energy_based_clustering¶

Bindings for protocols::energy_based_clustering namespace

class pyrosetta.rosetta.protocols.energy_based_clustering.EBC_ClusterType¶

Bases: pybind11_object

The type of clustering to perform.

Members:

EBC_bb_cartesian

EBC_bb_dihedral

EBC_end_of_list

EBC_bb_cartesian = <EBC_ClusterType.EBC_bb_cartesian: 1>¶

EBC_bb_dihedral = <EBC_ClusterType.EBC_bb_dihedral: 2>¶

EBC_end_of_list = <EBC_ClusterType.EBC_bb_dihedral: 2>¶

property name¶

property value¶

class pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions¶

Bases: pybind11_object

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.

assign(self: pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions, : pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions) → pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions¶: C++: protocols::energy_based_clustering::EnergyBasedClusteringOptions::operator=(const class protocols::energy_based_clustering::EnergyBasedClusteringOptions &) –> class protocols::energy_based_clustering::EnergyBasedClusteringOptions &

property chains_to_ignore_¶

clone(self: pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions) → pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions¶: C++: protocols::energy_based_clustering::EnergyBasedClusteringOptions::clone() const –> class std::shared_ptr<class protocols::energy_based_clustering::EnergyBasedClusteringOptions>

property cluster_by_¶

property cluster_cyclic_permutations_¶

property cluster_radius_¶

property cst_files_¶

property cyclic_¶

property cyclic_permutation_offset_¶

property cyclic_symmetry_¶

property cyclic_symmetry_mirroring_¶

property cyclic_symmetry_threshold_¶

property cyclic_symmetry_threshold_specified_¶

property disulfide_positions_¶

property extra_rms_atoms_¶

property homooligomer_swap_¶

initialize_from_global_options(self: pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions) → None¶

Initialize this option from the global options system.

Called by default constructor.

C++: protocols::energy_based_clustering::EnergyBasedClusteringOptions::initialize_from_global_options() –> void

property limit_clusters_¶

property limit_structures_per_cluster_¶

property mutate_to_ala_¶

property output_prefix_¶

property path_to_scores_file_¶

property perform_ABOXYZ_bin_analysis_¶

property prerelax_¶

property rebuild_all_in_dihedral_mode_¶

property relax_rounds_¶

property residues_to_ignore_¶

property silent_output_¶

property use_CB_¶

class pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol¶

Bases: pybind11_object

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.

assign(self: pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol, : pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol) → pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol¶: C++: protocols::energy_based_clustering::EnergyBasedClusteringProtocol::operator=(const class protocols::energy_based_clustering::EnergyBasedClusteringProtocol &) –> class protocols::energy_based_clustering::EnergyBasedClusteringProtocol &

clone(self: pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol) → pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol¶: C++: protocols::energy_based_clustering::EnergyBasedClusteringProtocol::clone() const –> class std::shared_ptr<class protocols::energy_based_clustering::EnergyBasedClusteringProtocol>

go(self: pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol) → None¶

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

C++: protocols::energy_based_clustering::EnergyBasedClusteringProtocol::go() –> void

n_clusters_from_last_run(self: pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringProtocol) → int¶

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

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

C++: protocols::energy_based_clustering::EnergyBasedClusteringProtocol::n_clusters_from_last_run() const –> unsigned long

static register_options() → None¶

Indicate which options-system options are relvant.

C++: protocols::energy_based_clustering::EnergyBasedClusteringProtocol::register_options() –> void