A generator for mainchain potentials. Inputs are a noncanonical residue type with an already-generated sidechain potential; outputs are a potential file suitable for use by the RamaPrePro scoreterm. More...

#include <GenerateMainchainPotential.hh>

Inheritance diagram for protocols::mainchain_potential::GenerateMainchainPotential:

[legend]

Public Member Functions
	GenerateMainchainPotential (GenerateMainchainPotentialOptionsCOP options=nullptr)
	Default constructor. More...

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

	~GenerateMainchainPotential () override
	Destructor. More...

GenerateMainchainPotentialOP	clone () const
	Clone function: make a copy of this object and return an owning pointer to the copy. More...

void	run ()
	Entry point into protocol execution. More...

void	write_last_generated_to_disk () const
	Write the last generated mainchain potential to disk. The output filename is given in the options_ object. More...

Private Member Functions
core::scoring::ScoreFunctionOP	generate_sfxn () const
	Get the scorefunction that we'll be using. More...

core::pose::PoseOP	generate_pose () const
	Generate the one-residue pose, based on options. More...

bool	protein_patches_can_apply (core::chemical::ResidueTypeCOP restype) const
	Can this residue type take protein terminal patches? More...

bool	patches_can_apply (core::chemical::ResidueTypeCOP restype, utility::vector1< core::chemical::VariantType > const &vartypes) const
	Can this residue type take specified terminal patches? More...

void	apply_protein_patches (core::pose::Pose &pose) const
	Given a one-residue pose, apply acetylated N-terminus and aminomethylated C-terminus patches. More...

void	generate_mainchain_potential (core::pose::PoseCOP pose, core::scoring::ScoreFunctionOP sfxn, core::chemical::mainchain_potential::MainchainScoreTableOP newtable, std::map< core::scoring::ScoreType, core::chemical::mainchain_potential::MainchainScoreTableOP > &last_generated_scoretables_by_scoreterm) const
	Given a pose, cycle through mainchain dihedrals and generate the mainchain potential. More...

Private Attributes
GenerateMainchainPotentialOptionsOP	options_
	This protocol's options. More...

core::chemical::mainchain_potential::MainchainScoreTableCOP	last_generated_scoretable_
	The last mainchain potential that this object generated. Nullptr if nothing has been generated. More...

std::map< core::scoring::ScoreType, core::chemical::mainchain_potential::MainchainScoreTableOP >	last_generated_scoretables_by_scoreterm_
	Mainchain potentials for each scoreterm, separately. More...

Friends
class	::GenerateMainchainPotentialTests

Detailed Description

A generator for mainchain potentials. Inputs are a noncanonical residue type with an already-generated sidechain potential; outputs are a potential file suitable for use by the RamaPrePro scoreterm.

Constructor & Destructor Documentation

◆ GenerateMainchainPotential() [1/2]

protocols::mainchain_potential::GenerateMainchainPotential::GenerateMainchainPotential ( GenerateMainchainPotentialOptionsCOP options = nullptr )

Default constructor.

Optionally takes a GenerageMainchainPotentialOptions const-owning pointer. If null, this object initializes itself to default values.

◆ GenerateMainchainPotential() [2/2]

protocols::mainchain_potential::GenerateMainchainPotential::GenerateMainchainPotential ( GenerateMainchainPotential const & src )

Copy constructor.

References last_generated_scoretables_by_scoreterm_.

◆ ~GenerateMainchainPotential()

protocols::mainchain_potential::GenerateMainchainPotential::~GenerateMainchainPotential ( )

override

Destructor.

Member Function Documentation

◆ apply_protein_patches()

void protocols::mainchain_potential::GenerateMainchainPotential::apply_protein_patches ( core::pose::Pose & pose ) const

private

Given a one-residue pose, apply acetylated N-terminus and aminomethylated C-terminus patches.

Applies aminomethylated or aminodimethylated C-terminus patches depending on settings in options.

References core::chemical::ACETYLATED_NTERMINUS_VARIANT, core::pose::add_variant_type_to_pose_residue(), core::chemical::DIMETHYLATED_CTERMINUS_VARIANT, core::chemical::ResidueTypeBase::has_variant_type(), core::chemical::METHYLATED_CTERMINUS_VARIANT, options_, core::pose::Pose::residue_type(), and core::pose::Pose::update_residue_neighbors().

Referenced by generate_pose().

◆ clone()

GenerateMainchainPotentialOP protocols::mainchain_potential::GenerateMainchainPotential::clone ( ) const

Clone function: make a copy of this object and return an owning pointer to the copy.

◆ generate_mainchain_potential()

void protocols::mainchain_potential::GenerateMainchainPotential::generate_mainchain_potential	(	core::pose::PoseCOP	pose,
		core::scoring::ScoreFunctionOP	sfxn,
		core::chemical::mainchain_potential::MainchainScoreTableOP	newtable,
		std::map< core::scoring::ScoreType, core::chemical::mainchain_potential::MainchainScoreTableOP > &	last_generated_scoretables_by_scoreterm
	)		const

private

Given a pose, cycle through mainchain dihedrals and generate the mainchain potential.

References core::id::BB, core::conformation::Residue::chi(), core::pack::create_packer_graph(), core::scoring::n_score_types, core::conformation::Residue::nchi(), options_, and protocols::TR().

Referenced by run().

◆ generate_pose()

core::pose::PoseOP protocols::mainchain_potential::GenerateMainchainPotential::generate_pose ( ) const

private

Generate the one-residue pose, based on options.

References apply_protein_patches(), core::chemical::FA_STANDARD, core::pose::make_pose_from_sequence(), options_, protein_patches_can_apply(), core::pose::remove_lower_terminus_type_from_pose_residue(), and core::pose::remove_upper_terminus_type_from_pose_residue().

Referenced by run().

◆ generate_sfxn()

core::scoring::ScoreFunctionOP protocols::mainchain_potential::GenerateMainchainPotential::generate_sfxn ( ) const

private

Get the scorefunction that we'll be using.

References core::scoring::ScoreFunctionFactory::create_score_function(), options_, and protocols::TR().

Referenced by run().

◆ patches_can_apply()

bool protocols::mainchain_potential::GenerateMainchainPotential::patches_can_apply	(	core::chemical::ResidueTypeCOP	restype,
		utility::vector1< core::chemical::VariantType > const &	vartypes
	)		const

private

Can this residue type take specified terminal patches?

References core::chemical::ResidueTypeFinder::base_type(), core::chemical::FA_STANDARD, core::chemical::ResidueTypeFinder::get_representative_type(), and core::chemical::ResidueTypeFinder::variants().

Referenced by protein_patches_can_apply().

◆ protein_patches_can_apply()

bool protocols::mainchain_potential::GenerateMainchainPotential::protein_patches_can_apply ( core::chemical::ResidueTypeCOP restype ) const

private

Can this residue type take protein terminal patches?

References core::chemical::ACETYLATED_NTERMINUS_VARIANT, core::chemical::METHYLATED_CTERMINUS_VARIANT, and patches_can_apply().

Referenced by generate_pose().

◆ run()

void protocols::mainchain_potential::GenerateMainchainPotential::run ( )

Entry point into protocol execution.

References generate_mainchain_potential(), generate_pose(), generate_sfxn(), last_generated_scoretable_, last_generated_scoretables_by_scoreterm_, and protocols::TR().

◆ write_last_generated_to_disk()

void protocols::mainchain_potential::GenerateMainchainPotential::write_last_generated_to_disk ( ) const

Write the last generated mainchain potential to disk. The output filename is given in the options_ object.

If we're writing individual scoretables for individual scoreterms, that happens here, too.

References last_generated_scoretable_, last_generated_scoretables_by_scoreterm_, core::scoring::name_from_score_type(), options_, and protocols::TR().

Friends And Related Function Documentation

◆ ::GenerateMainchainPotentialTests

friend class ::GenerateMainchainPotentialTests

friend

Member Data Documentation

◆ last_generated_scoretable_

core::chemical::mainchain_potential::MainchainScoreTableCOP protocols::mainchain_potential::GenerateMainchainPotential::last_generated_scoretable_

private

The last mainchain potential that this object generated. Nullptr if nothing has been generated.

Referenced by run(), and write_last_generated_to_disk().

◆ last_generated_scoretables_by_scoreterm_

std::map< core::scoring::ScoreType, core::chemical::mainchain_potential::MainchainScoreTableOP > protocols::mainchain_potential::GenerateMainchainPotential::last_generated_scoretables_by_scoreterm_

private

Mainchain potentials for each scoreterm, separately.

Note that these will be kept unnormalized. Moreover, each scoreterm's weight is treated as though it were 1.0.

Referenced by GenerateMainchainPotential(), run(), and write_last_generated_to_disk().

◆ options_

GenerateMainchainPotentialOptionsOP protocols::mainchain_potential::GenerateMainchainPotential::options_

private

This protocol's options.

Referenced by apply_protein_patches(), generate_mainchain_potential(), generate_pose(), generate_sfxn(), and write_last_generated_to_disk().

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

src/protocols/mainchain_potential/GenerateMainchainPotential.hh
src/protocols/mainchain_potential/GenerateMainchainPotential.cc

Public Member Functions

Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ GenerateMainchainPotential() [1/2]

◆ GenerateMainchainPotential() [2/2]

◆ ~GenerateMainchainPotential()

Member Function Documentation

◆ apply_protein_patches()

◆ clone()

◆ generate_mainchain_potential()

◆ generate_pose()

◆ generate_sfxn()

◆ patches_can_apply()

◆ protein_patches_can_apply()

◆ run()

◆ write_last_generated_to_disk()

Friends And Related Function Documentation

◆ ::GenerateMainchainPotentialTests

Member Data Documentation

◆ last_generated_scoretable_

◆ last_generated_scoretables_by_scoreterm_

◆ options_