energy_based_clustering

Bindings for protocols::energy_based_clustering namespace

class pyrosetta.rosetta.protocols.energy_based_clustering.EBC_ClusterType

Bases: pybind11_builtins.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
class pyrosetta.rosetta.protocols.energy_based_clustering.EnergyBasedClusteringOptions

Bases: pybind11_builtins.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 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_builtins.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