ligand_docking¶
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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.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
- 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
- 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
- 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
- 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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.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
- 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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.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
- 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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.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
- 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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.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
- 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
- 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
- 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
- class pyrosetta.rosetta.protocols.ligand_docking.HighResDocker¶
Bases:
Mover
- apply(*args, **kwargs)¶
Overloaded function.
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
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
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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.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
- 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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.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
- 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
- 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
- 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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.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
- 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
- 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.
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
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
C++: protocols::ligand_docking::LigandBaseProtocol::shared_from_this() –> class std::shared_ptr<class protocols::ligand_docking::LigandBaseProtocol>
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.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
- 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.
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
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.
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
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
C++: protocols::ligand_docking::LigandDockProtocol::shared_from_this() –> class std::shared_ptr<class protocols::ligand_docking::LigandDockProtocol>
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.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
- 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.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.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
- 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