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protocols::energy_based_clustering::EnergyBasedClusteringOptions Class Reference

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

#include <EnergyBasedClusteringOptions.hh>

Inheritance diagram for protocols::energy_based_clustering::EnergyBasedClusteringOptions:
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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::Sizeresidues_to_ignore_
 List of residues to ignore in alignments for clustering. Default empty list. More...
 
utility::vector1< core::Sizechains_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::Sizedisulfide_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...
 

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

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().

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

Destructor.

Member Function Documentation

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

Member Data Documentation

utility::vector1< core::Size > protocols::energy_based_clustering::EnergyBasedClusteringOptions::chains_to_ignore_
EBC_ClusterType protocols::energy_based_clustering::EnergyBasedClusteringOptions::cluster_by_
bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::cluster_cyclic_permutations_
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().

utility::vector1< std::string > protocols::energy_based_clustering::EnergyBasedClusteringOptions::cst_files_
bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::cyclic_
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().

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().

bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::cyclic_symmetry_mirroring_
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().

bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::cyclic_symmetry_threshold_specified_
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().

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().

bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::homooligomer_swap_
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().

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().

bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::mutate_to_ala_
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().

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().

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().

bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::rebuild_all_in_dihedral_mode_
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().

utility::vector1< core::Size > protocols::energy_based_clustering::EnergyBasedClusteringOptions::residues_to_ignore_
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().

bool protocols::energy_based_clustering::EnergyBasedClusteringOptions::use_CB_

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