align¶

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

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

Bases: pybind11_builtins.pybind11_object

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t) -> None
__init__(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClusterer, pose_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, moving_res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, options: pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions, force_align: bool) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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_builtins.pybind11_object

__delattr__¶: Implement delattr(self, name).

__dir__() → list¶: default dir() implementation

__eq__¶: Return self==value.

__format__()¶: default object formatter

__ge__¶: Return self>=value.

__getattribute__¶: Return getattr(self, name).

__gt__¶: Return self>value.

__hash__¶: Return hash(self).

__init__(*args, **kwargs)¶

Overloaded function.

__init__(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, silent_files_in: pyrosetta.rosetta.utility.vector1_std_string) -> None
__init__(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, silent_file_in: str) -> None
__init__(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, sfd: pyrosetta.rosetta.core.io.silent.SilentFileData) -> None
__init__(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, silent_file_data: pyrosetta.rosetta.core.io.silent.SilentFileData, moving_res_list: pyrosetta.rosetta.utility.vector1_unsigned_long, options: pyrosetta.rosetta.protocols.stepwise.modeler.options.StepWiseModelerOptions, force_align: bool) -> None
__init__(self: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased, arg0: pyrosetta.rosetta.protocols.stepwise.modeler.align.StepWiseLegacyClustererSilentBased) -> None

__init_subclass__()¶

This method is called when a class is subclassed.

The default implementation does nothing. It may be overridden to extend subclasses.

__le__¶: Return self<=value.

__lt__¶: Return self<value.

__ne__¶: Return self!=value.

__new__()¶: Create and return a new object. See help(type) for accurate signature.

__reduce__()¶: helper for pickle

__reduce_ex__()¶: helper for pickle

__repr__¶: Return repr(self).

__setattr__¶: Implement setattr(self, name, value).

__sizeof__() → int¶: size of object in memory, in bytes

__str__¶: Return str(self).

__subclasshook__()¶

Abstract classes can override this to customize issubclass().

This is invoked early on by abc.ABCMeta.__subclasscheck__(). It should return True, False or NotImplemented. If it returns NotImplemented, the normal algorithm is used. Otherwise, it overrides the normal algorithm (and the outcome is cached).

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¶: 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 class std::basic_string<char> &) –> 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_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 class std::basic_string<char> &) –> 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> > > &

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.

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>

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.

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

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

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