#include <RamaPrePro.hh>

Inheritance diagram for core::scoring::RamaPrePro:

Public Types
typedef pose::Pose	Pose

typedef chemical::AA	AA

Public Member Functions
	RamaPrePro ()

	~RamaPrePro () override=default

Real	eval_rpp_rama_score (core::conformation::Conformation const &conf, core::chemical::ResidueTypeCOP res1, core::chemical::ResidueTypeCOP res2, utility::vector1< core::Real > const &mainchain_torsions) const
	Evaluate the rama score for this residue (res1) given the identity of the next (res_aa2). More...

void	eval_rpp_rama_derivatives (core::conformation::Conformation const &conf, core::chemical::ResidueTypeCOP res1, core::chemical::ResidueTypeCOP res2, utility::vector1< core::Real > const &mainchain_torsions, utility::vector1< core::Real > &gradient) const
	Evaluate the rama score for this residue (res1) given the identity of the next (res_aa2). More...

void	eval_rpp_rama_score (AA const res_aa1, core::chemical::ResidueTypeCOP res2, Real const phi, Real const psi, Real &score_rama, Real &denergy_dphi, Real &denergy_dpsi, bool const return_derivs) const
	Evaluate the rama score for this residue (res_aa1) given the identity of the next (res_aa2). More...

void	random_mainchain_torsions (core::conformation::Conformation const &conf, core::chemical::ResidueTypeCOP res1, core::chemical::ResidueTypeCOP res2, utility::vector1< core::Real > &torsions) const
	Given the current residue (res1) and the next one (res2), randomly draw mainchain torsion values for the current residue, biased by the Ramachandran probabilities for its type. More...

utility::vector1< core::Size > const &	get_mainchain_torsions_covered (core::conformation::Conformation const &conf, core::chemical::ResidueTypeCOP res1, core::chemical::ResidueTypeCOP res2) const
	Get a const reference to the vector of mainchain torsions indices that the mainchain potential for a given noncanonical ResidueType covers. More...

utility::vector1 < id::PartialAtomID >	atoms_w_dof_derivatives (conformation::Residue const &res, pose::Pose const &) const
	Return a vector of the atoms that determine the DOFs covered by the RamaPrePro tables; these may extend beyond the residue in question and therefore must be described using PartialAtomIDs. More...

void	random_mainchain_torsions (core::chemical::AA const res_aa1, core::chemical::ResidueTypeCOP res2, utility::vector1< core::Real > &torsions) const
	Given the current residue (res1) and the next one (res2), randomly draw mainchain torsion values for the current residue, biased by the Ramachandran probabilities for its type. More...

bool	is_N_substituted (core::chemical::ResidueTypeCOP restype) const
	Returns true if this aa is aa_pro or aa_dpr, false otherwise. More...

Private Member Functions
void	read_canonical_rpp_tables ()
	Ensure that the RamaPrePro scoring tables for the 20 canonical amino acids are set up, and that we are storing pointers to them in a map of AA enum -> MainchainScoreTableCOP. More...

utility::vector1< core::Real >	invert_vector (utility::vector1< core::Real > const &input_vect) const
	Return the input vector multiplied by -1. More...

utility::vector1< core::Size > const &	get_mainchain_torsions_covered (core::conformation::Conformation const &conf, core::chemical::ResidueTypeCOP res, bool res_next_n_substituted) const
	Get a const reference to the vector of mainchain torsions indices that the mainchain potential for a given noncanonical ResidueType covers. More...

Private Attributes
std::map< core::chemical::AA, core::chemical::mainchain_potential::MainchainScoreTableCOP >	canonical_score_tables_
	Owning pointers to the MainchainScoreTables for the canonical amino acids. More...

std::map< core::chemical::AA, core::chemical::mainchain_potential::MainchainScoreTableCOP >	canonical_prepro_score_tables_
	Owning pointers to the MainchainScoreTables for the canonical amino acids, pre-proline versions. More...

Member Typedef Documentation

typedef chemical::AA core::scoring::RamaPrePro::AA

typedef pose::Pose core::scoring::RamaPrePro::Pose

Constructor & Destructor Documentation

core::scoring::RamaPrePro::RamaPrePro ( )

References read_canonical_rpp_tables().

core::scoring::RamaPrePro::~RamaPrePro ( )

overridedefault

Member Function Documentation

utility::vector1< id::PartialAtomID > core::scoring::RamaPrePro::atoms_w_dof_derivatives	(	conformation::Residue const &	res,
		pose::Pose const &	pose
	)		const

Return a vector of the atoms that determine the DOFs covered by the RamaPrePro tables; these may extend beyond the residue in question and therefore must be described using PartialAtomIDs.

The PartialAtomID is currently only able to represent the connect atoms themselves – they cannot specify the atoms away from the connect atoms that might also define torsions. If any RamaPrePro table were to use the last mainchain torsion in a residue (e.g. omega for amino acids), then the last atom defining that torsion would be excluded from the list.

References core::pose::Pose::conformation(), get_mainchain_torsions_covered(), core::conformation::insert_partial_atom_ids_for_mainchain_torsion(), and core::conformation::Residue::type_ptr().

Referenced by core::energy_methods::RamaPreProEnergy::atoms_with_dof_derivatives().

void core::scoring::RamaPrePro::eval_rpp_rama_derivatives	(	core::conformation::Conformation const &	conf,
		core::chemical::ResidueTypeCOP	res1,
		core::chemical::ResidueTypeCOP	res2,
		utility::vector1< core::Real > const &	input_mainchain_torsions,
		utility::vector1< core::Real > &	gradient
	)		const

Evaluate the rama score for this residue (res1) given the identity of the next (res_aa2).

Evaluate the rama score for this residue (res1) given the identity of the next (res2).

This version works for noncanonical or canonical residues with any number of mainchain torsions. If the next residue's identity is pro or d-pro, a different score table is used.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

This version works for noncanonical or canonical residues with any number of mainchain torsions. If the next residue's identity is pro or d-pro, a different score table is used.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).; some maintenece by Jack Maguire, jackm.nosp@m.agui.nosp@m.re144.nosp@m.4@gm.nosp@m.ail.c.nosp@m.om.

References core::chemical::aa_gly, eval_rpp_rama_score(), core::scoring::ScoringManager::get_rama_prepro_mainchain_torsion_potential(), invert_vector(), core::chemical::is_canonical_D_aa(), core::chemical::is_canonical_L_aa_or_gly(), is_N_substituted(), and core::conformation::Conformation::residue_type_set_for_conf().

Referenced by core::energy_methods::RamaPreProEnergy::eval_intraresidue_dof_derivative().

Real core::scoring::RamaPrePro::eval_rpp_rama_score	(	core::conformation::Conformation const &	conf,
		core::chemical::ResidueTypeCOP	res1,
		core::chemical::ResidueTypeCOP	res2,
		utility::vector1< core::Real > const &	input_mainchain_torsions
	)		const

Evaluate the rama score for this residue (res1) given the identity of the next (res_aa2).

Evaluate the rama score for this residue (res1) given the identity of the next (res2).

This version works for noncanonical or canonical residues with any number of mainchain torsions. If the next residue's identity is pro or d-pro, a different score table is used.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::chemical::aa_gly, core::scoring::ScoringManager::get_rama_prepro_mainchain_torsion_potential(), invert_vector(), core::chemical::is_canonical_D_aa(), core::chemical::is_canonical_L_aa_or_gly(), is_N_substituted(), and core::conformation::Conformation::residue_type_set_for_conf().

Referenced by protocols::generalized_kinematic_closure::filter::GeneralizedKICfilter::apply_rama_prepro_check(), eval_rpp_rama_derivatives(), protocols::stepwise::modeler::protein::StepWiseProteinBackboneSampler::rama_energy(), and core::energy_methods::RamaPreProEnergy::residue_pair_energy().

void core::scoring::RamaPrePro::eval_rpp_rama_score	(	AA const	res_aa1,
		core::chemical::ResidueTypeCOP	res2,
		Real const	phi,
		Real const	psi,
		Real &	score_rama,
		Real &	denergy_dphi,
		Real &	denergy_dpsi,
		bool const	return_derivs
	)		const

Evaluate the rama score for this residue (res_aa1) given the identity of the next (res_aa2).

Evaluate the rama score for this residue (res_aa1) given the identity of the next (res2).

This version only works for canonical L-amino acids, canonical D-amino acids, or glycine. If the next residue's identity is pro or d-pro, a different score table is used. Note: if return_derivs is true, the gradient vector is populated only. If it is false, then only the score_rama value is populated.

Author: Rewritten by Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::chemical::aa_gly, canonical_prepro_score_tables_, canonical_score_tables_, core::chemical::get_L_equivalent(), core::chemical::is_canonical_D_aa(), core::chemical::is_canonical_L_aa_or_gly(), is_N_substituted(), and core::chemical::num_canonical_aas.

utility::vector1< core::Size > const & core::scoring::RamaPrePro::get_mainchain_torsions_covered	(	core::conformation::Conformation const &	conf,
		core::chemical::ResidueTypeCOP	res1,
		core::chemical::ResidueTypeCOP	res2
	)		const

Get a const reference to the vector of mainchain torsions indices that the mainchain potential for a given noncanonical ResidueType covers.

For example, for an oligourea, this would return {1, 2, 3}, since the Rama maps for oligoureas cover phi, theta, and psi (mainchain torsions 1, 2, and 3, respectively), but not mu or omega (mainchain torsions 4 and 5).

Parameters

[in]	conf	The current conformation, for reference.
[in]	res1	The current residue, for which we're drawing mainchain torsions.
[in]	res2	The next residue, used to determine whether to use pre-proline tables or not.

References is_N_substituted().

Referenced by atoms_w_dof_derivatives(), and protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_mainchain_torsions().

utility::vector1< core::Size > const & core::scoring::RamaPrePro::get_mainchain_torsions_covered	(	core::conformation::Conformation const &	conf,
		core::chemical::ResidueTypeCOP	res,
		bool	res_next_n_substituted
	)		const

private

Get a const reference to the vector of mainchain torsions indices that the mainchain potential for a given noncanonical ResidueType covers.

For example, for an oligourea, this would return {1, 2, 3}, since the Rama maps for oligoureas cover phi, theta, and psi (mainchain torsions 1, 2, and 3, respectively), but not mu or omega (mainchain torsions 4 and 5).

Parameters

[in]	conf	The current conformation, for reference.
[in]	res1	The current residue, for which we're drawing mainchain torsions.
[in]	res2	The next residue, used to determine whether to use pre-proline tables or not.

References core::chemical::aa_unk, core::scoring::ScoringManager::get_rama_prepro_mainchain_torsion_potential(), and core::conformation::Conformation::residue_type_set_for_conf().

utility::vector1< core::Real > core::scoring::RamaPrePro::invert_vector ( utility::vector1< core::Real > const & input_vect ) const

private

Return the input vector multiplied by -1.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

Referenced by eval_rpp_rama_derivatives(), and eval_rpp_rama_score().

bool core::scoring::RamaPrePro::is_N_substituted ( core::chemical::ResidueTypeCOP restype ) const

Returns true if this aa is aa_pro or aa_dpr, false otherwise.

Also returns true for an N-methyl amino acid, peptoid, or proline-like oligourea.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References protocols::cluster::calibur::aa, core::chemical::aa_dpr, core::chemical::aa_pro, and core::chemical::ou3_pro.

Referenced by eval_rpp_rama_derivatives(), eval_rpp_rama_score(), get_mainchain_torsions_covered(), and random_mainchain_torsions().

void core::scoring::RamaPrePro::random_mainchain_torsions	(	core::conformation::Conformation const &	conf,
		core::chemical::ResidueTypeCOP	res1,
		core::chemical::ResidueTypeCOP	res2,
		utility::vector1< core::Real > &	torsions
	)		const

Given the current residue (res1) and the next one (res2), randomly draw mainchain torsion values for the current residue, biased by the Ramachandran probabilities for its type.

This version is general, usable for canonicals or noncanonicals.

Parameters

[in]	conf	The current conformation, for reference.
[in]	res1	The current residue, for which we're drawing mainchain torsions.
[in]	res2	The next residue, used to determine whether to use pre-proline tables or not.
[out]	torsions	A vector of mainchain torsions for the current residue.

Note: If the mainchain potential is a function of fewer than all of the mainchain torsions, the vector returned will not have random values for the torsions that the mainchain potential is not a function of. Rather, these torsions will be set to 0. Use the RamaPrePro::get_mainchain_torsions_covered() function to get a vector of torsion indices that were randomized based on the mainchain potential CDF.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

This version is general, usable for canonicals or noncanonicals.

Parameters

[in]	res1	The current residue, for which we're drawing mainchain torsions.
[in]	res2	The next residue, used to determine whether to use pre-proline tables or not.
[out]	torsions	A vector of mainchain torsions for the current residue.

Note: If the mainchain potential is a function of fewer than all of the mainchain torsions, the vector returned will not have random values for the torsions that the mainchain potential is not a function of. Rather, these torsions will be set to 0. Use the RamaPrePro::get_mainchain_torsions_covered() function to get a vector of torsion indices that were randomized based on the mainchain potential CDF.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References core::chemical::aa_gly, core::chemical::is_canonical_D_aa(), core::chemical::is_canonical_L_aa_or_gly(), is_N_substituted(), and core::conformation::Conformation::residue_type_set_for_conf().

Referenced by protocols::backbone_moves::RandomizeBBByRamaPrePro::apply(), and protocols::cyclic_peptide_predict::SimpleCycpepPredictApplication::set_mainchain_torsions().

void core::scoring::RamaPrePro::random_mainchain_torsions	(	core::chemical::AA const	res_aa1,
		core::chemical::ResidueTypeCOP	res2,
		utility::vector1< core::Real > &	torsions
	)		const

Given the current residue (res1) and the next one (res2), randomly draw mainchain torsion values for the current residue, biased by the Ramachandran probabilities for its type.

This version is for canonical residues only.

Parameters

[in]	res_aa1	The AA enum for a canonical residue type.
[in]	res2	The next residue, used to determine whether to use pre-proline tables or not.
[out]	torsions	A vector of mainchain torsions for the current residue.

Author: Vikram K. Mulligan (vmull.nosp@m.ig@u.nosp@m.w.edu).

References canonical_prepro_score_tables_, canonical_score_tables_, core::chemical::get_L_equivalent(), core::chemical::is_canonical_D_aa(), is_N_substituted(), and core::chemical::num_canonical_aas.

void core::scoring::RamaPrePro::read_canonical_rpp_tables ( )

private

Ensure that the RamaPrePro scoring tables for the 20 canonical amino acids are set up, and that we are storing pointers to them in a map of AA enum -> MainchainScoreTableCOP.