A container for the options used by the EnergyBasedClusteringProtocol. More...

#include <EnergyBasedClusteringOptions.hh>

Inheritance diagram for protocols::energy_based_clustering::EnergyBasedClusteringOptions:

Public Member Functions
	EnergyBasedClusteringOptions (bool const initialize_from_options=true)
	Default constructor. More...

	~EnergyBasedClusteringOptions () override
	Destructor. More...

EnergyBasedClusteringOptionsOP	clone () const

void	initialize_from_global_options ()
	Initialize this option from the global options system. More...

Public Attributes
bool	prerelax_
	Should imported structures be subjected to a round of fast relaxation? Default false. More...

core::Size	relax_rounds_
	The number of fastrelax rounds to apply if the prerelax_ option is used. Default 1. More...

EBC_ClusterType	cluster_by_
	What should I use as the basis for clustering? More...

bool	use_CB_
	If clustering by backbone Cartesian coordinates, should beta carbons be included? Default false. Note that if this option is used, none of the input structures can contain glycine. More...

core::Real	cluster_radius_
	The radius for clustering, in Angstroms for Cartesian clustering and degrees for dihedral clustering. Default 1.0. More...

utility::vector1< core::Size >	residues_to_ignore_
	List of residues to ignore in alignments for clustering. Default empty list. More...

utility::vector1< core::Size >	chains_to_ignore_
	List of chains to ignore in alignments for clustering. Default empty list. More...

core::Size	limit_structures_per_cluster_
	Maximum number of structures to output per cluster. Default no limit (0). More...

core::Size	limit_clusters_
	Maximum number of clusters to output. Default no limit (0). More...

bool	cyclic_
	If true, constraints are added to make a peptide bond between the N- and C-termini. If false (default), the termini are free. Default false. More...

core::Size	cyclic_symmetry_
	If provided, structures that do not have the desired symmetry are filtered out. Set to 2 for C2 or S2 symmetry, 3 for C3 symmetry, 4 for C4 or S4 symmetry, etc. Unused (0) if not specified. Can only be used with the cyclic_ option. More...

bool	cyclic_symmetry_mirroring_
	If true, then SN symmetry is used instead of CN. Unused if not specified. Can only be used with the cyclic_ and cyclic_symmetry_ options. More...

core::Real	cyclic_symmetry_threshold_
	The angle threshold, in degrees, for determining whether a cyclic peptide is symmetric. Can only be used with the cyclic_ and cyclic_symmetry_ flags. Defaults to 10.0 degrees. More...

bool	cyclic_symmetry_threshold_specified_
	Has the user specified a cyclic symmetry threshold? More...

bool	cluster_cyclic_permutations_
	If true, all cyclic permutations are tried when comparing two structures for clustering. Requires cyclic_ true. Default false. More...

core::Size	cyclic_permutation_offset_
	1 by default, meaning that every cyclic permutation is clustered if cluster_cyclic_permutations_ is true. Values X > 1 mean that cyclic permutations shifted by X residues will be clustered. More...

bool	perform_ABOXYZ_bin_analysis_
	If true, alpha-amino acid bin analysis is performed using the ABOXYZ bins defined in Hosseinzadeh, Bhardwaj, Mulligan, et al. (2018). False by default. More...

bool	mutate_to_ala_
	If true, the input structures will be converted to a chain of alanines (L- or D-) before scoring. Default false. More...

utility::vector1< core::Size >	disulfide_positions_
	A space-separated list of positions that are disulfide-bonded. For example, disulfide_positions_ 3 8 6 23 would mean that residues 3 and 8 are disulfide-bonded, as are residues 6 and 23. Default empty list. More...

bool	homooligomer_swap_
	If the structures contain multiple chains with identical sequence, setting this to true will test all permutations of chains when clustering. Default false. More...

bool	silent_output_
	Write output to a silent file instead of to separate PDBs. This will create two files: one that only contains the first member of each cluster, and one that contains everything. Default false. More...

utility::vector1< std::string >	cst_files_
	A user-specified set of one or more constraints file. Default unused. More...

utility::vector1< std::string >	extra_rms_atoms_
	A list of additional atoms to use in the RMSD calculation, each in the format residue:atomname separated by whitespace. For example, -v_extra_rms_atoms 7:SG 12:CG 12:CD 12:CE 12:NZ 14:OG. Default empty list. More...

bool	rebuild_all_in_dihedral_mode_
	In dihedral clustering mode, do we rebuild everything for output? More...

std::string	output_prefix_
	Prefix to prepend on output files. More...

std::string	path_to_scores_file_
	Holds the path to a file with alternative scores to sort by. More...

Detailed Description

A container for the options used by the EnergyBasedClusteringProtocol.

All data are public in this class. It's just a dumb bag for holding data.

Constructor & Destructor Documentation

◆ EnergyBasedClusteringOptions()

protocols::energy_based_clustering::EnergyBasedClusteringOptions::EnergyBasedClusteringOptions ( bool const initialize_from_options = true )

Default constructor.

Initializes from options system by default. Can be disabled by passing 'false'.

References initialize_from_global_options().

◆ ~EnergyBasedClusteringOptions()

protocols::energy_based_clustering::EnergyBasedClusteringOptions::~EnergyBasedClusteringOptions ( )

overridedefault

Destructor.

Member Function Documentation

◆ clone()

EnergyBasedClusteringOptionsOP protocols::energy_based_clustering::EnergyBasedClusteringOptions::clone ( ) const

◆ initialize_from_global_options()

void protocols::energy_based_clustering::EnergyBasedClusteringOptions::initialize_from_global_options ( )

Initialize this option from the global options system.

Called by default constructor.

References chains_to_ignore_, cluster_by_, cluster_cyclic_permutations_, cluster_radius_, cst_files_, cyclic_, cyclic_permutation_offset_, cyclic_symmetry_, cyclic_symmetry_mirroring_, cyclic_symmetry_threshold_, cyclic_symmetry_threshold_specified_, disulfide_positions_, protocols::energy_based_clustering::EBC_bb_cartesian, protocols::energy_based_clustering::EBC_bb_dihedral, extra_rms_atoms_, homooligomer_swap_, limit_clusters_, limit_structures_per_cluster_, mutate_to_ala_, output_prefix_, path_to_scores_file_, perform_ABOXYZ_bin_analysis_, prerelax_, rebuild_all_in_dihedral_mode_, relax_rounds_, residues_to_ignore_, silent_output_, and use_CB_.

Referenced by EnergyBasedClusteringOptions().

Member Data Documentation

◆ chains_to_ignore_

utility::vector1< core::Size > protocols::energy_based_clustering::EnergyBasedClusteringOptions::chains_to_ignore_

List of chains to ignore in alignments for clustering. Default empty list.

◆ cluster_by_

EBC_ClusterType protocols::energy_based_clustering::EnergyBasedClusteringOptions::cluster_by_

What should I use as the basis for clustering?

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_option_checks(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), initialize_from_global_options(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::swap_alignment_vector().

◆ cluster_cyclic_permutations_

bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::cluster_cyclic_permutations_

If true, all cyclic permutations are tried when comparing two structures for clustering. Requires cyclic_ true. Default false.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_ABOXYZ_bin_analysis(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_option_checks(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), and initialize_from_global_options().

◆ cluster_radius_

core::Real protocols::energy_based_clustering::EnergyBasedClusteringOptions::cluster_radius_

The radius for clustering, in Angstroms for Cartesian clustering and degrees for dihedral clustering. Default 1.0.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_option_checks(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), and initialize_from_global_options().

◆ cst_files_

utility::vector1< std::string > protocols::energy_based_clustering::EnergyBasedClusteringOptions::cst_files_

A user-specified set of one or more constraints file. Default unused.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::add_user_constraints(), initialize_from_global_options(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::set_up_scorefunction().

◆ cyclic_

bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::cyclic_

If true, constraints are added to make a peptide bond between the N- and C-termini. If false (default), the termini are free. Default false.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_option_checks(), initialize_from_global_options(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::set_up_scorefunction().

◆ cyclic_permutation_offset_

core::Size protocols::energy_based_clustering::EnergyBasedClusteringOptions::cyclic_permutation_offset_

1 by default, meaning that every cyclic permutation is clustered if cluster_cyclic_permutations_ is true. Values X > 1 mean that cyclic permutations shifted by X residues will be clustered.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), and initialize_from_global_options().

◆ cyclic_symmetry_

core::Size protocols::energy_based_clustering::EnergyBasedClusteringOptions::cyclic_symmetry_

If provided, structures that do not have the desired symmetry are filtered out. Set to 2 for C2 or S2 symmetry, 3 for C3 symmetry, 4 for C4 or S4 symmetry, etc. Unused (0) if not specified. Can only be used with the cyclic_ option.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_option_checks(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), and initialize_from_global_options().

◆ cyclic_symmetry_mirroring_

bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::cyclic_symmetry_mirroring_

If true, then SN symmetry is used instead of CN. Unused if not specified. Can only be used with the cyclic_ and cyclic_symmetry_ options.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_option_checks(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), and initialize_from_global_options().

◆ cyclic_symmetry_threshold_

core::Real protocols::energy_based_clustering::EnergyBasedClusteringOptions::cyclic_symmetry_threshold_

The angle threshold, in degrees, for determining whether a cyclic peptide is symmetric. Can only be used with the cyclic_ and cyclic_symmetry_ flags. Defaults to 10.0 degrees.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_option_checks(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), and initialize_from_global_options().

◆ cyclic_symmetry_threshold_specified_

bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::cyclic_symmetry_threshold_specified_

Has the user specified a cyclic symmetry threshold?

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_option_checks(), and initialize_from_global_options().

◆ disulfide_positions_

utility::vector1< core::Size > protocols::energy_based_clustering::EnergyBasedClusteringOptions::disulfide_positions_

A space-separated list of positions that are disulfide-bonded. For example, disulfide_positions_ 3 8 6 23 would mean that residues 3 and 8 are disulfide-bonded, as are residues 6 and 23. Default empty list.

Referenced by initialize_from_global_options(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::make_disulfides().

◆ extra_rms_atoms_

utility::vector1< std::string > protocols::energy_based_clustering::EnergyBasedClusteringOptions::extra_rms_atoms_

A list of additional atoms to use in the RMSD calculation, each in the format residue:atomname separated by whitespace. For example, -v_extra_rms_atoms 7:SG 12:CG 12:CD 12:CE 12:NZ 14:OG. Default empty list.

Referenced by initialize_from_global_options(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::parse_extra_atom_list().

◆ homooligomer_swap_

bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::homooligomer_swap_

If the structures contain multiple chains with identical sequence, setting this to true will test all permutations of chains when clustering. Default false.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::calc_dist(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_option_checks(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), and initialize_from_global_options().

◆ limit_clusters_

core::Size protocols::energy_based_clustering::EnergyBasedClusteringOptions::limit_clusters_

Maximum number of clusters to output. Default no limit (0).

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), and initialize_from_global_options().

◆ limit_structures_per_cluster_

core::Size protocols::energy_based_clustering::EnergyBasedClusteringOptions::limit_structures_per_cluster_

Maximum number of structures to output per cluster. Default no limit (0).

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), and initialize_from_global_options().

◆ mutate_to_ala_

bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::mutate_to_ala_

If true, the input structures will be converted to a chain of alanines (L- or D-) before scoring. Default false.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_option_checks(), and initialize_from_global_options().

◆ output_prefix_

std::string protocols::energy_based_clustering::EnergyBasedClusteringOptions::output_prefix_

Prefix to prepend on output files.

By default, read from options system.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), and initialize_from_global_options().

◆ path_to_scores_file_

std::string protocols::energy_based_clustering::EnergyBasedClusteringOptions::path_to_scores_file_

Holds the path to a file with alternative scores to sort by.

Expects one pose per line starting with the poses file name as returned by descriptor_string, whitespace separation and the score

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), initialize_from_global_options(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::parse_alternative_score_file().

◆ perform_ABOXYZ_bin_analysis_

bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::perform_ABOXYZ_bin_analysis_

If true, alpha-amino acid bin analysis is performed using the ABOXYZ bins defined in Hosseinzadeh, Bhardwaj, Mulligan, et al. (2018). False by default.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), and initialize_from_global_options().

◆ prerelax_

bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::prerelax_

Should imported structures be subjected to a round of fast relaxation? Default false.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), and initialize_from_global_options().

◆ rebuild_all_in_dihedral_mode_

bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::rebuild_all_in_dihedral_mode_

In dihedral clustering mode, do we rebuild everything for output?

Just rebuilds the mainchain if false. True by default.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), initialize_from_global_options(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::storeposedata().

◆ relax_rounds_

core::Size protocols::energy_based_clustering::EnergyBasedClusteringOptions::relax_rounds_

The number of fastrelax rounds to apply if the prerelax_ option is used. Default 1.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), and initialize_from_global_options().

◆ residues_to_ignore_

utility::vector1< core::Size > protocols::energy_based_clustering::EnergyBasedClusteringOptions::residues_to_ignore_

List of residues to ignore in alignments for clustering. Default empty list.

◆ silent_output_

bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::silent_output_

Write output to a silent file instead of to separate PDBs. This will create two files: one that only contains the first member of each cluster, and one that contains everything. Default false.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go(), and initialize_from_global_options().

◆ use_CB_

bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::use_CB_

If clustering by backbone Cartesian coordinates, should beta carbons be included? Default false. Note that if this option is used, none of the input structures can contain glycine.

Referenced by protocols::energy_based_clustering::EnergyBasedClusteringProtocol::alignment_atoms_in_res(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::do_initial_import_and_scoring(), initialize_from_global_options(), protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_in_rmsd(), and protocols::energy_based_clustering::EnergyBasedClusteringProtocol::use_this_atom().

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

src/protocols/energy_based_clustering/EnergyBasedClusteringOptions.hh
src/protocols/energy_based_clustering/EnergyBasedClusteringOptions.cc

Public Member Functions

Public Attributes

Detailed Description

Constructor & Destructor Documentation

◆ EnergyBasedClusteringOptions()

◆ ~EnergyBasedClusteringOptions()

Member Function Documentation

◆ clone()

◆ initialize_from_global_options()

Member Data Documentation

◆ chains_to_ignore_

◆ cluster_by_

◆ cluster_cyclic_permutations_

◆ cluster_radius_

◆ cst_files_

◆ cyclic_

◆ cyclic_permutation_offset_

◆ cyclic_symmetry_

◆ cyclic_symmetry_mirroring_

◆ cyclic_symmetry_threshold_

◆ cyclic_symmetry_threshold_specified_

◆ disulfide_positions_

◆ extra_rms_atoms_

◆ homooligomer_swap_

◆ limit_clusters_

◆ limit_structures_per_cluster_

◆ mutate_to_ala_

◆ output_prefix_

◆ path_to_scores_file_

◆ perform_ABOXYZ_bin_analysis_

◆ prerelax_

◆ rebuild_all_in_dihedral_mode_

◆ relax_rounds_

◆ residues_to_ignore_

◆ silent_output_

◆ use_CB_