antibody_legacy

Bindings for protocols::antibody_legacy namespace

class pyrosetta.rosetta.protocols.antibody_legacy.Antibody

Bases: pybind11_object

antibody definition

property Fv

property Fv_sequence_

property ab_movemap

align_to_native(self: pyrosetta.rosetta.protocols.antibody_legacy.Antibody, native: pyrosetta.rosetta.protocols.antibody_legacy.Antibody) → None

align current Fv to native.Fv

C++: protocols::antibody_legacy::Antibody::align_to_native(class protocols::antibody_legacy::Antibody &) –> void

all_cdr_fold_tree(self: pyrosetta.rosetta.protocols.antibody_legacy.Antibody) → None

C++: protocols::antibody_legacy::Antibody::all_cdr_fold_tree() –> void

property all_cdr_loops

assign(self: pyrosetta.rosetta.protocols.antibody_legacy.Antibody, : pyrosetta.rosetta.protocols.antibody_legacy.Antibody) → pyrosetta.rosetta.protocols.antibody_legacy.Antibody

C++: protocols::antibody_legacy::Antibody::operator=(const class protocols::antibody_legacy::Antibody &) –> class protocols::antibody_legacy::Antibody &

property current_end

property current_start

property extended_

property kinked_

populate_all_cdrs(self: pyrosetta.rosetta.protocols.antibody_legacy.Antibody) → None

C++: protocols::antibody_legacy::Antibody::populate_all_cdrs() –> void

set_Fv(*args, **kwargs)

Overloaded function.

1. set_Fv(self: pyrosetta.rosetta.protocols.antibody_legacy.Antibody, pose_in: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::antibody_legacy::Antibody::set_Fv(class core::pose::Pose &) –> void

2. set_Fv(self: pyrosetta.rosetta.protocols.antibody_legacy.Antibody, pose_in: pyrosetta.rosetta.core.pose.Pose, camelid: bool) -> None

C++: protocols::antibody_legacy::Antibody::set_Fv(class core::pose::Pose &, bool) –> void

set_defaults(self: pyrosetta.rosetta.protocols.antibody_legacy.Antibody) → None

C++: protocols::antibody_legacy::Antibody::set_defaults() –> void

class pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler

Bases: Mover

all_cdr_VL_VH_fold_tree(self: pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler, pose_in: pyrosetta.rosetta.core.pose.Pose, loops: pyrosetta.rosetta.protocols.loops.Loops) → None

C++: protocols::antibody_legacy::AntibodyModeler::all_cdr_VL_VH_fold_tree(class core::pose::Pose &, const class protocols::loops::Loops &) –> void

apply(self: pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::antibody_legacy::AntibodyModeler::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler, : pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler) → pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler

C++: protocols::antibody_legacy::AntibodyModeler::operator=(const class protocols::antibody_legacy::AntibodyModeler &) –> class protocols::antibody_legacy::AntibodyModeler &

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.antibody_legacy.AntibodyModeler) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::antibody_legacy::AntibodyModeler::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>

display_constraint_residues(self: pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler) → None

C++: protocols::antibody_legacy::AntibodyModeler::display_constraint_residues() –> 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.antibody_legacy.AntibodyModeler) → str

C++: protocols::antibody_legacy::AntibodyModeler::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

global_loop_rmsd(self: pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler, pose_in: pyrosetta.rosetta.core.pose.Pose, native_pose: pyrosetta.rosetta.core.pose.Pose, cdr_type: str) → float

C++: protocols::antibody_legacy::AntibodyModeler::global_loop_rmsd(const class core::pose::Pose &, const class core::pose::Pose &, std::string) –> double

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 > > &

init_from_options(self: pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler) → None

C++: protocols::antibody_legacy::AntibodyModeler::init_from_options() –> void

init_on_new_input(self: pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler) → None

C++: protocols::antibody_legacy::AntibodyModeler::init_on_new_input() –> void

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

read_and_store_fragments(self: pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler) → None

C++: protocols::antibody_legacy::AntibodyModeler::read_and_store_fragments() –> 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

relax_cdrs(self: pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler) → None

C++: protocols::antibody_legacy::AntibodyModeler::relax_cdrs() –> void

repulsive_ramp(self: pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler, pose_in: pyrosetta.rosetta.core.pose.Pose, loops_in: pyrosetta.rosetta.protocols.loops.Loops) → None

C++: protocols::antibody_legacy::AntibodyModeler::repulsive_ramp(class core::pose::Pose &, class protocols::loops::Loops) –> void

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_default(self: pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler) → None

C++: protocols::antibody_legacy::AntibodyModeler::set_default() –> 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_snugdock_foldtree(self: pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::antibody_legacy::AntibodyModeler::set_snugdock_foldtree(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_packer_task(self: pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::antibody_legacy::AntibodyModeler::setup_packer_task(class core::pose::Pose &) –> void

setup_simple_fold_tree(self: pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler, jumppoint1: int, cutpoint: int, jumppoint2: int, nres: int, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::antibody_legacy::AntibodyModeler::setup_simple_fold_tree(unsigned long, unsigned long, unsigned long, unsigned long, class core::pose::Pose &) –> 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

snugfit_MC_min(self: pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler, pose_in: pyrosetta.rosetta.core.pose.Pose, cdr_dock_map: pyrosetta.rosetta.core.kinematics.MoveMap, cycles: int, minimization_threshold: float, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, pack_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, is_flexible: pyrosetta.rosetta.utility.vector1_bool) → None

C++: protocols::antibody_legacy::AntibodyModeler::snugfit_MC_min(class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>, unsigned long, double, class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class core::scoring::ScoreFunction>, class utility::vector1<bool, class std::allocator<bool> >) –> void

snugfit_mcm_protocol(self: pyrosetta.rosetta.protocols.antibody_legacy.AntibodyModeler, pose_in: pyrosetta.rosetta.core.pose.Pose, loops_in: pyrosetta.rosetta.protocols.loops.Loops) → None

C++: protocols::antibody_legacy::AntibodyModeler::snugfit_mcm_protocol(class core::pose::Pose &, class protocols::loops::Loops) –> 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.antibody_legacy.CDRH3Modeler

Bases: Mover

Ab initio modeling of CDR H3 loop

CDR_H3_filter(*args, **kwargs)

Overloaded function.

1. CDR_H3_filter(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler, pose_in: pyrosetta.rosetta.core.pose.Pose, loop_begin: int, size: int) -> bool

2. CDR_H3_filter(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler, pose_in: pyrosetta.rosetta.core.pose.Pose, loop_begin: int, size: int, light_chain: str) -> bool

C++: protocols::antibody_legacy::CDRH3Modeler::CDR_H3_filter(const class core::pose::Pose &, const unsigned long, const unsigned long, const char) –> bool

property H3_base_library

antibody_modeling_insert_ter(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler) → None

insert C-terminal fragments

C++: protocols::antibody_legacy::CDRH3Modeler::antibody_modeling_insert_ter() –> void

apply(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::antibody_legacy::CDRH3Modeler::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler, : pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler) → pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler

C++: protocols::antibody_legacy::CDRH3Modeler::operator=(const class protocols::antibody_legacy::CDRH3Modeler &) –> class protocols::antibody_legacy::CDRH3Modeler &

build_centroid_loop(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler) → None

Build centroid mode CDR H3 loop

C++: protocols::antibody_legacy::CDRH3Modeler::build_centroid_loop() –> void

build_fullatom_loop(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler) → None

Build fullatom mode CDR H3 loop

C++: protocols::antibody_legacy::CDRH3Modeler::build_fullatom_loop() –> void

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>

cutpoint_separation(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler, pose_in: pyrosetta.rosetta.core.pose.Pose, cutpoint: int) → float

C++: protocols::antibody_legacy::CDRH3Modeler::cutpoint_separation(class core::pose::Pose &, unsigned long) –> double

cutpoints_separation(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler) → bool

return false if any cdr cutpoint is broken

C++: protocols::antibody_legacy::CDRH3Modeler::cutpoints_separation() –> bool

enable_benchmark_mode(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler, setting: bool) → None

enable benchmark mode

C++: protocols::antibody_legacy::CDRH3Modeler::enable_benchmark_mode(bool) –> 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.antibody_legacy.CDRH3Modeler) → str

C++: protocols::antibody_legacy::CDRH3Modeler::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

loop_centroid_relax(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler, pose_in: pyrosetta.rosetta.core.pose.Pose, loop_begin: int, loop_end: int) → None

C++: protocols::antibody_legacy::CDRH3Modeler::loop_centroid_relax(class core::pose::Pose &, const unsigned long, const unsigned long) –> void

loop_fa_relax(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler, pose_in: pyrosetta.rosetta.core.pose.Pose, loop_begin: int, loop_end: int) → None

C++: protocols::antibody_legacy::CDRH3Modeler::loop_fa_relax(class core::pose::Pose &, const unsigned long, const unsigned long) –> void

model_h3(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler, setting: bool) → None

enable CDR H3 loop building

C++: protocols::antibody_legacy::CDRH3Modeler::model_h3(bool) –> void

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

scored_frag_close(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler, pose_in: pyrosetta.rosetta.core.pose.Pose, trimmed_cdr_h3: pyrosetta.rosetta.protocols.loops.Loop) → None

C++: protocols::antibody_legacy::CDRH3Modeler::scored_frag_close(class core::pose::Pose &, const class protocols::loops::Loop) –> void

set_camelid(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler, setting: bool) → None

enable camelid modeling mode

C++: protocols::antibody_legacy::CDRH3Modeler::set_camelid(bool) –> void

set_centroid_loop_building(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler, setting: bool) → None

set centroid mode loop building

C++: protocols::antibody_legacy::CDRH3Modeler::set_centroid_loop_building(bool) –> 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_default(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler) → None

C++: protocols::antibody_legacy::CDRH3Modeler::set_default() –> void

set_fullatom_loop_building(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler, setting: bool) → None

set fullatom mode loop building

C++: protocols::antibody_legacy::CDRH3Modeler::set_fullatom_loop_building(bool) –> void

set_highres_score_func(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler, highres_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

set scorefunction for high resolution of CDR H3 modeling

C++: protocols::antibody_legacy::CDRH3Modeler::set_highres_score_func(class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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_lowres_score_func(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler, lowres_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

set scorefunction for low resolution of CDR H3 modeling

C++: protocols::antibody_legacy::CDRH3Modeler::set_lowres_score_func(class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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_packer_task(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::antibody_legacy::CDRH3Modeler::setup_packer_task(class core::pose::Pose &) –> 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

store_H3_cter_fragment(self: pyrosetta.rosetta.protocols.antibody_legacy.CDRH3Modeler, base_library_in: pyrosetta.rosetta.utility.vector1_core_fragment_FragData) → None

store CDR H3 C-terminal fragments

C++: protocols::antibody_legacy::CDRH3Modeler::store_H3_cter_fragment(class utility::vector1<class core::fragment::FragData, class std::allocator<class core::fragment::FragData> > &) –> 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.antibody_legacy.CloseOneMover

Bases: Mover

Closes only one CDR onto a framework

apply(self: pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::antibody_legacy::CloseOneMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover, : pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover) → pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover

C++: protocols::antibody_legacy::CloseOneMover::operator=(const class protocols::antibody_legacy::CloseOneMover &) –> class protocols::antibody_legacy::CloseOneMover &

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>

close_one_loop_stem(*args, **kwargs)

Overloaded function.

1. close_one_loop_stem(self: pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover, pose_in: pyrosetta.rosetta.core.pose.Pose, cutpoint_in: int, nter: bool) -> None

C++: protocols::antibody_legacy::CloseOneMover::close_one_loop_stem(class core::pose::Pose &, unsigned long, bool) –> void

2. close_one_loop_stem(self: pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover, pose_in: pyrosetta.rosetta.core.pose.Pose, loop_begin: int, loop_end: int, cutpoint: int) -> None

C++: protocols::antibody_legacy::CloseOneMover::close_one_loop_stem(class core::pose::Pose &, unsigned long, unsigned long, unsigned long) –> void

close_one_loop_stem_helper(self: pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover, loop_begin: int, loop_end: int, cutpoint: int, pose_in: pyrosetta.rosetta.core.pose.Pose, loop_map: pyrosetta.rosetta.core.kinematics.MoveMap) → None

C++: protocols::antibody_legacy::CloseOneMover::close_one_loop_stem_helper(unsigned long, unsigned long, unsigned long, class core::pose::Pose &, class std::shared_ptr<class core::kinematics::MoveMap>) –> void

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>

enable_benchmark_mode(self: pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover, setting: bool) → None

enable benchmark mode

C++: protocols::antibody_legacy::CloseOneMover::enable_benchmark_mode(bool) –> 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.antibody_legacy.CloseOneMover) → str

C++: protocols::antibody_legacy::CloseOneMover::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_default(self: pyrosetta.rosetta.protocols.antibody_legacy.CloseOneMover) → None

C++: protocols::antibody_legacy::CloseOneMover::set_default() –> 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.antibody_legacy.GraftMover

Bases: Mover

Grafts a series of CDR onto a framework

apply(self: pyrosetta.rosetta.protocols.antibody_legacy.GraftMover, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::antibody_legacy::GraftMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody_legacy.GraftMover, : pyrosetta.rosetta.protocols.antibody_legacy.GraftMover) → pyrosetta.rosetta.protocols.antibody_legacy.GraftMover

C++: protocols::antibody_legacy::GraftMover::operator=(const class protocols::antibody_legacy::GraftMover &) –> class protocols::antibody_legacy::GraftMover &

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>

enable_benchmark_mode(self: pyrosetta.rosetta.protocols.antibody_legacy.GraftMover, setting: bool) → None

enable benchmark mode

C++: protocols::antibody_legacy::GraftMover::enable_benchmark_mode(bool) –> void

enable_graft_h1(self: pyrosetta.rosetta.protocols.antibody_legacy.GraftMover, setting: bool) → None

C++: protocols::antibody_legacy::GraftMover::enable_graft_h1(bool) –> void

enable_graft_h2(self: pyrosetta.rosetta.protocols.antibody_legacy.GraftMover, setting: bool) → None

C++: protocols::antibody_legacy::GraftMover::enable_graft_h2(bool) –> void

enable_graft_h3(self: pyrosetta.rosetta.protocols.antibody_legacy.GraftMover, setting: bool) → None

C++: protocols::antibody_legacy::GraftMover::enable_graft_h3(bool) –> void

enable_graft_l1(self: pyrosetta.rosetta.protocols.antibody_legacy.GraftMover, setting: bool) → None

C++: protocols::antibody_legacy::GraftMover::enable_graft_l1(bool) –> void

enable_graft_l2(self: pyrosetta.rosetta.protocols.antibody_legacy.GraftMover, setting: bool) → None

C++: protocols::antibody_legacy::GraftMover::enable_graft_l2(bool) –> void

enable_graft_l3(self: pyrosetta.rosetta.protocols.antibody_legacy.GraftMover, setting: bool) → None

C++: protocols::antibody_legacy::GraftMover::enable_graft_l3(bool) –> 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.antibody_legacy.GraftMover) → str

C++: protocols::antibody_legacy::GraftMover::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

relax_optimized_CDR_grafts(self: pyrosetta.rosetta.protocols.antibody_legacy.GraftMover, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

relax optimized CDR grafted regions

C++: protocols::antibody_legacy::GraftMover::relax_optimized_CDR_grafts(class core::pose::Pose &) –> void

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_camelid(self: pyrosetta.rosetta.protocols.antibody_legacy.GraftMover, setting: bool) → None

C++: protocols::antibody_legacy::GraftMover::set_camelid(bool) –> 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_default(self: pyrosetta.rosetta.protocols.antibody_legacy.GraftMover) → None

C++: protocols::antibody_legacy::GraftMover::set_default() –> 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.antibody_legacy.GraftOneMover

Bases: Mover

Grafts only one CDR onto a framework

apply(self: pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::antibody_legacy::GraftOneMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover, : pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover) → pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover

C++: protocols::antibody_legacy::GraftOneMover::operator=(const class protocols::antibody_legacy::GraftOneMover &) –> class protocols::antibody_legacy::GraftOneMover &

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>

enable_benchmark_mode(self: pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover, setting: bool) → None

enable benchmark mode

C++: protocols::antibody_legacy::GraftOneMover::enable_benchmark_mode(bool) –> 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.antibody_legacy.GraftOneMover) → str

C++: protocols::antibody_legacy::GraftOneMover::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_default(self: pyrosetta.rosetta.protocols.antibody_legacy.GraftOneMover) → None

C++: protocols::antibody_legacy::GraftOneMover::set_default() –> 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.antibody_legacy.LoopRlxMover

Bases: Mover

Closes only one CDR onto a framework

apply(self: pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::antibody_legacy::LoopRlxMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover, : pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover) → pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover

C++: protocols::antibody_legacy::LoopRlxMover::operator=(const class protocols::antibody_legacy::LoopRlxMover &) –> class protocols::antibody_legacy::LoopRlxMover &

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>

enable_benchmark_mode(self: pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover, setting: bool) → None

enable benchmark mode

C++: protocols::antibody_legacy::LoopRlxMover::enable_benchmark_mode(bool) –> 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.antibody_legacy.LoopRlxMover) → str

C++: protocols::antibody_legacy::LoopRlxMover::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_default(self: pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover) → None

C++: protocols::antibody_legacy::LoopRlxMover::set_default() –> 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_packer_task(self: pyrosetta.rosetta.protocols.antibody_legacy.LoopRlxMover, pose_in: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::antibody_legacy::LoopRlxMover::setup_packer_task(class core::pose::Pose &) –> 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 &

pyrosetta.rosetta.protocols.antibody_legacy.read_H3_cter_fragment(antibody_in: pyrosetta.rosetta.protocols.antibody_legacy.Antibody, H3_base_library: pyrosetta.rosetta.utility.vector1_core_fragment_FragData, is_camelid: bool) → None

C++: protocols::antibody_legacy::read_H3_cter_fragment(class protocols::antibody_legacy::Antibody &, class utility::vector1<class core::fragment::FragData, class std::allocator<class core::fragment::FragData> > &, bool) –> void

pyrosetta.rosetta.protocols.antibody_legacy.simple_fold_tree(pose_in: pyrosetta.rosetta.core.pose.Pose, jumppoint1: int, cutpoint: int, jumppoint2: int) → None

C++: protocols::antibody_legacy::simple_fold_tree(class core::pose::Pose &, unsigned long, unsigned long, unsigned long) –> void

pyrosetta.rosetta.protocols.antibody_legacy.simple_one_loop_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose, loop: pyrosetta.rosetta.protocols.loops.Loop) → None

C++: protocols::antibody_legacy::simple_one_loop_fold_tree(class core::pose::Pose &, const class protocols::loops::Loop &) –> void