bundle_predict::HelicalBundlePredictApplication::apply_metropolis_criterion	(	core::Real const &	old_energy,
		core::Real const &	new_energy,
		core::Real const &	temperature
	)		const

private

Given the old energy, the new energy, and the temperature, apply the Metropolis criterion.

Referenced by do_a_simulated_annealing_round().

◆ check_ignore_residues_reasonable()

void protocols::helical_bundle_predict::HelicalBundlePredictApplication::check_ignore_residues_reasonable	(	utility::vector1< core::Size > const &	ignore_residues,
		core::pose::PoseCOP const &	pose
	)		const

private

Check that the list of residues to ignore in calculating RMSD is reasonable.

Throws if residues are outside the size of the posem or if residues are provided but there's no pose.

References core::id::to_string().

Referenced by run().

◆ clone()

HelicalBundlePredictApplicationOP protocols::helical_bundle_predict::HelicalBundlePredictApplication::clone ( ) const

Clone operator: copy this object and return a smart pointer to the copy.

◆ create_centroid_move_generator()

HBP_MoveGeneratorOP protocols::helical_bundle_predict::HelicalBundlePredictApplication::create_centroid_move_generator ( )

static

Create a new move generator. Static, so this can be called from other classes (e.g. HelicalBundlePredictApplication_MPI.)

Triggers read from disk!

◆ create_centroid_scorefunction()

core::scoring::ScoreFunctionOP protocols::helical_bundle_predict::HelicalBundlePredictApplication::create_centroid_scorefunction ( )

static

Create the scorefunction used during centroid mode.

Reads from disk! Do not use repeatedly! Store the result rather than regenerating it!

References core::scoring::ScoreFunctionFactory::create_score_function().

◆ create_final_fullatom_refinement_move_generator()

HBP_MoveGeneratorOP protocols::helical_bundle_predict::HelicalBundlePredictApplication::create_final_fullatom_refinement_move_generator ( ) const

Create the move generator used for the final fullatom refinement step.

Not static, since it depends on the options_ object.

Note: In its current form, this should not trigger a read from disk.

References fullatom_sfxn_, and options_.

◆ create_fullatom_scorefunction()

core::scoring::ScoreFunctionOP protocols::helical_bundle_predict::HelicalBundlePredictApplication::create_fullatom_scorefunction ( )

static

Create the scorefunction used during fullatom mode.

Reads from disk! Do not use repeatedly! Store the result rather than regenerating it!

Note: This returns whatever the current default fullatom scorefunction is, currently. This function is here to make it easy to hard-code a specialized scorefunction in the future if necessary.

References core::scoring::get_score_function().

◆ do_a_simulated_annealing_round()

void protocols::helical_bundle_predict::HelicalBundlePredictApplication::do_a_simulated_annealing_round	(	core::pose::PoseOP &	pose,
		core::Size	num_steps,
		HBP_MoveGeneratorCOP	move_generator,
		HBP_TemperatureScheduleGeneratorCOP	temperature_generator,
		core::scoring::ScoreFunction const &	sfxn
	)		const

private

Do a single simulated annealing round (a Monte Carlo trajectory with temperature ramping from high to low, once).

References core::io::pdb::add_to_multimodel_pdb(), apply_metropolis_criterion(), protocols::moves::MS_SUCCESS, and protocols::TR().

Referenced by do_simulated_annealing().

◆ do_final_fullatom_refinement()

void protocols::helical_bundle_predict::HelicalBundlePredictApplication::do_final_fullatom_refinement ( core::pose::PoseOP & pose ) const

private

Carry out the final full-atom refinement steps.

This is a single step, not a Monte Carlo trajectory.

References final_fullatom_refinement_move_generator_.

Referenced by run().

◆ do_simulated_annealing()

void protocols::helical_bundle_predict::HelicalBundlePredictApplication::do_simulated_annealing	(	core::pose::PoseOP &	pose,
		core::Size const	num_rounds,
		core::Size const	num_steps_per_round,
		HBP_MoveGeneratorOP	move_generator,
		HBP_TemperatureScheduleGeneratorOP	temperature_generator,
		core::scoring::ScoreFunction const &	sfxn
	)		const

private

Entry point into the simulated annealing.

Does multiple rounds of simulated annealing.

References do_a_simulated_annealing_round().

Referenced by run().

◆ load_native_pose_from_disk()

void protocols::helical_bundle_predict::HelicalBundlePredictApplication::load_native_pose_from_disk ( )

private

Read the native pose in from disk, based on the native_file_ set in the options_ object.

READS FROM DISK! This can be avoided by passing in a pointer to the native pose.

References native_pose_, options_, core::import_pose::pose_from_file(), and protocols::TR().

Referenced by run().

◆ make_pose_from_fasta_contents()

core::pose::PoseOP protocols::helical_bundle_predict::HelicalBundlePredictApplication::make_pose_from_fasta_contents ( ) const

private

Construct a pose from the contents of a FASTA file. The conformation is set to linear at this point.

References core::id::BB, core::chemical::CENTROID, core::pose::make_pose_from_sequence(), and options_.

Referenced by run().

◆ make_pose_from_sequence_file_contents()

core::pose::PoseOP protocols::helical_bundle_predict::HelicalBundlePredictApplication::make_pose_from_sequence_file_contents ( ) const

private

Construct a pose from the contents of a sequence file. The conformation is set to linear at this point.

References core::pose::add_lower_terminus_type_to_pose_residue(), protocols::cyclic_peptide::PeptideStubMover::add_residue(), core::pose::add_upper_terminus_type_to_pose_residue(), protocols::cyclic_peptide::PeptideStubMover::apply(), core::id::BB, core::chemical::CENTROID_t, options_, protocols::cyclic_peptide::PeptideStubMover::set_reset_mode(), and core::util::switch_to_residue_type_set().

Referenced by run().

◆ run()

void protocols::helical_bundle_predict::HelicalBundlePredictApplication::run ( )

◆ set_native()

void protocols::helical_bundle_predict::HelicalBundlePredictApplication::set_native ( core::pose::PoseCOP native )

Set the native pose.

Does not clone the input; sets owning pointer directly.

References native_pose_.

◆ set_nstruct()

void protocols::helical_bundle_predict::HelicalBundlePredictApplication::set_nstruct ( core::Size const nstruct_in )

inline

Set the number of repeats to try.

References nstruct_.

◆ set_output_format()

void protocols::helical_bundle_predict::HelicalBundlePredictApplication::set_output_format ( core::import_pose::FileType const type )

Set the output format. (Automatically sets extension.)

This one sets silent output to false.

References core::import_pose::end_of_filetype_list, core::import_pose::extension_from_filetype(), outfile_extension_, output_filetype_, silent_output_, and core::import_pose::SRLZ_file.

◆ set_output_prefix_and_suffix()

void protocols::helical_bundle_predict::HelicalBundlePredictApplication::set_output_prefix_and_suffix	(	std::string const &	prefix,
		std::string const &	suffix
	)

Set the prefix and suffix for output.

References outfile_prefix_, and outfile_suffix_.

◆ set_silent_output()

void protocols::helical_bundle_predict::HelicalBundlePredictApplication::set_silent_output ( )

Indicate that we're using silent output. This overrides set_ouput_format(), and sets the extension automatically.

References outfile_extension_, and silent_output_.

◆ set_up_centroid_move_generator()

void protocols::helical_bundle_predict::HelicalBundlePredictApplication::set_up_centroid_move_generator ( )

private

Given the helix assignment file's contents, set up the HBP_HelixCoilMoveGenerator used in centroid mode..

The helix_assignment_file_content_ variable must be populated first!

References centroid_move_generator_, and options_.

Referenced by HelicalBundlePredictApplication().

Member Data Documentation

◆ centroid_move_generator_

HBP_MoveGeneratorOP protocols::helical_bundle_predict::HelicalBundlePredictApplication::centroid_move_generator_

private

Move generator for centroid-mode Monte Carlo.

Referenced by HelicalBundlePredictApplication(), run(), and set_up_centroid_move_generator().

◆ centroid_sfxn_

core::scoring::ScoreFunctionOP protocols::helical_bundle_predict::HelicalBundlePredictApplication::centroid_sfxn_

private

The scorefunction to use in centroid mode.

Referenced by HelicalBundlePredictApplication(), and run().

◆ centroid_temperature_generator_

HBP_TemperatureScheduleGeneratorOP protocols::helical_bundle_predict::HelicalBundlePredictApplication::centroid_temperature_generator_

private

Temperature schedule generator for centroid-mode Monte Carlo.

Referenced by run().

◆ final_fullatom_refinement_move_generator_

HBP_MoveGeneratorOP protocols::helical_bundle_predict::HelicalBundlePredictApplication::final_fullatom_refinement_move_generator_

private

Move generator for the full-atom refinement move at the end.

Note: This generates a move that is applied ONCE.

Referenced by do_final_fullatom_refinement().

◆ fullatom_sfxn_

core::scoring::ScoreFunctionOP protocols::helical_bundle_predict::HelicalBundlePredictApplication::fullatom_sfxn_

private

The scoring function to use for fullatom refinement steps.

Referenced by create_final_fullatom_refinement_move_generator(), and HelicalBundlePredictApplication().

◆ native_pose_

core::pose::PoseCOP protocols::helical_bundle_predict::HelicalBundlePredictApplication::native_pose_

private

The native pose. Loaded from disk when run() is called unless provided separately.

Referenced by align_to_native_pose(), load_native_pose_from_disk(), run(), and set_native().

◆ nstruct_

core::Size protocols::helical_bundle_predict::HelicalBundlePredictApplication::nstruct_

private

Number of repeats to attempt.

Referenced by run(), and set_nstruct().

core::pose::PoseOP protocols::helical_bundle_predict::HelicalBundlePredictApplication::pose_

private

The pose that we're working on.

Referenced by run().

◆ silent_output_

bool protocols::helical_bundle_predict::HelicalBundlePredictApplication::silent_output_ = false

private

Are we doing silent output?

Not used in MPI build.

Referenced by run(), set_output_format(), and set_silent_output().

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

src/protocols/helical_bundle_predict/HelicalBundlePredictApplication.hh
src/protocols/helical_bundle_predict/HelicalBundlePredictApplication.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Private Attributes

Detailed Description

Constructor & Destructor Documentation

◆ HelicalBundlePredictApplication() [1/4]

◆ HelicalBundlePredictApplication() [2/4]

◆ HelicalBundlePredictApplication() [3/4]

◆ HelicalBundlePredictApplication() [4/4]

◆ ~HelicalBundlePredictApplication()

Member Function Documentation

◆ align_to_native_pose()

◆ apply_metropolis_criterion()

◆ check_ignore_residues_reasonable()

◆ clone()

◆ create_centroid_move_generator()

◆ create_centroid_scorefunction()

◆ create_final_fullatom_refinement_move_generator()

◆ create_fullatom_scorefunction()

◆ do_a_simulated_annealing_round()

◆ do_final_fullatom_refinement()

◆ do_simulated_annealing()

◆ load_native_pose_from_disk()

◆ make_pose_from_fasta_contents()

◆ make_pose_from_sequence_file_contents()

◆ run()

◆ set_native()

◆ set_nstruct()

◆ set_output_format()

◆ set_output_prefix_and_suffix()

◆ set_silent_output()

◆ set_up_centroid_move_generator()

Member Data Documentation

◆ centroid_move_generator_

◆ centroid_sfxn_

◆ centroid_temperature_generator_

◆ final_fullatom_refinement_move_generator_

◆ fullatom_sfxn_

◆ native_pose_

◆ nstruct_

◆ options_

◆ outfile_extension_

◆ outfile_prefix_

◆ outfile_suffix_

◆ output_filetype_

◆ pose_

◆ silent_output_