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 clas