comparative_modeling

• features

Bindings for protocols::comparative_modeling namespace

class pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator

Bases: EvaluatorCreator

creator for the AlignRmsdTargetEvaluatorCreator class

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator) -> None

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator, arg0: pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator) -> None

3. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator, arg0: pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator) -> None

_pybind11_conduit_v1_()

add_evaluators(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator, eval: pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator) → None

C++: protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator::add_evaluators(class protocols::evaluation::MetaPoseEvaluator &) const –> void

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator, : pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator) → pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator

C++: protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator::operator=(const class protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator &) –> class protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator &

register_options(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator) → None

C++: protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator::register_options() –> void

type_name(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignRmsdTargetEvaluatorCreator) → str

C++: protocols::comparative_modeling::AlignRmsdTargetEvaluatorCreator::type_name() const –> std::string

class pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator

Bases: AlignEvaluator

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, arg0: pyrosetta.rosetta.core.pose.Pose) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, arg0: pyrosetta.rosetta.core.pose.Pose, arg1: str) -> None

doc

3. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, arg0: pyrosetta.rosetta.core.pose.Pose, arg1: str, arg2: bool) -> None

doc

4. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, arg0: pyrosetta.rosetta.core.pose.Pose, arg1: str, arg2: bool, arg3: pyrosetta.rosetta.core.sequence.SequenceAlignment) -> None

doc

5. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, native_pose: pyrosetta.rosetta.core.pose.Pose, tag: str, calc_gdt: bool, aln: pyrosetta.rosetta.core.sequence.SequenceAlignment, gdt_by_TM: bool) -> None

6. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, arg0: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator) -> None

7. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, arg0: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator) -> None

_pybind11_conduit_v1_()

applicable(*args, **kwargs)

Overloaded function.

1. applicable(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : pyrosetta.rosetta.core.pose.Pose) -> bool

C++: protocols::evaluation::SingleValuePoseEvaluator<double>::applicable(const class core::pose::Pose &) const –> bool

2. applicable(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : pyrosetta.rosetta.core.pose.Pose) -> bool

C++: protocols::evaluation::PoseEvaluator::applicable(const class core::pose::Pose &) const –> bool

apply(*args, **kwargs)

Overloaded function.

1. apply(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, pose: pyrosetta.rosetta.core.pose.Pose, tag: str, ss: pyrosetta.rosetta.core.io.silent.SilentStruct) -> None

C++: protocols::comparative_modeling::Align_RmsdEvaluator::apply(class core::pose::Pose &, std::string, class core::io::silent::SilentStruct &) const –> void

2. apply(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, : pyrosetta.rosetta.core.pose.Pose) -> float

C++: protocols::comparative_modeling::Align_RmsdEvaluator::apply(class core::pose::Pose &) const –> double

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, : pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator) → pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator

C++: protocols::comparative_modeling::Align_RmsdEvaluator::operator=(const class protocols::comparative_modeling::Align_RmsdEvaluator &) –> class protocols::comparative_modeling::Align_RmsdEvaluator &

calc_gdt(*args, **kwargs)

Overloaded function.

1. calc_gdt(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, setting: bool) -> None

C++: protocols::comparative_modeling::Align_RmsdEvaluator::calc_gdt(const bool) –> void

2. calc_gdt(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator) -> bool

C++: protocols::comparative_modeling::Align_RmsdEvaluator::calc_gdt() const –> bool

gdt_by_TM(*args, **kwargs)

Overloaded function.

1. gdt_by_TM(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, setting: bool) -> None

C++: protocols::comparative_modeling::Align_RmsdEvaluator::gdt_by_TM(const bool) –> void

2. gdt_by_TM(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator) -> bool

C++: protocols::comparative_modeling::Align_RmsdEvaluator::gdt_by_TM() const –> bool

get_alignment(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.sequence.SequenceAlignment

C++: protocols::evaluation::AlignEvaluator::get_alignment(const class core::pose::Pose &) const –> class std::shared_ptr<class core::sequence::SequenceAlignment>

name(*args, **kwargs)

Overloaded function.

1. name(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : int) -> str

C++: protocols::evaluation::SingleValuePoseEvaluator<double>::name(unsigned long) const –> std::string

2. name(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : int) -> str

C++: protocols::evaluation::PoseEvaluator::name(unsigned long) const –> std::string

native_pose(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::evaluation::AlignEvaluator::native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

report_aln_components(*args, **kwargs)

Overloaded function.

1. report_aln_components(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator, setting: bool) -> None

C++: protocols::evaluation::AlignEvaluator::report_aln_components(const bool) –> void

2. report_aln_components(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator) -> bool

C++: protocols::evaluation::AlignEvaluator::report_aln_components() const –> bool

report_gdt_components(*args, **kwargs)

Overloaded function.

1. report_gdt_components(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator, setting: bool) -> None

C++: protocols::comparative_modeling::Align_RmsdEvaluator::report_gdt_components(const bool) –> void

2. report_gdt_components(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RmsdEvaluator) -> bool

C++: protocols::comparative_modeling::Align_RmsdEvaluator::report_gdt_components() const –> bool

size(*args, **kwargs)

Overloaded function.

1. size(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t) -> int

C++: protocols::evaluation::SingleValuePoseEvaluator<double>::size() const –> unsigned long

2. size(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t) -> int

C++: protocols::evaluation::PoseEvaluator::size() const –> unsigned long

tag(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator) → str

C++: protocols::evaluation::AlignEvaluator::tag() const –> std::string

class pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator

Bases: AlignEvaluator

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator, arg0: pyrosetta.rosetta.core.pose.Pose) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator, arg0: pyrosetta.rosetta.core.pose.Pose, arg1: str) -> None

doc

3. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator, arg0: pyrosetta.rosetta.core.pose.Pose, arg1: str, arg2: float) -> None

doc

4. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator, native_pose: pyrosetta.rosetta.core.pose.Pose, tag: str, chi_dev: float, aln: pyrosetta.rosetta.core.sequence.SequenceAlignment) -> None

5. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator, arg0: pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator) -> None

6. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator, arg0: pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator) -> None

_pybind11_conduit_v1_()

applicable(*args, **kwargs)

Overloaded function.

1. applicable(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : pyrosetta.rosetta.core.pose.Pose) -> bool

C++: protocols::evaluation::SingleValuePoseEvaluator<double>::applicable(const class core::pose::Pose &) const –> bool

2. applicable(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : pyrosetta.rosetta.core.pose.Pose) -> bool

C++: protocols::evaluation::PoseEvaluator::applicable(const class core::pose::Pose &) const –> bool

apply(*args, **kwargs)

Overloaded function.

1. apply(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator, pose: pyrosetta.rosetta.core.pose.Pose, tag: str, ss: pyrosetta.rosetta.core.io.silent.SilentStruct) -> None

C++: protocols::comparative_modeling::Align_RotamerEvaluator::apply(class core::pose::Pose &, std::string, class core::io::silent::SilentStruct &) const –> void

2. apply(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator, : pyrosetta.rosetta.core.pose.Pose) -> float

C++: protocols::comparative_modeling::Align_RotamerEvaluator::apply(class core::pose::Pose &) const –> double

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator, : pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator) → pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator

C++: protocols::comparative_modeling::Align_RotamerEvaluator::operator=(const class protocols::comparative_modeling::Align_RotamerEvaluator &) –> class protocols::comparative_modeling::Align_RotamerEvaluator &

chi_dev(self: pyrosetta.rosetta.protocols.comparative_modeling.Align_RotamerEvaluator) → float

C++: protocols::comparative_modeling::Align_RotamerEvaluator::chi_dev() const –> double

get_alignment(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.sequence.SequenceAlignment

C++: protocols::evaluation::AlignEvaluator::get_alignment(const class core::pose::Pose &) const –> class std::shared_ptr<class core::sequence::SequenceAlignment>

name(*args, **kwargs)

Overloaded function.

1. name(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : int) -> str

C++: protocols::evaluation::SingleValuePoseEvaluator<double>::name(unsigned long) const –> std::string

2. name(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t, : int) -> str

C++: protocols::evaluation::PoseEvaluator::name(unsigned long) const –> std::string

native_pose(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::evaluation::AlignEvaluator::native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

report_aln_components(*args, **kwargs)

Overloaded function.

1. report_aln_components(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator, setting: bool) -> None

C++: protocols::evaluation::AlignEvaluator::report_aln_components(const bool) –> void

2. report_aln_components(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator) -> bool

C++: protocols::evaluation::AlignEvaluator::report_aln_components() const –> bool

size(*args, **kwargs)

Overloaded function.

1. size(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t) -> int

C++: protocols::evaluation::SingleValuePoseEvaluator<double>::size() const –> unsigned long

2. size(self: pyrosetta.rosetta.protocols.evaluation.SingleValuePoseEvaluator_double_t) -> int

C++: protocols::evaluation::PoseEvaluator::size() const –> unsigned long

tag(self: pyrosetta.rosetta.protocols.evaluation.AlignEvaluator) → str

C++: protocols::evaluation::AlignEvaluator::tag() const –> std::string

class pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster

Bases: pybind11_object

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster, aln_in: pyrosetta.rosetta.core.sequence.SequenceAlignment) -> None

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster, arg0: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster) -> None

_pybind11_conduit_v1_()

add_aln(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster, aln_in: pyrosetta.rosetta.core.sequence.SequenceAlignment) → None

C++: protocols::comparative_modeling::AlignmentCluster::add_aln(class core::sequence::SequenceAlignment &) –> void

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster, : pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster) → pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster

C++: protocols::comparative_modeling::AlignmentCluster::operator=(const class protocols::comparative_modeling::AlignmentCluster &) –> class protocols::comparative_modeling::AlignmentCluster &

get_aln(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster, index: int) → pyrosetta.rosetta.core.sequence.SequenceAlignment

C++: protocols::comparative_modeling::AlignmentCluster::get_aln(unsigned long) –> class core::sequence::SequenceAlignment

get_clusterCenter(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster) → pyrosetta.rosetta.core.sequence.SequenceAlignment

C++: protocols::comparative_modeling::AlignmentCluster::get_clusterCenter() –> class core::sequence::SequenceAlignment

merge(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster, cluster_in: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster) → None

C++: protocols::comparative_modeling::AlignmentCluster::merge(class std::shared_ptr<class protocols::comparative_modeling::AlignmentCluster>) –> void

output(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster, alignment_out: pyrosetta.rosetta.std.ostream) → None

C++: protocols::comparative_modeling::AlignmentCluster::output(std::ostream &) –> void

overlap(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster, cluster_in: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster) → float

C++: protocols::comparative_modeling::AlignmentCluster::overlap(class std::shared_ptr<class protocols::comparative_modeling::AlignmentCluster>) –> double

size(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentCluster) → float

C++: protocols::comparative_modeling::AlignmentCluster::size() –> double

class pyrosetta.rosetta.protocols.comparative_modeling.AlignmentClustering

Bases: pybind11_object

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentClustering) -> None

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentClustering, arg0: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentClustering) -> None

_pybind11_conduit_v1_()

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentClustering, : pyrosetta.rosetta.protocols.comparative_modeling.AlignmentClustering) → pyrosetta.rosetta.protocols.comparative_modeling.AlignmentClustering

C++: protocols::comparative_modeling::AlignmentClustering::operator=(const class protocols::comparative_modeling::AlignmentClustering &) –> class protocols::comparative_modeling::AlignmentClustering &

class pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet

Bases: pybind11_object

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet) -> None

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet, arg0: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet) -> None

_pybind11_conduit_v1_()

alignments(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet) → pyrosetta.rosetta.utility.vector1_core_sequence_SequenceAlignment

Gets the next alignment from the stream. Might be the same

alignment every time, or might be a different alignment after each call to this function.

C++: protocols::comparative_modeling::AlignmentSet::alignments() const –> class utility::vector1<class core::sequence::SequenceAlignment, class std::allocator<class core::sequence::SequenceAlignment> >

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet, : pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet) → pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet

C++: protocols::comparative_modeling::AlignmentSet::operator=(const class protocols::comparative_modeling::AlignmentSet &) –> class protocols::comparative_modeling::AlignmentSet &

insert(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet, aln: pyrosetta.rosetta.core.sequence.SequenceAlignment) → None

C++: protocols::comparative_modeling::AlignmentSet::insert(class core::sequence::SequenceAlignment) –> void

size(self: pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet) → int

C++: protocols::comparative_modeling::AlignmentSet::size() const –> unsigned long

class pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover

Bases: Mover

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover, align: pyrosetta.rosetta.core.sequence.SequenceAlignment, template_pose: pyrosetta.rosetta.core.pose.Pose, residue_selection: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover, arg0: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover) -> None

3. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover, arg0: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover) -> None

_pybind11_conduit_v1_()

alignment(self: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover) → pyrosetta.rosetta.core.sequence.SequenceAlignment

Returns the SequenceAlignment object used in threading.

C++: protocols::comparative_modeling::ExtraThreadingMover::alignment() –> class core::sequence::SequenceAlignment

apply(self: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover, query_pose: pyrosetta.rosetta.core.pose.Pose) → None

Threads the given Pose onto the template_pose with the

SequenceAlignment provided.

C++: protocols::comparative_modeling::ExtraThreadingMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover, : pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover) → pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover

C++: protocols::comparative_modeling::ExtraThreadingMover::operator=(const class protocols::comparative_modeling::ExtraThreadingMover &) –> class protocols::comparative_modeling::ExtraThreadingMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover) → str

C++: protocols::comparative_modeling::ExtraThreadingMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_qt_mapping(self: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover, query_pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.id.SequenceMapping

Returns the SequenceMapping between query and template.

C++: protocols::comparative_modeling::ExtraThreadingMover::get_qt_mapping(const class core::pose::Pose &) const –> class core::id::SequenceMapping

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

query_index(self: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover) → int

Returns the index of the query sequence in SequenceAlignment

object.

C++: protocols::comparative_modeling::ExtraThreadingMover::query_index() const –> unsigned long

static register_options() → None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

template_index(self: pyrosetta.rosetta.protocols.comparative_modeling.ExtraThreadingMover) → int

Returns the index of the template sequence in SequenceAlignment

object.

C++: protocols::comparative_modeling::ExtraThreadingMover::template_index() const –> unsigned long

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter

Bases: JobInputter

This is the simplest implementation of JobInputter

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter) -> None

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter, arg0: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter) -> None

3. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter, arg0: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter) -> None

_pybind11_conduit_v1_()

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter, : pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter) → pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter

C++: protocols::comparative_modeling::GenericJobInputter::operator=(const class protocols::comparative_modeling::GenericJobInputter &) –> class protocols::comparative_modeling::GenericJobInputter &

fill_jobs(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter, jobs: protocols::jd2::JobsContainer) → None

this function determines what jobs exist

C++: protocols::comparative_modeling::GenericJobInputter::fill_jobs(class protocols::jd2::JobsContainer &) –> void

get_self_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) → pyrosetta.rosetta.protocols.jd2.JobInputter

Get self owning pointers.

C++: protocols::jd2::JobInputter::get_self_ptr() –> class std::shared_ptr<class protocols::jd2::JobInputter>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) → pyrosetta.rosetta.std.weak_ptr_protocols_jd2_JobInputter_t

Get self weak pointers.

C++: protocols::jd2::JobInputter::get_self_weak_ptr() –> class std::weak_ptr<class protocols::jd2::JobInputter>

input_source(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter) → pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum

Return the type of input source that the GenericJobInputter is currently

using.

Always POSE.

C++: protocols::comparative_modeling::GenericJobInputter::input_source() const –> enum protocols::jd2::JobInputterInputSource::Enum

static job_inputter_input_source_to_string(source: pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum) → str

call this with input_source() to get the input source of a

particular job inputter

C++: protocols::jd2::JobInputter::job_inputter_input_source_to_string(enum protocols::jd2::JobInputterInputSource::Enum) –> std::string

pose_from_job(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputter, pose: pyrosetta.rosetta.core.pose.Pose, job: protocols::jd2::Job) → None

this function is responsible for filling the pose reference with

the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference.

C++: protocols::comparative_modeling::GenericJobInputter::pose_from_job(class core::pose::Pose &, class std::shared_ptr<class protocols::jd2::Job>) –> void

update_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter, jobs: protocols::jd2::JobsContainer) → None

This function is only called by certain JobInputters to update the jobs list after it has already been created.

An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back.

C++: protocols::jd2::JobInputter::update_jobs_list(class std::shared_ptr<class protocols::jd2::JobsContainer>) –> void

updates_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter) → bool

Does this type of JobInputter update the jobs list?

False by default. Override this function in derived classes to make it true.

C++: protocols::jd2::JobInputter::updates_jobs_list() const –> bool

class pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator

Bases: JobInputterCreator

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator) -> None

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator, arg0: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator) -> None

3. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator, arg0: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator) -> None

_pybind11_conduit_v1_()

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator, : pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator) → pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator

C++: protocols::comparative_modeling::GenericJobInputterCreator::operator=(const class protocols::comparative_modeling::GenericJobInputterCreator &) –> class protocols::comparative_modeling::GenericJobInputterCreator &

create_JobInputter(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator) → pyrosetta.rosetta.protocols.jd2.JobInputter

C++: protocols::comparative_modeling::GenericJobInputterCreator::create_JobInputter() const –> class std::shared_ptr<class protocols::jd2::JobInputter>

keyname(self: pyrosetta.rosetta.protocols.comparative_modeling.GenericJobInputterCreator) → str

C++: protocols::comparative_modeling::GenericJobInputterCreator::keyname() const –> std::string

class pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet

Bases: ConstraintSet

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, arg0: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet) -> None

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, arg0: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet) -> None

3. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, residues_to_ignore: pyrosetta.rosetta.std.set_int_t, other: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) -> None

_pybind11_conduit_v1_()

add_constraint(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cst: pyrosetta.rosetta.core.scoring.constraints.Constraint) → None

C++: core::scoring::constraints::ConstraintSet::add_constraint(class std::shared_ptr<const class core::scoring::constraints::Constraint>) –> void

add_constraints(*args, **kwargs)

Overloaded function.

1. add_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cst_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t) -> None

C++: core::scoring::constraints::ConstraintSet::add_constraints(class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >) –> void

2. add_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cst_set: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) -> None

add another constraint set to this constraint set

C++: core::scoring::constraints::ConstraintSet::add_constraints(const class std::shared_ptr<const class core::scoring::constraints::ConstraintSet>) –> void

add_dof_constraint(*args, **kwargs)

Overloaded function.

1. add_dof_constraint(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, id: pyrosetta.rosetta.core.id.DOF_ID, func: pyrosetta.rosetta.core.scoring.func.Func) -> None

2. add_dof_constraint(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, id: pyrosetta.rosetta.core.id.DOF_ID, func: pyrosetta.rosetta.core.scoring.func.Func, t: pyrosetta.rosetta.core.scoring.ScoreType) -> None

Note – still hacky. Will not be included in packing, just scoring

and minimization

C++: core::scoring::constraints::ConstraintSet::add_dof_constraint(const class core::id::DOF_ID &, class std::shared_ptr<class core::scoring::func::Func>, const enum core::scoring::ScoreType &) –> void

assign(*args, **kwargs)

Overloaded function.

1. assign(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, rhs: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) -> pyrosetta.rosetta.core.scoring.constraints.ConstraintSet

C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::operator=(const class core::scoring::constraints::ConstraintSet &) –> class core::scoring::constraints::ConstraintSet &

2. assign(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, : pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet) -> pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet

C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::operator=(const class protocols::comparative_modeling::IgnoreSubsetConstraintSet &) –> class protocols::comparative_modeling::IgnoreSubsetConstraintSet &

attach_to_conformation(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, conformation: pyrosetta.rosetta.std.weak_ptr_const_core_conformation_Conformation_t) → None

C++: core::scoring::constraints::ConstraintSet::attach_to_conformation(class std::weak_ptr<const class core::conformation::Conformation>) –> void

clear(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → None

C++: core::scoring::constraints::ConstraintSet::clear() –> void

clear_sequence_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → None

Discard any and all sequence constraints in the sequence_constraints_ list.

C++: core::scoring::constraints::ConstraintSet::clear_sequence_constraints() –> void

clone(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet) → pyrosetta.rosetta.core.scoring.constraints.ConstraintSet

C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::clone() const –> class std::shared_ptr<class core::scoring::constraints::ConstraintSet>

deprecated_eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, atom_id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Switching over to a pairwise decomposable eval-atom-deriv system for

RTMin means deprecating the old “evaluate an atom’s derivative wrt the entire structure” This function is preserved (for now) for use by the RNA_TorsionEnergy

C++: core::scoring::constraints::ConstraintSet::deprecated_eval_atom_derivative(const class core::id::AtomID &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

detach_from_conformation(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → None

C++: core::scoring::constraints::ConstraintSet::detach_from_conformation() –> void

detached_clone(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet) → pyrosetta.rosetta.core.scoring.constraints.ConstraintSet

C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::detached_clone() const –> class std::shared_ptr<class core::scoring::constraints::ConstraintSet>

detached_copy(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, src: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → None

C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::detached_copy(const class core::scoring::constraints::ConstraintSet &) –> void

eval_intrares_energy(*args, **kwargs)

Overloaded function.

1. eval_intrares_energy(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::constraints::ConstraintSet::eval_intrares_energy(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

2. eval_intrares_energy(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, rsd: pyrosetta.rosetta.core.conformation.Residue, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

C++: core::scoring::constraints::ConstraintSet::eval_intrares_energy(const class core::conformation::Residue &, class core::scoring::EMapVector &) const –> void

eval_multibody_atom_derivative(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, atom_id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, weights: pyrosetta.rosetta.core.scoring.EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

evaluate the derivatives for an atom that contains 3- or higher-body

constraints. Such derivatives cannot be evalauated in an extra-posal context (e.g. such as in RTMin).

C++: core::scoring::constraints::ConstraintSet::eval_multibody_atom_derivative(const class core::id::AtomID &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::scoring::EMapVector &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

eval_non_residue_pair_energy(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

Does NOT zero the emap values, just adds the additional contribution to the

existing emap energies (so can be called inside finalize_total_energies)

C++: core::scoring::constraints::ConstraintSet::eval_non_residue_pair_energy(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

get_all_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t

Returns all constraints in the set as a flat list, regardless of

type.

C++: core::scoring::constraints::ConstraintSet::get_all_constraints() const –> class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >

has_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → bool

C++: core::scoring::constraints::ConstraintSet::has_constraints() const –> bool

has_dof_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → bool

C++: core::scoring::constraints::ConstraintSet::has_dof_constraints() const –> bool

has_intra_residue_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → bool

C++: core::scoring::constraints::ConstraintSet::has_intra_residue_constraints() const –> bool

has_non_residue_pair_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → bool

C++: core::scoring::constraints::ConstraintSet::has_non_residue_pair_constraints() const –> bool

has_residue_pair_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → bool

C++: core::scoring::constraints::ConstraintSet::has_residue_pair_constraints() const –> bool

ignore(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, pos: int) → bool

Returns true if we’re supposed to ignore this sequence position,

false otherwise.

C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::ignore(const int) const –> bool

ignore_list(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet) → pyrosetta.rosetta.std.set_int_t

C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::ignore_list() const –> class std::set<int, struct std::less<int>, class std::allocator<int> >

ignore_residue(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, pos: int) → None

C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::ignore_residue(const int) –> void

is_empty(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → bool

C++: core::scoring::constraints::ConstraintSet::is_empty() const –> bool

load(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, arc: pyrosetta.rosetta.cereal.BinaryInputArchive) → None

C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::load(class cereal::BinaryInputArchive &) –> void

n_sequence_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → int

Get the number of sequence constraints.

C++: core::scoring::constraints::ConstraintSet::n_sequence_constraints() const –> unsigned long

on_connection_change(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, event: pyrosetta.rosetta.core.conformation.signals.ConnectionEvent) → None

C++: core::scoring::constraints::ConstraintSet::on_connection_change(const struct core::conformation::signals::ConnectionEvent &) –> void

on_length_change(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, event: pyrosetta.rosetta.core.conformation.signals.LengthEvent) → None

C++: core::scoring::constraints::ConstraintSet::on_length_change(const struct core::conformation::signals::LengthEvent &) –> void

remap_residue_positions(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, smap: pyrosetta.rosetta.core.id.SequenceMapping) → None

remaps the constraints in this particular constraint set according

to brief the passed in sequence mapping — redundant with remapped_clone!!!

C++: core::scoring::constraints::ConstraintSet::remap_residue_positions(const class core::id::SequenceMapping &) –> void

remapped_clone(*args, **kwargs)

Overloaded function.

1. remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.ConstraintSet

2. remapped_clone(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose, smap: pyrosetta.rosetta.core.id.SequenceMapping) -> pyrosetta.rosetta.core.scoring.constraints.ConstraintSet

Copies the data from this ConstraintSet into a new object and

returns its OP; atoms are mapped to atoms with the same name in dest pose ( e.g. for switch from centroid to fullatom ) if a sequence_mapping is present it is used to map residue numbers .. nullptr = identity mapping to the new object. This will really clone all constraints since they have to change their atom-numbers and residue-numbers

C++: core::scoring::constraints::ConstraintSet::remapped_clone(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::id::SequenceMapping>) const –> class std::shared_ptr<class core::scoring::constraints::ConstraintSet>

remove_constraint(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cst: pyrosetta.rosetta.core.scoring.constraints.Constraint, object_comparison: bool) → bool

Returns true if the constraint was successfully found and removed.

if object comparison is set to true, the constraint to be removed is found through the Constraint::== operator and not through pointer comparison

C++: core::scoring::constraints::ConstraintSet::remove_constraint(class std::shared_ptr<const class core::scoring::constraints::Constraint>, bool) –> bool

remove_constraints(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, cst_list: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_constraints_Constraint_t, object_comparison: bool) → bool

C++: core::scoring::constraints::ConstraintSet::remove_constraints(class utility::vector1<class std::shared_ptr<const class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<const class core::scoring::constraints::Constraint> > >, bool) –> bool

residue_pair_constraint_exists(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, pos1: int, pos2: int) → bool

C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::residue_pair_constraint_exists(const int, const int) const –> bool

residue_pair_constraints_exists(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, pos: int) → bool

C++: core::scoring::constraints::ConstraintSet::residue_pair_constraints_exists(const unsigned long) const –> bool

residue_pair_energy(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) → None

C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::residue_pair_energy(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

revision_id(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) → int

C++: core::scoring::constraints::ConstraintSet::revision_id() const –> unsigned long

same_type_as_me(*args, **kwargs)

Overloaded function.

1. same_type_as_me(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, other: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet) -> bool

2. same_type_as_me(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, other: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, recurse: bool) -> bool

C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::same_type_as_me(const class core::scoring::constraints::ConstraintSet &, bool) const –> bool

save(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, arc: pyrosetta.rosetta.cereal.BinaryOutputArchive) → None

C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::save(class cereal::BinaryOutputArchive &) const –> void

sequence_constraint(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, index: int) → pyrosetta.rosetta.core.scoring.aa_composition_energy.SequenceConstraint

Get the owning pointer to the Nth sequence constraint.

C++: core::scoring::constraints::ConstraintSet::sequence_constraint(const unsigned long) const –> class std::shared_ptr<const class core::scoring::aa_composition_energy::SequenceConstraint>

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::scoring::constraints::ConstraintSet::setup_for_derivatives(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

setup_for_minimizing_for_residue(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, res_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData) → None

Allow the parent class implementation to add the residue constraints

for this residue to the res_data_cache if this residue is not being ignored.

C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::setup_for_minimizing_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &, class core::scoring::ResSingleMinimizationData &) const –> void

setup_for_minimizing_for_residue_pair(self: pyrosetta.rosetta.protocols.comparative_modeling.IgnoreSubsetConstraintSet, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, minmap: pyrosetta.rosetta.core.kinematics.MinimizerMapBase, res1_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, res2_data_cache: pyrosetta.rosetta.core.scoring.ResSingleMinimizationData, respair_data_cache: pyrosetta.rosetta.core.scoring.ResPairMinimizationData) → None

Allow the parent class implenetation to add the residue-pair constraints

for this residue pair to the respair_data_cache if neither residues are being ignored.

C++: protocols::comparative_modeling::IgnoreSubsetConstraintSet::setup_for_minimizing_for_residue_pair(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::kinematics::MinimizerMapBase &, const class core::scoring::ResSingleMinimizationData &, const class core::scoring::ResSingleMinimizationData &, class core::scoring::ResPairMinimizationData &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::scoring::constraints::ConstraintSet::setup_for_scoring(class core::pose::Pose &, const class core::scoring::ScoreFunction &) const –> void

show(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, out: pyrosetta.rosetta.std.ostream) → None

C++: core::scoring::constraints::ConstraintSet::show(std::ostream &) const –> void

show_definition(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) → None

C++: core::scoring::constraints::ConstraintSet::show_definition(std::ostream &, const class core::pose::Pose &) const –> void

show_numbers(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, out: pyrosetta.rosetta.std.ostream) → None

C++: core::scoring::constraints::ConstraintSet::show_numbers(std::ostream &) const –> void

show_violations(*args, **kwargs)

Overloaded function.

1. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, verbose_level: int) -> int

2. show_violations(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, out: pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose, verbose_level: int, threshold: float) -> int

C++: core::scoring::constraints::ConstraintSet::show_violations(std::ostream &, class core::pose::Pose &, unsigned long, double) const –> unsigned long

steal_def_clone(*args, **kwargs)

Overloaded function.

1. steal_def_clone(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.scoring.constraints.ConstraintSet

2. steal_def_clone(self: pyrosetta.rosetta.core.scoring.constraints.ConstraintSet, src: pyrosetta.rosetta.core.pose.Pose, dest: pyrosetta.rosetta.core.pose.Pose, smap: pyrosetta.rosetta.core.id.SequenceMapping) -> pyrosetta.rosetta.core.scoring.constraints.ConstraintSet

like remapped_clone, but constraints also steal_def from src-pose

use, e.g., to get a new set of CoordinateConstraints for given xyz coordinates in src-pose

C++: core::scoring::constraints::ConstraintSet::steal_def_clone(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::id::SequenceMapping>) const –> class std::shared_ptr<class core::scoring::constraints::ConstraintSet>

class pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover

Bases: Mover

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover) -> None

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover, arg0: pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover) -> None

3. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover, arg0: pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover) -> None

_pybind11_conduit_v1_()

apply(self: pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::comparative_modeling::LoopRelaxThreadingMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover, : pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover) → pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover

C++: protocols::comparative_modeling::LoopRelaxThreadingMover::operator=(const class protocols::comparative_modeling::LoopRelaxThreadingMover &) –> class protocols::comparative_modeling::LoopRelaxThreadingMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover) → str

C++: protocols::comparative_modeling::LoopRelaxThreadingMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

setup(self: pyrosetta.rosetta.protocols.comparative_modeling.LoopRelaxThreadingMover) → None

C++: protocols::comparative_modeling::LoopRelaxThreadingMover::setup() –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover

Bases: Mover

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover, aligns: pyrosetta.rosetta.utility.vector1_core_sequence_SequenceAlignment, template_poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose) -> None

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover, arg0: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover) -> None

3. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover, arg0: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover) -> None

_pybind11_conduit_v1_()

apply(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover, query_pose: pyrosetta.rosetta.core.pose.Pose) → None

Threads the given Pose onto the template_pose with the

SequenceAlignment provided.

C++: protocols::comparative_modeling::MultiThreadingMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover, : pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover) → pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover

C++: protocols::comparative_modeling::MultiThreadingMover::operator=(const class protocols::comparative_modeling::MultiThreadingMover &) –> class protocols::comparative_modeling::MultiThreadingMover &

build_loops(*args, **kwargs)

Overloaded function.

1. build_loops(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover, setting: bool) -> None

C++: protocols::comparative_modeling::MultiThreadingMover::build_loops(bool) –> void

2. build_loops(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover) -> bool

C++: protocols::comparative_modeling::MultiThreadingMover::build_loops() const –> bool

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

frag_libs(*args, **kwargs)

Overloaded function.

1. frag_libs(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t

C++: protocols::comparative_modeling::MultiThreadingMover::frag_libs() const –> class utility::vector1<class std::shared_ptr<class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<class core::fragment::FragSet> > >

2. frag_libs(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover, new_libs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t) -> None

C++: protocols::comparative_modeling::MultiThreadingMover::frag_libs(class utility::vector1<class std::shared_ptr<class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<class core::fragment::FragSet> > >) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover) → str

C++: protocols::comparative_modeling::MultiThreadingMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

min_loop_size(*args, **kwargs)

Overloaded function.

1. min_loop_size(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover, new_size: int) -> None

C++: protocols::comparative_modeling::MultiThreadingMover::min_loop_size(const unsigned long) –> void

2. min_loop_size(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover) -> int

C++: protocols::comparative_modeling::MultiThreadingMover::min_loop_size() const –> unsigned long

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

randomize_loop_coords(*args, **kwargs)

Overloaded function.

1. randomize_loop_coords(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover, setting: bool) -> None

C++: protocols::comparative_modeling::MultiThreadingMover::randomize_loop_coords(bool) –> void

2. randomize_loop_coords(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover) -> bool

C++: protocols::comparative_modeling::MultiThreadingMover::randomize_loop_coords() –> bool

static register_options() → None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

repack_query(*args, **kwargs)

Overloaded function.

1. repack_query(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover, setting: bool) -> None

C++: protocols::comparative_modeling::MultiThreadingMover::repack_query(bool) –> void

2. repack_query(self: pyrosetta.rosetta.protocols.comparative_modeling.MultiThreadingMover) -> bool

C++: protocols::comparative_modeling::MultiThreadingMover::repack_query() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover

Bases: Mover

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover, arg0: pyrosetta.rosetta.core.sequence.SequenceAlignment, arg1: pyrosetta.rosetta.core.pose.Pose) -> None

doc

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover, align: pyrosetta.rosetta.core.sequence.SequenceAlignment, template_pose: pyrosetta.rosetta.core.pose.Pose, skip_repack: bool) -> None

3. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover, arg0: pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover) -> None

4. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover, arg0: pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover) -> None

_pybind11_conduit_v1_()

apply(self: pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover, query_pose: pyrosetta.rosetta.core.pose.Pose) → None

Threads the given Pose onto the template_pose with the

SequenceAlignment provided.

C++: protocols::comparative_modeling::PartialThreadingMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover, : pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover) → pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover

C++: protocols::comparative_modeling::PartialThreadingMover::operator=(const class protocols::comparative_modeling::PartialThreadingMover &) –> class protocols::comparative_modeling::PartialThreadingMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.comparative_modeling.PartialThreadingMover) → str

C++: protocols::comparative_modeling::PartialThreadingMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover

Bases: Mover

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover, mover: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover, arg0: pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover) -> None

3. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover, arg0: pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover) -> None

_pybind11_conduit_v1_()

apply(self: pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::comparative_modeling::RecoverSideChainsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.comparative_modeling.RecoverSideChainsMover) → str

C++: protocols::comparative_modeling::RecoverSideChainsMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover

Bases: Mover

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover, source: pyrosetta.rosetta.core.pose.Pose, anchor_atom_dest: pyrosetta.rosetta.core.id.NamedAtomID, anchor_atom_source: pyrosetta.rosetta.core.id.NamedAtomID, ligand_indices: pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID) -> None

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover, arg0: pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover) -> None

3. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover, arg0: pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover) -> None

_pybind11_conduit_v1_()

apply(self: pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::comparative_modeling::StealLigandMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.comparative_modeling.StealLigandMover) → str

C++: protocols::comparative_modeling::StealLigandMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover

Bases: Mover

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover, source: pyrosetta.rosetta.core.pose.Pose, map: pyrosetta.rosetta.core.id.SequenceMapping) -> None

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover, arg0: pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover) -> None

3. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover, arg0: pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover) -> None

_pybind11_conduit_v1_()

apply(self: pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

maps from pose to source_

C++: protocols::comparative_modeling::StealSideChainsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.comparative_modeling.StealSideChainsMover) → str

C++: protocols::comparative_modeling::StealSideChainsMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob

Bases: InnerJob

The InnerThreadingJob class is responsible for knowing input requirements for a given job - how many nstruct, and what the input is. InnerThreadingJobs are relatively heavy; there is no need to duplicate a series of InnerThreadingJobs for each index into nstruct. The companion ThreadingJob class handles the nstruct index and has a pointer to an InnerThreadingJob (which is shared across many ThreadingJobs). InnerThreadingJob also holds a PoseOP to maintain the unmodified input pose for that job.

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob, template_pdb: pyrosetta.rosetta.core.pose.Pose, alignment: pyrosetta.rosetta.core.sequence.SequenceAlignment, input_tag: str, nstruct_max: int) -> None

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob, arg0: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob) -> None

3. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob, arg0: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob) -> None

_pybind11_conduit_v1_()

alignment(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob) → pyrosetta.rosetta.core.sequence.SequenceAlignment

the alignment for this Job

C++: protocols::comparative_modeling::ThreadingJob::alignment() const –> const class core::sequence::SequenceAlignment &

alignment_id(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob) → str

convenience : alignment id

C++: protocols::comparative_modeling::ThreadingJob::alignment_id() const –> std::string

bad(self: pyrosetta.rosetta.protocols.jd2.InnerJob) → bool

C++: protocols::jd2::InnerJob::bad() const –> bool

clone(self: pyrosetta.rosetta.protocols.jd2.InnerJob) → pyrosetta.rosetta.protocols.jd2.InnerJob

Return an owning pointer to a copy of this object.

C++: protocols::jd2::InnerJob::clone() const –> class std::shared_ptr<class protocols::jd2::InnerJob>

static current_job() → pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob

Convenience function to get the current ThreadingJob from JD2

Will return a nullptr if we can’t get a ThreadingJob from JD2

C++: protocols::comparative_modeling::ThreadingJob::current_job() –> const class protocols::comparative_modeling::ThreadingJob *

extra_residues_to_steal(*args, **kwargs)

Overloaded function.

1. extra_residues_to_steal(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob) -> pyrosetta.rosetta.utility.vector1_unsigned_long

returns list of extra residues to steal

C++: protocols::comparative_modeling::ThreadingJob::extra_residues_to_steal() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

2. extra_residues_to_steal(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob, res: pyrosetta.rosetta.utility.vector1_unsigned_long) -> None

C++: protocols::comparative_modeling::ThreadingJob::extra_residues_to_steal(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

get_pose(self: pyrosetta.rosetta.protocols.jd2.InnerJob) → pyrosetta.rosetta.core.pose.Pose

return a COP to the input pose

DO NOT USE OUTSIDE OF JD2 NAMESPACE

C++: protocols::jd2::InnerJob::get_pose() const –> class std::shared_ptr<const class core::pose::Pose>

input_tag(self: pyrosetta.rosetta.protocols.jd2.InnerJob) → str

return the input tag (a string of space separated PDB filenames)

C++: protocols::jd2::InnerJob::input_tag() const –> const std::string &

loops(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJob, nres: int) → pyrosetta.rosetta.protocols.loops.Loops

returns the “standard” loop definition (as conservative as possible)

C++: protocols::comparative_modeling::ThreadingJob::loops(unsigned long) const –> class protocols::loops::Loops

nstruct_max(self: pyrosetta.rosetta.protocols.jd2.InnerJob) → int

C++: protocols::jd2::InnerJob::nstruct_max() const –> unsigned long

optional_output_name(*args, **kwargs)

Overloaded function.

1. optional_output_name(self: pyrosetta.rosetta.protocols.jd2.InnerJob) -> str

returns a job name controlled by the mover. Must be turned with the optional_output_name out flag. This flag is typically used in conjuction with a mover

C++: protocols::jd2::InnerJob::optional_output_name() const –> const std::string &

2. optional_output_name(self: pyrosetta.rosetta.protocols.jd2.InnerJob, output_name: str) -> None

sets a job name controlled by the mover

C++: protocols::jd2::InnerJob::optional_output_name(std::string) –> void

same(self: pyrosetta.rosetta.protocols.jd2.InnerJob, other: pyrosetta.rosetta.protocols.jd2.InnerJob) → bool

returns true if this is the same as other;

does not call other.same()

C++: protocols::jd2::InnerJob::same(const class protocols::jd2::InnerJob &) const –> bool

set_bad(*args, **kwargs)

Overloaded function.

1. set_bad(self: pyrosetta.rosetta.protocols.jd2.InnerJob) -> None

2. set_bad(self: pyrosetta.rosetta.protocols.jd2.InnerJob, value: bool) -> None

C++: protocols::jd2::InnerJob::set_bad(bool) –> void

show(self: pyrosetta.rosetta.protocols.jd2.InnerJob, out: pyrosetta.rosetta.std.ostream) → None

C++: protocols::jd2::InnerJob::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter

Bases: JobInputter

This is the simplest implementation of JobInputter

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter) -> None

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter, arg0: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter) -> None

3. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter, arg0: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter) -> None

_pybind11_conduit_v1_()

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter, : pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter) → pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter

C++: protocols::comparative_modeling::ThreadingJobInputter::operator=(const class protocols::comparative_modeling::ThreadingJobInputter &) –> class protocols::comparative_modeling::ThreadingJobInputter &

fill_jobs(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter, jobs: protocols::jd2::JobsContainer) → None

this function determines what jobs exist

C++: protocols::comparative_modeling::ThreadingJobInputter::fill_jobs(class protocols::jd2::JobsContainer &) –> void

get_self_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) → pyrosetta.rosetta.protocols.jd2.JobInputter

Get self owning pointers.

C++: protocols::jd2::JobInputter::get_self_ptr() –> class std::shared_ptr<class protocols::jd2::JobInputter>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) → pyrosetta.rosetta.std.weak_ptr_protocols_jd2_JobInputter_t

Get self weak pointers.

C++: protocols::jd2::JobInputter::get_self_weak_ptr() –> class std::weak_ptr<class protocols::jd2::JobInputter>

input_source(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter) → pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum

Return the type of input source that the ThreadingJobInputter is

currently using for template structures.

C++: protocols::comparative_modeling::ThreadingJobInputter::input_source() const –> enum protocols::jd2::JobInputterInputSource::Enum

static job_inputter_input_source_to_string(source: pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum) → str

call this with input_source() to get the input source of a

particular job inputter

C++: protocols::jd2::JobInputter::job_inputter_input_source_to_string(enum protocols::jd2::JobInputterInputSource::Enum) –> std::string

pose_from_job(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputter, pose: pyrosetta.rosetta.core.pose.Pose, job: protocols::jd2::Job) → None

this function is responsible for filling the pose reference with

the pose indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference.

C++: protocols::comparative_modeling::ThreadingJobInputter::pose_from_job(class core::pose::Pose &, class std::shared_ptr<class protocols::jd2::Job>) –> void

update_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter, jobs: protocols::jd2::JobsContainer) → None

This function is only called by certain JobInputters to update the jobs list after it has already been created.

An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back.

C++: protocols::jd2::JobInputter::update_jobs_list(class std::shared_ptr<class protocols::jd2::JobsContainer>) –> void

updates_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter) → bool

Does this type of JobInputter update the jobs list?

False by default. Override this function in derived classes to make it true.

C++: protocols::jd2::JobInputter::updates_jobs_list() const –> bool

class pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator

Bases: JobInputterCreator

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator) -> None

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator, arg0: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator) -> None

3. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator, arg0: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator) -> None

_pybind11_conduit_v1_()

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator, : pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator) → pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator

C++: protocols::comparative_modeling::ThreadingJobInputterCreator::operator=(const class protocols::comparative_modeling::ThreadingJobInputterCreator &) –> class protocols::comparative_modeling::ThreadingJobInputterCreator &

create_JobInputter(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator) → pyrosetta.rosetta.protocols.jd2.JobInputter

C++: protocols::comparative_modeling::ThreadingJobInputterCreator::create_JobInputter() const –> class std::shared_ptr<class protocols::jd2::JobInputter>

keyname(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingJobInputterCreator) → str

C++: protocols::comparative_modeling::ThreadingJobInputterCreator::keyname() const –> std::string

class pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover

Bases: Mover

__init__(*args, **kwargs)

Overloaded function.

1. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> None

2. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, arg0: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> None

3. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, arg0: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> None

4. __init__(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, align: pyrosetta.rosetta.core.sequence.SequenceAlignment, template_pose: pyrosetta.rosetta.core.pose.Pose) -> None

_pybind11_conduit_v1_()

alignment(*args, **kwargs)

Overloaded function.

1. alignment(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> pyrosetta.rosetta.core.sequence.SequenceAlignment

Returns the SequenceAlignment object used in threading.

C++: protocols::comparative_modeling::ThreadingMover::alignment() –> class core::sequence::SequenceAlignment

2. alignment(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, new_align: pyrosetta.rosetta.core.sequence.SequenceAlignment) -> None

Sets the SequenceAlignment associated with this object.

C++: protocols::comparative_modeling::ThreadingMover::alignment(class core::sequence::SequenceAlignment) –> void

apply(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, query_pose: pyrosetta.rosetta.core.pose.Pose) → None

Threads the given Pose onto the template_pose with the

SequenceAlignment provided.

C++: protocols::comparative_modeling::ThreadingMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, : pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) → pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover

C++: protocols::comparative_modeling::ThreadingMover::operator=(const class protocols::comparative_modeling::ThreadingMover &) –> class protocols::comparative_modeling::ThreadingMover &

build_loops(*args, **kwargs)

Overloaded function.

1. build_loops(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, setting: bool) -> None

C++: protocols::comparative_modeling::ThreadingMover::build_loops(bool) –> void

2. build_loops(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> bool

C++: protocols::comparative_modeling::ThreadingMover::build_loops() const –> bool

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::comparative_modeling::ThreadingMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

frag_libs(*args, **kwargs)

Overloaded function.

1. frag_libs(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t

C++: protocols::comparative_modeling::ThreadingMover::frag_libs() const –> class utility::vector1<class std::shared_ptr<class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<class core::fragment::FragSet> > >

2. frag_libs(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, new_libs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_fragment_FragSet_t) -> None

C++: protocols::comparative_modeling::ThreadingMover::frag_libs(class utility::vector1<class std::shared_ptr<class core::fragment::FragSet>, class std::allocator<class std::shared_ptr<class core::fragment::FragSet> > >) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::comparative_modeling::ThreadingMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) → str

C++: protocols::comparative_modeling::ThreadingMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_qt_mapping(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, query_pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.id.SequenceMapping

Returns the SequenceMapping between query and template.

C++: protocols::comparative_modeling::ThreadingMover::get_qt_mapping(const class core::pose::Pose &) const –> class core::id::SequenceMapping

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

min_loop_size(*args, **kwargs)

Overloaded function.

1. min_loop_size(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, new_size: int) -> None

C++: protocols::comparative_modeling::ThreadingMover::min_loop_size(const unsigned long) –> void

2. min_loop_size(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> int

C++: protocols::comparative_modeling::ThreadingMover::min_loop_size() const –> unsigned long

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

query_index(*args, **kwargs)

Overloaded function.

1. query_index(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> int

Returns the index of the query sequence in SequenceAlignment

object.

C++: protocols::comparative_modeling::ThreadingMover::query_index() const –> unsigned long

2. query_index(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, new_index: int) -> None

Sets the index of the query sequence in SequenceAlignment object.

C++: protocols::comparative_modeling::ThreadingMover::query_index(unsigned long) –> void

randomize_loop_coords(*args, **kwargs)

Overloaded function.

1. randomize_loop_coords(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, setting: bool) -> None

C++: protocols::comparative_modeling::ThreadingMover::randomize_loop_coords(bool) –> void

2. randomize_loop_coords(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> bool

C++: protocols::comparative_modeling::ThreadingMover::randomize_loop_coords() –> bool

static register_options() → None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

repack_query(*args, **kwargs)

Overloaded function.

1. repack_query(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, setting: bool) -> None

C++: protocols::comparative_modeling::ThreadingMover::repack_query(bool) –> void

2. repack_query(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> bool

C++: protocols::comparative_modeling::ThreadingMover::repack_query() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

template_index(*args, **kwargs)

Overloaded function.

1. template_index(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover) -> int

Returns the index of the template sequence in SequenceAlignment

object.

C++: protocols::comparative_modeling::ThreadingMover::template_index() const –> unsigned long

2. template_index(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, new_index: int) -> None

Sets the index of the template sequence in SequenceAlignment

object.

C++: protocols::comparative_modeling::ThreadingMover::template_index(unsigned long) –> void

template_pose(self: pyrosetta.rosetta.protocols.comparative_modeling.ThreadingMover, template_pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::comparative_modeling::ThreadingMover::template_pose(class core::pose::Pose) –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

pyrosetta.rosetta.protocols.comparative_modeling.alignments_from_cmd_line() → pyrosetta.rosetta.protocols.comparative_modeling.AlignmentSet

C++: protocols::comparative_modeling::alignments_from_cmd_line() –> class protocols::comparative_modeling::AlignmentSet

pyrosetta.rosetta.protocols.comparative_modeling.bounded_loops_from_alignment(num_residues: int, min_size: int, alignment: pyrosetta.rosetta.core.sequence.SequenceAlignment, unaligned_regions: pyrosetta.rosetta.protocols.loops.Loops) → None

Identifies consecutive stretches of unaligned residues by scanning

the alignment. Each unaligned region is guaranteed to have length at least <min_size>. Aligned regions share this property as well, and can be obtained by calling the invert() method on the output parameter <unaligned_regions>.

C++: protocols::comparative_modeling::bounded_loops_from_alignment(const unsigned long, const unsigned long, const class core::sequence::SequenceAlignment &, class std::shared_ptr<class protocols::loops::Loops> &) –> void

pyrosetta.rosetta.protocols.comparative_modeling.cm_main() → None

Initiates LoopRelaxThreadingMover using the job distributor (jd2)

C++: protocols::comparative_modeling::cm_main() –> void

pyrosetta.rosetta.protocols.comparative_modeling.gather_coords(*args, **kwargs)

Overloaded function.

1. gather_coords(model: pyrosetta.rosetta.core.pose.Pose, native: pyrosetta.rosetta.core.pose.Pose, aln: pyrosetta.rosetta.core.sequence.SequenceAlignment, natoms: int, p1a: pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t, p2a: pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t) -> None

2. gather_coords(model: pyrosetta.rosetta.core.pose.Pose, native: pyrosetta.rosetta.core.pose.Pose, aln: pyrosetta.rosetta.core.sequence.SequenceAlignment, natoms: int, p1a: pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t, p2a: pyrosetta.rosetta.ObjexxFCL.FArray2D_double_t, atom_name: str) -> None

C++: protocols::comparative_modeling::gather_coords(const class core::pose::Pose &, const class core::pose::Pose &, const class core::sequence::SequenceAlignment &, int &, class ObjexxFCL::FArray2D<double> &, class ObjexxFCL::FArray2D<double> &, const std::string &) –> void

pyrosetta.rosetta.protocols.comparative_modeling.get_qt_mapping_general(query_pose: pyrosetta.rosetta.core.pose.Pose, align: pyrosetta.rosetta.core.sequence.SequenceAlignment, template_pose: pyrosetta.rosetta.core.pose.Pose, query_index: int, template_index: int) → pyrosetta.rosetta.core.id.SequenceMapping

C++: protocols::comparative_modeling::get_qt_mapping_general(const class core::pose::Pose &, const class core::sequence::SequenceAlignment &, const class core::pose::Pose &, const unsigned long, const unsigned long) –> class core::id::SequenceMapping

pyrosetta.rosetta.protocols.comparative_modeling.initialize_ss(pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::comparative_modeling::initialize_ss(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.comparative_modeling.loops_are_closed(pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::comparative_modeling::loops_are_closed(class core::pose::Pose &) –> bool

pyrosetta.rosetta.protocols.comparative_modeling.loops_from_alignment(nres: int, aln: pyrosetta.rosetta.core.sequence.SequenceAlignment, min_loop_size: int) → pyrosetta.rosetta.protocols.loops.Loops

C++: protocols::comparative_modeling::loops_from_alignment(unsigned long, const class core::sequence::SequenceAlignment &, const unsigned long) –> class std::shared_ptr<class protocols::loops::Loops>

pyrosetta.rosetta.protocols.comparative_modeling.loops_from_transitive_alignments(nres1: int, aln1: pyrosetta.rosetta.core.sequence.SequenceAlignment, nres2: int, aln2: pyrosetta.rosetta.core.sequence.SequenceAlignment, min_loop_size: int) → pyrosetta.rosetta.protocols.loops.Loops

C++: protocols::comparative_modeling::loops_from_transitive_alignments(unsigned long, const class core::sequence::SequenceAlignment &, unsigned long, const class core::sequence::SequenceAlignment &, const unsigned long) –> class std::shared_ptr<class protocols::loops::Loops>

pyrosetta.rosetta.protocols.comparative_modeling.poses_from_cmd_line(fn_list: pyrosetta.rosetta.utility.vector1_std_string) → pyrosetta.rosetta.std.map_std_string_core_pose_Pose

C++: protocols::comparative_modeling::poses_from_cmd_line(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> class std::map<std::string, class core::pose::Pose, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, class core::pose::Pose> > >

pyrosetta.rosetta.protocols.comparative_modeling.randomize_selected_atoms(query_pose: pyrosetta.rosetta.core.pose.Pose, selected: pyrosetta.rosetta.core.id.AtomID_Map_bool_t) → None

C++: protocols::comparative_modeling::randomize_selected_atoms(class core::pose::Pose &, const class core::id::AtomID_Map<bool> &) –> void

pyrosetta.rosetta.protocols.comparative_modeling.rebuild_loops_until_closed(query_pose: pyrosetta.rosetta.core.pose.Pose, min_loop_size: int, max_times: int, loop_mover_name: str) → None

C++: protocols::comparative_modeling::rebuild_loops_until_closed(class core::pose::Pose &, const unsigned long, const unsigned long, const std::string &) –> void

pyrosetta.rosetta.protocols.comparative_modeling.steal_ligands(dest_pose: pyrosetta.rosetta.core.pose.Pose, source_pose_in: pyrosetta.rosetta.core.pose.Pose, anchor_atom_dest: pyrosetta.rosetta.core.id.NamedAtomID, anchor_atom_source: pyrosetta.rosetta.core.id.NamedAtomID, ligand_indices: pyrosetta.rosetta.utility.vector1_core_id_NamedAtomID) → None

Function for stealing ligands from a given Pose

and adding them to source_pose.

: The parameters are:

dest_pose Pose to which ligands are added.

source_pose_in Pose from which ligands and orientations are taken.

anchor_atom_dest anchor atom providing reference in dest_pose for ligand orientation.

anchor_atom_source anchor atom providing reference in source_pose for ligand orientation.

ligand_indices list of AtomID entries for ligand, one per ligand. Ligand orientation is determined by orientation between anchor_atom_source and each ligand AtomID.

C++: protocols::comparative_modeling::steal_ligands(class core::pose::Pose &, const class core::pose::Pose &, const class core::id::NamedAtomID &, const class core::id::NamedAtomID &, const class utility::vector1<class core::id::NamedAtomID, class std::allocator<class core::id::NamedAtomID> > &) –> void

pyrosetta.rosetta.protocols.comparative_modeling.templates_from_cmd_line() → pyrosetta.rosetta.utility.vector1_core_pose_Pose

C++: protocols::comparative_modeling::templates_from_cmd_line() –> class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> >