flxbb

Bindings for protocols::flxbb namespace

class pyrosetta.rosetta.protocols.flxbb.CombinedTaskOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.TaskOperation

apply(self: pyrosetta.rosetta.protocols.flxbb.CombinedTaskOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) None

apply

C++: protocols::flxbb::CombinedTaskOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.flxbb.CombinedTaskOperation, : pyrosetta.rosetta.protocols.flxbb.CombinedTaskOperation) pyrosetta.rosetta.protocols.flxbb.CombinedTaskOperation

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

clone(self: pyrosetta.rosetta.protocols.flxbb.CombinedTaskOperation) pyrosetta.rosetta.core.pack.task.operation.TaskOperation

make clone

C++: protocols::flxbb::CombinedTaskOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

Used to parse an xml-like tag to load parameters and properties.

C++: core::pack::task::operation::TaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

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(std::ostream &) –> 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 std::string &) –> 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(std::ostream &) –> 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 std::string &) –> 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(std::ostream &) –> 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 std::string &) –> 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

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

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

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

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

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

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

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.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 std::string &) –> 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

static mover_name() str

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

static 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) None

C++: protocols::flxbb::FlxbbDesign::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 provide_xml_schema(xsd: 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

static 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

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_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 std::string &) –> 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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

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.FlxbbDesignCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesignCreator, : pyrosetta.rosetta.protocols.flxbb.FlxbbDesignCreator) pyrosetta.rosetta.protocols.flxbb.FlxbbDesignCreator

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

create_mover(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesignCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesignCreator) str

C++: protocols::flxbb::FlxbbDesignCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.flxbb.FlxbbDesignCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::flxbb::FlxbbDesignCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> 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>

static complex_type_generator_for_pack_rotamers_mover(xsd: utility::tag::XMLSchemaDefinition) 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.

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.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 > > &

initialize_task_factory_with_operations(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.std.list_std_shared_ptr_core_pack_task_operation_TaskOperation_std_allocator_std_shared_ptr_core_pack_task_operation_TaskOperation_t) None

C++: protocols::minimization_packing::PackRotamersMover::initialize_task_factory_with_operations(const class std::list<class std::shared_ptr<class core::pack::task::operation::TaskOperation>, class std::allocator<class std::shared_ptr<class core::pack::task::operation::TaskOperation> > > &) –> void

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

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

static mover_name() str

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

static 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

  1. 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) 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 &) –> void

parse_score_function(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) 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 &) –> void

parse_task_operations(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) 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 &) –> 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 provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

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

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

  1. 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_annealer_observer(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, observer: pyrosetta.rosetta.core.pack.annealer.AnnealerObserver) None

C++: protocols::minimization_packing::PackRotamersMover::set_annealer_observer(class std::shared_ptr<class core::pack::annealer::AnnealerObserver>) –> void

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

  1. show(self: pyrosetta.rosetta.protocols.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(std::ostream &) 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

  1. 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

  1. 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, type_in: str) -> None

Set the ‘type’ string

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

  1. 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.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.

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.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

static mover_name() str

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

static 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) None

C++: protocols::flxbb::InterlockAroma::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 provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

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

static register_options() None

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

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

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

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

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

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool
Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None
: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

  1. 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.flxbb.InterlockAromaCreator

Bases: pyrosetta.rosetta.protocols.moves.MoverCreator

assign(self: pyrosetta.rosetta.protocols.flxbb.InterlockAromaCreator, : pyrosetta.rosetta.protocols.flxbb.InterlockAromaCreator) pyrosetta.rosetta.protocols.flxbb.InterlockAromaCreator

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

create_mover(self: pyrosetta.rosetta.protocols.flxbb.InterlockAromaCreator) pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.flxbb.InterlockAromaCreator) str

C++: protocols::flxbb::InterlockAromaCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.flxbb.InterlockAromaCreator, xsd: utility::tag::XMLSchemaDefinition) None

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

class pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation

Bases: pyrosetta.rosetta.core.pack.task.operation.TaskOperation

DESIGN = <LayerOperationType.DESIGN: 0>
DESIGNABLE = <LayerSpecificationType.DESIGNABLE: 0>
FIXED = <LayerSpecificationType.FIXED: 2>
class LayerOperationType

Bases: pybind11_builtins.pybind11_object

Members:

DESIGN

NO_DESIGN

OMIT

DESIGN = <LayerOperationType.DESIGN: 0>
NO_DESIGN = <LayerOperationType.NO_DESIGN: 1>
OMIT = <LayerOperationType.OMIT: 2>
property name
class LayerSpecificationType

Bases: pybind11_builtins.pybind11_object

Members:

DESIGNABLE

PACKABLE

FIXED

DESIGNABLE = <LayerSpecificationType.DESIGNABLE: 0>
FIXED = <LayerSpecificationType.FIXED: 2>
PACKABLE = <LayerSpecificationType.PACKABLE: 1>
property name
NO_DESIGN = <LayerOperationType.NO_DESIGN: 1>
OMIT = <LayerOperationType.OMIT: 2>
PACKABLE = <LayerSpecificationType.PACKABLE: 1>
add_layer(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, layer_name: str, task: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, operation: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation.LayerOperationType, specification: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation.LayerSpecificationType) None

add a new layer which will be created based on a task operation

C++: protocols::flxbb::LayerDesignOperation::add_layer(const std::string &, class std::shared_ptr<class core::pack::task::operation::TaskOperation>, const enum protocols::flxbb::LayerDesignOperation::LayerOperationType, const enum protocols::flxbb::LayerDesignOperation::LayerSpecificationType) –> void

apply(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) None

apply

C++: protocols::flxbb::LayerDesignOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, : pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation) pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation

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

clone(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation) pyrosetta.rosetta.core.pack.task.operation.TaskOperation

make clone

C++: protocols::flxbb::LayerDesignOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

copy_layer_residues(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, src_layer: str, dest_layer: str) None

copies residues allowed from src to dest

C++: protocols::flxbb::LayerDesignOperation::copy_layer_residues(const std::string &, const std::string &) –> void

design_layer(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, dsgn_core: bool, dsgn_boundary: bool, dsgn_surface: bool) None

layer to be designed in internal SRBL object

C++: protocols::flxbb::LayerDesignOperation::design_layer(const bool, const bool, const bool) –> void

ignore_pikaa_natro(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation) bool

Returns whether residues set with PIKAA and NATRO in previously-applied resfiles are ignored.

Default behaviour is now FALSE to preserve commutativity.

C++: protocols::flxbb::LayerDesignOperation::ignore_pikaa_natro() const –> bool

static keyname() str

C++: protocols::flxbb::LayerDesignOperation::keyname() –> std::string

layer_residues(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, layer_name: str, ss_name: str) str

gets the residues allowed for a given secondary structure in a given layer

C++: protocols::flxbb::LayerDesignOperation::layer_residues(const std::string &, const std::string &) const –> const std::string &

make_pymol_script(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, value: bool) None

make pymol scripts showing the different layers

C++: protocols::flxbb::LayerDesignOperation::make_pymol_script(bool) –> void

parse_layer_secstruct_tag(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, secstruct_tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap, layer_name: str) None

C++: protocols::flxbb::LayerDesignOperation::parse_layer_secstruct_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &, const std::string &) –> void

parse_layer_tag(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, layer_tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::flxbb::LayerDesignOperation::parse_layer_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_tag(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None

C++: protocols::flxbb::LayerDesignOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

pore_radius(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, ps: float) None

set pore radius for colculating asa

C++: protocols::flxbb::LayerDesignOperation::pore_radius(double) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : 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 task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None

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

sasa_core(*args, **kwargs)

Overloaded function.

  1. sasa_core(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, r: float) -> None

  2. sasa_core(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, r: float, ss: str) -> None

accessible surface for evaluating residues are in core or not

C++: protocols::flxbb::LayerDesignOperation::sasa_core(const double, const std::string &) –> void

sasa_surface(*args, **kwargs)

Overloaded function.

  1. sasa_surface(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, r: float) -> None

  2. sasa_surface(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, r: float, ss: str) -> None

accessible surface for evaluating residues are in surface or not

C++: protocols::flxbb::LayerDesignOperation::sasa_surface(const double, const std::string &) –> void

set_design_layers(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, layers: pyrosetta.rosetta.utility.vector1_std_string) None

sets names of layers to design

C++: protocols::flxbb::LayerDesignOperation::set_design_layers(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

set_ignore_pikaa_natro(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, val: bool) None

Sets whether residues set with PIKAA and NATRO in previously-applied resfiles are ignored.

Default behaviour is now FALSE to preserve commutativity.

C++: protocols::flxbb::LayerDesignOperation::set_ignore_pikaa_natro(const bool) –> void

set_layer_operation(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, layer_name: str, operation: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation.LayerOperationType) None

sets layer operation

C++: protocols::flxbb::LayerDesignOperation::set_layer_operation(const std::string &, const enum protocols::flxbb::LayerDesignOperation::LayerOperationType) –> void

set_layer_residues(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, layer_name: str, ss_name: str, residues: str) None

sets residues allowed for a particular secondary structure in the given layer

C++: protocols::flxbb::LayerDesignOperation::set_layer_residues(const std::string &, const std::string &, const std::string &) –> void

set_layer_specification(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, layer_name: str, specification: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation.LayerSpecificationType) None

sets layer specification

C++: protocols::flxbb::LayerDesignOperation::set_layer_specification(const std::string &, const enum protocols::flxbb::LayerDesignOperation::LayerSpecificationType) –> void

set_restrict_restypes(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, b: bool) None

set restrict_restypes

C++: protocols::flxbb::LayerDesignOperation::set_restrict_restypes(const bool) –> void

set_sc_neighbor_angle_exponent(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, value: float) None

Set another parameter (the angle exponent) in the calculation that the sidechain neighbors algorithm uses.

See core::select::util::SelectResiduesByLayer class for details.

C++: protocols::flxbb::LayerDesignOperation::set_sc_neighbor_angle_exponent(const double &) –> void

set_sc_neighbor_angle_shift_factor(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, value: float) None

Set a parameter in the calculation that the sidechain neighbors algorithm uses.

See core::select::util::SelectResiduesByLayer class for details.

C++: protocols::flxbb::LayerDesignOperation::set_sc_neighbor_angle_shift_factor(const double &) –> void

set_sc_neighbor_denominator(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, value: float) None

Set the factor by which neighbor counts are divided when using the sidechain neighbors method.

C++: protocols::flxbb::LayerDesignOperation::set_sc_neighbor_denominator(const double &) –> void

set_sc_neighbor_dist_exponent(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, value: float) None

Set another parameter (the distance exponent) in the calculation that the sidechain neighbors algorithm uses.

See core::select::util::SelectResiduesByLayer class for details.

C++: protocols::flxbb::LayerDesignOperation::set_sc_neighbor_dist_exponent(const double &) –> void

set_sc_neighbor_dist_midpoint(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, value: float) None

Set the midpoint of the sigmoidal distance falloff for the sidechain neighbors method.

C++: protocols::flxbb::LayerDesignOperation::set_sc_neighbor_dist_midpoint(const double &) –> void

set_use_sidechain_neighbors(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, value: bool) None

Set whether to use sidechain neighbors to determine core/boundary/surface (default=false)

C++: protocols::flxbb::LayerDesignOperation::set_use_sidechain_neighbors(const bool) –> void

set_verbose(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, b: bool) None

set verbose

C++: protocols::flxbb::LayerDesignOperation::set_verbose(const bool) –> void

use_original_seq(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation) None

use original sequence for not designed layer

C++: protocols::flxbb::LayerDesignOperation::use_original_seq() –> void

class pyrosetta.rosetta.protocols.flxbb.LayerDesignOperationCreator

Bases: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperationCreator, : pyrosetta.rosetta.protocols.flxbb.LayerDesignOperationCreator) pyrosetta.rosetta.protocols.flxbb.LayerDesignOperationCreator

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

create_task_operation(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperationCreator) pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: protocols::flxbb::LayerDesignOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperationCreator) str

C++: protocols::flxbb::LayerDesignOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperationCreator, xsd: utility::tag::XMLSchemaDefinition) None

C++: protocols::flxbb::LayerDesignOperationCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> 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> > >

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

  2. 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> >