align

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

class pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer

Bases: pybind11_object

apply(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::stepwise::modeler::align::StepWiseClusterer::apply(const class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer, : pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer) → pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer

C++: protocols::stepwise::modeler::align::StepWiseClusterer::operator=(const class protocols::stepwise::modeler::align::StepWiseClusterer &) –> class protocols::stepwise::modeler::align::StepWiseClusterer &

cluster(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer) → None

C++: protocols::stepwise::modeler::align::StepWiseClusterer::cluster() –> void

cluster_rmsd(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer) → float

C++: protocols::stepwise::modeler::align::StepWiseClusterer::cluster_rmsd() const –> double

pose_list(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t

C++: protocols::stepwise::modeler::align::StepWiseClusterer::pose_list() –> class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >

set_assume_atom_ids_invariant(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer, setting: int) → None

C++: protocols::stepwise::modeler::align::StepWiseClusterer::set_assume_atom_ids_invariant(const unsigned long &) –> void

set_calc_rms_res(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::stepwise::modeler::align::StepWiseClusterer::set_calc_rms_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_do_checks(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer, setting: int) → None

C++: protocols::stepwise::modeler::align::StepWiseClusterer::set_do_checks(const unsigned long &) –> void

set_max_decoys(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer, setting: int) → None

C++: protocols::stepwise::modeler::align::StepWiseClusterer::set_max_decoys(const unsigned long &) –> void

set_pose_list(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer, setting: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) → None

C++: protocols::stepwise::modeler::align::StepWiseClusterer::set_pose_list(const class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &) –> void

set_silent_file(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer, setting: str) → None

C++: protocols::stepwise::modeler::align::StepWiseClusterer::set_silent_file(const std::string &) –> void

size(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseClusterer) → int

C++: protocols::stepwise::modeler::align::StepWiseClusterer::size() const –> unsigned long

class pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, : pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer) → pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer

C++: protocols::stepwise::modeler::align::StepWiseLegacyClusterer::operator=(const class protocols::stepwise::modeler::align::StepWiseLegacyClusterer &) –> class protocols::stepwise::modeler::align::StepWiseLegacyClusterer &

cluster(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClusterer::cluster() –> void

get_pose_list(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t

C++: protocols::stepwise::modeler::align::StepWiseLegacyClusterer::get_pose_list() –> class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >

rms_pose_list(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t

C++: protocols::stepwise::modeler::align::StepWiseLegacyClusterer::rms_pose_list() –> class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >

set_auto_tune(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, auto_tune: bool) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_auto_tune(const bool) –> void

set_calc_rms_res(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, calc_rms_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_calc_rms_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_cluster_by_all_atom_rmsd(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, setting: float) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_cluster_by_all_atom_rmsd(const double &) –> void

set_cluster_radius(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, setting: float) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_cluster_radius(const double &) –> void

set_force_align(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, force_align: bool) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_force_align(const bool) –> void

set_max_decoys(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, setting: int) → None

Filter a list of poses by score.

C++: protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_max_decoys(const unsigned long &) –> void

set_rename_tags(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, setting: float) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_rename_tags(const double &) –> void

set_score_diff_cut(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, setting: float) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClusterer::set_score_diff_cut(const double &) –> void

class pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, : pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased) → pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::operator=(const class protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased &) –> class protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased &

cluster(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::cluster() –> void

clustered_pose_list(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased) → pyrosetta.rosetta.std.map_std_string_std_shared_ptr_core_pose_Pose_t_std_allocator_std_pair_const_std_string_std_shared_ptr_core_pose_Pose_t

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::clustered_pose_list() –> class std::map<std::string, class std::shared_ptr<class core::pose::Pose>, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class std::shared_ptr<class core::pose::Pose> > > >

get_pose_list(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::get_pose_list() –> class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > >

output_silent_file(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, silent_file: str) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::output_silent_file(const std::string &) –> void

set_auto_tune(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, auto_tune: bool) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_auto_tune(const bool) –> void

set_calc_rms_res(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, calc_rms_res: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_calc_rms_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_cluster_by_all_atom_rmsd(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, setting: float) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_cluster_by_all_atom_rmsd(const double &) –> void

set_cluster_radius(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, setting: float) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_cluster_radius(const double &) –> void

set_force_align(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, force_align: bool) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_force_align(const bool) –> void

set_max_decoys(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, setting: int) → None

Filter a list of poses by score.

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_max_decoys(const unsigned long &) –> void

set_numbered_pdb_output(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, numbered_pdb_output: bool) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_numbered_pdb_output(const bool) –> void

set_rename_tags(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, setting: float) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_rename_tags(const double &) –> void

set_rsd_type_set(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, setting: str) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_rsd_type_set(const std::string &) –> void

set_score_diff_cut(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, setting: float) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_score_diff_cut(const double &) –> void

set_silent_file_data(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData) → None

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::set_silent_file_data(class std::shared_ptr<class core::io::silent::SilentFileData> &) –> void

silent_file_data(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased) → pyrosetta.rosetta.core.io.silent.SilentFileData

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::silent_file_data() –> class std::shared_ptr<class core::io::silent::SilentFileData>

silent_struct_output_list(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_io_silent_SilentStruct_t

C++: protocols::stepwise::modeler::align::StepWiseLegacyClustererSilentBased::silent_struct_output_list() –> class utility::vector1<class std::shared_ptr<class core::io::silent::SilentStruct>, class std::allocator<class std::shared_ptr<class core::io::silent::SilentStruct> > > &

class pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner

Bases: pybind11_object

apply(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::apply(class core::pose::Pose &) –> void

check_matching_atom_names(*args, **kwargs)

Overloaded function.

1. check_matching_atom_names(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) -> bool

2. check_matching_atom_names(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, verbose: bool) -> bool

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::check_matching_atom_names(const class core::pose::Pose &, const class core::pose::Pose &, const bool) –> bool

3. check_matching_atom_names(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, atom_id_map: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID) -> bool

4. check_matching_atom_names(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, atom_id_map: pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID, verbose: bool) -> bool

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::check_matching_atom_names(const class core::pose::Pose &, const class core::pose::Pose &, const class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > > &, const bool) –> bool

create_coordinate_constraint_atom_id_map(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::create_coordinate_constraint_atom_id_map(const class core::pose::Pose &) –> class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > >

create_coordinate_constraints(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose: pyrosetta.rosetta.core.pose.Pose, rmsd_screen: float) → None

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::create_coordinate_constraints(class core::pose::Pose &, const double) –> void

get_rmsd_no_superimpose(*args, **kwargs)

Overloaded function.

1. get_rmsd_no_superimpose(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose: pyrosetta.rosetta.core.pose.Pose) -> float

2. get_rmsd_no_superimpose(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose: pyrosetta.rosetta.core.pose.Pose, check_align: bool) -> float

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_no_superimpose(const class core::pose::Pose &, const bool) –> double

3. get_rmsd_no_superimpose(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose: pyrosetta.rosetta.core.pose.Pose, pose_reference: pyrosetta.rosetta.core.pose.Pose) -> float

4. get_rmsd_no_superimpose(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose: pyrosetta.rosetta.core.pose.Pose, pose_reference: pyrosetta.rosetta.core.pose.Pose, check_align: bool) -> float

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_no_superimpose(const class core::pose::Pose &, const class core::pose::Pose &, const bool) –> double

get_rmsd_over_all_poses(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose: pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::get_rmsd_over_all_poses(class core::pose::Pose &) –> double

initialize(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::initialize(const class core::pose::Pose &) –> void

natoms_rmsd(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) → int

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::natoms_rmsd() const –> unsigned long

natoms_superimpose_rmsd(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) → int

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::natoms_superimpose_rmsd() const –> unsigned long

rmsd(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) → float

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::rmsd() const –> double

rmsd_over_alignment_atoms(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) → float

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::rmsd_over_alignment_atoms() const –> double

rmsd_res_in_pose(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::rmsd_res_in_pose() –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

set_root_partition_res(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::set_root_partition_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

set_superimpose_over_all_instantiated(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, setting: bool) → None

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::set_superimpose_over_all_instantiated(const bool &) –> void

set_user_defined_calc_rms_res(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner, setting: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::set_user_defined_calc_rms_res(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

superimpose_atom_id_map(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) → pyrosetta.rosetta.std.map_core_id_AtomID_core_id_AtomID

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_atom_id_map() –> const class std::map<class core::id::AtomID, class core::id::AtomID, struct std::less<class core::id::AtomID>, class std::allocator<struct std::pair<const class core::id::AtomID, class core::id::AtomID> > > &

superimpose_over_all_instantiated(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) → bool

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_over_all_instantiated() const –> bool

superimpose_res_in_pose(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_res_in_pose() –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

superimpose_rmsd(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWisePoseAligner) → float

C++: protocols::stepwise::modeler::align::StepWisePoseAligner::superimpose_rmsd() const –> double

pyrosetta.rosetta.protocols.stepwise.modeler.align.align_pose_and_add_rmsd_constraints(pose: pyrosetta.rosetta.core.pose.Pose, align_pose: pyrosetta.rosetta.core.pose.Pose, moving_res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, rmsd_screen: float) → None

C++: protocols::stepwise::modeler::align::align_pose_and_add_rmsd_constraints(class core::pose::Pose &, class std::shared_ptr<const class core::pose::Pose>, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const double) –> void

pyrosetta.rosetta.protocols.stepwise.modeler.align.create_alignment_id_map_legacy(*args, **kwargs)

Overloaded function.

1. create_alignment_id_map_legacy(mod_pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, superimpose_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t

C++: protocols::stepwise::modeler::align::create_alignment_id_map_legacy(const class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> class core::id::AtomID_Map<class core::id::AtomID>

2. create_alignment_id_map_legacy(mod_pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, res_map: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long) -> pyrosetta.rosetta.core.id.AtomID_Map_core_id_AtomID_t

C++: protocols::stepwise::modeler::align::create_alignment_id_map_legacy(const class core::pose::Pose &, const class core::pose::Pose &, class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > >) –> class core::id::AtomID_Map<class core::id::AtomID>

pyrosetta.rosetta.protocols.stepwise.modeler.align.get_rmsd(*args, **kwargs)

Overloaded function.

1. get_rmsd(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, calc_rms_res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> float

2. get_rmsd(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, calc_rms_res: pyrosetta.rosetta.utility.vector1_unsigned_long, check_align_at_superimpose_res: bool) -> float

3. get_rmsd(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, calc_rms_res: pyrosetta.rosetta.utility.vector1_unsigned_long, check_align_at_superimpose_res: bool, check_switch: bool) -> float

C++: protocols::stepwise::modeler::align::get_rmsd(const class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const bool, const bool) –> double

4. get_rmsd(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) -> float

5. get_rmsd(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, check_align_at_superimpose_res: bool) -> float

6. get_rmsd(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose, check_align_at_superimpose_res: bool, check_switch: bool) -> float

C++: protocols::stepwise::modeler::align::get_rmsd(const class core::pose::Pose &, const class core::pose::Pose &, const bool, const bool) –> double

pyrosetta.rosetta.protocols.stepwise.modeler.align.superimpose_pose_legacy(mod_pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, res_map: pyrosetta.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

C++: protocols::stepwise::modeler::align::superimpose_pose_legacy(class core::pose::Pose &, const class core::pose::Pose &, const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &) –> double

pyrosetta.rosetta.protocols.stepwise.modeler.align.superimpose_with_stepwise_aligner(*args, **kwargs)

Overloaded function.

1. superimpose_with_stepwise_aligner(pose: pyrosetta.rosetta.core.pose.Pose, align_pose: pyrosetta.rosetta.core.pose.Pose) -> float

2. superimpose_with_stepwise_aligner(pose: pyrosetta.rosetta.core.pose.Pose, align_pose: pyrosetta.rosetta.core.pose.Pose, superimpose_over_all_instantiated: bool) -> float

C++: protocols::stepwise::modeler::align::superimpose_with_stepwise_aligner(class core::pose::Pose &, const class core::pose::Pose &, bool) –> double