Performs the work done by the energy_based_clustering app. Uses an energy-biased cookie-cutter approach to cluster a large number of structures without generating an all-by-all RMSD matrix. More...

#include <EnergyBasedClusteringProtocol.hh>

Inheritance diagram for protocols::energy_based_clustering::EnergyBasedClusteringProtocol:

[legend]

Public Member Functions
	EnergyBasedClusteringProtocol ()
	Default constructor – initializes from global options system. More...

	EnergyBasedClusteringProtocol (EnergyBasedClusteringOptions const &options)
	Options constructor – avoids access to global options system. More...

	~EnergyBasedClusteringProtocol () override

EnergyBasedClusteringProtocolOP	clone () const

void	go ()
	Perform the clustering, based on options set in the options object. More...

core::Size	n_clusters_from_last_run () const
	Get the number of clusters returned from the last call to go(). More...

Static Public Member Functions
static void	register_options ()
	Indicate which options-system options are relvant. More...

Private Member Functions
bool	is_in_list (core::Size const val, utility::vector1< core::Size > const &vallist) const
	Function to determine whether a value is in a list. More...

std::string	do_ABOXYZ_bin_analysis (core::pose::Pose const &pose) const
	Given a pose, generate a string for its ABOXYZ bins. More...

bool	is_all_alpha_aa_or_peptoid (core::pose::Pose const &pose) const
	Is a pose composed only of alpha amino acids and peptoid residues (returns true), or does it have other residues (returns false)? More...

void	align_with_offset (core::pose::Pose &pose1, core::pose::Pose const &pose2, core::Size const offset, utility::vector1< core::id::NamedAtomID > const &extra_atom_list) const
	Align one pose to another with an offset in the residue count. More...

void	pose_from_posedata (core::pose::Pose const &inputpose, core::pose::Pose &outputpose, EBC_ClusterType const clustermode, std::string const &pose_descriptor, utility::vector1< core::Real > const &posedata, utility::vector1< core::Real > const &reconstruction_data, bool const rebuild_all_in_dihedral_mode=false) const
	Reconstruct a pose from posedata. More...

void	sort_cluster_list (utility::vector1< core::Size > &statelist, utility::vector1< core::Real > &poseenergies) const
	Sort the list of states in a cluster by energies. More...

core::Real	calc_dist (utility::vector1< core::Real > const &vect1, utility::vector1< core::Real > const &vect2, EBC_ClusterType const clustmode, utility::vector1< numeric::xyzVector< core::Real > > const &alignmentvect1, utility::vector1< numeric::xyzVector< core::Real > > const &alignmentvect2, core::Size const nresidues, core::pose::Pose const &firstpose) const
	Function to calculate the RMSD between two poses, based on whatever is in "posedata" for the second only. This assumes that a pose already exists for the first, and that this is provided in refpose. More...

core::Real	calc_dist (utility::vector1< core::Real > const &vect1, utility::vector1< core::Real > const &vect2, EBC_ClusterType const clustmode, utility::vector1< numeric::xyzVector< core::Real > > const &alignmentvect1, utility::vector1< numeric::xyzVector< core::Real > > const &alignmentvect2, core::Size const nresidues, core::pose::Pose const &firstpose, core::Size &offset, core::Size &permutation) const
	Overloaded form of calc_dist for cyclic permutations and for homooligomer swapping. More...

void	swap_alignment_vector (utility::vector1< numeric::xyzVector< core::Real > > const &parentvect, utility::vector1< numeric::xyzVector< core::Real > > &swappedvect, core::pose::Pose const &refpose, core::Size const permutation_number) const
	Swap chains in an alignment vector (vector of x,y,z atom coordinates). More...

core::Size	alignment_atoms_in_res (core::pose::Pose const &pose, core::Size const position) const
	Returns the number of alignment atoms in a given residue. More...

core::Size	alignment_torsions_in_res (core::pose::Pose const &pose, core::Size const position) const
	Returns the number of alignment torsion angles stored for a given residue. More...

bool	use_this_atom (core::conformation::Residue const &res1, core::conformation::Residue const &res2, core::Size const atomno, std::string const &atname1, std::string const &atname2="") const
	Function containing the special-case logic for alpha, beta, and gamma-amino acids. More...

bool	use_in_rmsd (core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::Size resno, core::Size atomno, utility::vector1< core::id::NamedAtomID > const &extra_atom_list) const
	Given a residue number, and atom number, and a pose, determine whether that atom gets used in the RMSD calculation. More...

bool	use_in_rmsd_offset (core::pose::Pose const &pose1, core::pose::Pose const &pose2, core::Size resno2, core::Size atomno, core::Size const pose1_offset, utility::vector1< core::id::NamedAtomID > const &extra_atom_list) const
	Given two poses, a residue number in the second pose, and atom number, and and offset for circular permutation, determine whether the atom is to be used in RMSD calculation. More...

void	do_option_checks () const
	Check that options have been set sensibly. More...

core::scoring::ScoreFunctionOP	set_up_scorefunction () const
	Get the global scorefunction, and set up constraints energies appropriately. More...

void	parse_extra_atom_list (utility::vector1< core::id::NamedAtomID > &extra_atom_list) const
	Given a vector of strings of format resnum:atomname, parse this out into a vector of NamedAtomIDs. More...

void	add_user_constraints (core::pose::Pose &mypose) const
	Function to add user-specified constraints (specified with a CST file) to a pose. More...

void	swap_chains (core::pose::Pose &currentpose, core::Size const permutation_number) const
	Swap chains around in a pose (circular permutation of chain indices). More...

void	get_start_and_end_aa (core::Size const chain_index, core::pose::Pose const &pose, core::Size &startaa, core::Size &endaa) const
	Get the start and end indices of chain chain_index, and store these in startaa and endaa. More...

void	get_start_and_end_indices (core::Size const chain_index, core::pose::Pose const &pose, core::Size &startindex, core::Size &endindex) const
	Get the start and end indices of chain chain_index, and store these in startaa and endaa. More...

void	make_disulfides (core::pose::Pose &mypose) const
	Function to form the disulfides based on user-specified disulfide positions (if provided), or based on automatic detection (if not). More...

void	mutate_to_alanine (core::pose::Pose &mypose) const
	Function to mutate a pose to a chain of alanines. More...

void	check_backbones_match (core::pose::Pose const &pose1, core::pose::Pose const &pose2) const
	Function to check whether two poses have matching classes of residues at matching positions: More...

void	storeposedata (core::pose::Pose const &pose, utility::vector1< core::Real > &posedata, utility::vector1< numeric::xyzVector< core::Real > > &alignmentdata, utility::vector1< core::Real > &dihedral_mode_reconstruction_data, EBC_ClusterType const clustermode, utility::vector1< core::id::NamedAtomID > const &extra_atom_list) const
	Given an input pose, store only the relevant data needed for clustering. More...

void	do_initial_import_and_scoring (core::Size &count, core::Real &lowestE, core::Size &lowestE_index, core::pose::Pose &firstpose, protocols::cyclic_peptide::CycpepSymmetryFilter const &symmfilter, utility::vector1< core::Real > &poseenergies, utility::vector1< std::string > &pose_descriptors, utility::vector1< utility::vector1< core::Real > > &posedata, utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > &alignmentdata, utility::vector1< utility::vector1< core::Real > > &dihedral_reconstruction_data, utility::vector1< std::string > &pose_binstrings, utility::vector1< core::Size > &cluster_assignments, utility::vector1< core::Size > &cluster_offsets, utility::vector1< core::Size > &cluster_oligomer_permutations, core::scoring::ScoreFunctionOP sfxn, std::map< std::string, core::Real > const &loaded_scores, utility::vector1< core::id::NamedAtomID > const &extra_atom_list) const
	Import all structures and score them, setting up derived data. More...

void	remove_extraneous_virtuals (core::pose::Pose &pose) const
	Remove cutpoint variants that add extraneous virtual atoms that mess up atom indexing. More...

void	add_cyclic_constraints (core::pose::Pose &mypose) const
	Function to add cyclic constraints to a pose. More...

void	parse_alternative_score_file (std::map< std::string, core::Real > &scores) const
	Loads alternative scores from file and writes them into scores. More...

Static Private Member Functions
static core::Size	num_asymmetric_binstrings (std::set< std::string > const &binstrings, bool const circularly_permute)
	Count the number of binstrings which are not the same as their mirror image. More...

static core::Size	num_asymmetric_binstrings_with_mirror_counterpart_represented (std::set< std::string > const &binstrings, bool const circularly_permute)
	Count the number of asymmetric binstrings (binstrings which are not the same as their mirror image) for which the mirror image is also in the set. More...

static std::string	permute_string (std::string const &string_in)
	Given a string of the form "ABCDEFG", return "BCDEFGA". More...

static char	get_mirror_bin (char const bin_in)
	Given a bin, get its mirror. (A–X, B–Y, O–Z). More...

static std::string	get_mirror_bin_sequence (std::string const &binstring_in, bool const circularly_permuted_for_alphabetization)
	Given a bin string, get its mirror. More...

static char	determine_ABOXYZ_bin (core::Real const &phi, core::Real const &psi, core::Real const &omega)
	Given phi, psi, and omega, determine the ABOXYZ bin. More...

static std::string	get_circular_permutation_first_in_alphabetical_order (std::string const &string_in)
	Given an alpha-amino acid bin string, figure out all circular permutations and return the one that's first in alphabetical order. More...

Private Attributes
EnergyBasedClusteringOptions	options_
	Clustering options, either read from global options system or passed directly to the protocol. More...

std::string	constraints_file_contents_
	The contents of an optional constraints file. More...

core::Size	n_clusters_from_last_run_
	The number of clusters produced by the last run. More...

Friends
class	::EnergyBasedClusteringTests

Detailed Description

Performs the work done by the energy_based_clustering app. Uses an energy-biased cookie-cutter approach to cluster a large number of structures without generating an all-by-all RMSD matrix.

Constructor & Destructor Documentation

◆ EnergyBasedClusteringProtocol() [1/2]

protocols::energy_based_clustering::EnergyBasedClusteringProtocol::EnergyBasedClusteringProtocol ( )

Default constructor – initializes from global options system.

◆ EnergyBasedClusteringProtocol() [2/2]

protocols::energy_based_clustering::EnergyBasedClusteringProtocol::EnergyBasedClusteringProtocol ( EnergyBasedClusteringOptions const & options )

Options constructor – avoids access to global options system.

◆ ~EnergyBasedClusteringProtocol()

protocols::energy_based_clustering::EnergyBasedClusteringProtocol::~EnergyBasedClusteringProtocol ( )

overridedefault

Member Function Documentation

◆ add_cyclic_constraints()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_cyclic_constraints ( core::pose::Pose & mypose ) const

private

Function to add cyclic constraints to a pose.

References core::pose::Pose::add_constraint(), protocols::simple_moves::DeclareBond::apply(), core::conformation::Residue::atom_index(), CaCN_ANGLE, CNCa_ANGLE, core::conformation::Residue::has(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_upper_terminus(), core::pose::remove_lower_terminus_type_from_pose_residue(), core::pose::remove_upper_terminus_type_from_pose_residue(), core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::simple_moves::DeclareBond::set(), core::pose::Pose::size(), and core::pose::Pose::total_residue().

Referenced by do_initial_import_and_scoring().

◆ add_user_constraints()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_user_constraints ( core::pose::Pose & mypose ) const

private

Function to add user-specified constraints (specified with a CST file) to a pose.

References protocols::energy_based_clustering::EnergyBasedClusteringOptions::cst_files_, and options_.

Referenced by do_initial_import_and_scoring().

◆ align_with_offset()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::align_with_offset	(	core::pose::Pose &	pose1,
		core::pose::Pose const &	pose2,
		core::Size const	offset,
		utility::vector1< core::id::NamedAtomID > const &	extra_atom_list
	)		const

private

Align one pose to another with an offset in the residue count.

References core::id::AtomID::BOGUS_ATOM_ID(), core::pose::initialize_atomid_map(), core::chemical::ResidueType::nheavyatoms(), core::pose::Pose::residue_type(), core::scoring::superimpose_pose(), core::pose::Pose::total_residue(), and use_in_rmsd_offset().

Referenced by go().

◆ alignment_atoms_in_res()

core::Size protocols::energy_based_clustering::EnergyBasedClusteringProtocol::alignment_atoms_in_res	(	core::pose::Pose const &	pose,
		core::Size const	position
	)		const

private

Returns the number of alignment atoms in a given residue.

Some special-case logic here, since oxygens are counted in peptide-like building-blocks.

Referenced by calc_dist(), get_start_and_end_indices(), and swap_alignment_vector().

◆ alignment_torsions_in_res()

core::Size protocols::energy_based_clustering::EnergyBasedClusteringProtocol::alignment_torsions_in_res	(	core::pose::Pose const &	pose,
		core::Size const	position
	)		const

private

Returns the number of alignment torsion angles stored for a given residue.

References core::pose::Pose::chain(), protocols::energy_based_clustering::EnergyBasedClusteringOptions::chains_to_ignore_, core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::connected_residue_at_upper(), is_in_list(), core::chemical::ResidueType::is_ligand(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_metal(), core::chemical::ResidueType::is_upper_terminus(), core::conformation::Residue::mainchain_torsions(), options_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), and protocols::energy_based_clustering::EnergyBasedClusteringOptions::residues_to_ignore_.

Referenced by calc_dist().

◆ calc_dist() [1/2]

core::Real protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist	(	utility::vector1< core::Real > const &	vect1,
		utility::vector1< core::Real > const &	vect2,
		EBC_ClusterType const	clustmode,
		utility::vector1< numeric::xyzVector< core::Real > > const &	alignmentvect1,
		utility::vector1< numeric::xyzVector< core::Real > > const &	alignmentvect2,
		core::Size const	nresidues,
		core::pose::Pose const &	firstpose
	)		const

private

Function to calculate the RMSD between two poses, based on whatever is in "posedata" for the second only. This assumes that a pose already exists for the first, and that this is provided in refpose.

References core::conformation::Residue::chain(), protocols::energy_based_clustering::EnergyBasedClusteringOptions::chains_to_ignore_, core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::connected_residue_at_upper(), protocols::energy_based_clustering::EBC_bb_cartesian, protocols::energy_based_clustering::EBC_bb_dihedral, core::chemical::ResidueType::is_ligand(), core::conformation::Residue::is_lower_terminus(), core::chemical::ResidueType::is_metal(), core::conformation::Residue::is_upper_terminus(), core::conformation::Residue::mainchain_torsions(), options_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), and protocols::energy_based_clustering::EnergyBasedClusteringOptions::residues_to_ignore_.

Referenced by calc_dist(), and go().

◆ calc_dist() [2/2]

core::Real protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist	(	utility::vector1< core::Real > const &	vect1,
		utility::vector1< core::Real > const &	vect2,
		EBC_ClusterType const	clustmode,
		utility::vector1< numeric::xyzVector< core::Real > > const &	alignmentvect1,
		utility::vector1< numeric::xyzVector< core::Real > > const &	alignmentvect2,
		core::Size const	nresidues,
		core::pose::Pose const &	firstpose,
		core::Size &	offset,
		core::Size &	permutation
	)		const

private

Overloaded form of calc_dist for cyclic permutations and for homooligomer swapping.

References alignment_atoms_in_res(), alignment_torsions_in_res(), calc_dist(), protocols::energy_based_clustering::EnergyBasedClusteringOptions::cluster_cyclic_permutations_, protocols::energy_based_clustering::EnergyBasedClusteringOptions::cyclic_permutation_offset_, protocols::energy_based_clustering::EBC_bb_cartesian, protocols::energy_based_clustering::EBC_bb_dihedral, protocols::energy_based_clustering::EnergyBasedClusteringOptions::homooligomer_swap_, core::pose::Pose::num_chains(), options_, and swap_alignment_vector().

◆ check_backbones_match()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::check_backbones_match	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2
	)		const

private

Function to check whether two poses have matching classes of residues at matching positions:

References core::pose::Pose::chain(), protocols::energy_based_clustering::EnergyBasedClusteringOptions::chains_to_ignore_, core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueType::is_gamma_aa(), is_in_list(), core::chemical::ResidueType::is_ligand(), core::chemical::ResidueType::is_metal(), core::chemical::ResidueType::is_NA(), core::chemical::ResidueTypeBase::is_peptoid(), options_, core::pose::Pose::residue_type(), protocols::energy_based_clustering::EnergyBasedClusteringOptions::residues_to_ignore_, core::id::to_string(), and core::pose::Pose::total_residue().

Referenced by do_initial_import_and_scoring().

◆ clone()

EnergyBasedClusteringProtocolOP protocols::energy_based_clustering::EnergyBasedClusteringProtocol::clone ( ) const

◆ determine_ABOXYZ_bin()

char protocols::energy_based_clustering::EnergyBasedClusteringProtocol::determine_ABOXYZ_bin	(	core::Real const &	phi,
		core::Real const &	psi,
		core::Real const &	omega
	)

staticprivate

Given phi, psi, and omega, determine the ABOXYZ bin.

Based on the definition in David Baker's cyclic_utilities.py Python script from 2016, with slight modification for symmetry

If phi is in the interval (-180, 0], bin is A, B, or O. If it's in the interval (0, 180], the bin is X, Y, or Z.
In the negative phi case {
- If omega is in the range (-90, 90], it's O.

If psi is in the range (-80, 50], it's B.

Else, it's A. }

In the positive phi case {

If omega is in the range [-90, 90), it's Z.

If psi is in the range [-50, 80), it's Y.

Else, it's X. }

References core::scoring::omega.

Referenced by do_ABOXYZ_bin_analysis().

◆ do_ABOXYZ_bin_analysis()

std::string protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_ABOXYZ_bin_analysis ( core::pose::Pose const & pose ) const

private

Given a pose, generate a string for its ABOXYZ bins.

If the -cluster_cyclic_permutations flag is used, all cyclic permutations of the string are considered, and the first in alphabetical order is returned.

Note: Ignores ligands and virtual residues.

References protocols::energy_based_clustering::EnergyBasedClusteringOptions::cluster_cyclic_permutations_, determine_ABOXYZ_bin(), core::pose::Pose::empty(), get_circular_permutation_first_in_alphabetical_order(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_ligand(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueType::is_virtual_residue(), core::pose::Pose::omega(), options_, core::pose::Pose::phi(), core::pose::Pose::psi(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by do_initial_import_and_scoring().

◆ do_initial_import_and_scoring()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring	(	core::Size &	count,
		core::Real &	lowestE,
		core::Size &	lowestE_index,
		core::pose::Pose &	firstpose,
		protocols::cyclic_peptide::CycpepSymmetryFilter const &	symmfilter,
		utility::vector1< core::Real > &	poseenergies,
		utility::vector1< std::string > &	pose_descriptors,
		utility::vector1< utility::vector1< core::Real > > &	posedata,
		utility::vector1< utility::vector1< numeric::xyzVector< core::Real > > > &	alignmentdata,
		utility::vector1< utility::vector1< core::Real > > &	dihedral_reconstruction_data,
		utility::vector1< std::string > &	pose_binstrings,
		utility::vector1< core::Size > &	cluster_assignments,
		utility::vector1< core::Size > &	cluster_offsets,
		utility::vector1< core::Size > &	cluster_oligomer_permutations,
		core::scoring::ScoreFunctionOP	sfxn,
		std::map< std::string, core::Real > const &	loaded_scores,
		utility::vector1< core::id::NamedAtomID > const &	extra_atom_list
	)		const

private

Import all structures and score them, setting up derived data.

Performs disk access.

Referenced by go().

◆ do_option_checks()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_option_checks ( ) const

private

Check that options have been set sensibly.

Check that symmetry options have been set sensibly.

Referenced by go().

◆ get_circular_permutation_first_in_alphabetical_order()

std::string protocols::energy_based_clustering::EnergyBasedClusteringProtocol::get_circular_permutation_first_in_alphabetical_order ( std::string const & string_in )

staticprivate

Given an alpha-amino acid bin string, figure out all circular permutations and return the one that's first in alphabetical order.

Strings must be provided in uppercase only.

References permute_string().

Referenced by do_ABOXYZ_bin_analysis(), get_mirror_bin_sequence(), num_asymmetric_binstrings(), and num_asymmetric_binstrings_with_mirror_counterpart_represented().

◆ get_mirror_bin()

char protocols::energy_based_clustering::EnergyBasedClusteringProtocol::get_mirror_bin ( char const bin_in )

staticprivate

Given a bin, get its mirror. (A–X, B–Y, O–Z).

Referenced by get_mirror_bin_sequence().

◆ get_mirror_bin_sequence()

std::string protocols::energy_based_clustering::EnergyBasedClusteringProtocol::get_mirror_bin_sequence	(	std::string const &	binstring_in,
		bool const	circularly_permuted_for_alphabetization
	)

staticprivate

Given a bin string, get its mirror.

If the boolean is true, the sequence put through every circular permutation, and the one that's first alphabetically is selected and returned.

References get_circular_permutation_first_in_alphabetical_order(), and get_mirror_bin().

Referenced by go(), num_asymmetric_binstrings(), and num_asymmetric_binstrings_with_mirror_counterpart_represented().

◆ get_start_and_end_aa()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::get_start_and_end_aa	(	core::Size const	chain_index,
		core::pose::Pose const &	pose,
		core::Size &	startaa,
		core::Size &	endaa
	)		const

private

Get the start and end indices of chain chain_index, and store these in startaa and endaa.

References core::pose::Pose::chain(), and core::pose::Pose::total_residue().

Referenced by swap_alignment_vector(), and swap_chains().

◆ get_start_and_end_indices()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::get_start_and_end_indices	(	core::Size const	chain_index,
		core::pose::Pose const &	pose,
		core::Size &	startindex,
		core::Size &	endindex
	)		const

private

Get the start and end indices of chain chain_index, and store these in startaa and endaa.

References alignment_atoms_in_res(), core::pose::Pose::chain(), and core::pose::Pose::total_residue().

Referenced by swap_alignment_vector().

◆ go()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go ( )

Perform the clustering, based on options set in the options object.

◆ is_all_alpha_aa_or_peptoid()

bool protocols::energy_based_clustering::EnergyBasedClusteringProtocol::is_all_alpha_aa_or_peptoid ( core::pose::Pose const & pose ) const

private

Is a pose composed only of alpha amino acids and peptoid residues (returns true), or does it have other residues (returns false)?

Ignores virtual residues and ligands.

References core::pose::Pose::empty(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_ligand(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueType::is_virtual_residue(), core::pose::Pose::residue_type(), and core::pose::Pose::total_residue().

Referenced by do_initial_import_and_scoring().

◆ is_in_list()

bool protocols::energy_based_clustering::EnergyBasedClusteringProtocol::is_in_list	(	core::Size const	val,
		utility::vector1< core::Size > const &	vallist
	)		const

inlineprivate

Function to determine whether a value is in a list.

References protocols::hybridization::val.

Referenced by alignment_atoms_in_res(), alignment_torsions_in_res(), check_backbones_match(), pose_from_posedata(), storeposedata(), and use_this_atom().

◆ make_disulfides()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::make_disulfides ( core::pose::Pose & mypose ) const

private

Function to form the disulfides based on user-specified disulfide positions (if provided), or based on automatic detection (if not).

References core::pose::Pose::conformation(), core::conformation::Conformation::detect_disulfides(), protocols::energy_based_clustering::EnergyBasedClusteringOptions::disulfide_positions_, core::conformation::Conformation::fix_disulfides(), and options_.

Referenced by do_initial_import_and_scoring(), and pose_from_posedata().

◆ mutate_to_alanine()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::mutate_to_alanine ( core::pose::Pose & mypose ) const

private

Function to mutate a pose to a chain of alanines.

This does not mutate cysteine residues involved in disulfide bonds. Note that this assumes that disulfide bonds have already been built in the pose.

References protocols::simple_moves::MutateResidue::apply(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueTypeBase::is_d_aa(), core::chemical::ResidueType::is_disulfide_bonded(), core::chemical::ResidueType::is_oligourea(), core::chemical::ResidueTypeBase::is_peptoid(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::pose::Pose::update_residue_neighbors().

Referenced by do_initial_import_and_scoring().

◆ n_clusters_from_last_run()

core::Size protocols::energy_based_clustering::EnergyBasedClusteringProtocol::n_clusters_from_last_run ( ) const

inline

Get the number of clusters returned from the last call to go().

Will be zero if go() has not been called.

References n_clusters_from_last_run_.

◆ num_asymmetric_binstrings()

core::Size protocols::energy_based_clustering::EnergyBasedClusteringProtocol::num_asymmetric_binstrings	(	std::set< std::string > const &	binstrings,
		bool const	circularly_permute
	)

staticprivate

Count the number of binstrings which are not the same as their mirror image.

References get_circular_permutation_first_in_alphabetical_order(), and get_mirror_bin_sequence().

Referenced by go().

◆ num_asymmetric_binstrings_with_mirror_counterpart_represented()

core::Size protocols::energy_based_clustering::EnergyBasedClusteringProtocol::num_asymmetric_binstrings_with_mirror_counterpart_represented	(	std::set< std::string > const &	binstrings,
		bool const	circularly_permute
	)

staticprivate

Count the number of asymmetric binstrings (binstrings which are not the same as their mirror image) for which the mirror image is also in the set.

This should always be an even number.

References get_circular_permutation_first_in_alphabetical_order(), and get_mirror_bin_sequence().

Referenced by go().

◆ parse_alternative_score_file()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::parse_alternative_score_file ( std::map< std::string, core::Real > & scores ) const

private

Loads alternative scores from file and writes them into scores.

References options_, protocols::energy_based_clustering::EnergyBasedClusteringOptions::path_to_scores_file_, protocols::hybridization::score, and protocols::TR().

Referenced by go().

◆ parse_extra_atom_list()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::parse_extra_atom_list ( utility::vector1< core::id::NamedAtomID > & extra_atom_list ) const

private

Given a vector of strings of format resnum:atomname, parse this out into a vector of NamedAtomIDs.

References protocols::energy_based_clustering::EnergyBasedClusteringOptions::extra_rms_atoms_, options_, and protocols::TR().

Referenced by go().

◆ permute_string()

std::string protocols::energy_based_clustering::EnergyBasedClusteringProtocol::permute_string ( std::string const & string_in )

staticprivate

Given a string of the form "ABCDEFG", return "BCDEFGA".

Referenced by get_circular_permutation_first_in_alphabetical_order().

◆ pose_from_posedata()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::pose_from_posedata	(	core::pose::Pose const &	inputpose,
		core::pose::Pose &	outputpose,
		EBC_ClusterType const	clustermode,
		std::string const &	pose_descriptor,
		utility::vector1< core::Real > const &	posedata,
		utility::vector1< core::Real > const &	reconstruction_data,
		bool const	rebuild_all_in_dihedral_mode = `false`
	)		const

private

Reconstruct a pose from posedata.

The reconstruction_data vector is unused for anything except dihedral-based building whe rebuild_all_in_dihedral_mode is true. In that case, this must be a full vector of coordinates of atoms. Otherwise, it can be empty.

References protocols::analysis::simple_metrics::RunSimpleMetricsMover::apply(), core::id::BB, core::pose::Pose::chain(), protocols::energy_based_clustering::EnergyBasedClusteringOptions::chains_to_ignore_, core::conformation::Residue::connected_residue_at_lower(), core::conformation::Residue::connected_residue_at_upper(), protocols::energy_based_clustering::EBC_bb_cartesian, protocols::energy_based_clustering::EBC_bb_dihedral, is_in_list(), core::chemical::ResidueType::is_ligand(), core::chemical::ResidueType::is_lower_terminus(), core::chemical::ResidueType::is_metal(), core::chemical::ResidueType::is_upper_terminus(), core::conformation::Residue::mainchain_torsions(), make_disulfides(), core::conformation::Residue::natoms(), options_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::energy_based_clustering::EnergyBasedClusteringOptions::residues_to_ignore_, core::pose::Pose::set_torsion(), core::pose::Pose::set_xyz(), core::pose::Pose::size(), core::pose::Pose::total_residue(), and core::pose::Pose::update_residue_neighbors().

Referenced by go().

◆ register_options()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::register_options ( )

static

Indicate which options-system options are relvant.

◆ remove_extraneous_virtuals()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::remove_extraneous_virtuals ( core::pose::Pose & pose ) const

private

Remove cutpoint variants that add extraneous virtual atoms that mess up atom indexing.

References core::chemical::CUTPOINT_LOWER, core::chemical::CUTPOINT_UPPER, core::chemical::ResidueTypeBase::has_variant_type(), core::pose::remove_variant_type_from_pose_residue(), core::pose::Pose::residue_type(), core::pose::Pose::total_residue(), and core::pose::Pose::update_residue_neighbors().

Referenced by do_initial_import_and_scoring().

◆ set_up_scorefunction()

core::scoring::ScoreFunctionOP protocols::energy_based_clustering::EnergyBasedClusteringProtocol::set_up_scorefunction ( ) const

private

Get the global scorefunction, and set up constraints energies appropriately.

References core::scoring::angle_constraint, core::scoring::atom_pair_constraint, constraints_file_contents_, protocols::energy_based_clustering::EnergyBasedClusteringOptions::cst_files_, protocols::energy_based_clustering::EnergyBasedClusteringOptions::cyclic_, core::scoring::dihedral_constraint, core::scoring::get_score_function(), options_, and protocols::TR().

Referenced by go().

◆ sort_cluster_list()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::sort_cluster_list	(	utility::vector1< core::Size > &	statelist,
		utility::vector1< core::Real > &	poseenergies
	)		const

private

Sort the list of states in a cluster by energies.

Inefficient selection sort used. That's okay – this sorts small lists.

Referenced by go().

◆ storeposedata()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata	(	core::pose::Pose const &	pose,
		utility::vector1< core::Real > &	posedata,
		utility::vector1< numeric::xyzVector< core::Real > > &	alignmentdata,
		utility::vector1< core::Real > &	dihedral_mode_reconstruction_data,
		EBC_ClusterType const	clustermode,
		utility::vector1< core::id::NamedAtomID > const &	extra_atom_list
	)		const

private

Given an input pose, store only the relevant data needed for clustering.

The "alignmentdata" array is only used for Cartesian clustering.

Referenced by do_initial_import_and_scoring().

◆ swap_alignment_vector()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::swap_alignment_vector	(	utility::vector1< numeric::xyzVector< core::Real > > const &	parentvect,
		utility::vector1< numeric::xyzVector< core::Real > > &	swappedvect,
		core::pose::Pose const &	refpose,
		core::Size const	permutation_number
	)		const

private

Swap chains in an alignment vector (vector of x,y,z atom coordinates).

Can only be called if options_.cluster_by_ == EBC_bb_cartesian.

References alignment_atoms_in_res(), protocols::energy_based_clustering::EnergyBasedClusteringOptions::cluster_by_, protocols::energy_based_clustering::EBC_bb_cartesian, get_start_and_end_aa(), get_start_and_end_indices(), core::pose::Pose::num_chains(), and options_.

Referenced by calc_dist().

◆ swap_chains()

void protocols::energy_based_clustering::EnergyBasedClusteringProtocol::swap_chains	(	core::pose::Pose &	currentpose,
		core::Size const	permutation_number
	)		const

private

Swap chains around in a pose (circular permutation of chain indices).

References core::pose::append_subpose_to_pose(), get_start_and_end_aa(), core::pose::Pose::num_chains(), and core::pose::Pose::update_residue_neighbors().

Referenced by go().

◆ use_in_rmsd()

bool protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		core::Size	resno,
		core::Size	atomno,
		utility::vector1< core::id::NamedAtomID > const &	extra_atom_list
	)		const

private

Given a residue number, and atom number, and a pose, determine whether that atom gets used in the RMSD calculation.

References core::conformation::Residue::atom_index(), core::conformation::Residue::atom_name(), core::pose::Pose::chain(), protocols::energy_based_clustering::EnergyBasedClusteringOptions::chains_to_ignore_, core::conformation::Residue::has(), core::chemical::ResidueType::has(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_n_methylated(), options_, core::pose::Pose::residue(), core::pose::Pose::residue_type(), protocols::energy_based_clustering::EnergyBasedClusteringOptions::residues_to_ignore_, protocols::energy_based_clustering::EnergyBasedClusteringOptions::use_CB_, and use_this_atom().

Referenced by storeposedata().

◆ use_in_rmsd_offset()

bool protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd_offset	(	core::pose::Pose const &	pose1,
		core::pose::Pose const &	pose2,
		core::Size	resno2,
		core::Size	atomno,
		core::Size const	pose1_offset,
		utility::vector1< core::id::NamedAtomID > const &	extra_atom_list
	)		const

private

Given two poses, a residue number in the second pose, and atom number, and and offset for circular permutation, determine whether the atom is to be used in RMSD calculation.

References core::conformation::Residue::atom_name(), core::pose::Pose::chain(), protocols::energy_based_clustering::EnergyBasedClusteringOptions::chains_to_ignore_, core::conformation::Residue::has(), options_, core::pose::Pose::residue(), protocols::energy_based_clustering::EnergyBasedClusteringOptions::residues_to_ignore_, core::pose::Pose::total_residue(), and use_this_atom().

Referenced by align_with_offset().

◆ use_this_atom()

bool protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_this_atom	(	core::conformation::Residue const &	res1,
		core::conformation::Residue const &	res2,
		core::Size const	atomno,
		std::string const &	atname1,
		std::string const &	atname2 = `""`
	)		const

private

Function containing the special-case logic for alpha, beta, and gamma-amino acids.

References core::conformation::Residue::connected_residue_at_upper(), core::chemical::ResidueType::has(), core::conformation::Residue::has_upper_connect(), core::chemical::ResidueType::is_alpha_aa(), core::chemical::ResidueType::is_beta_aa(), core::chemical::ResidueType::is_gamma_aa(), is_in_list(), core::chemical::ResidueType::is_oligourea(), core::chemical::ResidueTypeBase::is_peptoid(), core::chemical::ResidueType::mainchain_atoms(), options_, core::conformation::Residue::type(), and protocols::energy_based_clustering::EnergyBasedClusteringOptions::use_CB_.

Referenced by use_in_rmsd(), and use_in_rmsd_offset().

Friends And Related Function Documentation

◆ ::EnergyBasedClusteringTests

friend class ::EnergyBasedClusteringTests

friend

Member Data Documentation

◆ constraints_file_contents_

std::string protocols::energy_based_clustering::EnergyBasedClusteringProtocol::constraints_file_contents_

private

The contents of an optional constraints file.

Referenced by set_up_scorefunction().

◆ n_clusters_from_last_run_

core::Size protocols::energy_based_clustering::EnergyBasedClusteringProtocol::n_clusters_from_last_run_

private

The number of clusters produced by the last run.

Referenced by go(), and n_clusters_from_last_run().

◆ options_

EnergyBasedClusteringOptions protocols::energy_based_clustering::EnergyBasedClusteringProtocol::options_

private

Clustering options, either read from global options system or passed directly to the protocol.

Referenced by add_user_constraints(), alignment_atoms_in_res(), alignment_torsions_in_res(), calc_dist(), check_backbones_match(), do_ABOXYZ_bin_analysis(), do_initial_import_and_scoring(), do_option_checks(), go(), make_disulfides(), parse_alternative_score_file(), parse_extra_atom_list(), pose_from_posedata(), set_up_scorefunction(), storeposedata(), swap_alignment_vector(), use_in_rmsd(), use_in_rmsd_offset(), and use_this_atom().

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

src/protocols/energy_based_clustering/EnergyBasedClusteringProtocol.hh
src/protocols/energy_based_clustering/EnergyBasedClusteringProtocol.cc

Public Member Functions

Static Public Member Functions

Private Member Functions

Static Private Member Functions

Private Attributes

Friends

Detailed Description

Constructor & Destructor Documentation

◆ EnergyBasedClusteringProtocol() [1/2]

◆ EnergyBasedClusteringProtocol() [2/2]

◆ ~EnergyBasedClusteringProtocol()

Member Function Documentation

◆ add_cyclic_constraints()

◆ add_user_constraints()

◆ align_with_offset()

◆ alignment_atoms_in_res()

◆ alignment_torsions_in_res()

◆ calc_dist() [1/2]

◆ calc_dist() [2/2]

◆ check_backbones_match()

◆ clone()

◆ determine_ABOXYZ_bin()

◆ do_ABOXYZ_bin_analysis()

◆ do_initial_import_and_scoring()

◆ do_option_checks()

◆ get_circular_permutation_first_in_alphabetical_order()

◆ get_mirror_bin()

◆ get_mirror_bin_sequence()

◆ get_start_and_end_aa()

◆ get_start_and_end_indices()

◆ go()

◆ is_all_alpha_aa_or_peptoid()

◆ is_in_list()

◆ make_disulfides()

◆ mutate_to_alanine()

◆ n_clusters_from_last_run()

◆ num_asymmetric_binstrings()

◆ num_asymmetric_binstrings_with_mirror_counterpart_represented()

◆ parse_alternative_score_file()

◆ parse_extra_atom_list()

◆ permute_string()

◆ pose_from_posedata()

◆ register_options()

◆ remove_extraneous_virtuals()

◆ set_up_scorefunction()

◆ sort_cluster_list()

◆ storeposedata()

◆ swap_alignment_vector()

◆ swap_chains()

◆ use_in_rmsd()

◆ use_in_rmsd_offset()

◆ use_this_atom()

Friends And Related Function Documentation

◆ ::EnergyBasedClusteringTests

Member Data Documentation

◆ constraints_file_contents_

◆ n_clusters_from_last_run_

◆ options_