flxbb

Bindings for protocols::flxbb namespace

class pyrosetta.rosetta.protocols.flxbb.DesignTask

Bases: pybind11_builtins.pybind11_object

add_task_operation(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, top: pyrosetta.rosetta.core.pack.task.operation.TaskOperation) → None

add task operation

C++: protocols::flxbb::DesignTask::add_task_operation(const class std::shared_ptr<class core::pack::task::operation::TaskOperation>) –> void

add_task_operations(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, top: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) → None

add task operations

C++: protocols::flxbb::DesignTask::add_task_operations(const class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > > &) –> void

assign(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, : pyrosetta.rosetta.protocols.flxbb.DesignTask) → pyrosetta.rosetta.protocols.flxbb.DesignTask

C++: protocols::flxbb::DesignTask::operator=(const class protocols::flxbb::DesignTask &) –> class protocols::flxbb::DesignTask &

dump_packertask(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, os: pyrosetta.rosetta.std.ostream) → None

output packertask

C++: protocols::flxbb::DesignTask::dump_packertask(class std::basic_ostream<char> &) –> void

filter_structs(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → protocols::flxbb::FilterStructs

filter during fixbb design

C++: protocols::flxbb::DesignTask::filter_structs() const –> class std::shared_ptr<class protocols::flxbb::FilterStructs>

mover(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → pyrosetta.rosetta.protocols.moves.Mover

mover after fixbb design

C++: protocols::flxbb::DesignTask::mover() const –> class std::shared_ptr<class protocols::moves::Mover>

ncycle(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → int

the number of cycles of fixbb design and mover

C++: protocols::flxbb::DesignTask::ncycle() const –> unsigned long

packertask(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → pyrosetta.rosetta.core.pack.task.PackerTask

packer task for fixbb design

C++: protocols::flxbb::DesignTask::packertask() const –> class std::shared_ptr<class core::pack::task::PackerTask>

resfile(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → str

resfile

C++: protocols::flxbb::DesignTask::resfile() const –> std::string

scorefxn(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → pyrosetta.rosetta.core.scoring.ScoreFunction

scorefxn for fixbb design

C++: protocols::flxbb::DesignTask::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

set_filter_structs(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, value: protocols::flxbb::FilterStructs) → None

filter during fixbb design

C++: protocols::flxbb::DesignTask::set_filter_structs(const class std::shared_ptr<class protocols::flxbb::FilterStructs>) –> void

set_mover(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, value: pyrosetta.rosetta.protocols.moves.Mover) → None

mover after fixbb design

C++: protocols::flxbb::DesignTask::set_mover(const class std::shared_ptr<class protocols::moves::Mover>) –> void

set_ncycle(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, ncycle: int) → None

the number of cycles of design and mover

C++: protocols::flxbb::DesignTask::set_ncycle(const unsigned long &) –> void

set_packertask(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, taskf: pyrosetta.rosetta.core.pack.task.PackerTask) → None

packer task

C++: protocols::flxbb::DesignTask::set_packertask(const class std::shared_ptr<class core::pack::task::PackerTask>) –> void

set_resfile(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, resfile: str) → None

set resfile

C++: protocols::flxbb::DesignTask::set_resfile(const class std::basic_string<char> &) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

scorefxn for fixbb design

C++: protocols::flxbb::DesignTask::set_scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

setup(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None

setup packer task

C++: protocols::flxbb::DesignTask::setup(const class core::pose::Pose &, const class std::shared_ptr<class core::pack::task::PackerTask>) –> void

class pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer

Bases: pyrosetta.rosetta.protocols.flxbb.DesignTask

add_task_operation(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, top: pyrosetta.rosetta.core.pack.task.operation.TaskOperation) → None

add task operation

C++: protocols::flxbb::DesignTask::add_task_operation(const class std::shared_ptr<class core::pack::task::operation::TaskOperation>) –> void

add_task_operations(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, top: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) → None

add task operations

C++: protocols::flxbb::DesignTask::add_task_operations(const class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > > &) –> void

assign(self: pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer, : pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer) → pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer

C++: protocols::flxbb::DesignTask_Layer::operator=(const class protocols::flxbb::DesignTask_Layer &) –> class protocols::flxbb::DesignTask_Layer &

dump_packertask(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, os: pyrosetta.rosetta.std.ostream) → None

output packertask

C++: protocols::flxbb::DesignTask::dump_packertask(class std::basic_ostream<char> &) –> void

filter_structs(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → protocols::flxbb::FilterStructs

filter during fixbb design

C++: protocols::flxbb::DesignTask::filter_structs() const –> class std::shared_ptr<class protocols::flxbb::FilterStructs>

mover(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → pyrosetta.rosetta.protocols.moves.Mover

mover after fixbb design

C++: protocols::flxbb::DesignTask::mover() const –> class std::shared_ptr<class protocols::moves::Mover>

ncycle(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → int

the number of cycles of fixbb design and mover

C++: protocols::flxbb::DesignTask::ncycle() const –> unsigned long

packertask(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → pyrosetta.rosetta.core.pack.task.PackerTask

packer task for fixbb design

C++: protocols::flxbb::DesignTask::packertask() const –> class std::shared_ptr<class core::pack::task::PackerTask>

resfile(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → str

resfile

C++: protocols::flxbb::DesignTask::resfile() const –> std::string

scorefxn(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → pyrosetta.rosetta.core.scoring.ScoreFunction

scorefxn for fixbb design

C++: protocols::flxbb::DesignTask::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

set_filter_structs(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, value: protocols::flxbb::FilterStructs) → None

filter during fixbb design

C++: protocols::flxbb::DesignTask::set_filter_structs(const class std::shared_ptr<class protocols::flxbb::FilterStructs>) –> void

set_mover(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, value: pyrosetta.rosetta.protocols.moves.Mover) → None

mover after fixbb design

C++: protocols::flxbb::DesignTask::set_mover(const class std::shared_ptr<class protocols::moves::Mover>) –> void

set_ncycle(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, ncycle: int) → None

the number of cycles of design and mover

C++: protocols::flxbb::DesignTask::set_ncycle(const unsigned long &) –> void

set_packertask(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, taskf: pyrosetta.rosetta.core.pack.task.PackerTask) → None

packer task

C++: protocols::flxbb::DesignTask::set_packertask(const class std::shared_ptr<class core::pack::task::PackerTask>) –> void

set_resfile(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, resfile: str) → None

set resfile

C++: protocols::flxbb::DesignTask::set_resfile(const class std::basic_string<char> &) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

scorefxn for fixbb design

C++: protocols::flxbb::DesignTask::set_scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

setup(self: pyrosetta.rosetta.protocols.flxbb.DesignTask_Layer, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: protocols::flxbb::DesignTask_Layer::setup(const class core::pose::Pose &, const class std::shared_ptr<class core::pack::task::PackerTask>) –> void

class pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal

Bases: pyrosetta.rosetta.protocols.flxbb.DesignTask

add_task_operation(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, top: pyrosetta.rosetta.core.pack.task.operation.TaskOperation) → None

add task operation

C++: protocols::flxbb::DesignTask::add_task_operation(const class std::shared_ptr<class core::pack::task::operation::TaskOperation>) –> void

add_task_operations(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, top: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_operation_TaskOperation_t) → None

add task operations

C++: protocols::flxbb::DesignTask::add_task_operations(const class utility::vector1<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > > &) –> void

assign(self: pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal, : pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal) → pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal

C++: protocols::flxbb::DesignTask_Normal::operator=(const class protocols::flxbb::DesignTask_Normal &) –> class protocols::flxbb::DesignTask_Normal &

dump_packertask(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, os: pyrosetta.rosetta.std.ostream) → None

output packertask

C++: protocols::flxbb::DesignTask::dump_packertask(class std::basic_ostream<char> &) –> void

filter_structs(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → protocols::flxbb::FilterStructs

filter during fixbb design

C++: protocols::flxbb::DesignTask::filter_structs() const –> class std::shared_ptr<class protocols::flxbb::FilterStructs>

mover(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → pyrosetta.rosetta.protocols.moves.Mover

mover after fixbb design

C++: protocols::flxbb::DesignTask::mover() const –> class std::shared_ptr<class protocols::moves::Mover>

ncycle(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → int

the number of cycles of fixbb design and mover

C++: protocols::flxbb::DesignTask::ncycle() const –> unsigned long

packertask(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → pyrosetta.rosetta.core.pack.task.PackerTask

packer task for fixbb design

C++: protocols::flxbb::DesignTask::packertask() const –> class std::shared_ptr<class core::pack::task::PackerTask>

resfile(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → str

resfile

C++: protocols::flxbb::DesignTask::resfile() const –> std::string

scorefxn(self: pyrosetta.rosetta.protocols.flxbb.DesignTask) → pyrosetta.rosetta.core.scoring.ScoreFunction

scorefxn for fixbb design

C++: protocols::flxbb::DesignTask::scorefxn() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

set_filter_structs(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, value: protocols::flxbb::FilterStructs) → None

filter during fixbb design

C++: protocols::flxbb::DesignTask::set_filter_structs(const class std::shared_ptr<class protocols::flxbb::FilterStructs>) –> void

set_mover(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, value: pyrosetta.rosetta.protocols.moves.Mover) → None

mover after fixbb design

C++: protocols::flxbb::DesignTask::set_mover(const class std::shared_ptr<class protocols::moves::Mover>) –> void

set_ncycle(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, ncycle: int) → None

the number of cycles of design and mover

C++: protocols::flxbb::DesignTask::set_ncycle(const unsigned long &) –> void

set_packertask(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, taskf: pyrosetta.rosetta.core.pack.task.PackerTask) → None

packer task

C++: protocols::flxbb::DesignTask::set_packertask(const class std::shared_ptr<class core::pack::task::PackerTask>) –> void

set_resfile(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, resfile: str) → None

set resfile

C++: protocols::flxbb::DesignTask::set_resfile(const class std::basic_string<char> &) –> void

set_scorefxn(self: pyrosetta.rosetta.protocols.flxbb.DesignTask, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

scorefxn for fixbb design

C++: protocols::flxbb::DesignTask::set_scorefxn(const class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

setup(self: pyrosetta.rosetta.protocols.flxbb.DesignTask_Normal, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: protocols::flxbb::DesignTask_Normal::setup(const class core::pose::Pose &, const class std::shared_ptr<class core::pack::task::PackerTask>) –> void

class pyrosetta.rosetta.protocols.flxbb.FilterStructs

Bases: pybind11_builtins.pybind11_object

apply(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::flxbb::FilterStructs::apply(const class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs, : pyrosetta.rosetta.protocols.flxbb.FilterStructs) → pyrosetta.rosetta.protocols.flxbb.FilterStructs

C++: protocols::flxbb::FilterStructs::operator=(const class protocols::flxbb::FilterStructs &) –> class protocols::flxbb::FilterStructs &

clone(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs) → pyrosetta.rosetta.protocols.flxbb.FilterStructs

C++: protocols::flxbb::FilterStructs::clone() const –> class std::shared_ptr<class protocols::flxbb::FilterStructs>

current_trial(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs) → int

C++: protocols::flxbb::FilterStructs::current_trial() const –> unsigned long

filter_on(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs) → bool

C++: protocols::flxbb::FilterStructs::filter_on() const –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs) → pyrosetta.rosetta.protocols.flxbb.FilterStructs

C++: protocols::flxbb::FilterStructs::fresh_instance() const –> class std::shared_ptr<class protocols::flxbb::FilterStructs>

get_bestpose(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::flxbb::FilterStructs::get_bestpose() const –> class std::shared_ptr<class core::pose::Pose>

name(*args, **kwargs)

Overloaded function.

1. name(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs) -> str

C++: protocols::flxbb::FilterStructs::name() const –> std::string

2. name(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs, name: str) -> None

C++: protocols::flxbb::FilterStructs::name(const class std::basic_string<char> &) –> void

reset(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::flxbb::FilterStructs::reset(const class core::pose::Pose &) –> void

set_ntrial(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs, ntrial: int) → None

C++: protocols::flxbb::FilterStructs::set_ntrial(const unsigned long) –> void

class pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat

Bases: pyrosetta.rosetta.protocols.flxbb.FilterStructs

apply(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::flxbb::FilterStructs_Packstat::apply(const class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat, : pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat) → pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat

C++: protocols::flxbb::FilterStructs_Packstat::operator=(const class protocols::flxbb::FilterStructs_Packstat &) –> class protocols::flxbb::FilterStructs_Packstat &

clone(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat) → pyrosetta.rosetta.protocols.flxbb.FilterStructs

C++: protocols::flxbb::FilterStructs_Packstat::clone() const –> class std::shared_ptr<class protocols::flxbb::FilterStructs>

current_trial(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs) → int

C++: protocols::flxbb::FilterStructs::current_trial() const –> unsigned long

filter_on(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs) → bool

C++: protocols::flxbb::FilterStructs::filter_on() const –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat) → pyrosetta.rosetta.protocols.flxbb.FilterStructs

C++: protocols::flxbb::FilterStructs_Packstat::fresh_instance() const –> class std::shared_ptr<class protocols::flxbb::FilterStructs>

get_bestpose(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::flxbb::FilterStructs::get_bestpose() const –> class std::shared_ptr<class core::pose::Pose>

name(*args, **kwargs)

Overloaded function.

1. name(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs) -> str

C++: protocols::flxbb::FilterStructs::name() const –> std::string

2. name(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs, name: str) -> None

C++: protocols::flxbb::FilterStructs::name(const class std::basic_string<char> &) –> void

reset(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs_Packstat, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::flxbb::FilterStructs_Packstat::reset(const class core::pose::Pose &) –> void

set_ntrial(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs, ntrial: int) → None

C++: protocols::flxbb::FilterStructs::set_ntrial(const unsigned long) –> void

class pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge

Bases: pyrosetta.rosetta.protocols.flxbb.FilterStructs

apply(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::flxbb::FilterStructs_TotalCharge::apply(const class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge, : pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge) → pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge

C++: protocols::flxbb::FilterStructs_TotalCharge::operator=(const class protocols::flxbb::FilterStructs_TotalCharge &) –> class protocols::flxbb::FilterStructs_TotalCharge &

clone(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge) → pyrosetta.rosetta.protocols.flxbb.FilterStructs

C++: protocols::flxbb::FilterStructs_TotalCharge::clone() const –> class std::shared_ptr<class protocols::flxbb::FilterStructs>

current_trial(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs) → int

C++: protocols::flxbb::FilterStructs::current_trial() const –> unsigned long

filter_on(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs) → bool

C++: protocols::flxbb::FilterStructs::filter_on() const –> bool

fresh_instance(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge) → pyrosetta.rosetta.protocols.flxbb.FilterStructs

C++: protocols::flxbb::FilterStructs_TotalCharge::fresh_instance() const –> class std::shared_ptr<class protocols::flxbb::FilterStructs>

get_bestpose(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::flxbb::FilterStructs::get_bestpose() const –> class std::shared_ptr<class core::pose::Pose>

name(*args, **kwargs)

Overloaded function.

1. name(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs) -> str

C++: protocols::flxbb::FilterStructs::name() const –> std::string

2. name(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs, name: str) -> None

C++: protocols::flxbb::FilterStructs::name(const class std::basic_string<char> &) –> void

reset(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs_TotalCharge, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::flxbb::FilterStructs_TotalCharge::reset(const class core::pose::Pose &) –> void

set_ntrial(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs, ntrial: int) → None

C++: protocols::flxbb::FilterStructs::set_ntrial(const unsigned long) –> void

class pyrosetta.rosetta.protocols.flxbb.FlxbbDesign

Bases: pyrosetta.rosetta.protocols.moves.Mover

add_design_task(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, design_task: pyrosetta.rosetta.protocols.flxbb.DesignTask) → None

add the design task which cotrols the iteration of fixbb design and relax

C++: protocols::flxbb::FlxbbDesign::add_design_task(const class std::shared_ptr<class protocols::flxbb::DesignTask>) –> void

apply(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, pose: pyrosetta.rosetta.core.pose.Pose) → None

mover apply

C++: protocols::flxbb::FlxbbDesign::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, : pyrosetta.rosetta.protocols.flxbb.FlxbbDesign) → pyrosetta.rosetta.protocols.flxbb.FlxbbDesign

C++: protocols::flxbb::FlxbbDesign::operator=(const class protocols::flxbb::FlxbbDesign &) –> class protocols::flxbb::FlxbbDesign &

clear_design_taskset(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign) → None

clear DesignTaskSet

C++: protocols::flxbb::FlxbbDesign::clear_design_taskset() –> 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.flxbb.FlxbbDesign) → pyrosetta.rosetta.protocols.moves.Mover

clone this object

C++: protocols::flxbb::FlxbbDesign::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.flxbb.FlxbbDesign) → pyrosetta.rosetta.protocols.moves.Mover

create this type of object

C++: protocols::flxbb::FlxbbDesign::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.

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.flxbb.FlxbbDesign) → str

C++: protocols::flxbb::FlxbbDesign::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_std_allocator_std_string_t

non-const accessor

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

initialize_filter(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, filter_trial: int, filter_type: str) → None

initialize filter parameters

C++: protocols::flxbb::FlxbbDesign::initialize_filter(const unsigned long, const class std::basic_string<char> &) –> void

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

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

movemap_from_blueprint(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, value: bool) → None

set movemap for relax

C++: protocols::flxbb::FlxbbDesign::movemap_from_blueprint(const bool) –> void

mover_name() → str

C++: protocols::flxbb::FlxbbDesign::mover_name() –> std::string

name() → str

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

no_design(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, no_design: bool) → None

design protocol will not be performed (default false)

C++: protocols::flxbb::FlxbbDesign::no_design(const bool) –> void

no_relax(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, no_relax: bool) → None

relax is not performed after design (default false)

C++: protocols::flxbb::FlxbbDesign::no_relax(const bool) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, : pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::flxbb::FlxbbDesign::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::flxbb::FlxbbDesign::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

read_options(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign) → None

read parameters

C++: protocols::flxbb::FlxbbDesign::read_options() –> void

register_options() → None

register options

C++: protocols::flxbb::FlxbbDesign::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_blueprint(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, blueprint: protocols::parser::BluePrint) → None

set BluePrintOP

C++: protocols::flxbb::FlxbbDesign::set_blueprint(const class std::shared_ptr<class protocols::parser::BluePrint>) –> void

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> void

set_design_taskset(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, design_taskset: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_flxbb_DesignTask_t) → None

set DesignTaskSet

Once you set DesignTaskSet, this controls almost every setups of this class

C++: protocols::flxbb::FlxbbDesign::set_design_taskset(const class utility::vector1<class std::shared_ptr<class protocols::flxbb::DesignTask>, class std::allocator<class std::shared_ptr<class protocols::flxbb::DesignTask> > > &) –> void

set_filter_during_design(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, filter_during_design: pyrosetta.rosetta.protocols.flxbb.FilterStructs) → None

filtering during design

C++: protocols::flxbb::FlxbbDesign::set_filter_during_design(const class std::shared_ptr<class protocols::flxbb::FilterStructs>) –> 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_layer_mode(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, layer_mode: str) → None

set layer mode

C++: protocols::flxbb::FlxbbDesign::set_layer_mode(const class std::basic_string<char> &) –> void

set_movemap(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, movemap: pyrosetta.rosetta.core.kinematics.MoveMap) → None

set movemap for relax

C++: protocols::flxbb::FlxbbDesign::set_movemap(const class std::shared_ptr<class core::kinematics::MoveMap>) –> void

set_movemap_factory(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) → None

set movemapi_factory for relax

C++: protocols::flxbb::FlxbbDesign::set_movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> 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_ncycles(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, ncycles: int) → None

the number of cycles of fixbb and relax

C++: protocols::flxbb::FlxbbDesign::set_ncycles(const unsigned long) –> void

set_scorefxn_design(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

set the score function for fixbb design

C++: protocols::flxbb::FlxbbDesign::set_scorefxn_design(const class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_scorefxn_relax(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

set the score function for relax

C++: protocols::flxbb::FlxbbDesign::set_scorefxn_relax(const class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> void

set_weight_constraints_NtoC(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, value: float) → None

set weight of constraints_NtoC which constrain between Ca atoms of C- and N-terminal

if this weight > 0.0, the constraints is applied ( default = -1.0 )

C++: protocols::flxbb::FlxbbDesign::set_weight_constraints_NtoC(const double) –> void

set_weight_constraints_sheet(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, value: float) → None

set weight of constraints_sheet which constrains between Ca atoms in beta-sheets

if this weight > 0.0, the constraints is applied ( default = -1.0 )

C++: protocols::flxbb::FlxbbDesign::set_weight_constraints_sheet(const double) –> 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(class std::basic_ostream<char> &) 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) -> str

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

use_origseq_for_not_dsgned_layer(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesign, use: bool) → None

use original sequence for not designed region in layer_mode,

otherwise the residues of the region turned into Ala ( default true )

C++: protocols::flxbb::FlxbbDesign::use_origseq_for_not_dsgned_layer(const bool) –> void

class pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack

Bases: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover

apply(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::flxbb::FlxbbDesignPack::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack, : pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack) → pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack

C++: protocols::flxbb::FlxbbDesignPack::operator=(const class protocols::flxbb::FlxbbDesignPack &) –> class protocols::flxbb::FlxbbDesignPack &

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.minimization_packing.PackRotamersMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

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

complex_type_generator_for_pack_rotamers_mover(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → pyrosetta.rosetta.utility.tag.XMLSchemaComplexTypeGenerator

C++: protocols::minimization_packing::PackRotamersMover::complex_type_generator_for_pack_rotamers_mover(class utility::tag::XMLSchemaDefinition &) –> class std::shared_ptr<class utility::tag::XMLSchemaComplexTypeGenerator>

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.minimization_packing.PackRotamersMover) → pyrosetta.rosetta.protocols.moves.Mover

required in the context of the parser/scripting scheme

C++: protocols::minimization_packing::PackRotamersMover::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.

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.flxbb.FlxbbDesignPack) → str

C++: protocols::flxbb::FlxbbDesignPack::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_std_allocator_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

mover_name() → str

C++: protocols::minimization_packing::PackRotamersMover::mover_name() –> std::string

name() → str

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

nloop(*args, **kwargs)

Overloaded function.

1. nloop(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, nloop_in: int) -> None

C++: protocols::minimization_packing::PackRotamersMover::nloop(unsigned long) –> void

2. nloop(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> int

C++: protocols::minimization_packing::PackRotamersMover::nloop() const –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, : pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, : pyrosetta.rosetta.core.pose.Pose) → None

parse XML (specifically in the context of the parser/scripting scheme)

C++: protocols::minimization_packing::PackRotamersMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

parse_score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, : pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, : pyrosetta.rosetta.core.pose.Pose) → None

parse “scorefxn” XML option (can be employed virtually by derived Packing movers)

C++: protocols::minimization_packing::PackRotamersMover::parse_score_function(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

parse_task_operations(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, : pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, : pyrosetta.rosetta.core.pose.Pose) → None

parse “task_operations” XML option (can be employed virtually by derived Packing movers)

C++: protocols::minimization_packing::PackRotamersMover::parse_task_operations(class std::shared_ptr<const class utility::tag::Tag>, const class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::minimization_packing::PackRotamersMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

rotamer_sets(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets

Returns the RotamerSets object being used for packing

• This is only valid after a call to setup or apply.

C++: protocols::minimization_packing::PackRotamersMover::rotamer_sets() const –> class std::shared_ptr<const class core::pack::rotamer_set::RotamerSets>

score_function(*args, **kwargs)

Overloaded function.

1. score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, sf: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

Sets the ScoreFunction to <sf>

example(s):

packmover.score_function(scorefxn)

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::minimization_packing::PackRotamersMover::score_function(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void

2. score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

Returns the ScoreFunction

example(s):

packmover.score_function()

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::minimization_packing::PackRotamersMover::score_function() const –> class std::shared_ptr<const class core::scoring::ScoreFunction>

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> None
2. show(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, output: pyrosetta.rosetta.std.ostream) -> None

C++: protocols::minimization_packing::PackRotamersMover::show(class std::basic_ostream<char> &) const –> void

task(*args, **kwargs)

Overloaded function.

1. task(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, t: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

Sets the PackerTask to <t>

example(s):

packmover.task(task_pack)

See Also:

PackRotamersMover PackRotamersMover.task_factory

C++: protocols::minimization_packing::PackRotamersMover::task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

2. task(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.PackerTask

Returns the PackerTask

example(s):

packmover.task()

See Also:

PackRotamersMover PackRotamersMover.task_factory

C++: protocols::minimization_packing::PackRotamersMover::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

task_factory(*args, **kwargs)

Overloaded function.

1. task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

Sets the TaskFactory to <tf>

example(s):

packmover.task_factory(task_design)

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::minimization_packing::PackRotamersMover::task_factory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> void

2. task_factory(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory

Returns the TaskFactory

example(s):

packmover.task_factory()

See Also:

PackRotamersMover PackRotamersMover.task

C++: protocols::minimization_packing::PackRotamersMover::task_factory() const –> class std::shared_ptr<const class core::pack::task::TaskFactory>

task_is_valid(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::minimization_packing::PackRotamersMover::task_is_valid(const class core::pose::Pose &) const –> bool

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) -> str

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.flxbb.FlxbbDesign_main() → None

C++: protocols::flxbb::FlxbbDesign_main() –> void

class pyrosetta.rosetta.protocols.flxbb.InterlockAroma

Bases: pyrosetta.rosetta.protocols.moves.Mover

apply(self: pyrosetta.rosetta.protocols.flxbb.InterlockAroma, pose: pyrosetta.rosetta.core.pose.Pose) → None

mover apply

C++: protocols::flxbb::InterlockAroma::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.flxbb.InterlockAroma, : pyrosetta.rosetta.protocols.flxbb.InterlockAroma) → pyrosetta.rosetta.protocols.flxbb.InterlockAroma

C++: protocols::flxbb::InterlockAroma::operator=(const class protocols::flxbb::InterlockAroma &) –> class protocols::flxbb::InterlockAroma &

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.flxbb.InterlockAroma) → pyrosetta.rosetta.protocols.moves.Mover

clone this object

C++: protocols::flxbb::InterlockAroma::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.flxbb.InterlockAroma) → pyrosetta.rosetta.protocols.moves.Mover

create this type of object

C++: protocols::flxbb::InterlockAroma::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.

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.flxbb.InterlockAroma) → str

C++: protocols::flxbb::InterlockAroma::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_std_allocator_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

mover_name() → str

C++: protocols::flxbb::InterlockAroma::mover_name() –> std::string

name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.flxbb.InterlockAroma, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap, : pyrosetta.rosetta.std.map_std_string_std_shared_ptr_protocols_filters_Filter_t, : pyrosetta.rosetta.std.map_const_std_string_std_shared_ptr_protocols_moves_Mover_t, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::flxbb::InterlockAroma::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const class std::map<class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter>, struct std::less<class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::filters::Filter> > > > &, const class std::map<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover>, struct std::less<const class std::basic_string<char> >, class std::allocator<struct std::pair<const class std::basic_string<char>, class std::shared_ptr<class protocols::moves::Mover> > > > &, const class core::pose::Pose &) –> void

provide_xml_schema(xsd: pyrosetta.rosetta.utility.tag.XMLSchemaDefinition) → None

C++: protocols::flxbb::InterlockAroma::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

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

////////////////////////////end Job Distributor interface////////////////////////////////////////

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 class std::basic_string<char> &) –> 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

C++: protocols::moves::Mover::set_type(const class std::basic_string<char> &) –> 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(class std::basic_ostream<char> &) 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) -> str

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

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

C++: protocols::moves::Mover::type(const class std::basic_string<char> &) –> void

pyrosetta.rosetta.protocols.flxbb.constraints_NtoC(*args, **kwargs)

Overloaded function.

1. constraints_NtoC(pose: pyrosetta.rosetta.core.pose.Pose, coef: float) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_constraints_Constraint_t
2. constraints_NtoC(pose: pyrosetta.rosetta.core.pose.Pose, coef: float, condist: float) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_constraints_Constraint_t

constraint between N- and C-terminal Ca atoms

C++: protocols::flxbb::constraints_NtoC(const class core::pose::Pose &, const double, const double) –> class utility::vector1<class std::shared_ptr<class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<class core::scoring::constraints::Constraint> > >

pyrosetta.rosetta.protocols.flxbb.constraints_sheet(*args, **kwargs)

Overloaded function.

1. constraints_sheet(pose: pyrosetta.rosetta.core.pose.Pose, blue: protocols::parser::BluePrint, coef: float) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_constraints_Constraint_t
2. constraints_sheet(pose: pyrosetta.rosetta.core.pose.Pose, blue: protocols::parser::BluePrint, coef: float, condist: float) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_constraints_Constraint_t

constrain between Ca atoms in beta sheet, which are specified in blueprint file

C++: protocols::flxbb::constraints_sheet(const class core::pose::Pose &, const class std::shared_ptr<class protocols::parser::BluePrint> &, const double, const double) –> class utility::vector1<class std::shared_ptr<class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<class core::scoring::constraints::Constraint> > >

3. constraints_sheet(pose: pyrosetta.rosetta.core.pose.Pose, coef: float) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_constraints_Constraint_t
4. constraints_sheet(pose: pyrosetta.rosetta.core.pose.Pose, coef: float, condist: float) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_constraints_Constraint_t

constrain between Ca atoms in beta sheet

C++: protocols::flxbb::constraints_sheet(const class core::pose::Pose &, const double, const double) –> class utility::vector1<class std::shared_ptr<class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<class core::scoring::constraints::Constraint> > >

pyrosetta.rosetta.protocols.flxbb.find_ligands(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

Looks for unknown amino acids in the pose and returns their indices

C++: protocols::flxbb::find_ligands(const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >