ligand_docking

• ga_ligand_dock
• ligand_options
• rdf

Bindings for protocols::ligand_docking namespace

class pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::AddHydrogen::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen, : pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen) → pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen

C++: protocols::ligand_docking::AddHydrogen::operator=(const class protocols::ligand_docking::AddHydrogen &) –> class protocols::ligand_docking::AddHydrogen &

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.ligand_docking.AddHydrogen) → str

C++: protocols::ligand_docking::AddHydrogen::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

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

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

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

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::AddHydrogens::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens, : pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens) → pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens

C++: protocols::ligand_docking::AddHydrogens::operator=(const class protocols::ligand_docking::AddHydrogens &) –> class protocols::ligand_docking::AddHydrogens &

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.ligand_docking.AddHydrogens) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::AddHydrogens::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.ligand_docking.AddHydrogens) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::AddHydrogens::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.ligand_docking.AddHydrogens) → str

C++: protocols::ligand_docking::AddHydrogens::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::ligand_docking::AddHydrogens::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.AddHydrogens, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::AddHydrogens::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::ligand_docking::AddHydrogens::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.AddHydrogensCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.AddHydrogensCreator, : pyrosetta.rosetta.protocols.ligand_docking.AddHydrogensCreator) → pyrosetta.rosetta.protocols.ligand_docking.AddHydrogensCreator

C++: protocols::ligand_docking::AddHydrogensCreator::operator=(const class protocols::ligand_docking::AddHydrogensCreator &) –> class protocols::ligand_docking::AddHydrogensCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.AddHydrogensCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.AddHydrogensCreator) → str

C++: protocols::ligand_docking::AddHydrogensCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.AddHydrogensCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilter

Bases: Filter

apply(self: pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::ligand_docking::AtomCountFilter::apply(const class core::pose::Pose &) const –> bool

static class_name() → str

C++: protocols::ligand_docking::AtomCountFilter::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.ligand_docking.AtomCountFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::AtomCountFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

fresh_instance(self: pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::AtomCountFilter::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.ligand_docking.AtomCountFilter) → str

C++: protocols::ligand_docking::AtomCountFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::AtomCountFilter::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::ligand_docking::AtomCountFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::filters::Filter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::filters::Filter::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

class pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilterCreator

Bases: FilterCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilterCreator, : pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilterCreator) → pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilterCreator

C++: protocols::ligand_docking::AtomCountFilterCreator::operator=(const class protocols::ligand_docking::AtomCountFilterCreator &) –> class protocols::ligand_docking::AtomCountFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilterCreator) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::AtomCountFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilterCreator) → str

C++: protocols::ligand_docking::AtomCountFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.AtomCountFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilter

Bases: Filter

apply(self: pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::ligand_docking::ChainExistsFilter::apply(const class core::pose::Pose &) const –> bool

static class_name() → str

C++: protocols::ligand_docking::ChainExistsFilter::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.ligand_docking.ChainExistsFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::ChainExistsFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

fresh_instance(self: pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::ChainExistsFilter::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.ligand_docking.ChainExistsFilter) → str

C++: protocols::ligand_docking::ChainExistsFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::ChainExistsFilter::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::ligand_docking::ChainExistsFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::filters::Filter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::filters::Filter::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

class pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilterCreator

Bases: FilterCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilterCreator, : pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilterCreator) → pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilterCreator

C++: protocols::ligand_docking::ChainExistsFilterCreator::operator=(const class protocols::ligand_docking::ChainExistsFilterCreator &) –> class protocols::ligand_docking::ChainExistsFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilterCreator) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::ChainExistsFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilterCreator) → str

C++: protocols::ligand_docking::ChainExistsFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.ChainExistsFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilter

Bases: Filter

apply(self: pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::ligand_docking::CompleteConnectionsFilter::apply(const class core::pose::Pose &) const –> bool

static class_name() → str

C++: protocols::ligand_docking::CompleteConnectionsFilter::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.ligand_docking.CompleteConnectionsFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::CompleteConnectionsFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

fresh_instance(self: pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::CompleteConnectionsFilter::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.ligand_docking.CompleteConnectionsFilter) → str

C++: protocols::ligand_docking::CompleteConnectionsFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::CompleteConnectionsFilter::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::ligand_docking::CompleteConnectionsFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::filters::Filter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::filters::Filter::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

class pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilterCreator

Bases: FilterCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilterCreator, : pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilterCreator) → pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilterCreator

C++: protocols::ligand_docking::CompleteConnectionsFilterCreator::operator=(const class protocols::ligand_docking::CompleteConnectionsFilterCreator &) –> class protocols::ligand_docking::CompleteConnectionsFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilterCreator) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::CompleteConnectionsFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilterCreator) → str

C++: protocols::ligand_docking::CompleteConnectionsFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.CompleteConnectionsFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::CompoundTranslate::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate, : pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate) → pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate

C++: protocols::ligand_docking::CompoundTranslate::operator=(const class protocols::ligand_docking::CompoundTranslate &) –> class protocols::ligand_docking::CompoundTranslate &

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.ligand_docking.CompoundTranslate) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::CompoundTranslate::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.ligand_docking.CompoundTranslate) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::CompoundTranslate::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.ligand_docking.CompoundTranslate) → str

C++: protocols::ligand_docking::CompoundTranslate::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::ligand_docking::CompoundTranslate::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslate, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::CompoundTranslate::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::ligand_docking::CompoundTranslate::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslateCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslateCreator, : pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslateCreator) → pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslateCreator

C++: protocols::ligand_docking::CompoundTranslateCreator::operator=(const class protocols::ligand_docking::CompoundTranslateCreator &) –> class protocols::ligand_docking::CompoundTranslateCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslateCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslateCreator) → str

C++: protocols::ligand_docking::CompoundTranslateCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.CompoundTranslateCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::ComputeLigandRDF::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF, : pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF) → pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF

C++: protocols::ligand_docking::ComputeLigandRDF::operator=(const class protocols::ligand_docking::ComputeLigandRDF &) –> class protocols::ligand_docking::ComputeLigandRDF &

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.ligand_docking.ComputeLigandRDF) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::ComputeLigandRDF::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.ligand_docking.ComputeLigandRDF) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::ComputeLigandRDF::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.ligand_docking.ComputeLigandRDF) → str

C++: protocols::ligand_docking::ComputeLigandRDF::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::ligand_docking::ComputeLigandRDF::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDF, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::ComputeLigandRDF::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::ligand_docking::ComputeLigandRDF::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDFCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDFCreator, : pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDFCreator) → pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDFCreator

C++: protocols::ligand_docking::ComputeLigandRDFCreator::operator=(const class protocols::ligand_docking::ComputeLigandRDFCreator &) –> class protocols::ligand_docking::ComputeLigandRDFCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDFCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDFCreator) → str

C++: protocols::ligand_docking::ComputeLigandRDFCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.ComputeLigandRDFCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.Distribution

Bases: pybind11_object

Members:

Uniform

Gaussian

Gaussian = <Distribution.Gaussian: 1>

Uniform = <Distribution.Uniform: 0>

property name

property value

class pyrosetta.rosetta.protocols.ligand_docking.DistributionMap

Bases: SingletonBase_protocols_ligand_docking_DistributionMap_t

A singleton class that returns a map of strings to enum types

static get_instance() → protocols::ligand_docking::DistributionMap

C++: utility::SingletonBase<protocols::ligand_docking::DistributionMap>::get_instance() –> class protocols::ligand_docking::DistributionMap *

class pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::FinalMinimizer::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer, : pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer) → pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer

C++: protocols::ligand_docking::FinalMinimizer::operator=(const class protocols::ligand_docking::FinalMinimizer &) –> class protocols::ligand_docking::FinalMinimizer &

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.ligand_docking.FinalMinimizer) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::FinalMinimizer::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.ligand_docking.FinalMinimizer) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::FinalMinimizer::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.ligand_docking.FinalMinimizer) → str

C++: protocols::ligand_docking::FinalMinimizer::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::ligand_docking::FinalMinimizer::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::FinalMinimizer::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizer, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide the citation.

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

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

C++: protocols::ligand_docking::FinalMinimizer::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizerCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizerCreator, : pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizerCreator) → pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizerCreator

C++: protocols::ligand_docking::FinalMinimizerCreator::operator=(const class protocols::ligand_docking::FinalMinimizerCreator &) –> class protocols::ligand_docking::FinalMinimizerCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizerCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizerCreator) → str

C++: protocols::ligand_docking::FinalMinimizerCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.FinalMinimizerCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.GrowLigand

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.GrowLigand, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::GrowLigand::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.GrowLigand, : pyrosetta.rosetta.protocols.ligand_docking.GrowLigand) → pyrosetta.rosetta.protocols.ligand_docking.GrowLigand

C++: protocols::ligand_docking::GrowLigand::operator=(const class protocols::ligand_docking::GrowLigand &) –> class protocols::ligand_docking::GrowLigand &

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.ligand_docking.GrowLigand) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::GrowLigand::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.ligand_docking.GrowLigand) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::GrowLigand::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.ligand_docking.GrowLigand) → str

C++: protocols::ligand_docking::GrowLigand::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::ligand_docking::GrowLigand::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.GrowLigand, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::GrowLigand::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::ligand_docking::GrowLigand::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.GrowLigandCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.GrowLigandCreator, : pyrosetta.rosetta.protocols.ligand_docking.GrowLigandCreator) → pyrosetta.rosetta.protocols.ligand_docking.GrowLigandCreator

C++: protocols::ligand_docking::GrowLigandCreator::operator=(const class protocols::ligand_docking::GrowLigandCreator &) –> class protocols::ligand_docking::GrowLigandCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.GrowLigandCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.GrowLigandCreator) → str

C++: protocols::ligand_docking::GrowLigandCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.GrowLigandCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilter

Bases: Filter

apply(self: pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::ligand_docking::HBondAcceptorFilter::apply(const class core::pose::Pose &) const –> bool

static class_name() → str

C++: protocols::ligand_docking::HBondAcceptorFilter::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.ligand_docking.HBondAcceptorFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::HBondAcceptorFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

fresh_instance(self: pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::HBondAcceptorFilter::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.ligand_docking.HBondAcceptorFilter) → str

C++: protocols::ligand_docking::HBondAcceptorFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::HBondAcceptorFilter::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::ligand_docking::HBondAcceptorFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::filters::Filter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::filters::Filter::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

class pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilterCreator

Bases: FilterCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilterCreator, : pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilterCreator) → pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilterCreator

C++: protocols::ligand_docking::HBondAcceptorFilterCreator::operator=(const class protocols::ligand_docking::HBondAcceptorFilterCreator &) –> class protocols::ligand_docking::HBondAcceptorFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilterCreator) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::HBondAcceptorFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilterCreator) → str

C++: protocols::ligand_docking::HBondAcceptorFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.HBondAcceptorFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilter

Bases: Filter

apply(self: pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::ligand_docking::HBondDonorFilter::apply(const class core::pose::Pose &) const –> bool

static class_name() → str

C++: protocols::ligand_docking::HBondDonorFilter::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.ligand_docking.HBondDonorFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::HBondDonorFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

fresh_instance(self: pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::HBondDonorFilter::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.ligand_docking.HBondDonorFilter) → str

C++: protocols::ligand_docking::HBondDonorFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::HBondDonorFilter::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::ligand_docking::HBondDonorFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::filters::Filter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::filters::Filter::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

class pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilterCreator

Bases: FilterCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilterCreator, : pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilterCreator) → pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilterCreator

C++: protocols::ligand_docking::HBondDonorFilterCreator::operator=(const class protocols::ligand_docking::HBondDonorFilterCreator &) –> class protocols::ligand_docking::HBondDonorFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilterCreator) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::HBondDonorFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilterCreator) → str

C++: protocols::ligand_docking::HBondDonorFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.HBondDonorFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilter

Bases: Filter

apply(self: pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::ligand_docking::HeavyAtomFilter::apply(const class core::pose::Pose &) const –> bool

static class_name() → str

C++: protocols::ligand_docking::HeavyAtomFilter::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.ligand_docking.HeavyAtomFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::HeavyAtomFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

fresh_instance(self: pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::HeavyAtomFilter::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.ligand_docking.HeavyAtomFilter) → str

C++: protocols::ligand_docking::HeavyAtomFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::HeavyAtomFilter::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::ligand_docking::HeavyAtomFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::filters::Filter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilter, : pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::ligand_docking::HeavyAtomFilter::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

class pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilterCreator

Bases: FilterCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilterCreator, : pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilterCreator) → pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilterCreator

C++: protocols::ligand_docking::HeavyAtomFilterCreator::operator=(const class protocols::ligand_docking::HeavyAtomFilterCreator &) –> class protocols::ligand_docking::HeavyAtomFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilterCreator) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::HeavyAtomFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilterCreator) → str

C++: protocols::ligand_docking::HeavyAtomFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.HeavyAtomFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.HighResDocker

Bases: Mover

apply(*args, **kwargs)

Overloaded function.

1. apply(self: pyrosetta.rosetta.protocols.ligand_docking.HighResDocker, pose: pyrosetta.rosetta.core.pose.Pose) -> None

C++: protocols::ligand_docking::HighResDocker::apply(class core::pose::Pose &) –> void

2. apply(self: pyrosetta.rosetta.protocols.ligand_docking.HighResDocker, poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, current_scores: pyrosetta.rosetta.utility.vector1_double, qsar_chars: pyrosetta.rosetta.utility.vector1_char, cycle: int) -> None

C++: protocols::ligand_docking::HighResDocker::apply(class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &, class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<char, class std::allocator<char> >, unsigned long) –> void

3. apply(self: pyrosetta.rosetta.protocols.ligand_docking.HighResDocker, pose: pyrosetta.rosetta.core.pose.Pose, current_score: float, qsar_char: str, cycle: int) -> None

C++: protocols::ligand_docking::HighResDocker::apply(class core::pose::Pose &, double &, char, unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.HighResDocker, : pyrosetta.rosetta.protocols.ligand_docking.HighResDocker) → pyrosetta.rosetta.protocols.ligand_docking.HighResDocker

C++: protocols::ligand_docking::HighResDocker::operator=(const class protocols::ligand_docking::HighResDocker &) –> class protocols::ligand_docking::HighResDocker &

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.ligand_docking.HighResDocker) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::HighResDocker::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.ligand_docking.HighResDocker) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::HighResDocker::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.ligand_docking.HighResDocker) → str

C++: protocols::ligand_docking::HighResDocker::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::ligand_docking::HighResDocker::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.HighResDocker, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::HighResDocker::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.ligand_docking.HighResDocker, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide the citation.

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

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

C++: protocols::ligand_docking::HighResDocker::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_all_residues(self: pyrosetta.rosetta.protocols.ligand_docking.HighResDocker, input: bool) → None

C++: protocols::ligand_docking::HighResDocker::set_all_residues(bool) –> void

set_allow_repacking(self: pyrosetta.rosetta.protocols.ligand_docking.HighResDocker, input: bool) → None

C++: protocols::ligand_docking::HighResDocker::set_allow_repacking(bool) –> void

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.HighResDockerCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.HighResDockerCreator, : pyrosetta.rosetta.protocols.ligand_docking.HighResDockerCreator) → pyrosetta.rosetta.protocols.ligand_docking.HighResDockerCreator

C++: protocols::ligand_docking::HighResDockerCreator::operator=(const class protocols::ligand_docking::HighResDockerCreator &) –> class protocols::ligand_docking::HighResDockerCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.HighResDockerCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.HighResDockerCreator) → str

C++: protocols::ligand_docking::HighResDockerCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.HighResDockerCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::HighResEnsemble::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble, : pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble) → pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble

C++: protocols::ligand_docking::HighResEnsemble::operator=(const class protocols::ligand_docking::HighResEnsemble &) –> class protocols::ligand_docking::HighResEnsemble &

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.ligand_docking.HighResEnsemble) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::HighResEnsemble::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.ligand_docking.HighResEnsemble) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::HighResEnsemble::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.ligand_docking.HighResEnsemble) → str

C++: protocols::ligand_docking::HighResEnsemble::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::ligand_docking::HighResEnsemble::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::HighResEnsemble::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.ligand_docking.HighResEnsemble, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide the citation.

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

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

C++: protocols::ligand_docking::HighResEnsemble::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.ligand_docking.HighResEnsemble) → bool

C++: protocols::ligand_docking::HighResEnsemble::reinitialize_for_each_job() const –> bool

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.HighResEnsembleCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.HighResEnsembleCreator, : pyrosetta.rosetta.protocols.ligand_docking.HighResEnsembleCreator) → pyrosetta.rosetta.protocols.ligand_docking.HighResEnsembleCreator

C++: protocols::ligand_docking::HighResEnsembleCreator::operator=(const class protocols::ligand_docking::HighResEnsembleCreator &) –> class protocols::ligand_docking::HighResEnsembleCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.HighResEnsembleCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.HighResEnsembleCreator) → str

C++: protocols::ligand_docking::HighResEnsembleCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.HighResEnsembleCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilder

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilder, : pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilder) → pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilder

C++: protocols::ligand_docking::InterfaceBuilder::operator=(const class protocols::ligand_docking::InterfaceBuilder &) –> class protocols::ligand_docking::InterfaceBuilder &

build(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilder, pose: pyrosetta.rosetta.core.pose.Pose) → protocols::ligand_docking::ligand_options::Interface

C++: protocols::ligand_docking::InterfaceBuilder::build(const class core::pose::Pose &) const –> class protocols::ligand_docking::ligand_options::Interface

static element_name() → str

C++: protocols::ligand_docking::InterfaceBuilder::element_name() –> std::string

get_ligand_areas(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilder) → pyrosetta.rosetta.std.map_char_std_shared_ptr_protocols_ligand_docking_LigandArea_t_std_allocator_std_pair_const_char_std_shared_ptr_protocols_ligand_docking_LigandArea_t

C++: protocols::ligand_docking::InterfaceBuilder::get_ligand_areas() const –> class std::map<char, class std::shared_ptr<class protocols::ligand_docking::LigandArea>, struct std::less<char>, class std::allocator<struct std::pair<const char, class std::shared_ptr<class protocols::ligand_docking::LigandArea> > > >

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilder, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::InterfaceBuilder::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

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

C++: protocols::ligand_docking::InterfaceBuilder::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader

Bases: DataLoader

A class for loading InterfaceBuilders into the XML parser’s basic::datacache::DataMap.

assign(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader, : pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader) → pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader

C++: protocols::ligand_docking::InterfaceBuilderLoader::operator=(const class protocols::ligand_docking::InterfaceBuilderLoader &) –> class protocols::ligand_docking::InterfaceBuilderLoader &

static interface_builder_ct_namer(element_name: str) → str

C++: protocols::ligand_docking::InterfaceBuilderLoader::interface_builder_ct_namer(const std::string &) –> std::string

load_data(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoader, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

The InterfaceBuilderLoader will create named InterfaceBuilders and load them into the basic::datacache::DataMap

C++: protocols::ligand_docking::InterfaceBuilderLoader::load_data(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) const –> void

static loader_name() → str

C++: protocols::ligand_docking::InterfaceBuilderLoader::loader_name() –> std::string

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

C++: protocols::ligand_docking::InterfaceBuilderLoader::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoaderCreator

Bases: DataLoaderCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoaderCreator, : pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoaderCreator) → pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoaderCreator

C++: protocols::ligand_docking::InterfaceBuilderLoaderCreator::operator=(const class protocols::ligand_docking::InterfaceBuilderLoaderCreator &) –> class protocols::ligand_docking::InterfaceBuilderLoaderCreator &

create_loader(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoaderCreator) → pyrosetta.rosetta.protocols.parser.DataLoader

C++: protocols::ligand_docking::InterfaceBuilderLoaderCreator::create_loader() const –> class std::shared_ptr<class protocols::parser::DataLoader>

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoaderCreator) → str

C++: protocols::ligand_docking::InterfaceBuilderLoaderCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoaderCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

schema_ct_naming_function(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilderLoaderCreator) → std::function<std::string (std::string const&)>

C++: protocols::ligand_docking::InterfaceBuilderLoaderCreator::schema_ct_naming_function() const –> class std::function<std::string (const std::string &)>

class pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::InterfaceScoreCalculator::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator, : pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator) → pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator

C++: protocols::ligand_docking::InterfaceScoreCalculator::operator=(const class protocols::ligand_docking::InterfaceScoreCalculator &) –> class protocols::ligand_docking::InterfaceScoreCalculator &

chains(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator, chains: pyrosetta.rosetta.std.vector_std_string) → None

C++: protocols::ligand_docking::InterfaceScoreCalculator::chains(const class std::vector<std::string, class std::allocator<std::string > > &) –> 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.ligand_docking.InterfaceScoreCalculator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::InterfaceScoreCalculator::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.ligand_docking.InterfaceScoreCalculator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::InterfaceScoreCalculator::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.ligand_docking.InterfaceScoreCalculator) → str

C++: protocols::ligand_docking::InterfaceScoreCalculator::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

grid_set_prototype(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator, grid_prototype: protocols::qsar::scoring_grid::GridSet) → None

C++: protocols::ligand_docking::InterfaceScoreCalculator::grid_set_prototype(class std::shared_ptr<const class protocols::qsar::scoring_grid::GridSet>) –> 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 > > &

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::ligand_docking::InterfaceScoreCalculator::mover_name() –> std::string

static name() → str

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

native_ensemble_best(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator, setting: bool) → None

C++: protocols::ligand_docking::InterfaceScoreCalculator::native_ensemble_best(bool) –> void

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::InterfaceScoreCalculator::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide the citation.

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

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

C++: protocols::ligand_docking::InterfaceScoreCalculator::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

score_fxn(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator, score_fxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: protocols::ligand_docking::InterfaceScoreCalculator::score_fxn(const 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(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculator, setting: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::InterfaceScoreCalculator::set_native(class std::shared_ptr<class core::pose::Pose>) –> void

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculatorCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculatorCreator, : pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculatorCreator) → pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculatorCreator

C++: protocols::ligand_docking::InterfaceScoreCalculatorCreator::operator=(const class protocols::ligand_docking::InterfaceScoreCalculatorCreator &) –> class protocols::ligand_docking::InterfaceScoreCalculatorCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculatorCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculatorCreator) → str

C++: protocols::ligand_docking::InterfaceScoreCalculatorCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.InterfaceScoreCalculatorCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.LigandArea

Bases: pybind11_object

property Calpha_restraints_

property add_nbr_radius_

property all_atom_mode_

assign(self: pyrosetta.rosetta.protocols.ligand_docking.LigandArea, : pyrosetta.rosetta.protocols.ligand_docking.LigandArea) → pyrosetta.rosetta.protocols.ligand_docking.LigandArea

C++: protocols::ligand_docking::LigandArea::operator=(const class protocols::ligand_docking::LigandArea &) –> class protocols::ligand_docking::LigandArea &

property chain_

property cutoff_

static element_name() → str

C++: protocols::ligand_docking::LigandArea::element_name() –> std::string

property high_res_angstroms_

property high_res_degrees_

property minimize_ligand_

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.LigandArea, tag: pyrosetta.rosetta.utility.tag.Tag) → None

C++: protocols::ligand_docking::LigandArea::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void

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

C++: protocols::ligand_docking::LigandArea::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

property tether_ligand_

class pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoader

Bases: DataLoader

assign(self: pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoader, : pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoader) → pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoader

C++: protocols::ligand_docking::LigandAreaLoader::operator=(const class protocols::ligand_docking::LigandAreaLoader &) –> class protocols::ligand_docking::LigandAreaLoader &

static ligand_area_ct_namer(element_name: str) → str

C++: protocols::ligand_docking::LigandAreaLoader::ligand_area_ct_namer(const std::string &) –> std::string

load_data(self: pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoader, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

The InterfaceBuilderLoader will create named InterfaceBuilders and load them into the basic::datacache::DataMap

C++: protocols::ligand_docking::LigandAreaLoader::load_data(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) const –> void

static loader_name() → str

C++: protocols::ligand_docking::LigandAreaLoader::loader_name() –> std::string

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

C++: protocols::ligand_docking::LigandAreaLoader::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoaderCreator

Bases: DataLoaderCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoaderCreator, : pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoaderCreator) → pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoaderCreator

C++: protocols::ligand_docking::LigandAreaLoaderCreator::operator=(const class protocols::ligand_docking::LigandAreaLoaderCreator &) –> class protocols::ligand_docking::LigandAreaLoaderCreator &

create_loader(self: pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoaderCreator) → pyrosetta.rosetta.protocols.parser.DataLoader

C++: protocols::ligand_docking::LigandAreaLoaderCreator::create_loader() const –> class std::shared_ptr<class protocols::parser::DataLoader>

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoaderCreator) → str

C++: protocols::ligand_docking::LigandAreaLoaderCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoaderCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

schema_ct_naming_function(self: pyrosetta.rosetta.protocols.ligand_docking.LigandAreaLoaderCreator) → std::function<std::string (std::string const&)>

C++: protocols::ligand_docking::LigandAreaLoaderCreator::schema_ct_naming_function() const –> class std::function<std::string (const std::string &)>

class pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol

Bases: Mover

Shared functionality for protocols that dock ligands.

Includes score function setup, interface definitions, and ligand flexibility.

apply(self: pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::LigandBaseProtocol::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol, : pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol) → pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol

C++: protocols::ligand_docking::LigandBaseProtocol::operator=(const class protocols::ligand_docking::LigandBaseProtocol &) –> class protocols::ligand_docking::LigandBaseProtocol &

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

static get_ligand_id(*args, **kwargs)

Overloaded function.

1. get_ligand_id(pose: pyrosetta.rosetta.core.pose.Pose) -> int

C++: protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(const class core::pose::Pose &) –> unsigned long

2. get_ligand_id(pose: pyrosetta.rosetta.core.pose.Pose, jump_id: int) -> int

C++: protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(const class core::pose::Pose &, unsigned long) –> unsigned long

static get_ligand_jump_id(pose: pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::ligand_docking::LigandBaseProtocol::get_ligand_jump_id(const class core::pose::Pose &) –> unsigned long

get_name(self: pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol) → str

C++: protocols::ligand_docking::LigandBaseProtocol::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_non_bb_clashing_rotamers(self: pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, scofx: pyrosetta.rosetta.core.scoring.ScoreFunction, accepted_rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) → None

C++: protocols::ligand_docking::LigandBaseProtocol::get_non_bb_clashing_rotamers(const class core::pose::Pose &, unsigned long, class std::shared_ptr<const class core::scoring::ScoreFunction>, class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &) const –> void

get_scorefxn(self: pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::ligand_docking::LigandBaseProtocol::get_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

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

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

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

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

reorder_foldtree_around_mobile_regions(self: pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, jump_id: int, mobile_bb: pyrosetta.rosetta.utility.vector1_bool, lig_id: int) → None

C++: protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(class core::pose::Pose &, const unsigned long &, const class utility::vector1<bool, class std::allocator<bool> > &, const unsigned long &) const –> 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

restrain_protein_Calphas(self: pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, is_restrained: pyrosetta.rosetta.utility.vector1_bool, restr_func: pyrosetta.rosetta.core.scoring.func.Func) → None

C++: protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, class std::shared_ptr<class core::scoring::func::Func>) –> 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

shared_from_this(self: pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol) → pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol

C++: protocols::ligand_docking::LigandBaseProtocol::shared_from_this() –> class std::shared_ptr<class protocols::ligand_docking::LigandBaseProtocol>

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.LigandDesign

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.LigandDesign, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::LigandDesign::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.LigandDesign, : pyrosetta.rosetta.protocols.ligand_docking.LigandDesign) → pyrosetta.rosetta.protocols.ligand_docking.LigandDesign

C++: protocols::ligand_docking::LigandDesign::operator=(const class protocols::ligand_docking::LigandDesign &) –> class protocols::ligand_docking::LigandDesign &

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.ligand_docking.LigandDesign) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::LigandDesign::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.ligand_docking.LigandDesign) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::LigandDesign::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.ligand_docking.LigandDesign) → str

C++: protocols::ligand_docking::LigandDesign::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::ligand_docking::LigandDesign::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.LigandDesign, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::LigandDesign::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::ligand_docking::LigandDesign::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.LigandDesignCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.LigandDesignCreator, : pyrosetta.rosetta.protocols.ligand_docking.LigandDesignCreator) → pyrosetta.rosetta.protocols.ligand_docking.LigandDesignCreator

C++: protocols::ligand_docking::LigandDesignCreator::operator=(const class protocols::ligand_docking::LigandDesignCreator &) –> class protocols::ligand_docking::LigandDesignCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.LigandDesignCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.LigandDesignCreator) → str

C++: protocols::ligand_docking::LigandDesignCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.LigandDesignCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol

Bases: LigandBaseProtocol

add_start_from(self: pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol, x: float, y: float, z: float) → None

C++: protocols::ligand_docking::LigandDockProtocol::add_start_from(double, double, double) –> void

append_ligand_docking_scores(*args, **kwargs)

Overloaded function.

1. append_ligand_docking_scores(self: pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol, before: pyrosetta.rosetta.core.pose.Pose, after: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, scores: pyrosetta.rosetta.std.map_std_string_double) -> None

2. append_ligand_docking_scores(self: pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol, before: pyrosetta.rosetta.core.pose.Pose, after: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, scores: pyrosetta.rosetta.std.map_std_string_double, constraint_io: pyrosetta.rosetta.protocols.toolbox.match_enzdes_util.EnzConstraintIO) -> None

C++: protocols::ligand_docking::LigandDockProtocol::append_ligand_docking_scores(const class core::pose::Pose &, const class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>, class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &, class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintIO>) const –> void

apply(self: pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::LigandDockProtocol::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol, : pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol) → pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol

C++: protocols::ligand_docking::LigandDockProtocol::operator=(const class protocols::ligand_docking::LigandDockProtocol &) –> class protocols::ligand_docking::LigandDockProtocol &

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

static get_ligand_id(*args, **kwargs)

Overloaded function.

1. get_ligand_id(pose: pyrosetta.rosetta.core.pose.Pose) -> int

C++: protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(const class core::pose::Pose &) –> unsigned long

2. get_ligand_id(pose: pyrosetta.rosetta.core.pose.Pose, jump_id: int) -> int

C++: protocols::ligand_docking::LigandBaseProtocol::get_ligand_id(const class core::pose::Pose &, unsigned long) –> unsigned long

static get_ligand_jump_id(pose: pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::ligand_docking::LigandBaseProtocol::get_ligand_jump_id(const class core::pose::Pose &) –> unsigned long

get_name(self: pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol) → str

C++: protocols::ligand_docking::LigandDockProtocol::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_non_bb_clashing_rotamers(self: pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int, scofx: pyrosetta.rosetta.core.scoring.ScoreFunction, accepted_rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) → None

C++: protocols::ligand_docking::LigandBaseProtocol::get_non_bb_clashing_rotamers(const class core::pose::Pose &, unsigned long, class std::shared_ptr<const class core::scoring::ScoreFunction>, class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &) const –> void

get_scorefxn(self: pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol) → pyrosetta.rosetta.core.scoring.ScoreFunction

C++: protocols::ligand_docking::LigandBaseProtocol::get_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

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

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

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

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

reorder_foldtree_around_mobile_regions(self: pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, jump_id: int, mobile_bb: pyrosetta.rosetta.utility.vector1_bool, lig_id: int) → None

C++: protocols::ligand_docking::LigandBaseProtocol::reorder_foldtree_around_mobile_regions(class core::pose::Pose &, const unsigned long &, const class utility::vector1<bool, class std::allocator<bool> > &, const unsigned long &) const –> 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

restrain_protein_Calphas(self: pyrosetta.rosetta.protocols.ligand_docking.LigandBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, is_restrained: pyrosetta.rosetta.utility.vector1_bool, restr_func: pyrosetta.rosetta.core.scoring.func.Func) → None

C++: protocols::ligand_docking::LigandBaseProtocol::restrain_protein_Calphas(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, class std::shared_ptr<class core::scoring::func::Func>) –> 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

shared_from_this(self: pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol) → pyrosetta.rosetta.protocols.ligand_docking.LigandDockProtocol

C++: protocols::ligand_docking::LigandDockProtocol::shared_from_this() –> class std::shared_ptr<class protocols::ligand_docking::LigandDockProtocol>

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.Ligand_info

Bases: pybind11_object

property atr

get_residues(self: pyrosetta.rosetta.protocols.ligand_docking.Ligand_info) → pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t

C++: protocols::ligand_docking::Ligand_info::get_residues() const –> const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &

property jump

property rep

property residues

property tag_along_residues

class pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::MinimizeBackbone::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone, : pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone) → pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone

C++: protocols::ligand_docking::MinimizeBackbone::operator=(const class protocols::ligand_docking::MinimizeBackbone &) –> class protocols::ligand_docking::MinimizeBackbone &

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.ligand_docking.MinimizeBackbone) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::MinimizeBackbone::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.ligand_docking.MinimizeBackbone) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::MinimizeBackbone::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.ligand_docking.MinimizeBackbone) → str

C++: protocols::ligand_docking::MinimizeBackbone::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::ligand_docking::MinimizeBackbone::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::MinimizeBackbone::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::ligand_docking::MinimizeBackbone::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

remove_constraints(self: pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone, pose: pyrosetta.rosetta.core.pose.Pose) → None

Remove any constraints which were added during the apply() call

C++: protocols::ligand_docking::MinimizeBackbone::remove_constraints(class core::pose::Pose &) –> void

remove_cutpoints(self: pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackbone, pose: pyrosetta.rosetta.core.pose.Pose) → None

Remove any cutpoint variants which were added during the apply() call

C++: protocols::ligand_docking::MinimizeBackbone::remove_cutpoints(class core::pose::Pose &) –> void

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackboneCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackboneCreator, : pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackboneCreator) → pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackboneCreator

C++: protocols::ligand_docking::MinimizeBackboneCreator::operator=(const class protocols::ligand_docking::MinimizeBackboneCreator &) –> class protocols::ligand_docking::MinimizeBackboneCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackboneCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackboneCreator) → str

C++: protocols::ligand_docking::MinimizeBackboneCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.MinimizeBackboneCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::MinimizeLigand::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand, : pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand) → pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand

C++: protocols::ligand_docking::MinimizeLigand::operator=(const class protocols::ligand_docking::MinimizeLigand &) –> class protocols::ligand_docking::MinimizeLigand &

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand) → str

C++: protocols::ligand_docking::MinimizeLigand::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

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

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

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

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

remove_constraints(self: pyrosetta.rosetta.protocols.ligand_docking.MinimizeLigand, pose: pyrosetta.rosetta.core.pose.Pose) → None

Remove the constraints added by this mover to the pose in apply, if any.

C++: protocols::ligand_docking::MinimizeLigand::remove_constraints(class core::pose::Pose &) –> void

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilter

Bases: Filter

apply(self: pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::ligand_docking::MolarMassFilter::apply(const class core::pose::Pose &) const –> bool

static class_name() → str

C++: protocols::ligand_docking::MolarMassFilter::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.ligand_docking.MolarMassFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::MolarMassFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

fresh_instance(self: pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::MolarMassFilter::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.ligand_docking.MolarMassFilter) → str

C++: protocols::ligand_docking::MolarMassFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::MolarMassFilter::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::ligand_docking::MolarMassFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::filters::Filter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::filters::Filter::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

class pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilterCreator

Bases: FilterCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilterCreator, : pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilterCreator) → pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilterCreator

C++: protocols::ligand_docking::MolarMassFilterCreator::operator=(const class protocols::ligand_docking::MolarMassFilterCreator &) –> class protocols::ligand_docking::MolarMassFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilterCreator) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::MolarMassFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilterCreator) → str

C++: protocols::ligand_docking::MolarMassFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.MolarMassFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilter

Bases: Filter

apply(self: pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilter, pose: pyrosetta.rosetta.core.pose.Pose) → bool

C++: protocols::ligand_docking::MolecularMassFilter::apply(const class core::pose::Pose &) const –> bool

static class_name() → str

C++: protocols::ligand_docking::MolecularMassFilter::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.ligand_docking.MolecularMassFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::MolecularMassFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>

fresh_instance(self: pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilter) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::MolecularMassFilter::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.ligand_docking.MolecularMassFilter) → str

C++: protocols::ligand_docking::MolecularMassFilter::name() const –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::MolecularMassFilter::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::ligand_docking::MolecularMassFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

report(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.std.ostream, : pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::filters::Filter::report(std::ostream &, const class core::pose::Pose &) const –> void

report_sm(self: pyrosetta.rosetta.protocols.filters.Filter, : pyrosetta.rosetta.core.pose.Pose) → float

C++: protocols::filters::Filter::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

class pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilterCreator

Bases: FilterCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilterCreator, : pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilterCreator) → pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilterCreator

C++: protocols::ligand_docking::MolecularMassFilterCreator::operator=(const class protocols::ligand_docking::MolecularMassFilterCreator &) –> class protocols::ligand_docking::MolecularMassFilterCreator &

create_filter(self: pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilterCreator) → pyrosetta.rosetta.protocols.filters.Filter

C++: protocols::ligand_docking::MolecularMassFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilterCreator) → str

C++: protocols::ligand_docking::MolecularMassFilterCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.MolecularMassFilterCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilder

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilder, : pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilder) → pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilder

C++: protocols::ligand_docking::MoveMapBuilder::operator=(const class protocols::ligand_docking::MoveMapBuilder &) –> class protocols::ligand_docking::MoveMapBuilder &

build(self: pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilder, : pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.kinematics.MoveMap

C++: protocols::ligand_docking::MoveMapBuilder::build(const class core::pose::Pose &) const –> class std::shared_ptr<class core::kinematics::MoveMap>

static element_name() → str

C++: protocols::ligand_docking::MoveMapBuilder::element_name() –> std::string

get_bb_interface_builder(self: pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilder) → pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilder

C++: protocols::ligand_docking::MoveMapBuilder::get_bb_interface_builder() const –> class std::shared_ptr<class protocols::ligand_docking::InterfaceBuilder>

get_sc_interface_builder(self: pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilder) → pyrosetta.rosetta.protocols.ligand_docking.InterfaceBuilder

C++: protocols::ligand_docking::MoveMapBuilder::get_sc_interface_builder() const –> class std::shared_ptr<class protocols::ligand_docking::InterfaceBuilder>

minimize_backbone(self: pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilder) → bool

C++: protocols::ligand_docking::MoveMapBuilder::minimize_backbone() –> bool

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilder, tag: pyrosetta.rosetta.utility.tag.Tag, datamap: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::MoveMapBuilder::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

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

C++: protocols::ligand_docking::MoveMapBuilder::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader

Bases: DataLoader

A class for loading MoveMapBuilders into the XML parser’s basic::datacache::DataMap. NOTE that in the input .xml file, the InterfaceBuilder must be specified before the MoveMapBuilder

assign(self: pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader, : pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader) → pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader

C++: protocols::ligand_docking::MoveMapBuilderLoader::operator=(const class protocols::ligand_docking::MoveMapBuilderLoader &) –> class protocols::ligand_docking::MoveMapBuilderLoader &

load_data(self: pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoader, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

The InterfaceBuilderLoader will create named InterfaceBuilders and load them into the basic::datacache::DataMap

C++: protocols::ligand_docking::MoveMapBuilderLoader::load_data(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) const –> void

static loader_name() → str

C++: protocols::ligand_docking::MoveMapBuilderLoader::loader_name() –> std::string

static movemap_builder_ct_namer(element_name: str) → str

C++: protocols::ligand_docking::MoveMapBuilderLoader::movemap_builder_ct_namer(const std::string &) –> std::string

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

C++: protocols::ligand_docking::MoveMapBuilderLoader::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

class pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoaderCreator

Bases: DataLoaderCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoaderCreator, : pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoaderCreator) → pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoaderCreator

C++: protocols::ligand_docking::MoveMapBuilderLoaderCreator::operator=(const class protocols::ligand_docking::MoveMapBuilderLoaderCreator &) –> class protocols::ligand_docking::MoveMapBuilderLoaderCreator &

create_loader(self: pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoaderCreator) → pyrosetta.rosetta.protocols.parser.DataLoader

C++: protocols::ligand_docking::MoveMapBuilderLoaderCreator::create_loader() const –> class std::shared_ptr<class protocols::parser::DataLoader>

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoaderCreator) → str

C++: protocols::ligand_docking::MoveMapBuilderLoaderCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoaderCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

schema_ct_naming_function(self: pyrosetta.rosetta.protocols.ligand_docking.MoveMapBuilderLoaderCreator) → std::function<std::string (std::string const&)>

C++: protocols::ligand_docking::MoveMapBuilderLoaderCreator::schema_ct_naming_function() const –> class std::function<std::string (const std::string &)>

class pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::ProtLigEnsemble::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble, : pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble) → pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble

C++: protocols::ligand_docking::ProtLigEnsemble::operator=(const class protocols::ligand_docking::ProtLigEnsemble &) –> class protocols::ligand_docking::ProtLigEnsemble &

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.ligand_docking.ProtLigEnsemble) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::ProtLigEnsemble::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.ligand_docking.ProtLigEnsemble) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::ProtLigEnsemble::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.ligand_docking.ProtLigEnsemble) → str

C++: protocols::ligand_docking::ProtLigEnsemble::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::ligand_docking::ProtLigEnsemble::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::ProtLigEnsemble::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsemble, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide the citation.

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

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

C++: protocols::ligand_docking::ProtLigEnsemble::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.ligand_docking.ProtLigEnsemble) → bool

C++: protocols::ligand_docking::ProtLigEnsemble::reinitialize_for_each_job() const –> bool

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsembleCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsembleCreator, : pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsembleCreator) → pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsembleCreator

C++: protocols::ligand_docking::ProtLigEnsembleCreator::operator=(const class protocols::ligand_docking::ProtLigEnsembleCreator &) –> class protocols::ligand_docking::ProtLigEnsembleCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsembleCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsembleCreator) → str

C++: protocols::ligand_docking::ProtLigEnsembleCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.ProtLigEnsembleCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info, : pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info) → pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info

C++: protocols::ligand_docking::ProtLigPair_info::operator=(const struct protocols::ligand_docking::ProtLigPair_info &) –> struct protocols::ligand_docking::ProtLigPair_info &

property bind_data

property has_bind

property lig_chain

property mut_resid

property mut_target

print_mut_string(self: pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info) → str

C++: protocols::ligand_docking::ProtLigPair_info::print_mut_string() –> std::string

print_string(self: pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info) → str

C++: protocols::ligand_docking::ProtLigPair_info::print_string() –> std::string

property wild_type

class pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover

Bases: Mover

Replace the residue at the given position with a randomly selected conformer from its rotamer library.

Only tested on ligand residues. If using torsion restraints, should be wrapped in an UnconstrainedTorsionsMover.

apply(self: pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::RandomConformerMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover, : pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover) → pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover

C++: protocols::ligand_docking::RandomConformerMover::operator=(const class protocols::ligand_docking::RandomConformerMover &) –> class protocols::ligand_docking::RandomConformerMover &

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.ligand_docking.RandomConformerMover) → str

C++: protocols::ligand_docking::RandomConformerMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

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

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

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

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.RandomConformers

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.RandomConformers, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::RandomConformers::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.RandomConformers, : pyrosetta.rosetta.protocols.ligand_docking.RandomConformers) → pyrosetta.rosetta.protocols.ligand_docking.RandomConformers

C++: protocols::ligand_docking::RandomConformers::operator=(const class protocols::ligand_docking::RandomConformers &) –> class protocols::ligand_docking::RandomConformers &

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.ligand_docking.RandomConformers) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::RandomConformers::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.ligand_docking.RandomConformers) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::RandomConformers::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.ligand_docking.RandomConformers) → str

C++: protocols::ligand_docking::RandomConformers::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::ligand_docking::RandomConformers::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.RandomConformers, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::RandomConformers::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::ligand_docking::RandomConformers::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.RandomConformersCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.RandomConformersCreator, : pyrosetta.rosetta.protocols.ligand_docking.RandomConformersCreator) → pyrosetta.rosetta.protocols.ligand_docking.RandomConformersCreator

C++: protocols::ligand_docking::RandomConformersCreator::operator=(const class protocols::ligand_docking::RandomConformersCreator &) –> class protocols::ligand_docking::RandomConformersCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.RandomConformersCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.RandomConformersCreator) → str

C++: protocols::ligand_docking::RandomConformersCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.RandomConformersCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints

Bases: pybind11_object

Manages harmonic restraints on torsions, so they can be turned off for packing.

Restraints are created when object is created, so they start off enabled. I had to change from a PoseOP in the constructor to Pose references in enable/disable because Movers only get Pose references, not PoseOPs. Do not try to use one of these with multiple different poses, or surely the C++ gods will smite thee.

assign(self: pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints, : pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints) → pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints

C++: protocols::ligand_docking::ResidueTorsionRestraints::operator=(const class protocols::ligand_docking::ResidueTorsionRestraints &) –> class protocols::ligand_docking::ResidueTorsionRestraints &

disable(self: pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints, pose: pyrosetta.rosetta.core.pose.Pose) → None

Remove residue torsions constraints added by this object (if any).

C++: protocols::ligand_docking::ResidueTorsionRestraints::disable(class core::pose::Pose &) –> void

enable(self: pyrosetta.rosetta.protocols.ligand_docking.ResidueTorsionRestraints, pose: pyrosetta.rosetta.core.pose.Pose) → None

Constrain residue torsions for specified pose.

C++: protocols::ligand_docking::ResidueTorsionRestraints::enable(class core::pose::Pose &) –> void

class pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover

Bases: Mover

An optimized mover for Monte Carlo trial of rigid body perturbations.

apply(self: pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::RigidSearchMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover, : pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover) → pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover

C++: protocols::ligand_docking::RigidSearchMover::operator=(const class protocols::ligand_docking::RigidSearchMover &) –> class protocols::ligand_docking::RigidSearchMover &

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover) → str

C++: protocols::ligand_docking::RigidSearchMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

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

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

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

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

recover_low(*args, **kwargs)

Overloaded function.

1. recover_low(self: pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover) -> bool

Will the absolute lowest-energy pose be recovered at the end of apply()?

C++: protocols::ligand_docking::RigidSearchMover::recover_low() const –> bool

2. recover_low(self: pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover, b: bool) -> None

Should the absolute lowest-energy pose be recovered at the end of apply()?

C++: protocols::ligand_docking::RigidSearchMover::recover_low(bool) –> 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

rotate_around_atom(self: pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover, rsd: int, atom: int) → None

Rotation occurs around the specified atom

C++: protocols::ligand_docking::RigidSearchMover::rotate_around_atom(unsigned long, unsigned long) –> void

rotate_around_downstream_centroid(self: pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover) → None

Rotation occurs around centroid of downstream half of the jump (default)

C++: protocols::ligand_docking::RigidSearchMover::rotate_around_downstream_centroid() –> void

rotation(*args, **kwargs)

Overloaded function.

1. rotation(self: pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover) -> float

Amount of random (Gaussian) rotation, in degrees

C++: protocols::ligand_docking::RigidSearchMover::rotation() const –> double

2. rotation(self: pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover, degrees: float) -> None

Amount of random (Gaussian) rotation, in degrees

C++: protocols::ligand_docking::RigidSearchMover::rotation(double) –> void

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

translation(*args, **kwargs)

Overloaded function.

1. translation(self: pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover) -> float

Amount of random (Gaussian) translation, in Angstroms

C++: protocols::ligand_docking::RigidSearchMover::translation() const –> double

2. translation(self: pyrosetta.rosetta.protocols.ligand_docking.RigidSearchMover, angstroms: float) -> None

Amount of random (Gaussian) translation, in Angstroms

C++: protocols::ligand_docking::RigidSearchMover::translation(double) –> void

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.Rotate

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.Rotate, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::Rotate::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.Rotate, : pyrosetta.rosetta.protocols.ligand_docking.Rotate) → pyrosetta.rosetta.protocols.ligand_docking.Rotate

C++: protocols::ligand_docking::Rotate::operator=(const class protocols::ligand_docking::Rotate &) –> class protocols::ligand_docking::Rotate &

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.ligand_docking.Rotate) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::Rotate::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.ligand_docking.Rotate) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::Rotate::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.ligand_docking.Rotate) → str

C++: protocols::ligand_docking::Rotate::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::ligand_docking::Rotate::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.Rotate, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::Rotate::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::ligand_docking::Rotate::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_chain(self: pyrosetta.rosetta.protocols.ligand_docking.Rotate, chain: str) → None

Reset the chain which the Rotate mover works on.

C++: protocols::ligand_docking::Rotate::set_chain(const std::string &) –> void

set_chain_id(self: pyrosetta.rosetta.protocols.ligand_docking.Rotate, chain_id: int) → None

Reset the chain which the Rotate mover works on.

C++: protocols::ligand_docking::Rotate::set_chain_id(unsigned long) –> void

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.RotateCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.RotateCreator, : pyrosetta.rosetta.protocols.ligand_docking.RotateCreator) → pyrosetta.rosetta.protocols.ligand_docking.RotateCreator

C++: protocols::ligand_docking::RotateCreator::operator=(const class protocols::ligand_docking::RotateCreator &) –> class protocols::ligand_docking::RotateCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.RotateCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.RotateCreator) → str

C++: protocols::ligand_docking::RotateCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.RotateCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.Rotate_info

Bases: pybind11_object

assign(self: pyrosetta.rosetta.protocols.ligand_docking.Rotate_info, : pyrosetta.rosetta.protocols.ligand_docking.Rotate_info) → pyrosetta.rosetta.protocols.ligand_docking.Rotate_info

C++: protocols::ligand_docking::Rotate_info::operator=(const struct protocols::ligand_docking::Rotate_info &) –> struct protocols::ligand_docking::Rotate_info &

chain_id(self: pyrosetta.rosetta.protocols.ligand_docking.Rotate_info, pose: pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::ligand_docking::Rotate_info::chain_id(const class core::pose::Pose &) const –> unsigned long

chain_letter(self: pyrosetta.rosetta.protocols.ligand_docking.Rotate_info, pose: pyrosetta.rosetta.core.pose.Pose) → str

C++: protocols::ligand_docking::Rotate_info::chain_letter(const class core::pose::Pose &) const –> char

property cycles

property degrees

property distribution

jump_id(self: pyrosetta.rosetta.protocols.ligand_docking.Rotate_info, pose: pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::ligand_docking::Rotate_info::jump_id(const class core::pose::Pose &) const –> unsigned long

set_chain_id(self: pyrosetta.rosetta.protocols.ligand_docking.Rotate_info, id: int) → None

C++: protocols::ligand_docking::Rotate_info::set_chain_id(unsigned long) –> void

set_chain_letter(self: pyrosetta.rosetta.protocols.ligand_docking.Rotate_info, str: str) → None

C++: protocols::ligand_docking::Rotate_info::set_chain_letter(const std::string &) –> void

set_tag_along_chains(self: pyrosetta.rosetta.protocols.ligand_docking.Rotate_info, setting: pyrosetta.rosetta.utility.vector1_std_string) → None

C++: protocols::ligand_docking::Rotate_info::set_tag_along_chains(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

tag_along_chain_ids(self: pyrosetta.rosetta.protocols.ligand_docking.Rotate_info, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

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

tag_along_jumps(self: pyrosetta.rosetta.protocols.ligand_docking.Rotate_info, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

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

tag_along_residues(self: pyrosetta.rosetta.protocols.ligand_docking.Rotate_info, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

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

class pyrosetta.rosetta.protocols.ligand_docking.Rotates

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.Rotates, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::Rotates::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.Rotates, : pyrosetta.rosetta.protocols.ligand_docking.Rotates) → pyrosetta.rosetta.protocols.ligand_docking.Rotates

C++: protocols::ligand_docking::Rotates::operator=(const class protocols::ligand_docking::Rotates &) –> class protocols::ligand_docking::Rotates &

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.ligand_docking.Rotates) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::Rotates::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.ligand_docking.Rotates) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::Rotates::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.ligand_docking.Rotates) → str

C++: protocols::ligand_docking::Rotates::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::ligand_docking::Rotates::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.Rotates, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::Rotates::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::ligand_docking::Rotates::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.RotatesCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.RotatesCreator, : pyrosetta.rosetta.protocols.ligand_docking.RotatesCreator) → pyrosetta.rosetta.protocols.ligand_docking.RotatesCreator

C++: protocols::ligand_docking::RotatesCreator::operator=(const class protocols::ligand_docking::RotatesCreator &) –> class protocols::ligand_docking::RotatesCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.RotatesCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.RotatesCreator) → str

C++: protocols::ligand_docking::RotatesCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.RotatesCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.SlideTogether

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.SlideTogether, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::SlideTogether::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.SlideTogether, : pyrosetta.rosetta.protocols.ligand_docking.SlideTogether) → pyrosetta.rosetta.protocols.ligand_docking.SlideTogether

C++: protocols::ligand_docking::SlideTogether::operator=(const class protocols::ligand_docking::SlideTogether &) –> class protocols::ligand_docking::SlideTogether &

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.ligand_docking.SlideTogether) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::SlideTogether::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.ligand_docking.SlideTogether) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::SlideTogether::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.ligand_docking.SlideTogether) → str

C++: protocols::ligand_docking::SlideTogether::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::ligand_docking::SlideTogether::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.SlideTogether, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::SlideTogether::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::ligand_docking::SlideTogether::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

class pyrosetta.rosetta.protocols.ligand_docking.SlideTogetherCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.SlideTogetherCreator, : pyrosetta.rosetta.protocols.ligand_docking.SlideTogetherCreator) → pyrosetta.rosetta.protocols.ligand_docking.SlideTogetherCreator

C++: protocols::ligand_docking::SlideTogetherCreator::operator=(const class protocols::ligand_docking::SlideTogetherCreator &) –> class protocols::ligand_docking::SlideTogetherCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.SlideTogetherCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.SlideTogetherCreator) → str

C++: protocols::ligand_docking::SlideTogetherCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.SlideTogetherCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.StartFrom

Bases: Mover

add_coords(*args, **kwargs)

Overloaded function.

1. add_coords(self: pyrosetta.rosetta.protocols.ligand_docking.StartFrom, coords: pyrosetta.rosetta.numeric.xyzVector_double_t) -> None

2. add_coords(self: pyrosetta.rosetta.protocols.ligand_docking.StartFrom, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, pdb_tag: str) -> None

Add the given coordinates as a valid starting position for the given pdb_tag

C++: protocols::ligand_docking::StartFrom::add_coords(const class numeric::xyzVector<double> &, const std::string &) –> void

add_coords_hash(self: pyrosetta.rosetta.protocols.ligand_docking.StartFrom, coords: pyrosetta.rosetta.numeric.xyzVector_double_t, hash_value: str) → None

Add the given coordinates as a valid starting position for the given structure hash

C++: protocols::ligand_docking::StartFrom::add_coords_hash(const class numeric::xyzVector<double> &, const std::string &) –> void

apply(self: pyrosetta.rosetta.protocols.ligand_docking.StartFrom, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::StartFrom::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.StartFrom, : pyrosetta.rosetta.protocols.ligand_docking.StartFrom) → pyrosetta.rosetta.protocols.ligand_docking.StartFrom

C++: protocols::ligand_docking::StartFrom::operator=(const class protocols::ligand_docking::StartFrom &) –> class protocols::ligand_docking::StartFrom &

chain(*args, **kwargs)

Overloaded function.

1. chain(self: pyrosetta.rosetta.protocols.ligand_docking.StartFrom, chains: pyrosetta.rosetta.utility.vector1_std_string) -> None

Set which chains the mover operates on.

C++: protocols::ligand_docking::StartFrom::chain(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> void

2. chain(self: pyrosetta.rosetta.protocols.ligand_docking.StartFrom, chain: str) -> None

Add a chain to the mover targets

C++: protocols::ligand_docking::StartFrom::chain(const std::string &) –> void

3. chain(self: pyrosetta.rosetta.protocols.ligand_docking.StartFrom) -> str

Get which chains the mover operates on

C++: protocols::ligand_docking::StartFrom::chain() –> std::string

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.ligand_docking.StartFrom) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::StartFrom::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.ligand_docking.StartFrom) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::StartFrom::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.ligand_docking.StartFrom) → str

C++: protocols::ligand_docking::StartFrom::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::ligand_docking::StartFrom::mover_name() –> std::string

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.StartFrom, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::StartFrom::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

parse_pdb_file(*args, **kwargs)

Overloaded function.

1. parse_pdb_file(self: pyrosetta.rosetta.protocols.ligand_docking.StartFrom, filename: str) -> None

2. parse_pdb_file(self: pyrosetta.rosetta.protocols.ligand_docking.StartFrom, filename: str, atom_name: str) -> None

3. parse_pdb_file(self: pyrosetta.rosetta.protocols.ligand_docking.StartFrom, filename: str, atom_name: str, tag: str) -> None

Parse a PDB file, grabbing the positions from the heavy atom coordinates.

If atom_name is not empty, only grab coordinates from the specified atom name.

C++: protocols::ligand_docking::StartFrom::parse_pdb_file(const std::string &, const std::string &, const std::string &) –> void

parse_startfrom_file(self: pyrosetta.rosetta.protocols.ligand_docking.StartFrom, filename: str) → None

Parse the json-format startfrom file

C++: protocols::ligand_docking::StartFrom::parse_startfrom_file(const std::string &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.ligand_docking.StartFrom, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide the citation.

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

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

C++: protocols::ligand_docking::StartFrom::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

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

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

Outputs details about the Mover, including current settings.

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

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

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

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

type(*args, **kwargs)

Overloaded function.

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

Set the ‘type’ string

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

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

Get the set ‘type’ string

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

use_nbr(*args, **kwargs)

Overloaded function.

1. use_nbr(self: pyrosetta.rosetta.protocols.ligand_docking.StartFrom, setting: bool) -> None

Set if we should use the neighbor atom or the all-atom centroid to center the ligand

C++: protocols::ligand_docking::StartFrom::use_nbr(bool) –> void

2. use_nbr(self: pyrosetta.rosetta.protocols.ligand_docking.StartFrom) -> bool

Get whether we should use the neighbor atom or the all-atom centroid to center the ligand

C++: protocols::ligand_docking::StartFrom::use_nbr() –> bool

class pyrosetta.rosetta.protocols.ligand_docking.StartFromCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.StartFromCreator, : pyrosetta.rosetta.protocols.ligand_docking.StartFromCreator) → pyrosetta.rosetta.protocols.ligand_docking.StartFromCreator

C++: protocols::ligand_docking::StartFromCreator::operator=(const class protocols::ligand_docking::StartFromCreator &) –> class protocols::ligand_docking::StartFromCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.StartFromCreator) → pyrosetta.rosetta.protocols.moves.Mover

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

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.StartFromCreator) → str

C++: protocols::ligand_docking::StartFromCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.StartFromCreator, xsd: utility::tag::XMLSchemaDefinition) → None

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

class pyrosetta.rosetta.protocols.ligand_docking.TetherLigand

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.TetherLigand, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::TetherLigand::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.TetherLigand, : pyrosetta.rosetta.protocols.ligand_docking.TetherLigand) → pyrosetta.rosetta.protocols.ligand_docking.TetherLigand

C++: protocols::ligand_docking::TetherLigand::operator=(const class protocols::ligand_docking::TetherLigand &) –> class protocols::ligand_docking::TetherLigand &

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

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

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

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

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

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

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

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

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

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

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

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

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

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_ligand_tether(self: pyrosetta.rosetta.protocols.ligand_docking.TetherLigand) → pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::ligand_docking::TetherLigand::get_ligand_tether() const –> const class std::shared_ptr<const class core::scoring::constraints::Constraint> &

get_name(self: pyrosetta.rosetta.protocols.ligand_docking.TetherLigand) → str

C++: protocols::ligand_docking::TetherLigand::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

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

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

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

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

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

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

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

static name() → str

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

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

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

static register_options() → None

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

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

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

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

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

each use.

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

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

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

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

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

release(self: pyrosetta.rosetta.protocols.ligand_docking.TetherLigand, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::TetherLigand::release(class core::pose::Pose &) –> void

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

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

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

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

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

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

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

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

setter for poses contained for rms

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

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

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

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

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

Set the ‘type’ string

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

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.ligand_docking.Transform

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::Transform::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, : pyrosetta.rosetta.protocols.ligand_docking.Transform) → pyrosetta.rosetta.protocols.ligand_docking.Transform

C++: protocols::ligand_docking::Transform::operator=(const class protocols::ligand_docking::Transform &) –> class protocols::ligand_docking::Transform &

change_conformer(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) → None

randomly change the ligand conformation

C++: protocols::ligand_docking::Transform::change_conformer(class core::conformation::UltraLightResidue &) –> void

check_conformers(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, starting_residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) → bool

Check that conformers are safely within the grids.

Returns true if good, false if bad.

C++: protocols::ligand_docking::Transform::check_conformers(class core::conformation::UltraLightResidue &) const –> bool

check_grid(*args, **kwargs)

Overloaded function.

1. check_grid(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, ligand_residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) -> bool

2. check_grid(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, ligand_residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, distance: float) -> bool

check ligand still inside the grid

C++: protocols::ligand_docking::Transform::check_grid(class core::conformation::UltraLightResidue &, double) –> bool

check_rmsd(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, start: pyrosetta.rosetta.core.conformation.UltraLightResidue, current: pyrosetta.rosetta.core.conformation.UltraLightResidue) → bool

return true if the rmsd is within the specified cutoff

C++: protocols::ligand_docking::Transform::check_rmsd(const class core::conformation::UltraLightResidue &, const class core::conformation::UltraLightResidue &) const –> bool

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.ligand_docking.Transform) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::Transform::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

convert_to_full_pose(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, pose: pyrosetta.rosetta.core.pose.Pose, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, chain_id: int) → float

copy the ligand into the desired receptor model and update conformation using the best model

C++: protocols::ligand_docking::Transform::convert_to_full_pose(class core::pose::Pose &, class core::conformation::UltraLightResidue &, unsigned long) –> double

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>

dump_conformer(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, output: pyrosetta.rosetta.utility.io.ozstream) → None

output the ligand residues to a pdb file

C++: protocols::ligand_docking::Transform::dump_conformer(class core::conformation::UltraLightResidue &, class utility::io::ozstream &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.ligand_docking.Transform) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::Transform::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.ligand_docking.Transform) → str

C++: protocols::ligand_docking::Transform::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

make_multi_pose_grids(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Generate all extra grids

C++: protocols::ligand_docking::Transform::make_multi_pose_grids(class numeric::xyzVector<double>) –> void

static mover_name() → str

C++: protocols::ligand_docking::Transform::mover_name() –> std::string

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::Transform::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide the citation.

C++: protocols::ligand_docking::Transform::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::ligand_docking::Transform::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

randomize_ligand(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, distance: float, angle: float) → None

Performa a randomization of the ligand residue, translating by some random value within a uniform distribution with a max of distance,

and rotating around a random axis with a uniformly random angle of between -angle/2 and +angle/2 (in degrees). Also randomizes starting conformer if available

C++: protocols::ligand_docking::Transform::randomize_ligand(class core::conformation::UltraLightResidue &, double, double) –> void

recommended_box_size(*args, **kwargs)

Overloaded function.

1. recommended_box_size(self: pyrosetta.rosetta.protocols.ligand_docking.Transform) -> float

2. recommended_box_size(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, success_rate: float) -> float

Return the recommended minimum box size for this particular setup.

• success_rate is the MC success rate. Will be bumped to a reasonable minimum

C++: protocols::ligand_docking::Transform::recommended_box_size(double) const –> double

recommended_grid_size(*args, **kwargs)

Overloaded function.

1. recommended_grid_size(self: pyrosetta.rosetta.protocols.ligand_docking.Transform) -> float

2. recommended_grid_size(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, success_rate: float) -> float

Return the recommended minimum size of the ligand grids for this particular setup.

• success_rate is the MC success rate. Will be bumped to a reasonable minimum

C++: protocols::ligand_docking::Transform::recommended_grid_size(double) const –> double

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

score_constraints(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, pose: pyrosetta.rosetta.core.pose.Pose, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → float

score constraints by updating pose and applying score_function_

C++: protocols::ligand_docking::Transform::score_constraints(class core::pose::Pose &, class core::conformation::UltraLightResidue &, class std::shared_ptr<class core::scoring::ScoreFunction> &) –> double

score_ligand(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, ligand_residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) → float

Calculate unconstrained score for given ligand

C++: protocols::ligand_docking::Transform::score_ligand(class core::conformation::UltraLightResidue &) –> double

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

setup_conformers(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, pose: pyrosetta.rosetta.core.pose.Pose, begin: int) → None

setup conformers for use

C++: protocols::ligand_docking::Transform::setup_conformers(class core::pose::Pose &, unsigned long) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

transform_ligand(self: pyrosetta.rosetta.protocols.ligand_docking.Transform, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue) → None

translate and rotate a random value by the distances specified in the Transform_info object, using a gaussian distribution

C++: protocols::ligand_docking::Transform::transform_ligand(class core::conformation::UltraLightResidue &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.ligand_docking.TransformCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.TransformCreator, : pyrosetta.rosetta.protocols.ligand_docking.TransformCreator) → pyrosetta.rosetta.protocols.ligand_docking.TransformCreator

C++: protocols::ligand_docking::TransformCreator::operator=(const class protocols::ligand_docking::TransformCreator &) –> class protocols::ligand_docking::TransformCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.TransformCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::TransformCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.TransformCreator) → str

C++: protocols::ligand_docking::TransformCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.TransformCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::ligand_docking::TransformCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::TransformEnsemble::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble, : pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble) → pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble

C++: protocols::ligand_docking::TransformEnsemble::operator=(const class protocols::ligand_docking::TransformEnsemble &) –> class protocols::ligand_docking::TransformEnsemble &

change_conformer(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble, ligand_residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, reference_residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, resid: int) → None

C++: protocols::ligand_docking::TransformEnsemble::change_conformer(class core::conformation::UltraLightResidue &, const class core::conformation::UltraLightResidue &, unsigned long) –> void

change_conformers(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble, ligand_residues: pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue, reference_residues: pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue) → None

C++: protocols::ligand_docking::TransformEnsemble::change_conformers(class utility::vector1<class core::conformation::UltraLightResidue, class std::allocator<class core::conformation::UltraLightResidue> > &, const class utility::vector1<class core::conformation::UltraLightResidue, class std::allocator<class core::conformation::UltraLightResidue> > &) –> void

check_grid(*args, **kwargs)

Overloaded function.

1. check_grid(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble, ligand_residues: pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue) -> bool

2. check_grid(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble, ligand_residues: pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue, distance: float) -> bool

C++: protocols::ligand_docking::TransformEnsemble::check_grid(class utility::vector1<class core::conformation::UltraLightResidue, class std::allocator<class core::conformation::UltraLightResidue> > &, double) –> bool

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.ligand_docking.TransformEnsemble) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::TransformEnsemble::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

convert_to_full_pose(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble, pose: pyrosetta.rosetta.core.pose.Pose, best_pose_count: int) → float

copy the ligand into the desired receptor model and update conformation using the best model

C++: protocols::ligand_docking::TransformEnsemble::convert_to_full_pose(class core::pose::Pose &, unsigned long &) –> double

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>

dump_conformer(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble, residue: pyrosetta.rosetta.core.conformation.UltraLightResidue, output: pyrosetta.rosetta.utility.io.ozstream) → None

C++: protocols::ligand_docking::TransformEnsemble::dump_conformer(const class core::conformation::UltraLightResidue &, class utility::io::ozstream &) –> void

fresh_instance(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::TransformEnsemble::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.ligand_docking.TransformEnsemble) → str

C++: protocols::ligand_docking::TransformEnsemble::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

make_multi_pose_grids(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble, center: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

Generate all extra grids

C++: protocols::ligand_docking::TransformEnsemble::make_multi_pose_grids(class numeric::xyzVector<double>) –> void

monte_carlo(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble, current: float, last: float) → bool

C++: protocols::ligand_docking::TransformEnsemble::monte_carlo(double &, double &) –> bool

static mover_name() → str

C++: protocols::ligand_docking::TransformEnsemble::mover_name() –> std::string

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::TransformEnsemble::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

print_xyz(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble, vector: pyrosetta.rosetta.numeric.xyzVector_double_t) → None

C++: protocols::ligand_docking::TransformEnsemble::print_xyz(class numeric::xyzVector<double>) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide the citation.

C++: protocols::ligand_docking::TransformEnsemble::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::ligand_docking::TransformEnsemble::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

score_ligands(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble, ligand_residues: pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue) → float

Calculate unconstrained score for given ligands

C++: protocols::ligand_docking::TransformEnsemble::score_ligands(class utility::vector1<class core::conformation::UltraLightResidue, class std::allocator<class core::conformation::UltraLightResidue> > &) –> double

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

transform_ligand(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble, ligand_residues: pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue, reference_residues: pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue) → None

C++: protocols::ligand_docking::TransformEnsemble::transform_ligand(class utility::vector1<class core::conformation::UltraLightResidue, class std::allocator<class core::conformation::UltraLightResidue> > &, class utility::vector1<class core::conformation::UltraLightResidue, class std::allocator<class core::conformation::UltraLightResidue> > &) –> void

translate_ligand(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble, ligand_residues: pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue, reference_residues: pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue, distance: float) → None

C++: protocols::ligand_docking::TransformEnsemble::translate_ligand(class utility::vector1<class core::conformation::UltraLightResidue, class std::allocator<class core::conformation::UltraLightResidue> > &, class utility::vector1<class core::conformation::UltraLightResidue, class std::allocator<class core::conformation::UltraLightResidue> > &, double) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

weighted_center(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble, residues: pyrosetta.rosetta.utility.vector1_core_conformation_UltraLightResidue) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::ligand_docking::TransformEnsemble::weighted_center(class utility::vector1<class core::conformation::UltraLightResidue, class std::allocator<class core::conformation::UltraLightResidue> > &) –> class numeric::xyzVector<double>

class pyrosetta.rosetta.protocols.ligand_docking.TransformEnsembleCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsembleCreator, : pyrosetta.rosetta.protocols.ligand_docking.TransformEnsembleCreator) → pyrosetta.rosetta.protocols.ligand_docking.TransformEnsembleCreator

C++: protocols::ligand_docking::TransformEnsembleCreator::operator=(const class protocols::ligand_docking::TransformEnsembleCreator &) –> class protocols::ligand_docking::TransformEnsembleCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsembleCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::TransformEnsembleCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsembleCreator) → str

C++: protocols::ligand_docking::TransformEnsembleCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsembleCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::ligand_docking::TransformEnsembleCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble_info

Bases: pybind11_object

property angle

assign(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble_info, : pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble_info) → pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble_info

C++: protocols::ligand_docking::TransformEnsemble_info::operator=(const struct protocols::ligand_docking::TransformEnsemble_info &) –> struct protocols::ligand_docking::TransformEnsemble_info &

property box_size

chain_ids(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble_info, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::ligand_docking::TransformEnsemble_info::chain_ids(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

property chains

property cycles

jump_ids(self: pyrosetta.rosetta.protocols.ligand_docking.TransformEnsemble_info, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::ligand_docking::TransformEnsemble_info::jump_ids(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

property move_distance

property repeats

property temperature

class pyrosetta.rosetta.protocols.ligand_docking.Transform_info

Bases: pybind11_object

property angle

assign(self: pyrosetta.rosetta.protocols.ligand_docking.Transform_info, : pyrosetta.rosetta.protocols.ligand_docking.Transform_info) → pyrosetta.rosetta.protocols.ligand_docking.Transform_info

C++: protocols::ligand_docking::Transform_info::operator=(const struct protocols::ligand_docking::Transform_info &) –> struct protocols::ligand_docking::Transform_info &

property box_size

property chain

property cycles

property move_distance

property repeats

property rmsd

property temperature

class pyrosetta.rosetta.protocols.ligand_docking.Translate

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.Translate, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::Translate::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.Translate, : pyrosetta.rosetta.protocols.ligand_docking.Translate) → pyrosetta.rosetta.protocols.ligand_docking.Translate

C++: protocols::ligand_docking::Translate::operator=(const class protocols::ligand_docking::Translate &) –> class protocols::ligand_docking::Translate &

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.ligand_docking.Translate) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::Translate::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.ligand_docking.Translate) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::Translate::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_chain_id(self: pyrosetta.rosetta.protocols.ligand_docking.Translate, pose: pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::ligand_docking::Translate::get_chain_id(const class core::pose::Pose &) –> unsigned long

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.ligand_docking.Translate) → str

C++: protocols::ligand_docking::Translate::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::ligand_docking::Translate::mover_name() –> std::string

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.Translate, tag: pyrosetta.rosetta.utility.tag.Tag, data_map: pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::Translate::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::ligand_docking::Translate::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.ligand_docking.TranslateCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.TranslateCreator, : pyrosetta.rosetta.protocols.ligand_docking.TranslateCreator) → pyrosetta.rosetta.protocols.ligand_docking.TranslateCreator

C++: protocols::ligand_docking::TranslateCreator::operator=(const class protocols::ligand_docking::TranslateCreator &) –> class protocols::ligand_docking::TranslateCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.TranslateCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::TranslateCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.TranslateCreator) → str

C++: protocols::ligand_docking::TranslateCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.TranslateCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::ligand_docking::TranslateCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

class pyrosetta.rosetta.protocols.ligand_docking.Translate_info

Bases: pybind11_object

property angstroms

assign(self: pyrosetta.rosetta.protocols.ligand_docking.Translate_info, : pyrosetta.rosetta.protocols.ligand_docking.Translate_info) → pyrosetta.rosetta.protocols.ligand_docking.Translate_info

C++: protocols::ligand_docking::Translate_info::operator=(const struct protocols::ligand_docking::Translate_info &) –> struct protocols::ligand_docking::Translate_info &

chain_id(self: pyrosetta.rosetta.protocols.ligand_docking.Translate_info, pose: pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::ligand_docking::Translate_info::chain_id(const class core::pose::Pose &) const –> unsigned long

chain_letter(self: pyrosetta.rosetta.protocols.ligand_docking.Translate_info, pose: pyrosetta.rosetta.core.pose.Pose) → str

C++: protocols::ligand_docking::Translate_info::chain_letter(const class core::pose::Pose &) const –> char

property cycles

property distribution

property force

jump_id(self: pyrosetta.rosetta.protocols.ligand_docking.Translate_info, pose: pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::ligand_docking::Translate_info::jump_id(const class core::pose::Pose &) const –> unsigned long

set_chain_id(self: pyrosetta.rosetta.protocols.ligand_docking.Translate_info, id: int) → None

C++: protocols::ligand_docking::Translate_info::set_chain_id(unsigned long) –> void

set_chain_letter(self: pyrosetta.rosetta.protocols.ligand_docking.Translate_info, str: str) → None

C++: protocols::ligand_docking::Translate_info::set_chain_letter(const std::string &) –> void

class pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover

Bases: Mover

Juggles torsional constraints with packing or rotamer trials.

Adds torsional constraints to the specified residue in the pose, but then removes them before running the supplied mover. They are then either restored (if no conformational change) or re-initialized. The supplied child_mover is expected to be either a full repack or rotamer trials.

apply(self: pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover, pose: pyrosetta.rosetta.core.pose.Pose) → None

Removes its constraints, runs mover, restores constraints.

C++: protocols::ligand_docking::UnconstrainedTorsionsMover::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover, : pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover) → pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover

C++: protocols::ligand_docking::UnconstrainedTorsionsMover::operator=(const class protocols::ligand_docking::UnconstrainedTorsionsMover &) –> class protocols::ligand_docking::UnconstrainedTorsionsMover &

clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) → None

Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.

clear_info is called by jd2 before calling apply

C++: protocols::moves::Mover::clear_info() –> void

clone(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Return a clone of the Mover object.

C++: protocols::moves::Mover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>

create(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>

fresh_instance(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

Generates a new Mover object freshly created with the default ctor.

C++: protocols::moves::Mover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>

get_additional_output(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

fpd

Mechanism by which a mover may return multiple output poses from a single input pose.

Supported in JD2. Will attempt to grab additional poses until a nullptr is returned.

C++: protocols::moves::Mover::get_additional_output() –> class std::shared_ptr<class core::pose::Pose>

get_current_job(self: pyrosetta.rosetta.protocols.moves.Mover) → protocols::jobdist::BasicJob

C++: protocols::moves::Mover::get_current_job() const –> class std::shared_ptr<const class protocols::jobdist::BasicJob>

get_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover) → str

A tag is a unique identifier used to identify structures produced

by this Mover. get_current_tag() returns the tag, and set_current_tag( std::string tag ) sets the tag. This functionality is not intended for use with the 2008 job distributor.

C++: protocols::moves::Mover::get_current_tag() const –> std::string

get_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_input_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_last_move_status(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.MoverStatus

returns status after an apply(). The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say “that run was no good, skip it” then use the protected last_move_status(MoverStatus) to change the value that this function will return.

C++: protocols::moves::Mover::get_last_move_status() const –> enum protocols::moves::MoverStatus

get_name(self: pyrosetta.rosetta.protocols.ligand_docking.UnconstrainedTorsionsMover) → str

C++: protocols::ligand_docking::UnconstrainedTorsionsMover::get_name() const –> std::string

get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.core.pose.Pose

C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>

get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>

get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t

C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>

get_type(self: pyrosetta.rosetta.protocols.moves.Mover) → str

C++: protocols::moves::Mover::get_type() const –> std::string

info(self: pyrosetta.rosetta.protocols.moves.Mover) → pyrosetta.rosetta.std.list_std_string_t

non-const accessor

C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &

last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) → float

C++: protocols::moves::Mover::last_proposal_density_ratio() –> double

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.moves.Mover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) → None

Called by MoverFactory when constructing new Movers. Takes care of the specific mover’s parsing.

C++: protocols::moves::Mover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.

C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

static register_options() → None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile

Bases: Mover

apply(self: pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::WriteLigandMolFile::apply(class core::pose::Pose &) –> void

assign(self: pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile, : pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile) → pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile

C++: protocols::ligand_docking::WriteLigandMolFile::operator=(const class protocols::ligand_docking::WriteLigandMolFile &) –> class protocols::ligand_docking::WriteLigandMolFile &

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.ligand_docking.WriteLigandMolFile) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::WriteLigandMolFile::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.ligand_docking.WriteLigandMolFile) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::WriteLigandMolFile::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.ligand_docking.WriteLigandMolFile) → str

C++: protocols::ligand_docking::WriteLigandMolFile::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::ligand_docking::WriteLigandMolFile::mover_name() –> std::string

static name() → str

C++: protocols::moves::Mover::name() –> std::string

parse_my_tag(self: pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFile, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

C++: protocols::ligand_docking::WriteLigandMolFile::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::ligand_docking::WriteLigandMolFile::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void

static register_options() → None

Overload this static method if you access options within the mover.

These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.

C++: protocols::moves::Mover::register_options() –> void

reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on

each use.

C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool

reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) → bool

Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input

pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).

C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool

reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) → None

resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.

C++: protocols::moves::Mover::reset_status() –> void

set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) → None

C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void

set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) → None

C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void

set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for poses contained for rms

C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe

C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) → None

Set the ‘type’ string

C++: protocols::moves::Mover::set_type(const std::string &) –> void

show(*args, **kwargs)

Overloaded function.

1. show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None

2. show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None

Outputs details about the Mover, including current settings.

C++: protocols::moves::Mover::show(std::ostream &) const –> void

test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) → None

: Unit test support function. Apply one move to a given pose.

Allows extra test specific functions to be called before applying

C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void

type(*args, **kwargs)

Overloaded function.

1. type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None

Set the ‘type’ string

C++: protocols::moves::Mover::type(const std::string &) –> void

2. type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str

Get the set ‘type’ string

C++: protocols::moves::Mover::type() const –> const std::string &

class pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFileCreator

Bases: MoverCreator

assign(self: pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFileCreator, : pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFileCreator) → pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFileCreator

C++: protocols::ligand_docking::WriteLigandMolFileCreator::operator=(const class protocols::ligand_docking::WriteLigandMolFileCreator &) –> class protocols::ligand_docking::WriteLigandMolFileCreator &

create_mover(self: pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFileCreator) → pyrosetta.rosetta.protocols.moves.Mover

C++: protocols::ligand_docking::WriteLigandMolFileCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>

keyname(self: pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFileCreator) → str

C++: protocols::ligand_docking::WriteLigandMolFileCreator::keyname() const –> std::string

provide_xml_schema(self: pyrosetta.rosetta.protocols.ligand_docking.WriteLigandMolFileCreator, xsd: utility::tag::XMLSchemaDefinition) → None

C++: protocols::ligand_docking::WriteLigandMolFileCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void

pyrosetta.rosetta.protocols.ligand_docking.apply_rotate(mover: pyrosetta.rosetta.protocols.rigid.RigidBodyMover, pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, jump_id: int, tag_along_chains: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: protocols::ligand_docking::apply_rotate(class std::shared_ptr<class protocols::rigid::RigidBodyMover>, class core::pose::Pose &, const class numeric::xyzVector<double> &, unsigned long, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

pyrosetta.rosetta.protocols.ligand_docking.check_score(ligand: pyrosetta.rosetta.protocols.ligand_docking.Ligand_info, heavy_atom_number: int) → bool

Convenience Functions for use with Rotate

C++: protocols::ligand_docking::check_score(const struct protocols::ligand_docking::Ligand_info &, const unsigned long) –> bool

pyrosetta.rosetta.protocols.ligand_docking.constrain_ligand_torsions(*args, **kwargs)

Overloaded function.

1. constrain_ligand_torsions(pose: pyrosetta.rosetta.core.pose.Pose, stddev_degrees: float) -> None

2. constrain_ligand_torsions(pose: pyrosetta.rosetta.core.pose.Pose, stddev_degrees: float, constrain_all_torsions_equally: bool) -> None

Call get_ligand_torsion_constraints() for all non-polymer residues

and add the resulting constraints to the Pose.

C++: protocols::ligand_docking::constrain_ligand_torsions(class core::pose::Pose &, double, bool) –> void

pyrosetta.rosetta.protocols.ligand_docking.find_attach_pt(jump_id: int, interface: protocols::ligand_docking::ligand_options::Interface, pose: pyrosetta.rosetta.core.pose.Pose) → int

C++: protocols::ligand_docking::find_attach_pt(const unsigned long, const class protocols::ligand_docking::ligand_options::Interface &, const class core::pose::Pose &) –> unsigned long

pyrosetta.rosetta.protocols.ligand_docking.find_peptide_attach_pt(start: int, stop: int, jump_to_attach: pyrosetta.rosetta.std.map_unsigned_long_unsigned_long) → int

C++: protocols::ligand_docking::find_peptide_attach_pt(const int &, const int &, const class std::map<unsigned long, unsigned long, struct std::less<unsigned long>, class std::allocator<struct std::pair<const unsigned long, unsigned long> > > &) –> unsigned long

pyrosetta.rosetta.protocols.ligand_docking.find_unconnected_residues(pose: pyrosetta.rosetta.core.pose.Pose, start: int, end: int) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::ligand_docking::find_unconnected_residues(const class core::pose::Pose &, unsigned long, const unsigned long) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.ligand_docking.frac_atoms_within(rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, cutoffs: pyrosetta.rosetta.utility.vector1_double, fractions_out: pyrosetta.rosetta.utility.vector1_double) → None

Without superimposing, automorphically computes the fraction of atoms

in these residues that are within the given cutoff(s) of each other.

C++: protocols::ligand_docking::frac_atoms_within(const class core::conformation::Residue &, const class core::conformation::Residue &, const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) –> void

pyrosetta.rosetta.protocols.ligand_docking.generate_unique_name(*args, **kwargs)

Overloaded function.

1. generate_unique_name() -> str

2. generate_unique_name(input_name: str) -> str

C++: protocols::ligand_docking::generate_unique_name(std::string) –> std::string

pyrosetta.rosetta.protocols.ligand_docking.get_automorphic_RMSDs(*args, **kwargs)

Overloaded function.

1. get_automorphic_RMSDs(test_pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, test_residue_id: int, ref_residue_ids: pyrosetta.rosetta.utility.vector1_unsigned_long) -> pyrosetta.rosetta.std.map_std_string_double

2. get_automorphic_RMSDs(test_pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, test_residue_id: int, ref_residue_ids: pyrosetta.rosetta.utility.vector1_unsigned_long, prefix: str) -> pyrosetta.rosetta.std.map_std_string_double

C++: protocols::ligand_docking::get_automorphic_RMSDs(const class core::pose::Pose &, const class core::pose::Pose &, unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const std::string &) –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

pyrosetta.rosetta.protocols.ligand_docking.get_distribution(distribution_str: str) → pyrosetta.rosetta.protocols.ligand_docking.Distribution

C++: protocols::ligand_docking::get_distribution(std::string) –> enum protocols::ligand_docking::Distribution

pyrosetta.rosetta.protocols.ligand_docking.get_incomplete_connections(residue: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: protocols::ligand_docking::get_incomplete_connections(class std::shared_ptr<const class core::conformation::Residue>) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.ligand_docking.get_interface_deltas(*args, **kwargs)

Overloaded function.

1. get_interface_deltas(chain: str, after: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.std.map_std_string_double

2. get_interface_deltas(chain: str, after: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, prefix: str) -> pyrosetta.rosetta.std.map_std_string_double

3. get_interface_deltas(chain: str, after: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, prefix: str, normalization_function: protocols::qsar::scoring_grid::ScoreNormalization) -> pyrosetta.rosetta.std.map_std_string_double

4. get_interface_deltas(chain: str, after: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, prefix: str, normalization_function: protocols::qsar::scoring_grid::ScoreNormalization, score_in_mem: bool) -> pyrosetta.rosetta.std.map_std_string_double

C++: protocols::ligand_docking::get_interface_deltas(char, const class core::pose::Pose &, const class std::shared_ptr<class core::scoring::ScoreFunction>, const std::string &, class std::shared_ptr<class protocols::qsar::scoring_grid::ScoreNormalization>, bool) –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

pyrosetta.rosetta.protocols.ligand_docking.get_ligand_RMSDs(*args, **kwargs)

Overloaded function.

1. get_ligand_RMSDs(chain: str, test_pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.std.map_std_string_double

2. get_ligand_RMSDs(chain: str, test_pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) -> pyrosetta.rosetta.std.map_std_string_double

3. get_ligand_RMSDs(chain: str, test_pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, use_ensemble_best: bool) -> pyrosetta.rosetta.std.map_std_string_double

C++: protocols::ligand_docking::get_ligand_RMSDs(char, const class core::pose::Pose &, const class core::pose::Pose &, const std::string &, bool) –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

pyrosetta.rosetta.protocols.ligand_docking.get_ligand_grid_scores(*args, **kwargs)

Overloaded function.

1. get_ligand_grid_scores(grid_set_prototype: protocols::qsar::scoring_grid::GridSet, jump_id: int, test_pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.std.map_std_string_double

2. get_ligand_grid_scores(grid_set_prototype: protocols::qsar::scoring_grid::GridSet, jump_id: int, test_pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) -> pyrosetta.rosetta.std.map_std_string_double

3. get_ligand_grid_scores(grid_set_prototype: protocols::qsar::scoring_grid::GridSet, jump_id: int, test_pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, normalization_function: protocols::qsar::scoring_grid::ScoreNormalization) -> pyrosetta.rosetta.std.map_std_string_double

normalizaton_function will only be used if the Grids do not have their own normalization

C++: protocols::ligand_docking::get_ligand_grid_scores(const class protocols::qsar::scoring_grid::GridSet &, unsigned long, const class core::pose::Pose &, const std::string &, class std::shared_ptr<class protocols::qsar::scoring_grid::ScoreNormalization>) –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

4. get_ligand_grid_scores(grid_set_prototype: protocols::qsar::scoring_grid::GridSet, chain: str, test_pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.std.map_std_string_double

5. get_ligand_grid_scores(grid_set_prototype: protocols::qsar::scoring_grid::GridSet, chain: str, test_pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) -> pyrosetta.rosetta.std.map_std_string_double

6. get_ligand_grid_scores(grid_set_prototype: protocols::qsar::scoring_grid::GridSet, chain: str, test_pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, normalization_function: protocols::qsar::scoring_grid::ScoreNormalization) -> pyrosetta.rosetta.std.map_std_string_double

normalizaton_function will only be used if the Grids do not have their own normalization

C++: protocols::ligand_docking::get_ligand_grid_scores(const class protocols::qsar::scoring_grid::GridSet &, char, const class core::pose::Pose &, const std::string &, class std::shared_ptr<class protocols::qsar::scoring_grid::ScoreNormalization>) –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

7. get_ligand_grid_scores(grid_set_prototype: protocols::qsar::scoring_grid::GridSet, residues: pyrosetta.rosetta.utility.vector1_unsigned_long, chain_label: str, test_pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, normalization_function: protocols::qsar::scoring_grid::ScoreNormalization) -> pyrosetta.rosetta.std.map_std_string_double

normalizaton_function will only be used if the Grids do not have their own normalization

C++: protocols::ligand_docking::get_ligand_grid_scores(const class protocols::qsar::scoring_grid::GridSet &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const std::string &, const class core::pose::Pose &, const std::string &, class std::shared_ptr<class protocols::qsar::scoring_grid::ScoreNormalization>) –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

pyrosetta.rosetta.protocols.ligand_docking.get_ligand_seqpos(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.utility.vector1_unsigned_long

simple function to scan the pose for all ligand residues

C++: protocols::ligand_docking::get_ligand_seqpos(const class core::pose::Pose &) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.protocols.ligand_docking.get_ligand_torsion_constraints(pose: pyrosetta.rosetta.core.pose.Pose, rsd_no: int, stddev_degrees: float, csts_out: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_scoring_constraints_Constraint_t, constrain_all_torsions_equally: bool) → None

Produce dihedral restraints for all chi angles in the specified

residue, from chi_rotamers() if available, and from the rotamer library otherwise.

C++: protocols::ligand_docking::get_ligand_torsion_constraints(class core::pose::Pose &, unsigned long, double, class utility::vector1<class std::shared_ptr<class core::scoring::constraints::Constraint>, class std::allocator<class std::shared_ptr<class core::scoring::constraints::Constraint> > > &, const bool) –> void

pyrosetta.rosetta.protocols.ligand_docking.get_ligand_travel(*args, **kwargs)

Overloaded function.

1. get_ligand_travel(chain: str, test_pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.std.map_std_string_double

2. get_ligand_travel(chain: str, test_pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) -> pyrosetta.rosetta.std.map_std_string_double

3. get_ligand_travel(chain: str, test_pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, prefix: str, use_ensemble_best: bool) -> pyrosetta.rosetta.std.map_std_string_double

Another interesting metric – how far does the ligand centroid move?

Large values indicate we’re outside of the intended binding site.

C++: protocols::ligand_docking::get_ligand_travel(char, const class core::pose::Pose &, const class core::pose::Pose &, const std::string &, bool) –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

pyrosetta.rosetta.protocols.ligand_docking.get_ligand_travel_ensemble_best(test_pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, test_residue_id: int, ref_residue_ids: pyrosetta.rosetta.utility.vector1_unsigned_long) → float

Another interesting metric – how far does the ligand centroid move?

Returns the smallest distance from any of the residues in the reference structure.

C++: protocols::ligand_docking::get_ligand_travel_ensemble_best(const class core::pose::Pose &, const class core::pose::Pose &, unsigned long, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> double

pyrosetta.rosetta.protocols.ligand_docking.get_multi_residue_ligand_RMSDs(*args, **kwargs)

Overloaded function.

1. get_multi_residue_ligand_RMSDs(test_pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, test_residue_ids: pyrosetta.rosetta.utility.vector1_unsigned_long, ref_residue_ids: pyrosetta.rosetta.utility.vector1_unsigned_long) -> pyrosetta.rosetta.std.map_std_string_double

2. get_multi_residue_ligand_RMSDs(test_pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, test_residue_ids: pyrosetta.rosetta.utility.vector1_unsigned_long, ref_residue_ids: pyrosetta.rosetta.utility.vector1_unsigned_long, chain: str) -> pyrosetta.rosetta.std.map_std_string_double

3. get_multi_residue_ligand_RMSDs(test_pose: pyrosetta.rosetta.core.pose.Pose, ref_pose: pyrosetta.rosetta.core.pose.Pose, test_residue_ids: pyrosetta.rosetta.utility.vector1_unsigned_long, ref_residue_ids: pyrosetta.rosetta.utility.vector1_unsigned_long, chain: str, prefix: str) -> pyrosetta.rosetta.std.map_std_string_double

C++: protocols::ligand_docking::get_multi_residue_ligand_RMSDs(const class core::pose::Pose &, const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, char, const std::string &) –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

pyrosetta.rosetta.protocols.ligand_docking.get_radius_of_gyration(chain: str, test_pose: pyrosetta.rosetta.core.pose.Pose, prefix: str) → pyrosetta.rosetta.std.map_std_string_double

Calculate radius of gyration for downstream non-H atoms

Ligands tend to bind in outstretched conformations…

C++: protocols::ligand_docking::get_radius_of_gyration(char, const class core::pose::Pose &, const std::string &) –> class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > >

pyrosetta.rosetta.protocols.ligand_docking.get_rb_atr_and_rep_scores(grid: pyrosetta.rosetta.core.grid.CartGrid_int_t, pose: pyrosetta.rosetta.core.pose.Pose, begin: int, end: int) → Tuple[int, int]

a cleaner implementation of rb_grid_score_atr_rep

C++: protocols::ligand_docking::get_rb_atr_and_rep_scores(const class core::grid::CartGrid<int> &, const class core::pose::Pose &, unsigned long, unsigned long) –> struct std::pair<int, int>

pyrosetta.rosetta.protocols.ligand_docking.grid_rotamer_trials(*args, **kwargs)

Overloaded function.

1. grid_rotamer_trials(grid: pyrosetta.rosetta.core.grid.CartGrid_int_t, pose: pyrosetta.rosetta.core.pose.Pose, rsd_no: int, packertask: pyrosetta.rosetta.core.pack.task.PackerTask) -> None

2. grid_rotamer_trials(grid: pyrosetta.rosetta.core.grid.CartGrid_int_t, pose: pyrosetta.rosetta.core.pose.Pose, rsd_no: int, packertask: pyrosetta.rosetta.core.pack.task.PackerTask, min_score: int) -> None

Try all rotamers for the specified residue and install the first one

that minimizes the grid score. Only tested with ligand residues w/ a conformer library.

C++: protocols::ligand_docking::grid_rotamer_trials(const class core::grid::CartGrid<int> &, class core::pose::Pose &, unsigned long, const class core::pack::task::PackerTask &, const int) –> void

pyrosetta.rosetta.protocols.ligand_docking.grid_rotamer_trials_atr_rep(grid: pyrosetta.rosetta.core.grid.CartGrid_int_t, pose: pyrosetta.rosetta.core.pose.Pose, rsd_no: int, packertask: pyrosetta.rosetta.core.pack.task.PackerTask) → None

Try all rotamers for the specified residue and install the first one

that minimizes the repulsive score, breaking ties by the attractive score. Only tested with ligand residues w/ a conformer library.

C++: protocols::ligand_docking::grid_rotamer_trials_atr_rep(const class core::grid::CartGrid<int> &, class core::pose::Pose &, unsigned long, const class core::pack::task::PackerTask &) –> void

pyrosetta.rosetta.protocols.ligand_docking.grid_score(*args, **kwargs)

Overloaded function.

1. grid_score(grid: pyrosetta.rosetta.core.grid.CartGrid_int_t, rsd: pyrosetta.rosetta.core.conformation.Residue) -> int

2. grid_score(grid: pyrosetta.rosetta.core.grid.CartGrid_int_t, rsd: pyrosetta.rosetta.core.conformation.Residue, max_score: int) -> int

Sum the grid values for all heavy atoms in the residue

C++: protocols::ligand_docking::grid_score(const class core::grid::CartGrid<int> &, const class core::conformation::Residue &, int) –> int

pyrosetta.rosetta.protocols.ligand_docking.grid_score_atr_rep(*args, **kwargs)

Overloaded function.

1. grid_score_atr_rep(grid: pyrosetta.rosetta.core.grid.CartGrid_int_t, rsd: pyrosetta.rosetta.core.conformation.Residue, atr_out: int, rep_out: int) -> None

2. grid_score_atr_rep(grid: pyrosetta.rosetta.core.grid.CartGrid_int_t, rsd: pyrosetta.rosetta.core.conformation.Residue, atr_out: int, rep_out: int, max_rep: int) -> None

Sum the grid values for all heavy atoms in the residue

C++: protocols::ligand_docking::grid_score_atr_rep(const class core::grid::CartGrid<int> &, const class core::conformation::Residue &, int &, int &, int) –> void

pyrosetta.rosetta.protocols.ligand_docking.grow(: pyrosetta.rosetta.core.pose.Pose, start: int, end: int) → bool

C++: protocols::ligand_docking::grow(class core::pose::Pose, unsigned long, unsigned long) –> bool

pyrosetta.rosetta.protocols.ligand_docking.has_incomplete_connections(pose: pyrosetta.rosetta.core.pose.Pose, start: int, end: int) → bool

C++: protocols::ligand_docking::has_incomplete_connections(class core::pose::Pose, unsigned long, const unsigned long) –> bool

pyrosetta.rosetta.protocols.ligand_docking.info_to_rank(vector: pyrosetta.rosetta.utility.vector1_protocols_ligand_docking_ProtLigPair_info) → None

C++: protocols::ligand_docking::info_to_rank(class utility::vector1<struct protocols::ligand_docking::ProtLigPair_info, class std::allocator<struct protocols::ligand_docking::ProtLigPair_info> > &) –> void

pyrosetta.rosetta.protocols.ligand_docking.make_atr_rep_grid(pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t) → pyrosetta.rosetta.core.grid.CartGrid_int_t

Make a grid around the specified point with attractive (negative)

and repulsive (positive) values for the protein backbone.

C++: protocols::ligand_docking::make_atr_rep_grid(const class core::pose::Pose &, const class numeric::xyzVector<double> &) –> class std::shared_ptr<class core::grid::CartGrid<int> >

pyrosetta.rosetta.protocols.ligand_docking.make_atr_rep_grid_without_ligand(pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_id_to_exclude: int) → pyrosetta.rosetta.core.grid.CartGrid_int_t

Make a grid around the specified point with attractive (negative)

and repulsive (positive) values for all heavy atoms not in ligand_chain_id_to_exclude

C++: protocols::ligand_docking::make_atr_rep_grid_without_ligand(const class core::pose::Pose &, const class numeric::xyzVector<double> &, const unsigned long &) –> class std::shared_ptr<class core::grid::CartGrid<int> >

pyrosetta.rosetta.protocols.ligand_docking.make_atr_rep_grid_without_ligands(pose: pyrosetta.rosetta.core.pose.Pose, center: pyrosetta.rosetta.numeric.xyzVector_double_t, ligand_chain_ids_to_exclude: pyrosetta.rosetta.utility.vector1_unsigned_long) → pyrosetta.rosetta.core.grid.CartGrid_int_t

Make a grid around the specified point with attractive (negative)

and repulsive (positive) values for all heavy atoms not in ligand_chain_ids_to_exclude

C++: protocols::ligand_docking::make_atr_rep_grid_without_ligands(const class core::pose::Pose &, const class numeric::xyzVector<double> &, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> class std::shared_ptr<class core::grid::CartGrid<int> >

pyrosetta.rosetta.protocols.ligand_docking.move_ligand_neighbor_to_desired_position(*args, **kwargs)

Overloaded function.

1. move_ligand_neighbor_to_desired_position(chains: pyrosetta.rosetta.utility.vector1_std_string, desired_position: pyrosetta.rosetta.numeric.xyzVector_double_t, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Move the neighbor atom of the specified multiple chains to the desired_position

C++: protocols::ligand_docking::move_ligand_neighbor_to_desired_position(const class utility::vector1<std::string, class std::allocator<std::string > > &, const class numeric::xyzVector<double> &, class core::pose::Pose &) –> void

2. move_ligand_neighbor_to_desired_position(chain: str, desired_position: pyrosetta.rosetta.numeric.xyzVector_double_t, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Move the neighbor atom of the specified chain to the desired_position

C++: protocols::ligand_docking::move_ligand_neighbor_to_desired_position(const std::string &, const class numeric::xyzVector<double> &, class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.ligand_docking.move_ligand_to_desired_centroid(*args, **kwargs)

Overloaded function.

1. move_ligand_to_desired_centroid(chain: str, desired_centroid: pyrosetta.rosetta.numeric.xyzVector_double_t, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Move the center of specified chain to the desired_centroid

C++: protocols::ligand_docking::move_ligand_to_desired_centroid(const std::string &, const class numeric::xyzVector<double> &, class core::pose::Pose &) –> void

2. move_ligand_to_desired_centroid(chains: pyrosetta.rosetta.utility.vector1_std_string, desired_centroid: pyrosetta.rosetta.numeric.xyzVector_double_t, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Move the center of specified multiple chains to the desired_centroid

C++: protocols::ligand_docking::move_ligand_to_desired_centroid(const class utility::vector1<std::string, class std::allocator<std::string > > &, const class numeric::xyzVector<double> &, class core::pose::Pose &) –> void

3. move_ligand_to_desired_centroid(jump_id: int, desired_centroid: pyrosetta.rosetta.numeric.xyzVector_double_t, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Move the center of the object(s) downstream of jump_id to the desired_centroid

C++: protocols::ligand_docking::move_ligand_to_desired_centroid(const unsigned long, const class numeric::xyzVector<double> &, class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.ligand_docking.output_interface_deltas(*args, **kwargs)

Overloaded function.

1. output_interface_deltas(score_map: pyrosetta.rosetta.std.map_std_string_double, chain: str, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, together_energies: pyrosetta.rosetta.core.scoring.EMapVector, separated_energies: pyrosetta.rosetta.core.scoring.EMapVector, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> None

2. output_interface_deltas(score_map: pyrosetta.rosetta.std.map_std_string_double, chain: str, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, together_energies: pyrosetta.rosetta.core.scoring.EMapVector, separated_energies: pyrosetta.rosetta.core.scoring.EMapVector, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, prefix: str) -> None

3. output_interface_deltas(score_map: pyrosetta.rosetta.std.map_std_string_double, chain: str, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, together_energies: pyrosetta.rosetta.core.scoring.EMapVector, separated_energies: pyrosetta.rosetta.core.scoring.EMapVector, residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, prefix: str, normalization_function: protocols::qsar::scoring_grid::ScoreNormalization) -> None

C++: protocols::ligand_docking::output_interface_deltas(class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > &, char, const class std::shared_ptr<class core::scoring::ScoreFunction>, const class core::scoring::EMapVector &, const class core::scoring::EMapVector &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const std::string &, class std::shared_ptr<class protocols::qsar::scoring_grid::ScoreNormalization>) –> void

pyrosetta.rosetta.protocols.ligand_docking.passes_filters(pose: pyrosetta.rosetta.core.pose.Pose, start: int, end: int) → bool

C++: protocols::ligand_docking::passes_filters(const class core::pose::Pose &, unsigned long, const unsigned long) –> bool

pyrosetta.rosetta.protocols.ligand_docking.process_line(line: str) → pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info

C++: protocols::ligand_docking::process_line(std::string &) –> struct protocols::ligand_docking::ProtLigPair_info

pyrosetta.rosetta.protocols.ligand_docking.random_connection(residue: pyrosetta.rosetta.core.conformation.Residue) → int

C++: protocols::ligand_docking::random_connection(class std::shared_ptr<const class core::conformation::Residue>) –> unsigned long

pyrosetta.rosetta.protocols.ligand_docking.rb_grid_rotamer_trials_atr_rep(grid: pyrosetta.rosetta.core.grid.CartGrid_int_t, pose: pyrosetta.rosetta.core.pose.Pose, begin: int, end: int, packertask: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: protocols::ligand_docking::rb_grid_rotamer_trials_atr_rep(const class core::grid::CartGrid<int> &, class core::pose::Pose &, unsigned long, unsigned long, const class core::pack::task::PackerTask &) –> void

pyrosetta.rosetta.protocols.ligand_docking.rb_grid_score_atr_rep(*args, **kwargs)

Overloaded function.

1. rb_grid_score_atr_rep(grid: pyrosetta.rosetta.core.grid.CartGrid_int_t, pose: pyrosetta.rosetta.core.pose.Pose, begin: int, end: int, atr_out: int, rep_out: int) -> None

2. rb_grid_score_atr_rep(grid: pyrosetta.rosetta.core.grid.CartGrid_int_t, pose: pyrosetta.rosetta.core.pose.Pose, begin: int, end: int, atr_out: int, rep_out: int, max_rep: int) -> None

Sum the grid values for all heavy atoms in the residue

C++: protocols::ligand_docking::rb_grid_score_atr_rep(const class core::grid::CartGrid<int> &, const class core::pose::Pose &, unsigned long, const unsigned long, int &, int &, int) –> void

pyrosetta.rosetta.protocols.ligand_docking.reorder_with_first_non_mobile_as_root(f: pyrosetta.rosetta.core.kinematics.FoldTree, interface: protocols::ligand_docking::ligand_options::Interface, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::reorder_with_first_non_mobile_as_root(class std::shared_ptr<class core::kinematics::FoldTree>, const class protocols::ligand_docking::ligand_options::Interface &, class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.ligand_docking.restrain_ligand_nbr_atom(lig_id: int, stddev_Angstroms: float, pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.scoring.constraints.Constraint

C++: protocols::ligand_docking::restrain_ligand_nbr_atom(const unsigned long, const double, class core::pose::Pose &) –> class std::shared_ptr<const class core::scoring::constraints::Constraint>

pyrosetta.rosetta.protocols.ligand_docking.restrict_to_protein_residues(interface: protocols::ligand_docking::ligand_options::Interface, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: protocols::ligand_docking::restrict_to_protein_residues(class protocols::ligand_docking::ligand_options::Interface &, const class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.ligand_docking.rotamers_for_trials(pose: pyrosetta.rosetta.core.pose.Pose, rsd_no: int, conformers_out: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, packertask: pyrosetta.rosetta.core.pack.task.PackerTask) → None

Internal helper function for rotamer trials; fills conformers_out.

C++: protocols::ligand_docking::rotamers_for_trials(class core::pose::Pose &, unsigned long, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, const class core::pack::task::PackerTask &) –> void

pyrosetta.rosetta.protocols.ligand_docking.select_best_poses(*args, **kwargs)

Overloaded function.

1. select_best_poses(atdiff: pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff, tags_out: pyrosetta.rosetta.std.set_std_string_t) -> None

Convenience wrapper: selects the best ligand docking results

from a silent file and appends their tags to the supplied set.

C++: protocols::ligand_docking::select_best_poses(const class core::import_pose::atom_tree_diffs::AtomTreeDiff &, class std::set<std::string, struct std::less<std::string >, class std::allocator<std::string > > &) –> void

2. select_best_poses(atdiff: pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff, scores_out: pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t) -> None

3. select_best_poses(atdiff: pyrosetta.rosetta.core.import_pose.atom_tree_diffs.AtomTreeDiff, scores_out: pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t, to_keep: float) -> None

Selects the best ligand docking results from a silent file

and appends their scores to the supplied list.

C++: protocols::ligand_docking::select_best_poses(const class core::import_pose::atom_tree_diffs::AtomTreeDiff &, class utility::vector1<struct std::pair<std::string, class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > >, class std::allocator<struct std::pair<std::string, class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > > > > &, double) –> void

4. select_best_poses(scores_in: pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t, scores_out: pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t) -> None

5. select_best_poses(scores_in: pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t, scores_out: pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_map_std_string_double_std_less_std_string_std_allocator_std_pair_const_std_string_double_t, to_keep: float) -> None

Trims scores_in based on ligand_is_touching (if present) and

then by total_score.

C++: protocols::ligand_docking::select_best_poses(const class utility::vector1<struct std::pair<std::string, class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > >, class std::allocator<struct std::pair<std::string, class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > > > > &, class utility::vector1<struct std::pair<std::string, class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > >, class std::allocator<struct std::pair<std::string, class std::map<std::string, double, struct std::less<std::string >, class std::allocator<struct std::pair<const std::string, double> > > > > > &, double) –> void

pyrosetta.rosetta.protocols.ligand_docking.sort_by_binding(left_lig: pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info, right_lig: pyrosetta.rosetta.protocols.ligand_docking.ProtLigPair_info) → bool

C++: protocols::ligand_docking::sort_by_binding(const struct protocols::ligand_docking::ProtLigPair_info &, const struct protocols::ligand_docking::ProtLigPair_info &) –> bool

pyrosetta.rosetta.protocols.ligand_docking.sort_by_second(left_lig: Tuple[int, float], right_lig: Tuple[int, float]) → bool

C++: protocols::ligand_docking::sort_by_second(struct std::pair<unsigned long, double>, struct std::pair<unsigned long, double>) –> bool

pyrosetta.rosetta.protocols.ligand_docking.spearman(vector_exp: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_double_t, vector_rosetta: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_double_t) → float

C++: protocols::ligand_docking::spearman(class utility::vector1<struct std::pair<unsigned long, double>, class std::allocator<struct std::pair<unsigned long, double> > >, class utility::vector1<struct std::pair<unsigned long, double>, class std::allocator<struct std::pair<unsigned long, double> > >) –> double

pyrosetta.rosetta.protocols.ligand_docking.torsion_constraints_from_chi_rotamers(rsd_no: int, chino: int, rsdtype: pyrosetta.rosetta.core.chemical.ResidueType) → pyrosetta.rosetta.core.scoring.constraints.Constraint

Produce an ambiguous dihedral restraint for the specified chi angle,

assuming that ResidueType.chi_rotamers() lists (all) energetic minima.

C++: protocols::ligand_docking::torsion_constraints_from_chi_rotamers(unsigned long, unsigned long, const class core::chemical::ResidueType &) –> class std::shared_ptr<class core::scoring::constraints::Constraint>

pyrosetta.rosetta.protocols.ligand_docking.torsion_constraints_from_rotamers(rsd_no: int, chino: int, rsds: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, stddev_degrees: float) → pyrosetta.rosetta.core.scoring.constraints.Constraint

Produce an ambiguous dihedral restraint for the specified chi angle,

assuming that the provided conformations represent (all) energetic minima.

C++: protocols::ligand_docking::torsion_constraints_from_rotamers(unsigned long, unsigned long, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, double) –> class std::shared_ptr<class core::scoring::constraints::Constraint>

pyrosetta.rosetta.protocols.ligand_docking.vector_to_rank(vector: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_double_t) → None

C++: protocols::ligand_docking::vector_to_rank(class utility::vector1<struct std::pair<unsigned long, double>, class std::allocator<struct std::pair<unsigned long, double> > > &) –> void