matdes¶

Bindings for protocols::matdes namespace

class pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperation¶

Bases: TaskOperation

apply(self: pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperation, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) → None¶: C++: protocols::matdes::BuildingBlockInterfaceOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperation, : pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperation) → pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperation¶: C++: protocols::matdes::BuildingBlockInterfaceOperation::operator=(const class protocols::matdes::BuildingBlockInterfaceOperation &) –> class protocols::matdes::BuildingBlockInterfaceOperation &

clone(self: pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::matdes::BuildingBlockInterfaceOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

static keyname() → str¶: C++: protocols::matdes::BuildingBlockInterfaceOperation::keyname() –> std::string

parse_tag(self: pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperation, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::matdes::BuildingBlockInterfaceOperation::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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::matdes::BuildingBlockInterfaceOperation::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator¶

Bases: TaskOperationCreator

assign(self: pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator, : pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator) → pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator¶: C++: protocols::matdes::BuildingBlockInterfaceOperationCreator::operator=(const class protocols::matdes::BuildingBlockInterfaceOperationCreator &) –> class protocols::matdes::BuildingBlockInterfaceOperationCreator &

create_task_operation(self: pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation¶: C++: protocols::matdes::BuildingBlockInterfaceOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

keyname(self: pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator) → str¶: C++: protocols::matdes::BuildingBlockInterfaceOperationCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.matdes.BuildingBlockInterfaceOperationCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::matdes::BuildingBlockInterfaceOperationCreator::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

class pyrosetta.rosetta.protocols.matdes.ClashCheckFilter¶

Bases: Filter

apply(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::matdes::ClashCheckFilter::apply(const class core::pose::Pose &) const –> bool

clash_dist(*args, **kwargs)¶

Overloaded function.

clash_dist(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter, c: float) -> None

C++: protocols::matdes::ClashCheckFilter::clash_dist(const double) –> void

clash_dist(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter) -> float

C++: protocols::matdes::ClashCheckFilter::clash_dist() const –> double

static class_name() → str¶: C++: protocols::matdes::ClashCheckFilter::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::ClashCheckFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compute(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter, pose: pyrosetta.rosetta.core.pose.Pose, v: bool, w: bool) → int¶

calc oligomeric AverageDegree

C++: protocols::matdes::ClashCheckFilter::compute(const class core::pose::Pose &, const bool &, const bool &) const –> unsigned long

fresh_instance(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::ClashCheckFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

name(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter) → str¶: C++: protocols::matdes::ClashCheckFilter::name() const –> std::string

nsub_bblock(*args, **kwargs)¶

Overloaded function.

nsub_bblock(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter, n: int) -> None

C++: protocols::matdes::ClashCheckFilter::nsub_bblock(const unsigned long) –> void

nsub_bblock(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter) -> int

C++: protocols::matdes::ClashCheckFilter::nsub_bblock() const –> unsigned long

parse_my_tag(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::matdes::ClashCheckFilter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : 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 filters wishing to provide citation information.

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::matdes::ClashCheckFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::matdes::ClashCheckFilter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::matdes::ClashCheckFilter::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

sym_dof_names(*args, **kwargs)¶

Overloaded function.

sym_dof_names(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter, s: str) -> None

C++: protocols::matdes::ClashCheckFilter::sym_dof_names(const std::string &) –> void

sym_dof_names(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter) -> str

C++: protocols::matdes::ClashCheckFilter::sym_dof_names() const –> std::string

task_factory(*args, **kwargs)¶

Overloaded function.

task_factory(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::matdes::ClashCheckFilter::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

task_factory(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter) -> pyrosetta.rosetta.core.pack.task.TaskFactory

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

threshold(*args, **kwargs)¶

Overloaded function.

threshold(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter, t: int) -> None

C++: protocols::matdes::ClashCheckFilter::threshold(const unsigned long) –> void

threshold(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter) -> int

C++: protocols::matdes::ClashCheckFilter::threshold() const –> unsigned long

verbose(*args, **kwargs)¶

Overloaded function.

verbose(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter, v: bool) -> None

C++: protocols::matdes::ClashCheckFilter::verbose(const bool) –> void

verbose(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter) -> bool

C++: protocols::matdes::ClashCheckFilter::verbose() const –> bool

write(*args, **kwargs)¶

Overloaded function.

write(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter, w: bool) -> None

C++: protocols::matdes::ClashCheckFilter::write(const bool) –> void

write(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter) -> bool

C++: protocols::matdes::ClashCheckFilter::write() const –> bool

write_pymol_string_to_pdb(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter, pymol_selection: str) → None¶: C++: protocols::matdes::ClashCheckFilter::write_pymol_string_to_pdb(const std::string &) const –> void

write_to_pdb(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilter, pose: pyrosetta.rosetta.core.pose.Pose, residue_name: str, residue: int, atom_name: str) → None¶: C++: protocols::matdes::ClashCheckFilter::write_to_pdb(const class core::pose::Pose &, const std::string &, const unsigned long, const std::string &) const –> void

class pyrosetta.rosetta.protocols.matdes.ClashCheckFilterCreator¶

Bases: FilterCreator

assign(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilterCreator, : pyrosetta.rosetta.protocols.matdes.ClashCheckFilterCreator) → pyrosetta.rosetta.protocols.matdes.ClashCheckFilterCreator¶: C++: protocols::matdes::ClashCheckFilterCreator::operator=(const class protocols::matdes::ClashCheckFilterCreator &) –> class protocols::matdes::ClashCheckFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilterCreator) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::ClashCheckFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilterCreator) → str¶: C++: protocols::matdes::ClashCheckFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.matdes.ClashCheckFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::matdes::ClashCheckFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::matdes::ExtractSubposeMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover, : pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover) → pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover¶: C++: protocols::matdes::ExtractSubposeMover::operator=(const class protocols::matdes::ExtractSubposeMover &) –> class protocols::matdes::ExtractSubposeMover &

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.matdes.ExtractSubposeMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::matdes::ExtractSubposeMover::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.matdes.ExtractSubposeMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::matdes::ExtractSubposeMover::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.matdes.ExtractSubposeMover) → str¶: C++: protocols::matdes::ExtractSubposeMover::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::matdes::ExtractSubposeMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.matdes.ExtractSubposeMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::matdes::ExtractSubposeMover::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::matdes::ExtractSubposeMover::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.matdes.ExtractSubposeMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.matdes.ExtractSubposeMoverCreator, : pyrosetta.rosetta.protocols.matdes.ExtractSubposeMoverCreator) → pyrosetta.rosetta.protocols.matdes.ExtractSubposeMoverCreator¶: C++: protocols::matdes::ExtractSubposeMoverCreator::operator=(const class protocols::matdes::ExtractSubposeMoverCreator &) –> class protocols::matdes::ExtractSubposeMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.matdes.ExtractSubposeMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::matdes::ExtractSubposeMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.matdes.ExtractSubposeMoverCreator) → str¶: C++: protocols::matdes::ExtractSubposeMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.matdes.ExtractSubposeMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::matdes::ExtractSubposeMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.matdes.GetRBDOFValues¶

Bases: Filter

WARNING WARNING WARNING THIS CLASS USES THE THREAD UNSAFE SymDofMoverSampler AND MAKES ANY PROTOCOL THAT USES THIS CLASS THREAD UNSAFE.

angle(*args, **kwargs)¶

Overloaded function.

angle(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, ang: bool) -> None

C++: protocols::matdes::GetRBDOFValues::angle(const bool) –> void

angle(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> bool

C++: protocols::matdes::GetRBDOFValues::angle() const –> bool

apply(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::matdes::GetRBDOFValues::apply(const class core::pose::Pose &) const –> bool

axis(*args, **kwargs)¶

Overloaded function.

axis(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, ax: str) -> None

C++: protocols::matdes::GetRBDOFValues::axis(const char) –> void

axis(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> str

C++: protocols::matdes::GetRBDOFValues::axis() const –> char

static class_name() → str¶: C++: protocols::matdes::GetRBDOFValues::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::GetRBDOFValues::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compute(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, pose: pyrosetta.rosetta.core.pose.Pose, verb: bool, dof_name: str, jump: int, ax: str, disp: bool, ang: bool, init_d: float, init_a: float, get_init: bool) → float¶

get the translation and rotation for a user specified jump

C++: protocols::matdes::GetRBDOFValues::compute(const class core::pose::Pose &, const bool &, const std::string &, const int &, const char &, const bool &, const bool &, const double &, const double &, const bool &) const –> double

fresh_instance(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::GetRBDOFValues::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_init_value(*args, **kwargs)¶

Overloaded function.

get_init_value(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, get_init: bool) -> None

C++: protocols::matdes::GetRBDOFValues::get_init_value(const bool) –> void

get_init_value(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> bool

C++: protocols::matdes::GetRBDOFValues::get_init_value() const –> bool

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

init_angle(*args, **kwargs)¶

Overloaded function.

init_angle(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, init_a: float) -> None

C++: protocols::matdes::GetRBDOFValues::init_angle(const double) –> void

init_angle(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> float

C++: protocols::matdes::GetRBDOFValues::init_angle() const –> double

init_disp(*args, **kwargs)¶

Overloaded function.

init_disp(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, init_d: float) -> None

C++: protocols::matdes::GetRBDOFValues::init_disp(const double) –> void

init_disp(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> float

C++: protocols::matdes::GetRBDOFValues::init_disp() const –> double

jump_id(*args, **kwargs)¶

Overloaded function.

jump_id(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, jump: int) -> None

C++: protocols::matdes::GetRBDOFValues::jump_id(const unsigned long) –> void

jump_id(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> int

C++: protocols::matdes::GetRBDOFValues::jump_id() const –> unsigned long

name(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) → str¶: C++: protocols::matdes::GetRBDOFValues::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::matdes::GetRBDOFValues::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : 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 filters wishing to provide citation information.

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::matdes::GetRBDOFValues::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

radial_disp(*args, **kwargs)¶

Overloaded function.

radial_disp(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, disp: bool) -> None

C++: protocols::matdes::GetRBDOFValues::radial_disp(const bool) –> void

radial_disp(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> bool

C++: protocols::matdes::GetRBDOFValues::radial_disp() const –> bool

report(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::matdes::GetRBDOFValues::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::matdes::GetRBDOFValues::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

sym_dof_name(*args, **kwargs)¶

Overloaded function.

sym_dof_name(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, dof_name: str) -> None

C++: protocols::matdes::GetRBDOFValues::sym_dof_name(const std::string &) –> void

sym_dof_name(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> str

C++: protocols::matdes::GetRBDOFValues::sym_dof_name() const –> std::string

verbose(*args, **kwargs)¶

Overloaded function.

verbose(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues, verb: bool) -> None

C++: protocols::matdes::GetRBDOFValues::verbose(const bool) –> void

verbose(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValues) -> bool

C++: protocols::matdes::GetRBDOFValues::verbose() const –> bool

class pyrosetta.rosetta.protocols.matdes.GetRBDOFValuesCreator¶

Bases: FilterCreator

assign(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValuesCreator, : pyrosetta.rosetta.protocols.matdes.GetRBDOFValuesCreator) → pyrosetta.rosetta.protocols.matdes.GetRBDOFValuesCreator¶: C++: protocols::matdes::GetRBDOFValuesCreator::operator=(const class protocols::matdes::GetRBDOFValuesCreator &) –> class protocols::matdes::GetRBDOFValuesCreator &

create_filter(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValuesCreator) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::GetRBDOFValuesCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValuesCreator) → str¶: C++: protocols::matdes::GetRBDOFValuesCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.matdes.GetRBDOFValuesCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::matdes::GetRBDOFValuesCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter¶

Bases: Filter

apply(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::matdes::InterfacePackingFilter::apply(const class core::pose::Pose &) const –> bool

static class_name() → str¶: C++: protocols::matdes::InterfacePackingFilter::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::InterfacePackingFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compute(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::matdes::InterfacePackingFilter::compute(const class core::pose::Pose &) const –> double

contact_dist(*args, **kwargs)¶

Overloaded function.

contact_dist(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter) -> float

C++: protocols::matdes::InterfacePackingFilter::contact_dist() const –> double

contact_dist(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter, c: float) -> None

C++: protocols::matdes::InterfacePackingFilter::contact_dist(const double) –> void

distance_cutoff(*args, **kwargs)¶

Overloaded function.

distance_cutoff(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter) -> float

C++: protocols::matdes::InterfacePackingFilter::distance_cutoff() const –> double

distance_cutoff(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter, d: float) -> None

C++: protocols::matdes::InterfacePackingFilter::distance_cutoff(const double) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::InterfacePackingFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

lower_threshold(*args, **kwargs)¶

Overloaded function.

lower_threshold(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter) -> float

C++: protocols::matdes::InterfacePackingFilter::lower_threshold() const –> double

lower_threshold(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter, l: float) -> None

C++: protocols::matdes::InterfacePackingFilter::lower_threshold(const double) –> void

multicomp(*args, **kwargs)¶

Overloaded function.

multicomp(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter) -> bool

C++: protocols::matdes::InterfacePackingFilter::multicomp() const –> bool

multicomp(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter, multicomp: bool) -> None

C++: protocols::matdes::InterfacePackingFilter::multicomp(const bool) –> void

name(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter) → str¶: C++: protocols::matdes::InterfacePackingFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::matdes::InterfacePackingFilter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : 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 filters wishing to provide citation information.

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::matdes::InterfacePackingFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::matdes::InterfacePackingFilter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::matdes::InterfacePackingFilter::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

sym_dof_names(*args, **kwargs)¶

Overloaded function.

sym_dof_names(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter) -> str

C++: protocols::matdes::InterfacePackingFilter::sym_dof_names() const –> std::string

sym_dof_names(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter, s: str) -> None

C++: protocols::matdes::InterfacePackingFilter::sym_dof_names(const std::string) –> void

upper_threshold(*args, **kwargs)¶

Overloaded function.

upper_threshold(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter) -> float

C++: protocols::matdes::InterfacePackingFilter::upper_threshold() const –> double

upper_threshold(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilter, u: float) -> None

C++: protocols::matdes::InterfacePackingFilter::upper_threshold(const double) –> void

class pyrosetta.rosetta.protocols.matdes.InterfacePackingFilterCreator¶

Bases: FilterCreator

assign(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilterCreator, : pyrosetta.rosetta.protocols.matdes.InterfacePackingFilterCreator) → pyrosetta.rosetta.protocols.matdes.InterfacePackingFilterCreator¶: C++: protocols::matdes::InterfacePackingFilterCreator::operator=(const class protocols::matdes::InterfacePackingFilterCreator &) –> class protocols::matdes::InterfacePackingFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilterCreator) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::InterfacePackingFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilterCreator) → str¶: C++: protocols::matdes::InterfacePackingFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.matdes.InterfacePackingFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::matdes::InterfacePackingFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover¶

Bases: Mover

add_filter(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, : pyrosetta.rosetta.protocols.filters.Filter, sample_type: str, filter_delta: float) → None¶: C++: protocols::matdes::MatDesGreedyOptMutationMover::add_filter(class std::shared_ptr<class protocols::filters::Filter>, const std::string, double) –> void

apply(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::matdes::MatDesGreedyOptMutationMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, : pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) → pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover¶: C++: protocols::matdes::MatDesGreedyOptMutationMover::operator=(const class protocols::matdes::MatDesGreedyOptMutationMover &) –> class protocols::matdes::MatDesGreedyOptMutationMover &

calc_pfront_poses_filter_ranks(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) → None¶: C++: protocols::matdes::MatDesGreedyOptMutationMover::calc_pfront_poses_filter_ranks() –> void

clear_cached_data(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) → None¶: C++: protocols::matdes::MatDesGreedyOptMutationMover::clear_cached_data() –> 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.matdes.MatDesGreedyOptMutationMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::matdes::MatDesGreedyOptMutationMover::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>

delta_filters(*args, **kwargs)¶

Overloaded function.

delta_filters(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_DeltaFilter_t

C++: protocols::matdes::MatDesGreedyOptMutationMover::delta_filters() const –> class utility::vector1<class std::shared_ptr<class protocols::simple_filters::DeltaFilter>, class std::allocator<class std::shared_ptr<class protocols::simple_filters::DeltaFilter> > >

delta_filters(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, d: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_DeltaFilter_t) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::delta_filters(const class utility::vector1<class std::shared_ptr<class protocols::simple_filters::DeltaFilter>, class std::allocator<class std::shared_ptr<class protocols::simple_filters::DeltaFilter> > >) –> void

diversify(*args, **kwargs)¶

Overloaded function.

diversify(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool

C++: protocols::matdes::MatDesGreedyOptMutationMover::diversify() const –> bool

diversify(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, b: bool) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::diversify(const bool) –> void

dump_pdb(*args, **kwargs)¶

Overloaded function.

dump_pdb(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool

C++: protocols::matdes::MatDesGreedyOptMutationMover::dump_pdb() const –> bool

dump_pdb(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, dump_pdb: bool) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::dump_pdb(const bool) –> void

dump_scoring_table(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, filename: str, ref_pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::matdes::MatDesGreedyOptMutationMover::dump_scoring_table(std::string, const class core::pose::Pose &) const –> void

dump_table(*args, **kwargs)¶

Overloaded function.

dump_table(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool

C++: protocols::matdes::MatDesGreedyOptMutationMover::dump_table() const –> bool

dump_table(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, dump_table: bool) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::dump_table(const bool) –> void

filter_deltas(*args, **kwargs)¶

Overloaded function.

filter_deltas(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> pyrosetta.rosetta.utility.vector1_double

C++: protocols::matdes::MatDesGreedyOptMutationMover::filter_deltas() const –> class utility::vector1<double, class std::allocator<double> >

filter_deltas(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, filter_deltas: pyrosetta.rosetta.utility.vector1_double) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::filter_deltas(const class utility::vector1<double, class std::allocator<double> >) –> void

filter_pareto_opt_poses(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) → None¶: C++: protocols::matdes::MatDesGreedyOptMutationMover::filter_pareto_opt_poses() –> void

filter_seqpos_pareto_opt_ptmuts(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) → None¶: C++: protocols::matdes::MatDesGreedyOptMutationMover::filter_seqpos_pareto_opt_ptmuts() –> void

filter_thresholds(*args, **kwargs)¶

Overloaded function.

filter_thresholds(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> pyrosetta.rosetta.utility.vector1_std_pair_std_string_double_t

C++: protocols::matdes::MatDesGreedyOptMutationMover::filter_thresholds() const –> class utility::vector1<struct std::pair<std::string, double>, class std::allocator<struct std::pair<std::string, double> > >

filter_thresholds(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, filter_thresholds: pyrosetta.rosetta.utility.vector1_std_pair_std_string_double_t) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::filter_thresholds(class utility::vector1<struct std::pair<std::string, double>, class std::allocator<struct std::pair<std::string, double> > >) –> void

filters(*args, **kwargs)¶

Overloaded function.

filters(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t

C++: protocols::matdes::MatDesGreedyOptMutationMover::filters() const –> class utility::vector1<class std::shared_ptr<class protocols::filters::Filter>, class std::allocator<class std::shared_ptr<class protocols::filters::Filter> > >

filters(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, filters: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::filters(class utility::vector1<class std::shared_ptr<class protocols::filters::Filter>, class std::allocator<class std::shared_ptr<class protocols::filters::Filter> > >) –> void

force_natro(*args, **kwargs)¶

Overloaded function.

force_natro(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool

C++: protocols::matdes::MatDesGreedyOptMutationMover::force_natro() const –> bool

force_natro(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, f: bool) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::force_natro(const bool) –> void

force_natro_for_stored_task_names(*args, **kwargs)¶

Overloaded function.

force_natro_for_stored_task_names(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::matdes::MatDesGreedyOptMutationMover::force_natro_for_stored_task_names() const –> class utility::vector1<std::string, class std::allocator<std::string > >

force_natro_for_stored_task_names(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, force_natro_for_stored_task_names: pyrosetta.rosetta.utility.vector1_std_string) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::force_natro_for_stored_task_names(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::matdes::MatDesGreedyOptMutationMover::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.matdes.MatDesGreedyOptMutationMover) → str¶: C++: protocols::matdes::MatDesGreedyOptMutationMover::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

incl_nonopt(*args, **kwargs)¶

Overloaded function.

incl_nonopt(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool

C++: protocols::matdes::MatDesGreedyOptMutationMover::incl_nonopt() const –> bool

incl_nonopt(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, b: bool) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::incl_nonopt(const bool) –> void

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 > > &

keep_trying(*args, **kwargs)¶

Overloaded function.

keep_trying(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool

C++: protocols::matdes::MatDesGreedyOptMutationMover::keep_trying() const –> bool

keep_trying(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, k: bool) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::keep_trying(const bool) –> 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::matdes::MatDesGreedyOptMutationMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parallel(*args, **kwargs)¶

Overloaded function.

parallel(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool

C++: protocols::matdes::MatDesGreedyOptMutationMover::parallel() const –> bool

parallel(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, parallel: bool) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::parallel(const bool) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::matdes::MatDesGreedyOptMutationMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

pose_coords_are_same(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::matdes::MatDesGreedyOptMutationMover::pose_coords_are_same(const class core::pose::Pose &, const class core::pose::Pose &) –> bool

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::matdes::MatDesGreedyOptMutationMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

reference_pose(*args, **kwargs)¶

Overloaded function.

reference_pose(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::matdes::MatDesGreedyOptMutationMover::reference_pose() const –> class std::shared_ptr<class core::pose::Pose>

reference_pose(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, reference_pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::reference_pose(const class std::shared_ptr<class core::pose::Pose>) –> void

static register_options() → None¶

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

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

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

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

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

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input: pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

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

relax_mover(*args, **kwargs)¶

Overloaded function.

relax_mover(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::matdes::MatDesGreedyOptMutationMover::relax_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

relax_mover(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, relax_mover: pyrosetta.rosetta.protocols.moves.Mover) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::relax_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

reset_delta_filter_baselines(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::matdes::MatDesGreedyOptMutationMover::reset_delta_filter_baselines(class core::pose::Pose &) –> void

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

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

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

rtmin(*args, **kwargs)¶

Overloaded function.

rtmin(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool

C++: protocols::matdes::MatDesGreedyOptMutationMover::rtmin() const –> bool

rtmin(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, b: bool) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::rtmin(const bool) –> void

sample_types(*args, **kwargs)¶

Overloaded function.

sample_types(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::matdes::MatDesGreedyOptMutationMover::sample_types() const –> class utility::vector1<std::string, class std::allocator<std::string > >

sample_types(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, sample_types: pyrosetta.rosetta.utility.vector1_std_string) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::sample_types(const class utility::vector1<std::string, class std::allocator<std::string > >) –> void

scorefxn(*args, **kwargs)¶

Overloaded function.

scorefxn(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> pyrosetta.rosetta.core.scoring.ScoreFunction

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

scorefxn(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> 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_task_for_filters(*args, **kwargs)¶

Overloaded function.

set_task_for_filters(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t

C++: protocols::matdes::MatDesGreedyOptMutationMover::set_task_for_filters() const –> class utility::vector1<class std::shared_ptr<class protocols::simple_filters::TaskAwareScoreTypeFilter>, class std::allocator<class std::shared_ptr<class protocols::simple_filters::TaskAwareScoreTypeFilter> > >

set_task_for_filters(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, set_task_for_filters: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::set_task_for_filters(class utility::vector1<class std::shared_ptr<class protocols::simple_filters::TaskAwareScoreTypeFilter>, class std::allocator<class std::shared_ptr<class protocols::simple_filters::TaskAwareScoreTypeFilter> > >) –> 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

shuffle_order(*args, **kwargs)¶

Overloaded function.

shuffle_order(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool

C++: protocols::matdes::MatDesGreedyOptMutationMover::shuffle_order() const –> bool

shuffle_order(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, b: bool) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::shuffle_order(const bool) –> void

skip_best_check(*args, **kwargs)¶

Overloaded function.

skip_best_check(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool

C++: protocols::matdes::MatDesGreedyOptMutationMover::skip_best_check() const –> bool

skip_best_check(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, skip_best_check: bool) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::skip_best_check(const bool) –> void

stop_before_condition(*args, **kwargs)¶

Overloaded function.

stop_before_condition(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> bool

C++: protocols::matdes::MatDesGreedyOptMutationMover::stop_before_condition() const –> bool

stop_before_condition(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, stop_before_condition: bool) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::stop_before_condition(const bool) –> void

stopping_condition(*args, **kwargs)¶

Overloaded function.

stopping_condition(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, f: pyrosetta.rosetta.protocols.filters.Filter) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::stopping_condition(class std::shared_ptr<class protocols::filters::Filter>) –> void

stopping_condition(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::matdes::MatDesGreedyOptMutationMover::stopping_condition() const –> class std::shared_ptr<class protocols::filters::Filter>

task_factory(*args, **kwargs)¶

Overloaded function.

task_factory(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover) -> pyrosetta.rosetta.core.pack.task.TaskFactory

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

task_factory(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMover, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::matdes::MatDesGreedyOptMutationMover::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> 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.matdes.MatDesGreedyOptMutationMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMoverCreator, : pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMoverCreator) → pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMoverCreator¶: C++: protocols::matdes::MatDesGreedyOptMutationMoverCreator::operator=(const class protocols::matdes::MatDesGreedyOptMutationMoverCreator &) –> class protocols::matdes::MatDesGreedyOptMutationMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::matdes::MatDesGreedyOptMutationMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMoverCreator) → str¶: C++: protocols::matdes::MatDesGreedyOptMutationMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.matdes.MatDesGreedyOptMutationMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::matdes::MatDesGreedyOptMutationMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator¶

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, : pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator) → pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator¶: C++: protocols::matdes::MatDesPointMutationCalculator::operator=(const class protocols::matdes::MatDesPointMutationCalculator &) –> class protocols::matdes::MatDesPointMutationCalculator &

calc_point_mut_filters(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, start_pose: pyrosetta.rosetta.core.pose.Pose, seqpos_aa_vals_vec: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_utility_vector1_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_std_allocator_std_pair_core_chemical_AA_utility_vector1_double_std_allocator_double_t) → None¶: C++: protocols::matdes::MatDesPointMutationCalculator::calc_point_mut_filters(const class core::pose::Pose &, class utility::vector1<struct std::pair<unsigned long, class utility::vector1<struct std::pair<enum core::chemical::AA, class utility::vector1<double, class std::allocator<double> > >, class std::allocator<struct std::pair<enum core::chemical::AA, class utility::vector1<double, class std::allocator<double> > > > > >, class std::allocator<struct std::pair<unsigned long, class utility::vector1<struct std::pair<enum core::chemical::AA, class utility::vector1<double, class std::allocator<double> > >, class std::allocator<struct std::pair<enum core::chemical::AA, class utility::vector1<double, class std::allocator<double> > > > > > > > &) –> void

clone(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator) → pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator¶: C++: protocols::matdes::MatDesPointMutationCalculator::clone() const –> class std::shared_ptr<class protocols::matdes::MatDesPointMutationCalculator>

dump_pdb(*args, **kwargs)¶

Overloaded function.

dump_pdb(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator) -> bool

C++: protocols::matdes::MatDesPointMutationCalculator::dump_pdb() const –> bool

dump_pdb(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, dump_pdb: bool) -> None

C++: protocols::matdes::MatDesPointMutationCalculator::dump_pdb(const bool) –> void

eval_filters(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, pose: pyrosetta.rosetta.core.pose.Pose, filter_pass: bool, vals: pyrosetta.rosetta.utility.vector1_double, always_eval: bool) → None¶: C++: protocols::matdes::MatDesPointMutationCalculator::eval_filters(class core::pose::Pose &, bool &, class utility::vector1<double, class std::allocator<double> > &, bool) –> void

filter_thresholds(*args, **kwargs)¶

Overloaded function.

filter_thresholds(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator) -> pyrosetta.rosetta.utility.vector1_std_pair_std_string_double_t

C++: protocols::matdes::MatDesPointMutationCalculator::filter_thresholds() const –> class utility::vector1<struct std::pair<std::string, double>, class std::allocator<struct std::pair<std::string, double> > >

filter_thresholds(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, filter_thresholds: pyrosetta.rosetta.utility.vector1_std_pair_std_string_double_t) -> None

C++: protocols::matdes::MatDesPointMutationCalculator::filter_thresholds(class utility::vector1<struct std::pair<std::string, double>, class std::allocator<struct std::pair<std::string, double> > >) –> void

filters(*args, **kwargs)¶

Overloaded function.

filters(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t

C++: protocols::matdes::MatDesPointMutationCalculator::filters() const –> class utility::vector1<class std::shared_ptr<class protocols::filters::Filter>, class std::allocator<class std::shared_ptr<class protocols::filters::Filter> > >

filters(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, filters: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_filters_Filter_t) -> None

C++: protocols::matdes::MatDesPointMutationCalculator::filters(class utility::vector1<class std::shared_ptr<class protocols::filters::Filter>, class std::allocator<class std::shared_ptr<class protocols::filters::Filter> > >) –> void

force_natro(*args, **kwargs)¶

Overloaded function.

force_natro(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, force_natro: bool) -> None

C++: protocols::matdes::MatDesPointMutationCalculator::force_natro(const bool) –> void

force_natro(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator) -> bool

C++: protocols::matdes::MatDesPointMutationCalculator::force_natro() const –> bool

mutate_and_relax(*args, **kwargs)¶

Overloaded function.

mutate_and_relax(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, pose: pyrosetta.rosetta.core.pose.Pose, resi: int, target_aa: pyrosetta.rosetta.core.chemical.AA) -> None

C++: protocols::matdes::MatDesPointMutationCalculator::mutate_and_relax(class core::pose::Pose &, const unsigned long &, const enum core::chemical::AA &) –> void

mutate_and_relax(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, pose: pyrosetta.rosetta.core.pose.Pose, resi: int, target_aa: pyrosetta.rosetta.core.chemical.AA, green_packer: protocols::minimization_packing::GreenPacker) -> None

C++: protocols::matdes::MatDesPointMutationCalculator::mutate_and_relax(class core::pose::Pose &, const unsigned long &, const enum core::chemical::AA &, class std::shared_ptr<class protocols::minimization_packing::GreenPacker>) –> void

new_tasks(*args, **kwargs)¶

Overloaded function.

new_tasks(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, new_tasks: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_PackerTask_t) -> None

C++: protocols::matdes::MatDesPointMutationCalculator::new_tasks(class utility::vector1<class std::shared_ptr<class core::pack::task::PackerTask>, class std::allocator<class std::shared_ptr<class core::pack::task::PackerTask> > >) –> void

new_tasks(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pack_task_PackerTask_t

C++: protocols::matdes::MatDesPointMutationCalculator::new_tasks() const –> class utility::vector1<class std::shared_ptr<class core::pack::task::PackerTask>, class std::allocator<class std::shared_ptr<class core::pack::task::PackerTask> > >

parallel(*args, **kwargs)¶

Overloaded function.

parallel(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, r: bool) -> None

C++: protocols::matdes::MatDesPointMutationCalculator::parallel(const bool) –> void

parallel(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator) -> bool

C++: protocols::matdes::MatDesPointMutationCalculator::parallel() const –> bool

reference_pose(*args, **kwargs)¶

Overloaded function.

reference_pose(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::matdes::MatDesPointMutationCalculator::reference_pose() const –> class std::shared_ptr<class core::pose::Pose>

reference_pose(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, reference_pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::matdes::MatDesPointMutationCalculator::reference_pose(const class std::shared_ptr<class core::pose::Pose>) –> void

relax_mover(*args, **kwargs)¶

Overloaded function.

relax_mover(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator) -> pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::matdes::MatDesPointMutationCalculator::relax_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

relax_mover(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, relax_mover: pyrosetta.rosetta.protocols.moves.Mover) -> None

C++: protocols::matdes::MatDesPointMutationCalculator::relax_mover(class std::shared_ptr<class protocols::moves::Mover>) –> void

rtmin(*args, **kwargs)¶

Overloaded function.

rtmin(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, r: bool) -> None

C++: protocols::matdes::MatDesPointMutationCalculator::rtmin(const bool) –> void

rtmin(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator) -> bool

C++: protocols::matdes::MatDesPointMutationCalculator::rtmin() const –> bool

sample_types(*args, **kwargs)¶

Overloaded function.

sample_types(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator) -> pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::matdes::MatDesPointMutationCalculator::sample_types() const –> class utility::vector1<std::string, class std::allocator<std::string > >

sample_types(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, sample_types: pyrosetta.rosetta.utility.vector1_std_string) -> None

C++: protocols::matdes::MatDesPointMutationCalculator::sample_types(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

scorefxn(*args, **kwargs)¶

Overloaded function.

scorefxn(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator) -> pyrosetta.rosetta.core.scoring.ScoreFunction

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

scorefxn(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

C++: protocols::matdes::MatDesPointMutationCalculator::scorefxn(class std::shared_ptr<class core::scoring::ScoreFunction>) –> void

set_design_shell(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, dz_shell: float) → None¶: C++: protocols::matdes::MatDesPointMutationCalculator::set_design_shell(double) –> void

set_repack_shell(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, rp_shell: float) → None¶: C++: protocols::matdes::MatDesPointMutationCalculator::set_repack_shell(double) –> void

set_task_for_filters(*args, **kwargs)¶

Overloaded function.

set_task_for_filters(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t

C++: protocols::matdes::MatDesPointMutationCalculator::set_task_for_filters() const –> class utility::vector1<class std::shared_ptr<class protocols::simple_filters::TaskAwareScoreTypeFilter>, class std::allocator<class std::shared_ptr<class protocols::simple_filters::TaskAwareScoreTypeFilter> > >

set_task_for_filters(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, set_task_for_filters: pyrosetta.rosetta.utility.vector1_std_shared_ptr_protocols_simple_filters_TaskAwareScoreTypeFilter_t) -> None

C++: protocols::matdes::MatDesPointMutationCalculator::set_task_for_filters(class utility::vector1<class std::shared_ptr<class protocols::simple_filters::TaskAwareScoreTypeFilter>, class std::allocator<class std::shared_ptr<class protocols::simple_filters::TaskAwareScoreTypeFilter> > >) –> void

stored_task_names(*args, **kwargs)¶

Overloaded function.

stored_task_names(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, stored_task_names: pyrosetta.rosetta.utility.vector1_std_string) -> None

C++: protocols::matdes::MatDesPointMutationCalculator::stored_task_names(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

stored_task_names(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator) -> pyrosetta.rosetta.utility.vector1_std_string

C++: protocols::matdes::MatDesPointMutationCalculator::stored_task_names() const –> class utility::vector1<std::string, class std::allocator<std::string > >

task_factory(*args, **kwargs)¶

Overloaded function.

task_factory(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator) -> pyrosetta.rosetta.core.pack.task.TaskFactory

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

task_factory(self: pyrosetta.rosetta.protocols.matdes.MatDesPointMutationCalculator, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::matdes::MatDesPointMutationCalculator::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

class pyrosetta.rosetta.protocols.matdes.MotifHitsRotamersOperation¶

Bases: RotamerSetOperation

alter_rotamer_set(self: pyrosetta.rosetta.protocols.matdes.MotifHitsRotamersOperation, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, rotamer_set: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → None¶: C++: protocols::matdes::MotifHitsRotamersOperation::alter_rotamer_set(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class core::pack::rotamer_set::RotamerSet &) –> void

assign(self: pyrosetta.rosetta.protocols.matdes.MotifHitsRotamersOperation, : pyrosetta.rosetta.protocols.matdes.MotifHitsRotamersOperation) → pyrosetta.rosetta.protocols.matdes.MotifHitsRotamersOperation¶: C++: protocols::matdes::MotifHitsRotamersOperation::operator=(const class protocols::matdes::MotifHitsRotamersOperation &) –> class protocols::matdes::MotifHitsRotamersOperation &

clone(self: pyrosetta.rosetta.protocols.matdes.MotifHitsRotamersOperation) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation¶: C++: protocols::matdes::MotifHitsRotamersOperation::clone() const –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSetOperation>

increase_packer_residue_radius(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, the_task: pyrosetta.rosetta.core.pack.task.PackerTask, residue_in: int) → float¶: C++: core::pack::rotamer_set::RotamerSetOperation::increase_packer_residue_radius(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, unsigned long) const –> double

class pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter¶

Bases: Filter

apply(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::matdes::OligomericAverageDegreeFilter::apply(const class core::pose::Pose &) const –> bool

static class_name() → str¶: C++: protocols::matdes::OligomericAverageDegreeFilter::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::OligomericAverageDegreeFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compute(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter, pose: pyrosetta.rosetta.core.pose.Pose, verbose: bool, write: bool) → float¶

calc oligomeric AverageDegree

C++: protocols::matdes::OligomericAverageDegreeFilter::compute(const class core::pose::Pose &, const bool &, const bool &) const –> double

distance_threshold(*args, **kwargs)¶

Overloaded function.

distance_threshold(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter, d: float) -> None

C++: protocols::matdes::OligomericAverageDegreeFilter::distance_threshold(const double) –> void

distance_threshold(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> float

C++: protocols::matdes::OligomericAverageDegreeFilter::distance_threshold() const –> double

fresh_instance(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::OligomericAverageDegreeFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

jump_id(*args, **kwargs)¶

Overloaded function.

jump_id(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter, jump: int) -> None

C++: protocols::matdes::OligomericAverageDegreeFilter::jump_id(const unsigned long) –> void

jump_id(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> int

C++: protocols::matdes::OligomericAverageDegreeFilter::jump_id() const –> unsigned long

jump_set(*args, **kwargs)¶

Overloaded function.

jump_set(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter, jump_set: bool) -> None

C++: protocols::matdes::OligomericAverageDegreeFilter::jump_set(const bool) –> void

jump_set(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> bool

C++: protocols::matdes::OligomericAverageDegreeFilter::jump_set() const –> bool

multicomp(*args, **kwargs)¶

Overloaded function.

multicomp(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter, multicomp: bool) -> None

C++: protocols::matdes::OligomericAverageDegreeFilter::multicomp(const bool) –> void

multicomp(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> bool

C++: protocols::matdes::OligomericAverageDegreeFilter::multicomp() const –> bool

name(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter) → str¶: C++: protocols::matdes::OligomericAverageDegreeFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::matdes::OligomericAverageDegreeFilter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : 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 filters wishing to provide citation information.

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::matdes::OligomericAverageDegreeFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::matdes::OligomericAverageDegreeFilter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::matdes::OligomericAverageDegreeFilter::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

sym_dof_names(*args, **kwargs)¶

Overloaded function.

sym_dof_names(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter, dof_names: str) -> None

C++: protocols::matdes::OligomericAverageDegreeFilter::sym_dof_names(const std::string &) –> void

sym_dof_names(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> str

C++: protocols::matdes::OligomericAverageDegreeFilter::sym_dof_names() const –> std::string

task_factory(*args, **kwargs)¶

Overloaded function.

task_factory(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter, task_factory: pyrosetta.rosetta.core.pack.task.TaskFactory) -> None

C++: protocols::matdes::OligomericAverageDegreeFilter::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void

task_factory(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> pyrosetta.rosetta.core.pack.task.TaskFactory

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

threshold(*args, **kwargs)¶

Overloaded function.

threshold(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter, t: float) -> None

C++: protocols::matdes::OligomericAverageDegreeFilter::threshold(const double) –> void

threshold(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> float

C++: protocols::matdes::OligomericAverageDegreeFilter::threshold() const –> double

verbose(*args, **kwargs)¶

Overloaded function.

verbose(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter, verb: bool) -> None

C++: protocols::matdes::OligomericAverageDegreeFilter::verbose(const bool) –> void

verbose(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> bool

C++: protocols::matdes::OligomericAverageDegreeFilter::verbose() const –> bool

write2pdb(*args, **kwargs)¶

Overloaded function.

write2pdb(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter, write: bool) -> None

C++: protocols::matdes::OligomericAverageDegreeFilter::write2pdb(const bool) –> void

write2pdb(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter) -> bool

C++: protocols::matdes::OligomericAverageDegreeFilter::write2pdb() const –> bool

write_to_pdb(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilter, pose: pyrosetta.rosetta.core.pose.Pose, residue: int, residue_name: str, neighbors: int) → None¶: C++: protocols::matdes::OligomericAverageDegreeFilter::write_to_pdb(const class core::pose::Pose &, const unsigned long, const std::string &, const unsigned long) const –> void

class pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilterCreator¶

Bases: FilterCreator

assign(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilterCreator, : pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilterCreator) → pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilterCreator¶: C++: protocols::matdes::OligomericAverageDegreeFilterCreator::operator=(const class protocols::matdes::OligomericAverageDegreeFilterCreator &) –> class protocols::matdes::OligomericAverageDegreeFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilterCreator) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::OligomericAverageDegreeFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilterCreator) → str¶: C++: protocols::matdes::OligomericAverageDegreeFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.matdes.OligomericAverageDegreeFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::matdes::OligomericAverageDegreeFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover¶

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::matdes::SchemePlaceMotifsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover, : pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover) → pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover¶: C++: protocols::matdes::SchemePlaceMotifsMover::operator=(const class protocols::matdes::SchemePlaceMotifsMover &) –> class protocols::matdes::SchemePlaceMotifsMover &

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.matdes.SchemePlaceMotifsMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::matdes::SchemePlaceMotifsMover::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.matdes.SchemePlaceMotifsMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::matdes::SchemePlaceMotifsMover::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.matdes.SchemePlaceMotifsMover) → str¶: C++: protocols::matdes::SchemePlaceMotifsMover::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::matdes::SchemePlaceMotifsMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMover, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::matdes::SchemePlaceMotifsMover::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::matdes::SchemePlaceMotifsMover::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.matdes.SchemePlaceMotifsMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMoverCreator, : pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMoverCreator) → pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMoverCreator¶: C++: protocols::matdes::SchemePlaceMotifsMoverCreator::operator=(const class protocols::matdes::SchemePlaceMotifsMoverCreator &) –> class protocols::matdes::SchemePlaceMotifsMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::matdes::SchemePlaceMotifsMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMoverCreator) → str¶: C++: protocols::matdes::SchemePlaceMotifsMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.matdes.SchemePlaceMotifsMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::matdes::SchemePlaceMotifsMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.matdes.SymDofMover¶

Bases: Mover

WARNING WARNING WARNING THIS IS A THREAD-UNSAFE CLASS SINCE IT USES THE SymDofMoverSampler, A NON-CONSTANT SINGLETON. ANY PROTOCOL THAT RELIES ON THIS MOVER IS THREAD-UNSAFE.

add_components_to_pose_if_necessary(self: pyrosetta.rosetta.protocols.matdes.SymDofMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::matdes::SymDofMover::add_components_to_pose_if_necessary(class core::pose::Pose &) –> void

apply(self: pyrosetta.rosetta.protocols.matdes.SymDofMover, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::matdes::SymDofMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.matdes.SymDofMover, : pyrosetta.rosetta.protocols.matdes.SymDofMover) → pyrosetta.rosetta.protocols.matdes.SymDofMover¶: C++: protocols::matdes::SymDofMover::operator=(const class protocols::matdes::SymDofMover &) –> class protocols::matdes::SymDofMover &

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.matdes.SymDofMover) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::matdes::SymDofMover::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.matdes.SymDofMover) → pyrosetta.rosetta.protocols.moves.Mover¶

create this type of object

C++: protocols::matdes::SymDofMover::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.matdes.SymDofMover) → str¶: C++: protocols::matdes::SymDofMover::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::matdes::SymDofMover::mover_name() –> std::string

static name() → str¶: C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.matdes.SymDofMover, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::matdes::SymDofMover::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::matdes::SymDofMover::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.matdes.SymDofMoverCreator¶

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverCreator, : pyrosetta.rosetta.protocols.matdes.SymDofMoverCreator) → pyrosetta.rosetta.protocols.matdes.SymDofMoverCreator¶: C++: protocols::matdes::SymDofMoverCreator::operator=(const class protocols::matdes::SymDofMoverCreator &) –> class protocols::matdes::SymDofMoverCreator &

create_mover(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverCreator) → pyrosetta.rosetta.protocols.moves.Mover¶: C++: protocols::matdes::SymDofMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverCreator) → str¶: C++: protocols::matdes::SymDofMoverCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::matdes::SymDofMoverCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler¶

Bases: SingletonBase_protocols_matdes_SymDofMoverSampler_t

WARNING WARNING WARNING THIS SINGLETON CLASS HOLDS NON-CONST, JOB SPECIFIC DATA AND MAKES EVERY CLASS THAT USES THIS DATA THREAD UNSAFE. THIS IS NOT HOW SINGLETONS SHOULD BE USED.

get_angle_diffs(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::matdes::SymDofMoverSampler::get_angle_diffs() –> class utility::vector1<double, class std::allocator<double> >

get_angles(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::matdes::SymDofMoverSampler::get_angles() –> class utility::vector1<double, class std::allocator<double> >

static get_instance() → protocols::matdes::SymDofMoverSampler¶: C++: utility::SingletonBase<protocols::matdes::SymDofMoverSampler>::get_instance() –> class protocols::matdes::SymDofMoverSampler *

get_radial_disp_diffs(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::matdes::SymDofMoverSampler::get_radial_disp_diffs() –> class utility::vector1<double, class std::allocator<double> >

get_radial_disps(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler) → pyrosetta.rosetta.utility.vector1_double¶: C++: protocols::matdes::SymDofMoverSampler::get_radial_disps() –> class utility::vector1<double, class std::allocator<double> >

get_sym_dof_names(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler) → pyrosetta.rosetta.utility.vector1_std_string¶: C++: protocols::matdes::SymDofMoverSampler::get_sym_dof_names() –> class utility::vector1<std::string, class std::allocator<std::string > >

set_angle_ranges(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler, angles_range_min: pyrosetta.rosetta.utility.vector1_double, angles_range_max: pyrosetta.rosetta.utility.vector1_double, angle_steps: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: protocols::matdes::SymDofMoverSampler::set_angle_ranges(class utility::vector1<double, class std::allocator<double> >, class utility::vector1<double, class std::allocator<double> >, class utility::vector1<double, class std::allocator<double> >) –> void

set_angles(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler, angles: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: protocols::matdes::SymDofMoverSampler::set_angles(class utility::vector1<double, class std::allocator<double> >) –> void

set_radial_disp_ranges(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler, radial_disps_range_min: pyrosetta.rosetta.utility.vector1_double, radial_disps_range_max: pyrosetta.rosetta.utility.vector1_double, radial_disp_steps: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: protocols::matdes::SymDofMoverSampler::set_radial_disp_ranges(class utility::vector1<double, class std::allocator<double> >, class utility::vector1<double, class std::allocator<double> >, class utility::vector1<double, class std::allocator<double> >) –> void

set_radial_disps(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler, radial_disps: pyrosetta.rosetta.utility.vector1_double) → None¶: C++: protocols::matdes::SymDofMoverSampler::set_radial_disps(class utility::vector1<double, class std::allocator<double> >) –> void

set_sym_dof_names(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler, sym_dof_names: pyrosetta.rosetta.utility.vector1_std_string) → None¶: C++: protocols::matdes::SymDofMoverSampler::set_sym_dof_names(class utility::vector1<std::string, class std::allocator<std::string > >) –> void

step(self: pyrosetta.rosetta.protocols.matdes.SymDofMoverSampler) → None¶: C++: protocols::matdes::SymDofMoverSampler::step() –> void

class pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter¶

Bases: Filter

filters based on an upper bound # of buried unsatisfied polar residues

apply(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool¶: C++: protocols::matdes::SymUnsatHbondFilter::apply(const class core::pose::Pose &) const –> bool

static class_name() → str¶: C++: protocols::matdes::SymUnsatHbondFilter::class_name() –> std::string

clear(self: pyrosetta.rosetta.protocols.filters.Filter) → None¶

used to clear internal variables if needed. Using fresh_instance is preferred since it’s a pure virtual

C++: protocols::filters::Filter::clear() –> void

clone(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::SymUnsatHbondFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

compare_to_ref(*args, **kwargs)¶

Overloaded function.

compare_to_ref(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, compare_to_ref: bool) -> None

C++: protocols::matdes::SymUnsatHbondFilter::compare_to_ref(const bool) –> void

compare_to_ref(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> bool

C++: protocols::matdes::SymUnsatHbondFilter::compare_to_ref() const –> bool

compute(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, pose: pyrosetta.rosetta.core.pose.Pose, verb: bool, write: bool) → float¶: C++: protocols::matdes::SymUnsatHbondFilter::compute(const class core::pose::Pose &, const bool &, const bool &) const –> double

fresh_instance(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::SymUnsatHbondFilter::fresh_instance() const –> class std::shared_ptr<class protocols::filters::Filter>

get_type(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_type() const –> std::string

get_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter) → str¶: C++: protocols::filters::Filter::get_user_defined_name() const –> std::string

jump_num(*args, **kwargs)¶

Overloaded function.

jump_num(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, jump: int) -> None

C++: protocols::matdes::SymUnsatHbondFilter::jump_num(const unsigned long) –> void

jump_num(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> int

C++: protocols::matdes::SymUnsatHbondFilter::jump_num() const –> unsigned long

mode(*args, **kwargs)¶

Overloaded function.

mode(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, mode: str) -> None

C++: protocols::matdes::SymUnsatHbondFilter::mode(const std::string) –> void

mode(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> str

C++: protocols::matdes::SymUnsatHbondFilter::mode() const –> std::string

name(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) → str¶: C++: protocols::matdes::SymUnsatHbondFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None¶: C++: protocols::matdes::SymUnsatHbondFilter::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.filters.Filter, : 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 filters wishing to provide citation information.

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

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::matdes::SymUnsatHbondFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

reference_pose(*args, **kwargs)¶

Overloaded function.

reference_pose(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, reference_pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::matdes::SymUnsatHbondFilter::reference_pose(const class std::shared_ptr<class core::pose::Pose>) –> void

reference_pose(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> pyrosetta.rosetta.core.pose.Pose

C++: protocols::matdes::SymUnsatHbondFilter::reference_pose() const –> class std::shared_ptr<class core::pose::Pose>

report(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) → None¶: C++: protocols::matdes::SymUnsatHbondFilter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::matdes::SymUnsatHbondFilter::report_sm(const class core::pose::Pose &) const –> double

score(self: pyrosetta.rosetta.protocols.filters.Filter, pose: pyrosetta.rosetta.core.pose.Pose) → float¶: C++: protocols::filters::Filter::score(class core::pose::Pose &) –> double

set_user_defined_name(self: pyrosetta.rosetta.protocols.filters.Filter, name: str) → None¶: C++: protocols::filters::Filter::set_user_defined_name(const std::string &) –> void

sym_dof_names(*args, **kwargs)¶

Overloaded function.

sym_dof_names(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, sym_dofs: str) -> None

C++: protocols::matdes::SymUnsatHbondFilter::sym_dof_names(const std::string) –> void

sym_dof_names(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> str

C++: protocols::matdes::SymUnsatHbondFilter::sym_dof_names() const –> std::string

upper_threshold(*args, **kwargs)¶

Overloaded function.

upper_threshold(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, upper_cutoff: int) -> None

C++: protocols::matdes::SymUnsatHbondFilter::upper_threshold(const unsigned long) –> void

upper_threshold(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> int

C++: protocols::matdes::SymUnsatHbondFilter::upper_threshold() const –> unsigned long

verbose(*args, **kwargs)¶

Overloaded function.

verbose(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, verb: bool) -> None

C++: protocols::matdes::SymUnsatHbondFilter::verbose(const bool) –> void

verbose(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> bool

C++: protocols::matdes::SymUnsatHbondFilter::verbose() const –> bool

write2pdb(*args, **kwargs)¶

Overloaded function.

write2pdb(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, write: bool) -> None

C++: protocols::matdes::SymUnsatHbondFilter::write2pdb(const bool) –> void

write2pdb(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter) -> bool

C++: protocols::matdes::SymUnsatHbondFilter::write2pdb() const –> bool

write_pymol_string_to_pdb(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, pymol_selection: str) → None¶: C++: protocols::matdes::SymUnsatHbondFilter::write_pymol_string_to_pdb(const std::string) const –> void

write_to_pdb(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilter, pose: pyrosetta.rosetta.core.pose.Pose, mode: str, residue_name: str, residue: int, atom_name: str) → None¶: C++: protocols::matdes::SymUnsatHbondFilter::write_to_pdb(const class core::pose::Pose &, const std::string, const std::string, const unsigned long, const std::string) const –> void

class pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilterCreator¶

Bases: FilterCreator

assign(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilterCreator, : pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilterCreator) → pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilterCreator¶: C++: protocols::matdes::SymUnsatHbondFilterCreator::operator=(const class protocols::matdes::SymUnsatHbondFilterCreator &) –> class protocols::matdes::SymUnsatHbondFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilterCreator) → pyrosetta.rosetta.protocols.filters.Filter¶: C++: protocols::matdes::SymUnsatHbondFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilterCreator) → str¶: C++: protocols::matdes::SymUnsatHbondFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.matdes.SymUnsatHbondFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None¶: C++: protocols::matdes::SymUnsatHbondFilterCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void