flxbb¶
Bindings for protocols::flxbb namespace
- class pyrosetta.rosetta.protocols.flxbb.CombinedTaskOperation¶
Bases:
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_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:
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:
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_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.
name(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs) -> str
C++: protocols::flxbb::FilterStructs::name() const –> std::string
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:
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.
name(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs) -> str
C++: protocols::flxbb::FilterStructs::name() const –> std::string
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:
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.
name(self: pyrosetta.rosetta.protocols.flxbb.FilterStructs) -> str
C++: protocols::flxbb::FilterStructs::name() const –> std::string
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:
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_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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
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.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
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:
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
- class pyrosetta.rosetta.protocols.flxbb.FlxbbDesignPack¶
Bases:
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_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_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 list_options_read(opts: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) None ¶
C++: protocols::minimization_packing::PackRotamersMover::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void
- 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.
nloop(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover, nloop_in: int) -> None
C++: protocols::minimization_packing::PackRotamersMover::nloop(unsigned long) –> void
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.
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
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.
show(self: pyrosetta.rosetta.protocols.minimization_packing.PackRotamersMover) -> None
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.
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
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.
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
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.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
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:
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_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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
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.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
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:
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
- class pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation¶
Bases:
TaskOperation
- DESIGN = <LayerOperationType.DESIGN: 0>¶
- DESIGNABLE = <LayerSpecificationType.DESIGNABLE: 0>¶
- FIXED = <LayerSpecificationType.FIXED: 2>¶
- class LayerOperationType¶
Bases:
pybind11_object
Members:
DESIGN
NO_DESIGN
OMIT
- DESIGN = <LayerOperationType.DESIGN: 0>¶
- NO_DESIGN = <LayerOperationType.NO_DESIGN: 1>¶
- OMIT = <LayerOperationType.OMIT: 2>¶
- property name¶
- property value¶
- class LayerSpecificationType¶
Bases:
pybind11_object
Members:
DESIGNABLE
PACKABLE
FIXED
- DESIGNABLE = <LayerSpecificationType.DESIGNABLE: 0>¶
- FIXED = <LayerSpecificationType.FIXED: 2>¶
- PACKABLE = <LayerSpecificationType.PACKABLE: 1>¶
- property name¶
- property value¶
- 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.
sasa_core(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, r: float) -> None
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.
sasa_surface(self: pyrosetta.rosetta.protocols.flxbb.LayerDesignOperation, r: float) -> None
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:
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
- skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) bool ¶
Indicate whether we skip adding citation information to the XML schema.
False for any real task operation. True only for dummy task operations created for unit tests.
C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool
- pyrosetta.rosetta.protocols.flxbb.constraints_NtoC(*args, **kwargs)¶
Overloaded function.
constraints_NtoC(pose: pyrosetta.rosetta.core.pose.Pose, coef: float) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_constraints_Constraint_t
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.
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
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> > >
constraints_sheet(pose: pyrosetta.rosetta.core.pose.Pose, coef: float) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_constraints_Constraint_t
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> >