Bindings for protocols::stepwise::modeler::align namespace

Classes
		builtins.object StepWiseClusterer StepWiseLegacyClusterer StepWiseLegacyClustererSilentBased StepWisePoseAligner   class StepWiseClusterer(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.protocols.stepwise.modeler.align.StepWiseClusterer) -> NoneType   2. __init__(self : rosetta.protocols.stepwise.modeler.align.StepWiseClusterer, options : protocols::stepwise::modeler::options::StepWiseModelerOptions) -> NoneType   3. __init__(self : rosetta.protocols.stepwise.modeler.align.StepWiseClusterer,  : rosetta.protocols.stepwise.modeler.align.StepWiseClusterer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.stepwise.modeler.align.StepWiseClusterer, pose : rosetta.core.pose.Pose) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.stepwise.modeler.align.StepWiseClusterer,  : rosetta.protocols.stepwise.modeler.align.StepWiseClusterer) -> rosetta.protocols.stepwise.modeler.align.StepWiseClusterer cluster(...) from builtins.PyCapsule cluster(rosetta.protocols.stepwise.modeler.align.StepWiseClusterer) -> NoneType cluster_rmsd(...) from builtins.PyCapsule cluster_rmsd(rosetta.protocols.stepwise.modeler.align.StepWiseClusterer) -> float pose_list(...) from builtins.PyCapsule pose_list(rosetta.protocols.stepwise.modeler.align.StepWiseClusterer) -> rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t set_assume_atom_ids_invariant(...) from builtins.PyCapsule set_assume_atom_ids_invariant(self : rosetta.protocols.stepwise.modeler.align.StepWiseClusterer, setting : int) -> NoneType set_calc_rms_res(...) from builtins.PyCapsule set_calc_rms_res(self : rosetta.protocols.stepwise.modeler.align.StepWiseClusterer, setting : rosetta.utility.vector1_unsigned_long) -> NoneType set_do_checks(...) from builtins.PyCapsule set_do_checks(self : rosetta.protocols.stepwise.modeler.align.StepWiseClusterer, setting : int) -> NoneType set_max_decoys(...) from builtins.PyCapsule set_max_decoys(self : rosetta.protocols.stepwise.modeler.align.StepWiseClusterer, setting : int) -> NoneType set_pose_list(...) from builtins.PyCapsule set_pose_list(self : rosetta.protocols.stepwise.modeler.align.StepWiseClusterer, setting : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) -> NoneType set_silent_file(...) from builtins.PyCapsule set_silent_file(self : rosetta.protocols.stepwise.modeler.align.StepWiseClusterer, setting : str) -> NoneType size(...) from builtins.PyCapsule size(rosetta.protocols.stepwise.modeler.align.StepWiseClusterer) -> int   class StepWiseLegacyClusterer(builtins.object)     ////////////////////////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, pose_list : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) -> NoneType   2. __init__(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, pose_list : rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, moving_res_list : rosetta.utility.vector1_unsigned_long, options : rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions, force_align : bool) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer,  : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer) -> rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer cluster(...) from builtins.PyCapsule cluster(rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer) -> NoneType get_pose_list(...) from builtins.PyCapsule get_pose_list(rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer) -> rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t rms_pose_list(...) from builtins.PyCapsule rms_pose_list(rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer) -> rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t set_auto_tune(...) from builtins.PyCapsule set_auto_tune(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, auto_tune : bool) -> NoneType set_calc_rms_res(...) from builtins.PyCapsule set_calc_rms_res(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, calc_rms_res : rosetta.utility.vector1_unsigned_long) -> NoneType set_cluster_by_all_atom_rmsd(...) from builtins.PyCapsule set_cluster_by_all_atom_rmsd(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, setting : float) -> NoneType set_cluster_radius(...) from builtins.PyCapsule set_cluster_radius(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, setting : float) -> NoneType set_force_align(...) from builtins.PyCapsule set_force_align(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, force_align : bool) -> NoneType set_max_decoys(...) from builtins.PyCapsule set_max_decoys(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, setting : int) -> NoneType   Filter a list of poses by score. set_rename_tags(...) from builtins.PyCapsule set_rename_tags(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, setting : float) -> NoneType set_score_diff_cut(...) from builtins.PyCapsule set_score_diff_cut(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, setting : float) -> NoneType   class StepWiseLegacyClustererSilentBased(builtins.object)     ////////////////////////////////////////////////////////////////////////////////////////////// //////////////////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, silent_files_in : rosetta.utility.vector1_std_string) -> NoneType   2. __init__(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, silent_file_in : str) -> NoneType   3. __init__(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, sfd : rosetta.core.io.silent.SilentFileData) -> NoneType   4. __init__(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, silent_file_data : rosetta.core.io.silent.SilentFileData, moving_res_list : rosetta.utility.vector1_unsigned_long, options : rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions, force_align : bool) -> NoneType   5. __init__(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased,  : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased,  : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased) -> rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased cluster(...) from builtins.PyCapsule cluster(rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased) -> NoneType clustered_pose_list(...) from builtins.PyCapsule clustered_pose_list(rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased) -> rosetta.std.map_std_string_std_shared_ptr_core_pose_Pose_t get_pose_list(...) from builtins.PyCapsule get_pose_list(rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased) -> rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t output_silent_file(...) from builtins.PyCapsule output_silent_file(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, silent_file : str) -> NoneType set_auto_tune(...) from builtins.PyCapsule set_auto_tune(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, auto_tune : bool) -> NoneType set_calc_rms_res(...) from builtins.PyCapsule set_calc_rms_res(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, calc_rms_res : rosetta.utility.vector1_unsigned_long) -> NoneType set_cluster_by_all_atom_rmsd(...) from builtins.PyCapsule set_cluster_by_all_atom_rmsd(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, setting : float) -> NoneType set_cluster_radius(...) from builtins.PyCapsule set_cluster_radius(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, setting : float) -> NoneType set_force_align(...) from builtins.PyCapsule set_force_align(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, force_align : bool) -> NoneType set_max_decoys(...) from builtins.PyCapsule set_max_decoys(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, setting : int) -> NoneType   Filter a list of poses by score. set_rename_tags(...) from builtins.PyCapsule set_rename_tags(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, setting : float) -> NoneType set_rsd_type_set(...) from builtins.PyCapsule set_rsd_type_set(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, setting : str) -> NoneType set_score_diff_cut(...) from builtins.PyCapsule set_score_diff_cut(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, setting : float) -> NoneType set_silent_file_data(...) from builtins.PyCapsule set_silent_file_data(self : rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, sfd : rosetta.core.io.silent.SilentFileData) -> NoneType silent_file_data(...) from builtins.PyCapsule silent_file_data(rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased) -> rosetta.core.io.silent.SilentFileData silent_struct_output_list(...) from builtins.PyCapsule silent_struct_output_list(rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased) -> rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t   class StepWisePoseAligner(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, reference_pose : rosetta.core.pose.Pose) -> NoneType   2. __init__(self : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner,  : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. apply(...) from builtins.PyCapsule apply(self : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose : rosetta.core.pose.Pose) -> NoneType check_matching_atom_names(...) from builtins.PyCapsule check_matching_atom_names(*args, **kwargs) Overloaded function.   1. check_matching_atom_names(self : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose) -> bool   2. check_matching_atom_names(self : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, verbose : bool) -> bool   3. check_matching_atom_names(self : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, atom_id_map : rosetta.std.map_core_id_AtomID_core_id_AtomID) -> bool   4. check_matching_atom_names(self : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, atom_id_map : rosetta.std.map_core_id_AtomID_core_id_AtomID, verbose : bool) -> bool create_coordinate_constraints(...) from builtins.PyCapsule create_coordinate_constraints(self : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose : rosetta.core.pose.Pose, rmsd_screen : float) -> NoneType get_rmsd_no_superimpose(...) from builtins.PyCapsule get_rmsd_no_superimpose(*args, **kwargs) Overloaded function.   1. get_rmsd_no_superimpose(self : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose : rosetta.core.pose.Pose) -> float   2. get_rmsd_no_superimpose(self : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose : rosetta.core.pose.Pose, check_align : bool) -> float   3. get_rmsd_no_superimpose(self : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose : rosetta.core.pose.Pose, pose_reference : rosetta.core.pose.Pose) -> float   4. get_rmsd_no_superimpose(self : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose : rosetta.core.pose.Pose, pose_reference : rosetta.core.pose.Pose, check_align : bool) -> float get_rmsd_over_all_poses(...) from builtins.PyCapsule get_rmsd_over_all_poses(self : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose : rosetta.core.pose.Pose) -> float initialize(...) from builtins.PyCapsule initialize(self : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose : rosetta.core.pose.Pose) -> NoneType natoms_rmsd(...) from builtins.PyCapsule natoms_rmsd(rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) -> int natoms_superimpose_rmsd(...) from builtins.PyCapsule natoms_superimpose_rmsd(rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) -> int rmsd(...) from builtins.PyCapsule rmsd(rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) -> float rmsd_over_alignment_atoms(...) from builtins.PyCapsule rmsd_over_alignment_atoms(rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) -> float rmsd_res_in_pose(...) from builtins.PyCapsule rmsd_res_in_pose(rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) -> rosetta.utility.vector1_unsigned_long set_root_partition_res(...) from builtins.PyCapsule set_root_partition_res(self : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, setting : rosetta.utility.vector1_unsigned_long) -> NoneType set_superimpose_over_all_instantiated(...) from builtins.PyCapsule set_superimpose_over_all_instantiated(self : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, setting : bool) -> NoneType set_user_defined_calc_rms_res(...) from builtins.PyCapsule set_user_defined_calc_rms_res(self : rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, setting : rosetta.utility.vector1_unsigned_long) -> NoneType superimpose_atom_id_map(...) from builtins.PyCapsule superimpose_atom_id_map(rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) -> rosetta.std.map_core_id_AtomID_core_id_AtomID superimpose_over_all_instantiated(...) from builtins.PyCapsule superimpose_over_all_instantiated(rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) -> bool superimpose_res_in_pose(...) from builtins.PyCapsule superimpose_res_in_pose(rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) -> rosetta.utility.vector1_unsigned_long superimpose_rmsd(...) from builtins.PyCapsule superimpose_rmsd(rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) -> float

Functions
		align_pose_and_add_rmsd_constraints(...) method of builtins.PyCapsule instance align_pose_and_add_rmsd_constraints(pose : rosetta.core.pose.Pose, align_pose : rosetta.core.pose.Pose, moving_res_list : rosetta.utility.vector1_unsigned_long, rmsd_screen : float) -> NoneType create_alignment_id_map_legacy(...) method of builtins.PyCapsule instance create_alignment_id_map_legacy(*args, **kwargs) Overloaded function.   1. create_alignment_id_map_legacy(mod_pose : rosetta.core.pose.Pose, ref_pose : rosetta.core.pose.Pose, superimpose_res : rosetta.utility.vector1_unsigned_long) -> rosetta.core.id.AtomID_Map_core_id_AtomID_t   2. create_alignment_id_map_legacy(mod_pose : rosetta.core.pose.Pose, ref_pose : rosetta.core.pose.Pose, res_map : rosetta.std.map_unsigned_long_unsigned_long) -> rosetta.core.id.AtomID_Map_core_id_AtomID_t get_rmsd(...) method of builtins.PyCapsule instance get_rmsd(*args, **kwargs) Overloaded function.   1. get_rmsd(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, calc_rms_res : rosetta.utility.vector1_unsigned_long) -> float   2. get_rmsd(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, calc_rms_res : rosetta.utility.vector1_unsigned_long, check_align_at_superimpose_res : bool) -> float   3. get_rmsd(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, calc_rms_res : rosetta.utility.vector1_unsigned_long, check_align_at_superimpose_res : bool, check_switch : bool) -> float   4. get_rmsd(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose) -> float   5. get_rmsd(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, check_align_at_superimpose_res : bool) -> float   6. get_rmsd(pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, check_align_at_superimpose_res : bool, check_switch : bool) -> float superimpose_pose_legacy(...) method of builtins.PyCapsule instance superimpose_pose_legacy(mod_pose : rosetta.core.pose.Pose, ref_pose : rosetta.core.pose.Pose, res_map : rosetta.std.map_unsigned_long_unsigned_long) -> float   ////////////////////////////////////////////////////////////////////////////////////////       Superimpose mod_pose onto ref_pose using the mapping of residues from  mod_pose to ref_pose given by res_map superimpose_with_stepwise_aligner(...) method of builtins.PyCapsule instance superimpose_with_stepwise_aligner(*args, **kwargs) Overloaded function.   1. superimpose_with_stepwise_aligner(pose : rosetta.core.pose.Pose, align_pose : rosetta.core.pose.Pose) -> float   2. superimpose_with_stepwise_aligner(pose : rosetta.core.pose.Pose, align_pose : rosetta.core.pose.Pose, superimpose_over_all_instantiated : bool) -> float