enzdes¶
Bindings for protocols::enzdes namespace
- class pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamers¶
Bases:
TaskOperation
- apply(self: pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamers, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) None ¶
- Change a packer task in some way. The input pose is the one to which the input
task will be later applied.
C++: protocols::enzdes::AddLigandMotifRotamers::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void
- assign(self: pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamers, : pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamers) pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamers ¶
C++: protocols::enzdes::AddLigandMotifRotamers::operator=(const class protocols::enzdes::AddLigandMotifRotamers &) –> class protocols::enzdes::AddLigandMotifRotamers &
- clone(self: pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamers) pyrosetta.rosetta.core.pack.task.operation.TaskOperation ¶
C++: protocols::enzdes::AddLigandMotifRotamers::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>
- static keyname() str ¶
C++: protocols::enzdes::AddLigandMotifRotamers::keyname() –> std::string
- parse_tag(self: pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamers, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::enzdes::AddLigandMotifRotamers::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by task operations wishing to provide citation information.
C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- class pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamersOperationCreator¶
Bases:
TaskOperationCreator
- assign(self: pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamersOperationCreator, : pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamersOperationCreator) pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamersOperationCreator ¶
C++: protocols::enzdes::AddLigandMotifRotamersOperationCreator::operator=(const class protocols::enzdes::AddLigandMotifRotamersOperationCreator &) –> class protocols::enzdes::AddLigandMotifRotamersOperationCreator &
- create_task_operation(self: pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamersOperationCreator) pyrosetta.rosetta.core.pack.task.operation.TaskOperation ¶
C++: protocols::enzdes::AddLigandMotifRotamersOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>
- keyname(self: pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamersOperationCreator) str ¶
C++: protocols::enzdes::AddLigandMotifRotamersOperationCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.enzdes.AddLigandMotifRotamersOperationCreator, xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::enzdes::AddLigandMotifRotamersOperationCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) bool ¶
Indicate whether we skip adding citation information to the XML schema.
False for any real task operation. True only for dummy task operations created for unit tests.
C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool
- class pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts¶
Bases:
Mover
A simple wrapper to get the functionality in EnzConstraintIO into mover format
- apply(self: pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::enzdes::AddOrRemoveMatchCsts::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts, : pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts) pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts ¶
C++: protocols::enzdes::AddOrRemoveMatchCsts::operator=(const class protocols::enzdes::AddOrRemoveMatchCsts &) –> class protocols::enzdes::AddOrRemoveMatchCsts &
- 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.enzdes.AddOrRemoveMatchCsts) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::enzdes::AddOrRemoveMatchCsts::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>
- cstfile(self: pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts, setting: str) None ¶
C++: protocols::enzdes::AddOrRemoveMatchCsts::cstfile(const std::string &) –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::enzdes::AddOrRemoveMatchCsts::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>
- static get_const_EnzConstraintIO_for_cstfile(*args, **kwargs)¶
Overloaded function.
get_const_EnzConstraintIO_for_cstfile() -> protocols::toolbox::match_enzdes_util::EnzConstraintIO
get_const_EnzConstraintIO_for_cstfile(cstfile: str) -> protocols::toolbox::match_enzdes_util::EnzConstraintIO
C++: protocols::enzdes::AddOrRemoveMatchCsts::get_const_EnzConstraintIO_for_cstfile(std::string) –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintIO>
- 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.enzdes.AddOrRemoveMatchCsts) str ¶
C++: protocols::enzdes::AddOrRemoveMatchCsts::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::enzdes::AddOrRemoveMatchCsts::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::enzdes::AddOrRemoveMatchCsts::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::enzdes::AddOrRemoveMatchCsts::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_accept_blocks_missing_header(self: pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts, setting: bool) None ¶
C++: protocols::enzdes::AddOrRemoveMatchCsts::set_accept_blocks_missing_header(bool) –> void
- set_cst_action(self: pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts, action: pyrosetta.rosetta.protocols.enzdes.CstAction) None ¶
C++: protocols::enzdes::AddOrRemoveMatchCsts::set_cst_action(enum protocols::enzdes::CstAction) –> 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_keep_covalent(self: pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCsts, setting: bool) None ¶
C++: protocols::enzdes::AddOrRemoveMatchCsts::set_keep_covalent(bool) –> 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.enzdes.AddOrRemoveMatchCstsCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCstsCreator, : pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCstsCreator) pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCstsCreator ¶
C++: protocols::enzdes::AddOrRemoveMatchCstsCreator::operator=(const class protocols::enzdes::AddOrRemoveMatchCstsCreator &) –> class protocols::enzdes::AddOrRemoveMatchCstsCreator &
- create_mover(self: pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCstsCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::enzdes::AddOrRemoveMatchCstsCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.enzdes.AddOrRemoveMatchCstsCreator) str ¶
C++: protocols::enzdes::AddOrRemoveMatchCstsCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfs¶
Bases:
TaskOperation
- apply(self: pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfs, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask) None ¶
- Change a packer task in some way. The input pose is the one to which the input
task will be later applied.
C++: protocols::enzdes::AddRigidBodyLigandConfs::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void
- assign(self: pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfs, : pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfs) pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfs ¶
C++: protocols::enzdes::AddRigidBodyLigandConfs::operator=(const class protocols::enzdes::AddRigidBodyLigandConfs &) –> class protocols::enzdes::AddRigidBodyLigandConfs &
- clone(self: pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfs) pyrosetta.rosetta.core.pack.task.operation.TaskOperation ¶
C++: protocols::enzdes::AddRigidBodyLigandConfs::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>
- static keyname() str ¶
C++: protocols::enzdes::AddRigidBodyLigandConfs::keyname() –> std::string
- parse_tag(self: pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfs, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::enzdes::AddRigidBodyLigandConfs::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by task operations wishing to provide citation information.
C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- class pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfsCreator¶
Bases:
TaskOperationCreator
- assign(self: pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfsCreator, : pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfsCreator) pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfsCreator ¶
C++: protocols::enzdes::AddRigidBodyLigandConfsCreator::operator=(const class protocols::enzdes::AddRigidBodyLigandConfsCreator &) –> class protocols::enzdes::AddRigidBodyLigandConfsCreator &
- create_task_operation(self: pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfsCreator) pyrosetta.rosetta.core.pack.task.operation.TaskOperation ¶
C++: protocols::enzdes::AddRigidBodyLigandConfsCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>
- keyname(self: pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfsCreator) str ¶
C++: protocols::enzdes::AddRigidBodyLigandConfsCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.enzdes.AddRigidBodyLigandConfsCreator, xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::enzdes::AddRigidBodyLigandConfsCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) bool ¶
Indicate whether we skip adding citation information to the XML schema.
False for any real task operation. True only for dummy task operations created for unit tests.
C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool
- class pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf¶
Bases:
ModifyStoredRBConfs
for every ligand that has additional stored rb conformations in the enzdes cacheable observer, the one currently in the pose gets exchanged with a random stored one
- apply(self: pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::enzdes::ApplyRandomStoredRBConf::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf, : pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf) pyrosetta.rosetta.protocols.enzdes.ApplyRandomStoredRBConf ¶
C++: protocols::enzdes::ApplyRandomStoredRBConf::operator=(const class protocols::enzdes::ApplyRandomStoredRBConf &) –> class protocols::enzdes::ApplyRandomStoredRBConf &
- 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>
- closest_orient_atoms_msd(self: pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs, pose: pyrosetta.rosetta.core.pose.Pose, confs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) pyrosetta.rosetta.utility.vector1_double ¶
- calculates the closest orient atom (i.e. atoms used in rotamer placement
msd between every conf and the confs coming before it in the pose or in the vector
C++: protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(const class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &) const –> class utility::vector1<double, class std::allocator<double> >
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- 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.enzdes.ApplyRandomStoredRBConf) str ¶
C++: protocols::enzdes::ApplyRandomStoredRBConf::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
- swap_coordinates_in_pose(self: pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs, pose: pyrosetta.rosetta.core.pose.Pose, rescoords: pyrosetta.rosetta.core.conformation.Residue) None ¶
- helper function to exchange coordinates in a pose
this function doesn’t actually exchange the residues, but sets all the coords of pose.residue( rescoords.seqpos() ) to what is in rescoords and vice versa
C++: protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(class core::pose::Pose &, class core::conformation::Residue &) 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.enzdes.BackboneSampler¶
Bases:
LigandBaseProtocol
- apply(self: pyrosetta.rosetta.protocols.enzdes.BackboneSampler, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::enzdes::BackboneSampler::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.enzdes.BackboneSampler, : pyrosetta.rosetta.protocols.enzdes.BackboneSampler) pyrosetta.rosetta.protocols.enzdes.BackboneSampler ¶
C++: protocols::enzdes::BackboneSampler::operator=(const class protocols::enzdes::BackboneSampler &) –> class protocols::enzdes::BackboneSampler &
- 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.enzdes.BackboneSampler) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::enzdes::BackboneSampler::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.enzdes.BackboneSampler) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::enzdes::BackboneSampler::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.enzdes.BackboneSampler) str ¶
C++: protocols::enzdes::BackboneSampler::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 mover_name() str ¶
C++: protocols::enzdes::BackboneSampler::mover_name() –> std::string
- 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 provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::enzdes::BackboneSampler::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
- 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.enzdes.BackboneSamplerCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.enzdes.BackboneSamplerCreator, : pyrosetta.rosetta.protocols.enzdes.BackboneSamplerCreator) pyrosetta.rosetta.protocols.enzdes.BackboneSamplerCreator ¶
C++: protocols::enzdes::BackboneSamplerCreator::operator=(const class protocols::enzdes::BackboneSamplerCreator &) –> class protocols::enzdes::BackboneSamplerCreator &
- create_mover(self: pyrosetta.rosetta.protocols.enzdes.BackboneSamplerCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::enzdes::BackboneSamplerCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.enzdes.BackboneSamplerCreator) str ¶
C++: protocols::enzdes::BackboneSamplerCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.enzdes.CstAction¶
Bases:
pybind11_object
Members:
_VOID
ADD_NEW
ADD_PREGENERATED
REMOVE
- ADD_NEW = <CstAction.ADD_NEW: 2>¶
- ADD_PREGENERATED = <CstAction.ADD_PREGENERATED: 3>¶
- REMOVE = <CstAction.REMOVE: 4>¶
- _VOID = <CstAction._VOID: 1>¶
- property name¶
- property value¶
- class pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison¶
Bases:
pybind11_object
class that holds a bunch of native poses and compares them
against a given input pose on request
- assign(self: pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison, : pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison) pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison ¶
C++: protocols::enzdes::DesignVsNativeComparison::operator=(const class protocols::enzdes::DesignVsNativeComparison &) –> class protocols::enzdes::DesignVsNativeComparison &
- compare_to_native(self: pyrosetta.rosetta.protocols.enzdes.DesignVsNativeComparison, pose: pyrosetta.rosetta.core.pose.Pose, calculators: pyrosetta.rosetta.utility.vector1_std_pair_std_string_std_string_t, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, silent_Es: pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy) None ¶
C++: protocols::enzdes::DesignVsNativeComparison::compare_to_native(const class core::pose::Pose &, const class utility::vector1<struct std::pair<std::string, std::string >, class std::allocator<struct std::pair<std::string, std::string > > > &, class std::shared_ptr<const class core::scoring::ScoreFunction>, class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> > &) –> void
- class pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface¶
Bases:
TaskOperation
Given a set of cut1/cut2/cut3/cut4 distance specifications, alter a packing task to set residues within alpha carbons within cut1 of a ligand (or within cut2 with beta carbons facing inwards) to redesign, and within cut3 (or cut4 facing inwards) to repack, and all others to fixed. If a resfile is provided, only do the detection for those residues set to AUTO in the resfile.
- static add_observer_cache_segments_to_set(pose: pyrosetta.rosetta.core.pose.Pose, set: pyrosetta.rosetta.std.set_unsigned_long_t) None ¶
C++: protocols::enzdes::DetectProteinLigandInterface::add_observer_cache_segments_to_set(const class core::pose::Pose &, class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) –> void
- apply(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) None ¶
- Change a packer task in some way. The input pose is the one to which the input
task will be later applied.
C++: protocols::enzdes::DetectProteinLigandInterface::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void
- assign(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface, : pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface) pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface ¶
C++: protocols::enzdes::DetectProteinLigandInterface::operator=(const class protocols::enzdes::DetectProteinLigandInterface &) –> class protocols::enzdes::DetectProteinLigandInterface &
- clone(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface) pyrosetta.rosetta.core.pack.task.operation.TaskOperation ¶
C++: protocols::enzdes::DetectProteinLigandInterface::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>
- find_design_interface(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface, pose: pyrosetta.rosetta.core.pose.Pose, interface_target_res: pyrosetta.rosetta.std.set_unsigned_long_t, cut1: float, cut2: float, cut3: float, cut4: float, repack_res: pyrosetta.rosetta.utility.vector1_bool, design_res: pyrosetta.rosetta.utility.vector1_bool) None ¶
C++: protocols::enzdes::DetectProteinLigandInterface::find_design_interface(const class core::pose::Pose &, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, double, double, double, double, class utility::vector1<bool, class std::allocator<bool> > &, class utility::vector1<bool, class std::allocator<bool> > &) const –> void
- find_design_interface_arg_sweep(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface, pose: pyrosetta.rosetta.core.pose.Pose, interface_target_res: pyrosetta.rosetta.std.set_unsigned_long_t, cut1: float, cut2: float, cut3: float, cut4: float, arg_sweep_cutoff: float, repack_res: pyrosetta.rosetta.utility.vector1_bool, design_res: pyrosetta.rosetta.utility.vector1_bool) None ¶
C++: protocols::enzdes::DetectProteinLigandInterface::find_design_interface_arg_sweep(const class core::pose::Pose &, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, double, double, double, double, double, class utility::vector1<bool, class std::allocator<bool> > &, class utility::vector1<bool, class std::allocator<bool> > &) const –> void
- get_design(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface) bool ¶
C++: protocols::enzdes::DetectProteinLigandInterface::get_design() const –> bool
- get_detect_interface(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface) bool ¶
C++: protocols::enzdes::DetectProteinLigandInterface::get_detect_interface() const –> bool
- get_no_design_cys(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface) bool ¶
C++: protocols::enzdes::DetectProteinLigandInterface::get_no_design_cys() const –> bool
- init_from_options(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface) None ¶
Initialize the class based on the command line options.
C++: protocols::enzdes::DetectProteinLigandInterface::init_from_options() –> void
- static keyname() str ¶
C++: protocols::enzdes::DetectProteinLigandInterface::keyname() –> std::string
- parse_tag(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::enzdes::DetectProteinLigandInterface::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by task operations wishing to provide citation information.
C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::enzdes::DetectProteinLigandInterface::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
C++: protocols::enzdes::DetectProteinLigandInterface::register_options() –> void
- set_design(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface, design_in: bool) None ¶
C++: protocols::enzdes::DetectProteinLigandInterface::set_design(const bool) –> void
- set_design_target_res(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface, target_res: pyrosetta.rosetta.std.set_unsigned_long_t) None ¶
C++: protocols::enzdes::DetectProteinLigandInterface::set_design_target_res(const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &) –> void
- set_detect_interface(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface, setting: bool) None ¶
C++: protocols::enzdes::DetectProteinLigandInterface::set_detect_interface(bool) –> void
- set_no_design_cys(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterface, no_design_cys_in: bool) None ¶
C++: protocols::enzdes::DetectProteinLigandInterface::set_no_design_cys(const bool) –> void
- class pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterfaceOperationCreator¶
Bases:
TaskOperationCreator
- assign(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterfaceOperationCreator, : pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterfaceOperationCreator) pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterfaceOperationCreator ¶
C++: protocols::enzdes::DetectProteinLigandInterfaceOperationCreator::operator=(const class protocols::enzdes::DetectProteinLigandInterfaceOperationCreator &) –> class protocols::enzdes::DetectProteinLigandInterfaceOperationCreator &
- create_task_operation(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterfaceOperationCreator) pyrosetta.rosetta.core.pack.task.operation.TaskOperation ¶
C++: protocols::enzdes::DetectProteinLigandInterfaceOperationCreator::create_task_operation() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>
- keyname(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterfaceOperationCreator) str ¶
C++: protocols::enzdes::DetectProteinLigandInterfaceOperationCreator::keyname() const –> std::string
- provide_xml_schema(self: pyrosetta.rosetta.protocols.enzdes.DetectProteinLigandInterfaceOperationCreator, xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::enzdes::DetectProteinLigandInterfaceOperationCreator::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) const –> void
- skip_citation_info_in_schema(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperationCreator) bool ¶
Indicate whether we skip adding citation information to the XML schema.
False for any real task operation. True only for dummy task operations created for unit tests.
C++: core::pack::task::operation::TaskOperationCreator::skip_citation_info_in_schema() const –> bool
- class pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter¶
Bases:
Filter
- apply(self: pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::enzdes::DiffAtomSasaFilter::apply(const class core::pose::Pose &) const –> bool
- static class_name() str ¶
C++: protocols::enzdes::DiffAtomSasaFilter::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.enzdes.DiffAtomSasaFilter) pyrosetta.rosetta.protocols.filters.Filter ¶
C++: protocols::enzdes::DiffAtomSasaFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>
- compute(self: pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::enzdes::DiffAtomSasaFilter::compute(const class core::pose::Pose &) const –> bool
- fresh_instance(self: pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter) pyrosetta.rosetta.protocols.filters.Filter ¶
C++: protocols::enzdes::DiffAtomSasaFilter::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.enzdes.DiffAtomSasaFilter) str ¶
C++: protocols::enzdes::DiffAtomSasaFilter::name() const –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::enzdes::DiffAtomSasaFilter::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::enzdes::DiffAtomSasaFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report(self: pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::enzdes::DiffAtomSasaFilter::report(std::ostream &, const class core::pose::Pose &) const –> void
- report_sm(self: pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilter, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::enzdes::DiffAtomSasaFilter::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.enzdes.DiffAtomSasaFilterCreator¶
Bases:
FilterCreator
- assign(self: pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilterCreator, : pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilterCreator) pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilterCreator ¶
C++: protocols::enzdes::DiffAtomSasaFilterCreator::operator=(const class protocols::enzdes::DiffAtomSasaFilterCreator &) –> class protocols::enzdes::DiffAtomSasaFilterCreator &
- create_filter(self: pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilterCreator) pyrosetta.rosetta.protocols.filters.Filter ¶
C++: protocols::enzdes::DiffAtomSasaFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>
- keyname(self: pyrosetta.rosetta.protocols.enzdes.DiffAtomSasaFilterCreator) str ¶
C++: protocols::enzdes::DiffAtomSasaFilterCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs¶
Bases:
ModifyStoredRBConfs
uses a docking mover to diversiy the stored confs until they’re all min_rms_ away from each other note: no scorefunction used here
- apply(self: pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::enzdes::DiversifyStoredRBConfs::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs, : pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs) pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs ¶
C++: protocols::enzdes::DiversifyStoredRBConfs::operator=(const class protocols::enzdes::DiversifyStoredRBConfs &) –> class protocols::enzdes::DiversifyStoredRBConfs &
- 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>
- closest_orient_atoms_msd(self: pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs, pose: pyrosetta.rosetta.core.pose.Pose, confs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) pyrosetta.rosetta.utility.vector1_double ¶
- calculates the closest orient atom (i.e. atoms used in rotamer placement
msd between every conf and the confs coming before it in the pose or in the vector
C++: protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(const class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &) const –> class utility::vector1<double, class std::allocator<double> >
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- diversify_all_confs(self: pyrosetta.rosetta.protocols.enzdes.DiversifyStoredRBConfs, pose: pyrosetta.rosetta.core.pose.Pose, confs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) None ¶
C++: protocols::enzdes::DiversifyStoredRBConfs::diversify_all_confs(const class core::pose::Pose &, 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
- 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.enzdes.DiversifyStoredRBConfs) str ¶
C++: protocols::enzdes::DiversifyStoredRBConfs::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
- swap_coordinates_in_pose(self: pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs, pose: pyrosetta.rosetta.core.pose.Pose, rescoords: pyrosetta.rosetta.core.conformation.Residue) None ¶
- helper function to exchange coordinates in a pose
this function doesn’t actually exchange the residues, but sets all the coords of pose.residue( rescoords.seqpos() ) to what is in rescoords and vice versa
C++: protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(class core::pose::Pose &, class core::conformation::Residue &) 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.enzdes.EnzRepackMinimize¶
Bases:
Mover
- apply(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::enzdes::EnzRepackMinimize::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize, : pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize) pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize ¶
C++: protocols::enzdes::EnzRepackMinimize::operator=(const class protocols::enzdes::EnzRepackMinimize &) –> class protocols::enzdes::EnzRepackMinimize &
- 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.enzdes.EnzRepackMinimize) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::enzdes::EnzRepackMinimize::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>
- create_ptask(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.pack.task.PackerTask ¶
C++: protocols::enzdes::EnzRepackMinimize::create_ptask(class core::pose::Pose &) –> class std::shared_ptr<class core::pack::task::PackerTask>
- ensure_scofx_cstfication(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- turns on constraint score terms in case the pose
has an enzdes cst cache
C++: protocols::enzdes::EnzRepackMinimize::ensure_scofx_cstfication(const class core::pose::Pose &) –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::enzdes::EnzRepackMinimize::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_design(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize) bool ¶
C++: protocols::enzdes::EnzRepackMinimize::get_design() const –> bool
- 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_min_bb(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize) bool ¶
C++: protocols::enzdes::EnzRepackMinimize::get_min_bb() const –> bool
- get_min_lig(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize) bool ¶
C++: protocols::enzdes::EnzRepackMinimize::get_min_lig() const –> bool
- get_min_rb(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize) bool ¶
C++: protocols::enzdes::EnzRepackMinimize::get_min_rb() const –> bool
- get_min_sc(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize) bool ¶
C++: protocols::enzdes::EnzRepackMinimize::get_min_sc() const –> bool
- get_name(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize) str ¶
C++: protocols::enzdes::EnzRepackMinimize::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
- minimize_in_stages(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, cstopt: bool, min_sc: bool, min_rb: bool, min_lig: bool) None ¶
C++: protocols::enzdes::EnzRepackMinimize::minimize_in_stages(class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, const bool &, const bool &, const bool &, const bool &) –> void
- static mover_name() str ¶
C++: protocols::enzdes::EnzRepackMinimize::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::enzdes::EnzRepackMinimize::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::enzdes::EnzRepackMinimize::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- rb_min_jumps(*args, **kwargs)¶
Overloaded function.
rb_min_jumps(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize) -> pyrosetta.rosetta.utility.vector1_unsigned_long
C++: protocols::enzdes::EnzRepackMinimize::rb_min_jumps() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
rb_min_jumps(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize, : pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
C++: protocols::enzdes::EnzRepackMinimize::rb_min_jumps(const class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> 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
- scorefxn_minimize(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::enzdes::EnzRepackMinimize::scorefxn_minimize() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- scorefxn_repack(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::enzdes::EnzRepackMinimize::scorefxn_repack() const –> class std::shared_ptr<class core::scoring::ScoreFunction>
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_design(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize, des: bool) None ¶
C++: protocols::enzdes::EnzRepackMinimize::set_design(const bool) –> 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_min_bb(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize, min_bb: bool) None ¶
C++: protocols::enzdes::EnzRepackMinimize::set_min_bb(const bool) –> void
- set_min_lig(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize, min_lig: bool) None ¶
C++: protocols::enzdes::EnzRepackMinimize::set_min_lig(const bool) –> void
- set_min_rb(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize, min_rb: bool) None ¶
C++: protocols::enzdes::EnzRepackMinimize::set_min_rb(const bool) –> void
- set_min_sc(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize, min_sc: bool) None ¶
C++: protocols::enzdes::EnzRepackMinimize::set_min_sc(const bool) –> 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_scorefxn_minimize(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::enzdes::EnzRepackMinimize::set_scorefxn_minimize(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- set_scorefxn_repack(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::enzdes::EnzRepackMinimize::set_scorefxn_repack(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- 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
- task_factory(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimize, p: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
C++: protocols::enzdes::EnzRepackMinimize::task_factory(class std::shared_ptr<class core::pack::task::TaskFactory>) –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimizeCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimizeCreator, : pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimizeCreator) pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimizeCreator ¶
C++: protocols::enzdes::EnzRepackMinimizeCreator::operator=(const class protocols::enzdes::EnzRepackMinimizeCreator &) –> class protocols::enzdes::EnzRepackMinimizeCreator &
- create_mover(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimizeCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::enzdes::EnzRepackMinimizeCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.enzdes.EnzRepackMinimizeCreator) str ¶
C++: protocols::enzdes::EnzRepackMinimizeCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter¶
Bases:
Filter
- apply(self: pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::enzdes::EnzScoreFilter::apply(const class core::pose::Pose &) const –> bool
- static class_name() str ¶
C++: protocols::enzdes::EnzScoreFilter::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.enzdes.EnzScoreFilter) pyrosetta.rosetta.protocols.filters.Filter ¶
C++: protocols::enzdes::EnzScoreFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>
- compute(self: pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::enzdes::EnzScoreFilter::compute(const class core::pose::Pose &) const –> double
- static default_value_for_cstid() str ¶
C++: protocols::enzdes::EnzScoreFilter::default_value_for_cstid() –> std::string
- static default_value_for_is_cstE() bool ¶
C++: protocols::enzdes::EnzScoreFilter::default_value_for_is_cstE() –> bool
- static default_value_for_resnum() str ¶
C++: protocols::enzdes::EnzScoreFilter::default_value_for_resnum() –> std::string
- static default_value_for_score_type() str ¶
C++: protocols::enzdes::EnzScoreFilter::default_value_for_score_type() –> std::string
- static default_value_for_threshold() float ¶
C++: protocols::enzdes::EnzScoreFilter::default_value_for_threshold() –> double
- static default_value_for_whole_pose() bool ¶
C++: protocols::enzdes::EnzScoreFilter::default_value_for_whole_pose() –> bool
- fresh_instance(self: pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter) pyrosetta.rosetta.protocols.filters.Filter ¶
C++: protocols::enzdes::EnzScoreFilter::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.enzdes.EnzScoreFilter) str ¶
C++: protocols::enzdes::EnzScoreFilter::name() const –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::enzdes::EnzScoreFilter::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::enzdes::EnzScoreFilter::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- report(self: pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::enzdes::EnzScoreFilter::report(std::ostream &, const class core::pose::Pose &) const –> void
- report_sm(self: pyrosetta.rosetta.protocols.enzdes.EnzScoreFilter, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::enzdes::EnzScoreFilter::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.enzdes.EnzScoreFilterCreator¶
Bases:
FilterCreator
- assign(self: pyrosetta.rosetta.protocols.enzdes.EnzScoreFilterCreator, : pyrosetta.rosetta.protocols.enzdes.EnzScoreFilterCreator) pyrosetta.rosetta.protocols.enzdes.EnzScoreFilterCreator ¶
C++: protocols::enzdes::EnzScoreFilterCreator::operator=(const class protocols::enzdes::EnzScoreFilterCreator &) –> class protocols::enzdes::EnzScoreFilterCreator &
- create_filter(self: pyrosetta.rosetta.protocols.enzdes.EnzScoreFilterCreator) pyrosetta.rosetta.protocols.filters.Filter ¶
C++: protocols::enzdes::EnzScoreFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>
- keyname(self: pyrosetta.rosetta.protocols.enzdes.EnzScoreFilterCreator) str ¶
C++: protocols::enzdes::EnzScoreFilterCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol¶
Bases:
LigandBaseProtocol
- add_pregenerated_enzdes_constraints(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::add_pregenerated_enzdes_constraints(class core::pose::Pose &) const –> void
- 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.enzdes.EnzdesBaseProtocol, : pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol) pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol ¶
C++: protocols::enzdes::EnzdesBaseProtocol::operator=(const class protocols::enzdes::EnzdesBaseProtocol &) –> class protocols::enzdes::EnzdesBaseProtocol &
- catalytic_res(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
C++: protocols::enzdes::EnzdesBaseProtocol::catalytic_res(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- 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>
- create_enzdes_movemap(*args, **kwargs)¶
Overloaded function.
create_enzdes_movemap(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) -> pyrosetta.rosetta.core.kinematics.MoveMap
create_enzdes_movemap(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, min_all_jumps: bool) -> pyrosetta.rosetta.core.kinematics.MoveMap
C++: protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, bool) –> class std::shared_ptr<class core::kinematics::MoveMap>
- create_enzdes_pack_task(*args, **kwargs)¶
Overloaded function.
create_enzdes_pack_task(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.pack.task.PackerTask
create_enzdes_pack_task(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, design: bool) -> pyrosetta.rosetta.core.pack.task.PackerTask
C++: protocols::enzdes::EnzdesBaseProtocol::create_enzdes_pack_task(class core::pose::Pose &, bool) –> class std::shared_ptr<class core::pack::task::PackerTask>
- cst_minimize(*args, **kwargs)¶
Overloaded function.
cst_minimize(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) -> None
cst_minimize(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, cst_opt: bool) -> None
C++: protocols::enzdes::EnzdesBaseProtocol::cst_minimize(class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, bool) –> void
- design_targets(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.set_unsigned_long_t ¶
C++: protocols::enzdes::EnzdesBaseProtocol::design_targets(const class core::pose::Pose &) const –> const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &
- design_targets_score(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::enzdes::EnzdesBaseProtocol::design_targets_score(const class core::pose::Pose &) const –> double
- enzdes_pack(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, cycles: int, minimize_after_packing: bool, pack_unconstrained: bool, favor_native: bool) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::enzdes_pack(class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, class std::shared_ptr<const class core::scoring::ScoreFunction>, unsigned long, bool, bool, bool) –> void
- 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>
- generate_explicit_ligand_rotamer_poses(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, orig_pose: pyrosetta.rosetta.core.pose.Pose, ligrot_poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, scofx: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::generate_explicit_ligand_rotamer_poses(const class core::pose::Pose &, class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &, class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- 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.enzdes.EnzdesBaseProtocol) str ¶
C++: protocols::enzdes::EnzdesBaseProtocol::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 > > &
- is_catalytic_position(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) bool ¶
C++: protocols::enzdes::EnzdesBaseProtocol::is_catalytic_position(const class core::pose::Pose &, const unsigned long) const –> bool
- 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
- rb_min_jumps(*args, **kwargs)¶
Overloaded function.
rb_min_jumps(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol) -> pyrosetta.rosetta.utility.vector1_unsigned_long
C++: protocols::enzdes::EnzdesBaseProtocol::rb_min_jumps() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
rb_min_jumps(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, : pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
C++: protocols::enzdes::EnzdesBaseProtocol::rb_min_jumps(const class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void
- reduced_scorefxn(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::enzdes::EnzdesBaseProtocol::reduced_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>
- static register_options() None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::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
- remap_resid(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, smap: pyrosetta.rosetta.core.id.SequenceMapping) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::remap_resid(const class core::pose::Pose &, const class core::id::SequenceMapping &) –> void
- remove_enzdes_constraints(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, keep_covalent: bool) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::remove_enzdes_constraints(class core::pose::Pose &, bool) const –> void
- 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
- restype_set(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol) pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t ¶
C++: protocols::enzdes::EnzdesBaseProtocol::restype_set() const –> class std::weak_ptr<const class core::chemical::ResidueTypeSet>
- set_all_jumps_minimizable(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, setting: bool) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::set_all_jumps_minimizable(const 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_fix_cataa(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, setting: bool) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::set_fix_cataa(const bool &) –> 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_minimize_options(*args, **kwargs)¶
Overloaded function.
set_minimize_options(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, min_sc: bool, min_bb: bool, min_rb: bool, min_lig: bool) -> None
set_minimize_options(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, min_sc: bool, min_bb: bool, min_rb: bool, min_lig: bool, backrub: bool) -> None
C++: protocols::enzdes::EnzdesBaseProtocol::set_minimize_options(const bool &, const bool &, const bool &, const bool &, bool) –> 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_scorefxn(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- setup_bbmin_ft_and_csts(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, allow_move_bb: pyrosetta.rosetta.utility.vector1_bool, jump_id: int) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::setup_bbmin_ft_and_csts(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >, unsigned long) –> void
- setup_sequence_recovery_cache(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::setup_sequence_recovery_cache(class core::pose::Pose &, const class core::pack::task::PackerTask &) const –> 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.enzdes.EnzdesConstraintReporter¶
Bases:
pybind11_object
- assign(self: pyrosetta.rosetta.protocols.enzdes.EnzdesConstraintReporter, : pyrosetta.rosetta.protocols.enzdes.EnzdesConstraintReporter) pyrosetta.rosetta.protocols.enzdes.EnzdesConstraintReporter ¶
C++: protocols::enzdes::EnzdesConstraintReporter::operator=(const class protocols::enzdes::EnzdesConstraintReporter &) –> class protocols::enzdes::EnzdesConstraintReporter &
- constrained_lig_atoms(self: pyrosetta.rosetta.protocols.enzdes.EnzdesConstraintReporter) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
- Read access to the set of atoms that participate in distance constraints
to ligand atoms.
C++: protocols::enzdes::EnzdesConstraintReporter::constrained_lig_atoms() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &
- constrained_nonligand_atoms(self: pyrosetta.rosetta.protocols.enzdes.EnzdesConstraintReporter) pyrosetta.rosetta.utility.vector1_core_id_AtomID ¶
C++: protocols::enzdes::EnzdesConstraintReporter::constrained_nonligand_atoms() const –> const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &
- find_constraints_to_ligand(self: pyrosetta.rosetta.protocols.enzdes.EnzdesConstraintReporter, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Recurse through all the constraints in the pose to the ligand,
through all the constraint-container constraints (e.g. Ambiguous constraints and multi-constraints) to find all the atoms that participate in various constraints to ligand atoms in the input Pose.
C++: protocols::enzdes::EnzdesConstraintReporter::find_constraints_to_ligand(const class core::pose::Pose &) –> void
- ligand_resno(*args, **kwargs)¶
Overloaded function.
ligand_resno(self: pyrosetta.rosetta.protocols.enzdes.EnzdesConstraintReporter, res_no: int) -> None
Set the (one) ligand residue index
C++: protocols::enzdes::EnzdesConstraintReporter::ligand_resno(unsigned long) –> void
ligand_resno(self: pyrosetta.rosetta.protocols.enzdes.EnzdesConstraintReporter) -> int
Get the (one) ligand residue index
C++: protocols::enzdes::EnzdesConstraintReporter::ligand_resno() const –> unsigned long
- class pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol¶
Bases:
EnzdesBaseProtocol
- add_pregenerated_enzdes_constraints(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::add_pregenerated_enzdes_constraints(class core::pose::Pose &) const –> void
- apply(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::enzdes::EnzdesFixBBProtocol::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol, : pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol) pyrosetta.rosetta.protocols.enzdes.EnzdesFixBBProtocol ¶
C++: protocols::enzdes::EnzdesFixBBProtocol::operator=(const class protocols::enzdes::EnzdesFixBBProtocol &) –> class protocols::enzdes::EnzdesFixBBProtocol &
- catalytic_res(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
C++: protocols::enzdes::EnzdesBaseProtocol::catalytic_res(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- 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>
- create_enzdes_movemap(*args, **kwargs)¶
Overloaded function.
create_enzdes_movemap(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) -> pyrosetta.rosetta.core.kinematics.MoveMap
create_enzdes_movemap(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, min_all_jumps: bool) -> pyrosetta.rosetta.core.kinematics.MoveMap
C++: protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, bool) –> class std::shared_ptr<class core::kinematics::MoveMap>
- create_enzdes_pack_task(*args, **kwargs)¶
Overloaded function.
create_enzdes_pack_task(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.pack.task.PackerTask
create_enzdes_pack_task(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, design: bool) -> pyrosetta.rosetta.core.pack.task.PackerTask
C++: protocols::enzdes::EnzdesBaseProtocol::create_enzdes_pack_task(class core::pose::Pose &, bool) –> class std::shared_ptr<class core::pack::task::PackerTask>
- cst_minimize(*args, **kwargs)¶
Overloaded function.
cst_minimize(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) -> None
cst_minimize(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, cst_opt: bool) -> None
C++: protocols::enzdes::EnzdesBaseProtocol::cst_minimize(class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, bool) –> void
- design_targets(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.set_unsigned_long_t ¶
C++: protocols::enzdes::EnzdesBaseProtocol::design_targets(const class core::pose::Pose &) const –> const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &
- design_targets_score(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::enzdes::EnzdesBaseProtocol::design_targets_score(const class core::pose::Pose &) const –> double
- enzdes_pack(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, cycles: int, minimize_after_packing: bool, pack_unconstrained: bool, favor_native: bool) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::enzdes_pack(class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, class std::shared_ptr<const class core::scoring::ScoreFunction>, unsigned long, bool, bool, bool) –> void
- 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>
- generate_explicit_ligand_rotamer_poses(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, orig_pose: pyrosetta.rosetta.core.pose.Pose, ligrot_poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, scofx: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::generate_explicit_ligand_rotamer_poses(const class core::pose::Pose &, class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &, class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- 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.enzdes.EnzdesFixBBProtocol) str ¶
C++: protocols::enzdes::EnzdesFixBBProtocol::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 > > &
- is_catalytic_position(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) bool ¶
C++: protocols::enzdes::EnzdesBaseProtocol::is_catalytic_position(const class core::pose::Pose &, const unsigned long) const –> bool
- 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
- rb_min_jumps(*args, **kwargs)¶
Overloaded function.
rb_min_jumps(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol) -> pyrosetta.rosetta.utility.vector1_unsigned_long
C++: protocols::enzdes::EnzdesBaseProtocol::rb_min_jumps() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
rb_min_jumps(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, : pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
C++: protocols::enzdes::EnzdesBaseProtocol::rb_min_jumps(const class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void
- reduced_scorefxn(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::enzdes::EnzdesBaseProtocol::reduced_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>
- static register_options() None ¶
C++: protocols::enzdes::EnzdesFixBBProtocol::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
- remap_resid(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, smap: pyrosetta.rosetta.core.id.SequenceMapping) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::remap_resid(const class core::pose::Pose &, const class core::id::SequenceMapping &) –> void
- remove_enzdes_constraints(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, keep_covalent: bool) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::remove_enzdes_constraints(class core::pose::Pose &, bool) const –> void
- 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
- restype_set(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol) pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t ¶
C++: protocols::enzdes::EnzdesBaseProtocol::restype_set() const –> class std::weak_ptr<const class core::chemical::ResidueTypeSet>
- set_all_jumps_minimizable(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, setting: bool) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::set_all_jumps_minimizable(const 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_fix_cataa(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, setting: bool) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::set_fix_cataa(const bool &) –> 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_minimize_options(*args, **kwargs)¶
Overloaded function.
set_minimize_options(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, min_sc: bool, min_bb: bool, min_rb: bool, min_lig: bool) -> None
set_minimize_options(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, min_sc: bool, min_bb: bool, min_rb: bool, min_lig: bool, backrub: bool) -> None
C++: protocols::enzdes::EnzdesBaseProtocol::set_minimize_options(const bool &, const bool &, const bool &, const bool &, bool) –> 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_scorefxn(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- setup_bbmin_ft_and_csts(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, allow_move_bb: pyrosetta.rosetta.utility.vector1_bool, jump_id: int) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::setup_bbmin_ft_and_csts(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >, unsigned long) –> void
- setup_sequence_recovery_cache(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::setup_sequence_recovery_cache(class core::pose::Pose &, const class core::pack::task::PackerTask &) const –> 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.enzdes.EnzdesFlexBBProtocol¶
Bases:
EnzdesBaseProtocol
- add_flexible_region(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol, start: int, end: int, pose: pyrosetta.rosetta.core.pose.Pose, clear_existing: bool) None ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::add_flexible_region(unsigned long, unsigned long, const class core::pose::Pose &, bool) –> void
- add_pregenerated_enzdes_constraints(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::add_pregenerated_enzdes_constraints(class core::pose::Pose &) const –> void
- apply(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol, : pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol) pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::operator=(const class protocols::enzdes::EnzdesFlexBBProtocol &) –> class protocols::enzdes::EnzdesFlexBBProtocol &
- catalytic_res(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
C++: protocols::enzdes::EnzdesBaseProtocol::catalytic_res(const class core::pose::Pose &) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
- 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>
- create_enzdes_movemap(*args, **kwargs)¶
Overloaded function.
create_enzdes_movemap(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) -> pyrosetta.rosetta.core.kinematics.MoveMap
create_enzdes_movemap(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, min_all_jumps: bool) -> pyrosetta.rosetta.core.kinematics.MoveMap
C++: protocols::enzdes::EnzdesBaseProtocol::create_enzdes_movemap(class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, bool) –> class std::shared_ptr<class core::kinematics::MoveMap>
- create_enzdes_pack_task(*args, **kwargs)¶
Overloaded function.
create_enzdes_pack_task(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.pack.task.PackerTask
create_enzdes_pack_task(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, design: bool) -> pyrosetta.rosetta.core.pack.task.PackerTask
C++: protocols::enzdes::EnzdesBaseProtocol::create_enzdes_pack_task(class core::pose::Pose &, bool) –> class std::shared_ptr<class core::pack::task::PackerTask>
- cst_minimize(*args, **kwargs)¶
Overloaded function.
cst_minimize(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) -> None
cst_minimize(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, cst_opt: bool) -> None
C++: protocols::enzdes::EnzdesBaseProtocol::cst_minimize(class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, bool) –> void
- design_targets(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.set_unsigned_long_t ¶
C++: protocols::enzdes::EnzdesBaseProtocol::design_targets(const class core::pose::Pose &) const –> const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &
- design_targets_score(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::enzdes::EnzdesBaseProtocol::design_targets_score(const class core::pose::Pose &) const –> double
- determine_flexible_regions(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) None ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::determine_flexible_regions(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>) –> void
- enz_flexible_region(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol, region: int) protocols::enzdes::EnzdesFlexibleRegion ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::enz_flexible_region(unsigned long) const –> class std::shared_ptr<const class protocols::enzdes::EnzdesFlexibleRegion>
- enz_loops_file(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol) protocols::toolbox::match_enzdes_util::EnzdesLoopsFile ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::enz_loops_file() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzdesLoopsFile>
- enzdes_pack(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.pack.task.PackerTask, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, cycles: int, minimize_after_packing: bool, pack_unconstrained: bool, favor_native: bool) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::enzdes_pack(class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, class std::shared_ptr<const class core::scoring::ScoreFunction>, unsigned long, bool, bool, bool) –> void
- 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>
- generate_alc_ensemble_for_region(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose: pyrosetta.rosetta.core.pose.Pose, region: int) None ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::generate_alc_ensemble_for_region(class core::pose::Pose &, unsigned long) –> void
- generate_backrub_ensemble_for_region(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose: pyrosetta.rosetta.core.pose.Pose, region: int) None ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::generate_backrub_ensemble_for_region(class core::pose::Pose &, unsigned long) –> void
- generate_ensemble_for_region(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose: pyrosetta.rosetta.core.pose.Pose, region: int) None ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::generate_ensemble_for_region(class core::pose::Pose &, unsigned long) –> void
- generate_explicit_ligand_rotamer_poses(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, orig_pose: pyrosetta.rosetta.core.pose.Pose, ligrot_poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, scofx: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::generate_explicit_ligand_rotamer_poses(const class core::pose::Pose &, class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &, class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- 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.enzdes.EnzdesFlexBBProtocol) str ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::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_tenA_neighbor_residues(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose: pyrosetta.rosetta.core.pose.Pose, residue_positions: pyrosetta.rosetta.utility.vector1_bool) None ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::get_tenA_neighbor_residues(const class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> > &) const –> void
- 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 > > &
- is_catalytic_position(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, seqpos: int) bool ¶
C++: protocols::enzdes::EnzdesBaseProtocol::is_catalytic_position(const class core::pose::Pose &, const unsigned long) const –> bool
- is_flexible(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol, seqpos: int) bool ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::is_flexible(unsigned long) const –> bool
- is_remodelable(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol, seqpos: int) bool ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::is_remodelable(unsigned long) const –> bool
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- minimize_flexible_region(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose: pyrosetta.rosetta.core.pose.Pose, region: int, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, chi_to_move: pyrosetta.rosetta.std.set_unsigned_long_t, including_CA_angles: bool, min_tolerance: float) bool ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::minimize_flexible_region(class core::pose::Pose &, unsigned long, class std::shared_ptr<const class core::scoring::ScoreFunction>, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, const bool, double) –> bool
- modified_task(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose: pyrosetta.rosetta.core.pose.Pose, orig_task: pyrosetta.rosetta.core.pack.task.PackerTask) pyrosetta.rosetta.core.pack.task.PackerTask ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::modified_task(const class core::pose::Pose &, const class core::pack::task::PackerTask &) –> class std::shared_ptr<class core::pack::task::PackerTask>
- 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
- rb_min_jumps(*args, **kwargs)¶
Overloaded function.
rb_min_jumps(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol) -> pyrosetta.rosetta.utility.vector1_unsigned_long
C++: protocols::enzdes::EnzdesBaseProtocol::rb_min_jumps() const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >
rb_min_jumps(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, : pyrosetta.rosetta.utility.vector1_unsigned_long) -> None
C++: protocols::enzdes::EnzdesBaseProtocol::rb_min_jumps(const class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void
- reduced_scorefxn(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol) pyrosetta.rosetta.core.scoring.ScoreFunction ¶
C++: protocols::enzdes::EnzdesBaseProtocol::reduced_scorefxn() –> class std::shared_ptr<class core::scoring::ScoreFunction>
- static register_options() None ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::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
- remap_resid(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose: pyrosetta.rosetta.core.pose.Pose, smap: pyrosetta.rosetta.core.id.SequenceMapping) None ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::remap_resid(const class core::pose::Pose &, const class core::id::SequenceMapping &) –> void
- remove_enzdes_constraints(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, keep_covalent: bool) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::remove_enzdes_constraints(class core::pose::Pose &, bool) const –> void
- 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
- restype_set(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol) pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t ¶
C++: protocols::enzdes::EnzdesBaseProtocol::restype_set() const –> class std::weak_ptr<const class core::chemical::ResidueTypeSet>
- set_all_jumps_minimizable(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, setting: bool) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::set_all_jumps_minimizable(const 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_fix_cataa(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, setting: bool) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::set_fix_cataa(const bool &) –> 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_minimize_options(*args, **kwargs)¶
Overloaded function.
set_minimize_options(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, min_sc: bool, min_bb: bool, min_rb: bool, min_lig: bool) -> None
set_minimize_options(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, min_sc: bool, min_bb: bool, min_rb: bool, min_lig: bool, backrub: bool) -> None
C++: protocols::enzdes::EnzdesBaseProtocol::set_minimize_options(const bool &, const bool &, const bool &, const bool &, bool) –> 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_scorefxn(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- setup_bbmin_ft_and_csts(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, allow_move_bb: pyrosetta.rosetta.utility.vector1_bool, jump_id: int) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::setup_bbmin_ft_and_csts(class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> >, unsigned long) –> void
- setup_sequence_recovery_cache(self: pyrosetta.rosetta.protocols.enzdes.EnzdesBaseProtocol, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) None ¶
C++: protocols::enzdes::EnzdesBaseProtocol::setup_sequence_recovery_cache(class core::pose::Pose &, const class core::pack::task::PackerTask &) const –> 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_flexbb_rotamer_sets(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexBBProtocol, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) None ¶
C++: protocols::enzdes::EnzdesFlexBBProtocol::test_flexbb_rotamer_sets(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>) –> 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.enzdes.EnzdesFlexibleRegion¶
Bases:
Frame
- static _static_type_name() str ¶
C++: core::fragment::Frame::_static_type_name() –> std::string
- add_fragment(*args, **kwargs)¶
Overloaded function.
add_fragment(self: pyrosetta.rosetta.core.fragment.Frame, new_frag: core::fragment::FragData) -> int
add a fragment .. return new frag_nr
C++: core::fragment::Frame::add_fragment(class std::shared_ptr<const class core::fragment::FragData>) –> unsigned long
add_fragment(self: pyrosetta.rosetta.core.fragment.Frame, new_frags: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_fragment_FragData_t) -> bool
add all fragments in list
C++: core::fragment::Frame::add_fragment(class utility::vector1<class std::shared_ptr<const class core::fragment::FragData>, class std::allocator<class std::shared_ptr<const class core::fragment::FragData> > >) –> bool
- align(self: pyrosetta.rosetta.core.fragment.Frame, map: pyrosetta.rosetta.core.id.SequenceMapping) bool ¶
change frames residue numbers accoriding to map
C++: core::fragment::Frame::align(const class core::id::SequenceMapping &) –> bool
- apply(*args, **kwargs)¶
Overloaded function.
apply(self: pyrosetta.rosetta.core.fragment.Frame, : core::kinematics::MoveMap, frag_num: int, pose: pyrosetta.rosetta.core.pose.Pose) -> int
insert fragment frag_num into pose
C++: core::fragment::Frame::apply(const class core::kinematics::MoveMap &, unsigned long, class core::pose::Pose &) const –> unsigned long
apply(self: pyrosetta.rosetta.core.fragment.Frame, frag_num: int, pose: pyrosetta.rosetta.core.pose.Pose) -> int
insert fragment frag_num into pose — ignore movemap
C++: core::fragment::Frame::apply(unsigned long, class core::pose::Pose &) const –> unsigned long
- apply_ranked_fragment(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose: pyrosetta.rosetta.core.pose.Pose, frag_rank: int) None ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::apply_ranked_fragment(class core::pose::Pose &, unsigned long) –> void
- apply_ss(self: pyrosetta.rosetta.core.fragment.Frame, : core::kinematics::MoveMap, frag_num: int, ss: str) int ¶
change ss-string according to sec-struct info in fragments
C++: core::fragment::Frame::apply_ss(const class core::kinematics::MoveMap &, unsigned long, std::string &) const –> unsigned long
- assemble_enzdes_fragdata(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.core.fragment.FragData ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::assemble_enzdes_fragdata(const class core::pose::Pose &) –> class std::shared_ptr<class core::fragment::FragData>
- assign(self: pyrosetta.rosetta.core.fragment.Frame, : pyrosetta.rosetta.core.fragment.Frame) pyrosetta.rosetta.core.fragment.Frame ¶
C++: core::fragment::Frame::operator=(const class core::fragment::Frame &) –> class core::fragment::Frame &
- cache(self: pyrosetta.rosetta.core.fragment.Frame, tag: str, new_cache: pyrosetta.rosetta.core.fragment.BaseCacheUnit) pyrosetta.rosetta.core.fragment.BaseCacheUnit ¶
- return handle to cached data stored under “tag”
shouldn’t be called directly
C++: core::fragment::Frame::cache(std::string, const class std::shared_ptr<class core::fragment::BaseCacheUnit> &) const –> class core::fragment::BaseCacheUnit &
- calculate_rotamer_set_design_targets_partition_sum(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, threads_to_request: int) float ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::calculate_rotamer_set_design_targets_partition_sum(const class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>, class std::shared_ptr<const class core::pack::task::PackerTask>, const unsigned long) const –> double
- clear(self: pyrosetta.rosetta.core.fragment.Frame) None ¶
remove all valid fragments, a template fragment will be left over
C++: core::fragment::Frame::clear() –> void
- clone(self: pyrosetta.rosetta.core.fragment.Frame) pyrosetta.rosetta.core.fragment.Frame ¶
clone method, new frame with same alignment position, fragments are not copied!
C++: core::fragment::Frame::clone() const –> class std::shared_ptr<class core::fragment::Frame>
- clone_cache_data(self: pyrosetta.rosetta.core.fragment.Frame, source: pyrosetta.rosetta.core.fragment.Frame, sid: int, nid: int) None ¶
copies all entries in the Frame-Cache for fragment “sid” of Frame “source” to fragment “nid” of “this” frame
C++: core::fragment::Frame::clone_cache_data(const class core::fragment::Frame &, unsigned long, unsigned long) –> void
- clone_with_frags(self: pyrosetta.rosetta.core.fragment.Frame) pyrosetta.rosetta.core.fragment.Frame ¶
clone method, new frame with same alignment position, fragments are not copied!
C++: core::fragment::Frame::clone_with_frags() const –> class std::shared_ptr<class core::fragment::Frame>
- clone_with_template(self: pyrosetta.rosetta.core.fragment.Frame) pyrosetta.rosetta.core.fragment.Frame ¶
clone method, new frame with same alignment position, one fragments is copied as template ( valid() == false )
C++: core::fragment::Frame::clone_with_template() –> class std::shared_ptr<class core::fragment::Frame>
- static compare_SizeRealPairs(first: Tuple[int, float], second: Tuple[int, float]) bool ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::compare_SizeRealPairs(const struct std::pair<unsigned long, double> &, const struct std::pair<unsigned long, double> &) –> bool
- contains_catalytic_res(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion) bool ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::contains_catalytic_res() const –> bool
- contains_seqpos(self: pyrosetta.rosetta.core.fragment.Frame, seqpos: int) bool ¶
whether this fragment contains a certain position
C++: core::fragment::Frame::contains_seqpos(unsigned long) const –> bool
- declare_remodelable(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion, min_length: int, max_length: int) None ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::declare_remodelable(unsigned long, unsigned long) –> void
- deltaE_best(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion, frag_rank: int) float ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::deltaE_best(const unsigned long) const –> double
- end(self: pyrosetta.rosetta.core.fragment.Frame) int ¶
last sequence position affected by this frame
C++: core::fragment::Frame::end() const –> unsigned long
- enz_loop_info(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion) protocols::toolbox::match_enzdes_util::EnzdesLoopInfo ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::enz_loop_info() const –> class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzdesLoopInfo>
- examine_new_loopconf(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose: pyrosetta.rosetta.core.pose.Pose, template_pose: pyrosetta.rosetta.core.pose.Pose, compare_poses: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_pose_Pose_t, rmsd_to_native: pyrosetta.rosetta.utility.vector1_double) bool ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::examine_new_loopconf(const class core::pose::Pose &, class core::pose::Pose &, class utility::vector1<class std::shared_ptr<class core::pose::Pose>, class std::allocator<class std::shared_ptr<class core::pose::Pose> > > &, class utility::vector1<double, class std::allocator<double> > &) –> bool
- extract_lig_designability_score(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, backgroundE: float) float ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::extract_lig_designability_score(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, double &) –> double
- frag_id(self: pyrosetta.rosetta.core.fragment.Frame, frag_num: int) int ¶
- a unique id for every fragment in the list.
his is silly, but would enable later on to avoid cache_clearence on deletion of FragData entries in this case, we would require that the ID of a certain fragment never changes, even if the position in FragList changes
C++: core::fragment::Frame::frag_id(unsigned long) const –> unsigned long
- fragment(self: pyrosetta.rosetta.core.fragment.Frame, frag_num: int) core::fragment::FragData ¶
accesors for underlying FragData
C++: core::fragment::Frame::fragment(unsigned long) const –> const class core::fragment::FragData &
- fragment_as_pose(self: pyrosetta.rosetta.core.fragment.Frame, frag_num: int, pose: pyrosetta.rosetta.core.pose.Pose, restype_set: pyrosetta.rosetta.std.weak_ptr_const_core_chemical_ResidueTypeSet_t) None ¶
returns a (small) pose with fragment ( continous from seqpos 1 … nr_res_affected() )
C++: core::fragment::Frame::fragment_as_pose(unsigned long, class core::pose::Pose &, class std::weak_ptr<const class core::chemical::ResidueTypeSet>) const –> void
- fragment_ptr(self: pyrosetta.rosetta.core.fragment.Frame, frag_num: int) core::fragment::FragData ¶
accessor for underlying FragData as owning ptr
C++: core::fragment::Frame::fragment_ptr(unsigned long) const –> class std::shared_ptr<const class core::fragment::FragData>
- generate_sub_frame(*args, **kwargs)¶
Overloaded function.
generate_sub_frame(self: pyrosetta.rosetta.core.fragment.Frame, length: int) -> pyrosetta.rosetta.core.fragment.Frame
generate_sub_frame(self: pyrosetta.rosetta.core.fragment.Frame, length: int, start: int) -> pyrosetta.rosetta.core.fragment.Frame
generate_sub_frame of length from start ( internal numbers )
C++: core::fragment::Frame::generate_sub_frame(unsigned long, unsigned long) const –> class std::shared_ptr<class core::fragment::Frame>
- get_10A_neighbors(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.std.set_unsigned_long_t ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::get_10A_neighbors(const class core::pose::Pose &) const –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >
- get_region_mm_bend_score(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::get_region_mm_bend_score(const class core::pose::Pose &) const –> double
- get_region_total_score(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose: pyrosetta.rosetta.core.pose.Pose) float ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::get_region_total_score(const class core::pose::Pose &) const –> double
- hack_fillup_frag_designabilities(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion) None ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::hack_fillup_frag_designabilities() –> void
- index(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion) int ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::index() const –> unsigned long
- is_applicable(self: pyrosetta.rosetta.core.fragment.Frame, : core::kinematics::MoveMap) int ¶
is the Frame applicable to the pose with the given movemap?
C++: core::fragment::Frame::is_applicable(const class core::kinematics::MoveMap &) const –> unsigned long
- is_continuous(self: pyrosetta.rosetta.core.fragment.Frame) bool ¶
true if frame is continuous (always true for base class)
C++: core::fragment::Frame::is_continuous() const –> bool
- is_mergeable(self: pyrosetta.rosetta.core.fragment.Frame, other: pyrosetta.rosetta.core.fragment.Frame) bool ¶
C++: core::fragment::Frame::is_mergeable(const class core::fragment::Frame &) const –> bool
- is_valid(self: pyrosetta.rosetta.core.fragment.Frame) bool ¶
- a frame is considered valid if at least one fragment is contained and this fragment is also valid
(not an empty template fragment)
C++: core::fragment::Frame::is_valid() const –> bool
- length(self: pyrosetta.rosetta.core.fragment.Frame) int ¶
number of residues in this frame ( for continuous frames it is the same as end()-start() + 1 )
C++: core::fragment::Frame::length() const –> unsigned long
- merge(self: pyrosetta.rosetta.core.fragment.Frame, other: pyrosetta.rosetta.core.fragment.Frame) bool ¶
C++: core::fragment::Frame::merge(const class core::fragment::Frame &) –> bool
- minimize_region(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, chi_to_move: pyrosetta.rosetta.std.set_unsigned_long_t, including_CA_angles: bool, min_tolerance: float) bool ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::minimize_region(class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, const bool, double) –> bool
- moves_residue(self: pyrosetta.rosetta.core.fragment.Frame, pos: int) bool ¶
C++: core::fragment::Frame::moves_residue(unsigned long) const –> bool
- no_ranked_frags(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion) int ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::no_ranked_frags() const –> unsigned long
- nr_frags(self: pyrosetta.rosetta.core.fragment.Frame) int ¶
number of fragments attached to this frame
C++: core::fragment::Frame::nr_frags() const –> unsigned long
- nr_res_affected(self: pyrosetta.rosetta.core.fragment.Frame, mm: core::kinematics::MoveMap) int ¶
number of residues affected by this frame
C++: core::fragment::Frame::nr_res_affected(const class core::kinematics::MoveMap &) const –> unsigned long
- positions(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion) pyrosetta.rosetta.utility.vector1_unsigned_long ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::positions() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &
- read(self: pyrosetta.rosetta.core.fragment.Frame, in: pyrosetta.rosetta.std.istream) None ¶
C++: core::fragment::Frame::read(std::istream &) –> void
- remap_resid(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion, pose: pyrosetta.rosetta.core.pose.Pose, smap: pyrosetta.rosetta.core.id.SequenceMapping) bool ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::remap_resid(const class core::pose::Pose &, const class core::id::SequenceMapping &) –> bool
- remodel_max_length(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion) int ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::remodel_max_length() const –> unsigned long
- remodel_min_length(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion) int ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::remodel_min_length() const –> unsigned long
- remodelable(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion) bool ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::remodelable() const –> bool
- scale_target_proximity_to_other_conformations(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion, factor: float) None ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::scale_target_proximity_to_other_conformations(double) –> void
- scale_target_proximity_to_starting_conformation(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion, factor: float) None ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::scale_target_proximity_to_starting_conformation(double) –> void
- seqpos(self: pyrosetta.rosetta.core.fragment.Frame, intra_pos: int) int ¶
translate intra-frame position into sequence position. (trivial for base-class)
C++: core::fragment::Frame::seqpos(unsigned long) const –> unsigned long
- set_target_proximity_to_starting_conformation(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion, proximity: float) None ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::set_target_proximity_to_starting_conformation(double) –> void
- shift_by(self: pyrosetta.rosetta.core.fragment.Frame, offset: int) None ¶
shift frame by offset relative to current start position ( change end accordingly )
C++: core::fragment::Frame::shift_by(int) –> void
- shift_to(self: pyrosetta.rosetta.core.fragment.Frame, setting: int) None ¶
shift to new start position ( change end accordingly )
C++: core::fragment::Frame::shift_to(unsigned long) –> void
- show(self: pyrosetta.rosetta.core.fragment.Frame, out: pyrosetta.rosetta.std.ostream) None ¶
C++: core::fragment::Frame::show(std::ostream &) const –> void
- show_classic(self: pyrosetta.rosetta.core.fragment.Frame, out: pyrosetta.rosetta.std.ostream) None ¶
C++: core::fragment::Frame::show_classic(std::ostream &) const –> void
- show_header(self: pyrosetta.rosetta.core.fragment.Frame, out: pyrosetta.rosetta.std.ostream) None ¶
C++: core::fragment::Frame::show_header(std::ostream &) const –> void
- sort_ensemble_by_designability(self: pyrosetta.rosetta.protocols.enzdes.EnzdesFlexibleRegion, ref_pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask) None ¶
C++: protocols::enzdes::EnzdesFlexibleRegion::sort_ensemble_by_designability(const class core::pose::Pose &, class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<const class core::pack::task::PackerTask>) –> void
- start(self: pyrosetta.rosetta.core.fragment.Frame) int ¶
first seqpos of this frame
C++: core::fragment::Frame::start() const –> unsigned long
- steal(self: pyrosetta.rosetta.core.fragment.Frame, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
obtain fragment from pose at frame position
C++: core::fragment::Frame::steal(const class core::pose::Pose &) –> bool
- stop(self: pyrosetta.rosetta.core.fragment.Frame) int ¶
last sequence position affected by this frame
C++: core::fragment::Frame::stop() const –> unsigned long
- type(self: pyrosetta.rosetta.core.fragment.Frame) str ¶
type() is specifying the output name of the Frame in FragmentIO (“FRAME”, “JUMPFRAME”, etc)
C++: core::fragment::Frame::type() const –> std::string
- class pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputter¶
Bases:
PDBJobInputter
- assign(self: pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputter, : pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputter) pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputter ¶
C++: protocols::enzdes::EnzdesJobInputter::operator=(const class protocols::enzdes::EnzdesJobInputter &) –> class protocols::enzdes::EnzdesJobInputter &
- fill_jobs(self: pyrosetta.rosetta.protocols.jd2.PDBJobInputter, jobs: protocols::jd2::JobsContainer) None ¶
this function determines what jobs exist from -s/-l
C++: protocols::jd2::PDBJobInputter::fill_jobs(class protocols::jd2::JobsContainer &) –> void
- get_self_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) pyrosetta.rosetta.protocols.jd2.JobInputter ¶
Get self owning pointers.
C++: protocols::jd2::JobInputter::get_self_ptr() –> class std::shared_ptr<class protocols::jd2::JobInputter>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.jd2.JobInputter) pyrosetta.rosetta.std.weak_ptr_protocols_jd2_JobInputter_t ¶
Get self weak pointers.
C++: protocols::jd2::JobInputter::get_self_weak_ptr() –> class std::weak_ptr<class protocols::jd2::JobInputter>
- input_source(self: pyrosetta.rosetta.protocols.jd2.PDBJobInputter) pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum ¶
- Return the type of input source that the PDBJobInputter is currently
using.
Always PDB_FILE.
C++: protocols::jd2::PDBJobInputter::input_source() const –> enum protocols::jd2::JobInputterInputSource::Enum
- static job_inputter_input_source_to_string(source: pyrosetta.rosetta.protocols.jd2.JobInputterInputSource.Enum) str ¶
- call this with input_source() to get the input source of a
particular job inputter
C++: protocols::jd2::JobInputter::job_inputter_input_source_to_string(enum protocols::jd2::JobInputterInputSource::Enum) –> std::string
- pose_from_job(self: pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputter, pose: pyrosetta.rosetta.core.pose.Pose, job: protocols::jd2::Job) None ¶
- this function is responsible for filling the pose reference with the pose
indicated by the job. The Job object (within its InnerJob) contains a PoseCOP. This function needs to either fill the pose reference from the InnerJob or, on first demand of a pose from that InnerJob, instantiate the pose, hand off a COP to the InnerJob, and fill the reference. This implementation uses pose_from_pdb
C++: protocols::enzdes::EnzdesJobInputter::pose_from_job(class core::pose::Pose &, class std::shared_ptr<class protocols::jd2::Job>) –> void
- update_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter, jobs: protocols::jd2::JobsContainer) None ¶
This function is only called by certain JobInputters to update the jobs list after it has already been created.
An example case would be the LargeNstructJobInputter, which uses this function to load additional jobs after the first N have started to come back.
C++: protocols::jd2::JobInputter::update_jobs_list(class std::shared_ptr<class protocols::jd2::JobsContainer>) –> void
- updates_jobs_list(self: pyrosetta.rosetta.protocols.jd2.JobInputter) bool ¶
Does this type of JobInputter update the jobs list?
False by default. Override this function in derived classes to make it true.
C++: protocols::jd2::JobInputter::updates_jobs_list() const –> bool
- class pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputterCreator¶
Bases:
JobInputterCreator
- assign(self: pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputterCreator, : pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputterCreator) pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputterCreator ¶
C++: protocols::enzdes::EnzdesJobInputterCreator::operator=(const class protocols::enzdes::EnzdesJobInputterCreator &) –> class protocols::enzdes::EnzdesJobInputterCreator &
- create_JobInputter(self: pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputterCreator) pyrosetta.rosetta.protocols.jd2.JobInputter ¶
C++: protocols::enzdes::EnzdesJobInputterCreator::create_JobInputter() const –> class std::shared_ptr<class protocols::jd2::JobInputter>
- keyname(self: pyrosetta.rosetta.protocols.enzdes.EnzdesJobInputterCreator) str ¶
C++: protocols::enzdes::EnzdesJobInputterCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter¶
Bases:
PDBJobOutputter
- for now this class only writes a different scorefile
than the default one written by the FileJobOutputter. the structure output format is pdb
SML Feb 4 2016 note. I moved most of PDBJobOutputter into an intermediate class wwPDBJobOutputter to share functions with mmCIFJobOutputter. This class is not being modified (doesn’t appear to need it). Its use of dump_pdb forces that function to be protected rather than private.
- add_evaluation(self: pyrosetta.rosetta.protocols.jd2.JobOutputter, : pyrosetta.rosetta.protocols.evaluation.PoseEvaluator) None ¶
////////////////////////////// evaluator interface ////////////////////////////////////////////
C++: protocols::jd2::JobOutputter::add_evaluation(class std::shared_ptr<class protocols::evaluation::PoseEvaluator>) –> void
- call_output_observers(self: pyrosetta.rosetta.protocols.jd2.JobOutputter, pose: pyrosetta.rosetta.core.pose.Pose, job: protocols::jd2::Job) None ¶
call all output_observers
C++: protocols::jd2::JobOutputter::call_output_observers(const class core::pose::Pose &, class std::shared_ptr<class protocols::jd2::Job>) const –> void
- clear_evaluators(self: pyrosetta.rosetta.protocols.jd2.JobOutputter) None ¶
C++: protocols::jd2::JobOutputter::clear_evaluators() –> void
- evaluate(self: pyrosetta.rosetta.protocols.jd2.JobOutputter, pose: pyrosetta.rosetta.core.pose.Pose, tag: str, pss: pyrosetta.rosetta.core.io.silent.SilentStruct) None ¶
C++: protocols::jd2::JobOutputter::evaluate(class core::pose::Pose &, std::string, class core::io::silent::SilentStruct &) const –> void
- evaluators(self: pyrosetta.rosetta.protocols.jd2.JobOutputter) pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator ¶
C++: protocols::jd2::JobOutputter::evaluators() const –> class std::shared_ptr<const class protocols::evaluation::MetaPoseEvaluator>
- file(self: pyrosetta.rosetta.protocols.jd2.FileJobOutputter, job: protocols::jd2::Job, data: str) None ¶
this function takes a string and writes it to disk (separately from Tracer output).
C++: protocols::jd2::FileJobOutputter::file(class std::shared_ptr<const class protocols::jd2::Job>, const std::string &) –> void
- filename(self: pyrosetta.rosetta.protocols.jd2.JobOutputter, : protocols::jd2::Job) str ¶
C++: protocols::jd2::JobOutputter::filename(class std::shared_ptr<const class protocols::jd2::Job>) const –> std::string
- final_pose(self: pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter, job: protocols::jd2::Job, pose: pyrosetta.rosetta.core.pose.Pose, tag: str) None ¶
C++: protocols::enzdes::EnzdesJobOutputter::final_pose(class std::shared_ptr<class protocols::jd2::Job>, const class core::pose::Pose &, const std::string &) –> void
- flush(self: pyrosetta.rosetta.protocols.jd2.JobOutputter) None ¶
- this function is meant to be redefined in child classes to allow for flushing of memory buffers.
Here’s the long version: The SilentFileJobOutputter wanted to buffer output, but needed to guaruntee that the output would be flushed at end of runtime. The original implementation was to A) bend over backward to ensure that the destructor was run (JobOutputter lives inside static JobDistributor, which was previously not destructed because it’s static) and B) flush the buffers in the destructor. This caused a problem because the buffer-flushing tried to use the Tracers, which had already been destructed…boom crash.
New solution: re-forbid use of destructors within the static JobDistributor system, and create a flush function to force this stuff out. So here it is:
C++: protocols::jd2::JobOutputter::flush() –> void
- job_has_completed(self: pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputter, job: protocols::jd2::Job) bool ¶
C++: protocols::enzdes::EnzdesJobOutputter::job_has_completed(class std::shared_ptr<const class protocols::jd2::Job>) –> bool
- other_pose(*args, **kwargs)¶
Overloaded function.
other_pose(self: pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter, job: protocols::jd2::Job, pose: pyrosetta.rosetta.core.pose.Pose, tag: str) -> None
other_pose(self: pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter, job: protocols::jd2::Job, pose: pyrosetta.rosetta.core.pose.Pose, tag: str, copy_count: int) -> None
other_pose(self: pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter, job: protocols::jd2::Job, pose: pyrosetta.rosetta.core.pose.Pose, tag: str, copy_count: int, score_only: bool) -> None
this function is intended for saving mid-protocol poses; for example the final centroid structure in a combined centroid/fullatom protocol. This implementation will write a wwPDB-format file (plus scores). It calls a pure virtual so that child classes can write PDB or mmCIF format.
C++: protocols::jd2::wwPDBJobOutputter::other_pose(class std::shared_ptr<class protocols::jd2::Job>, const class core::pose::Pose &, const std::string &, int, bool) –> void
- output_name(self: pyrosetta.rosetta.protocols.jd2.wwPDBJobOutputter, job: protocols::jd2::Job) str ¶
this is the master function for determining the unique output identifier for a job
C++: protocols::jd2::wwPDBJobOutputter::output_name(class std::shared_ptr<const class protocols::jd2::Job>) –> std::string
- scorefile_name(self: pyrosetta.rosetta.protocols.jd2.FileJobOutputter) pyrosetta.rosetta.utility.file.FileName ¶
C++: protocols::jd2::FileJobOutputter::scorefile_name() –> const class utility::file::FileName &
- set_defaults(self: pyrosetta.rosetta.protocols.jd2.FileJobOutputter) None ¶
C++: protocols::jd2::FileJobOutputter::set_defaults() –> void
- set_evaluators(self: pyrosetta.rosetta.protocols.jd2.JobOutputter, : pyrosetta.rosetta.protocols.evaluation.MetaPoseEvaluator) None ¶
C++: protocols::jd2::JobOutputter::set_evaluators(const class protocols::evaluation::MetaPoseEvaluator &) –> void
- starting_pose(self: pyrosetta.rosetta.protocols.jd2.JobOutputter, : pyrosetta.rosetta.core.pose.Pose) None ¶
- optionally pass a starting (reference) pose to a JobOutputter for later comparison
purposes and/or as interface for initializing evaluators
C++: protocols::jd2::JobOutputter::starting_pose(const class core::pose::Pose &) –> void
- write_scorefile(self: pyrosetta.rosetta.protocols.jd2.FileJobOutputter) bool ¶
C++: protocols::jd2::FileJobOutputter::write_scorefile() const –> bool
- class pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputterCreator¶
Bases:
JobOutputterCreator
- assign(self: pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputterCreator, : pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputterCreator) pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputterCreator ¶
C++: protocols::enzdes::EnzdesJobOutputterCreator::operator=(const class protocols::enzdes::EnzdesJobOutputterCreator &) –> class protocols::enzdes::EnzdesJobOutputterCreator &
- create_JobOutputter(self: pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputterCreator) pyrosetta.rosetta.protocols.jd2.JobOutputter ¶
C++: protocols::enzdes::EnzdesJobOutputterCreator::create_JobOutputter() const –> class std::shared_ptr<class protocols::jd2::JobOutputter>
- keyname(self: pyrosetta.rosetta.protocols.enzdes.EnzdesJobOutputterCreator) str ¶
C++: protocols::enzdes::EnzdesJobOutputterCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter¶
Bases:
Filter
brief Class that calculates silent energies for an enzdes type scorefile these silent energies can then be written into a scorefile. class is derived from Filter because eventually it should be possible to have this class read in a requirement file and return false if any of the silent energies don’t have the required value
- apply(self: pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::enzdes::EnzdesScorefileFilter::apply(const class core::pose::Pose &) const –> bool
- static class_name() str ¶
C++: protocols::enzdes::EnzdesScorefileFilter::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
- clear_rnl_pose(self: pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter) None ¶
clear rnl pose to save some memory
C++: protocols::enzdes::EnzdesScorefileFilter::clear_rnl_pose() –> void
- clone(self: pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter) pyrosetta.rosetta.protocols.filters.Filter ¶
C++: protocols::enzdes::EnzdesScorefileFilter::clone() const –> class std::shared_ptr<class protocols::filters::Filter>
- examine_pose(self: pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::enzdes::EnzdesScorefileFilter::examine_pose(const class core::pose::Pose &) const –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter) pyrosetta.rosetta.protocols.filters.Filter ¶
C++: protocols::enzdes::EnzdesScorefileFilter::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.enzdes.EnzdesScorefileFilter) str ¶
C++: protocols::enzdes::EnzdesScorefileFilter::name() const –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter, tag: pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::enzdes::EnzdesScorefileFilter::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::enzdes::EnzdesScorefileFilter::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
- rnl_pose(self: pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::enzdes::EnzdesScorefileFilter::rnl_pose() –> class std::shared_ptr<class core::pose::Pose>
- 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_cstio(self: pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter, enzcst_io: protocols::toolbox::match_enzdes_util::EnzConstraintIO) None ¶
C++: protocols::enzdes::EnzdesScorefileFilter::set_cstio(class std::shared_ptr<const class protocols::toolbox::match_enzdes_util::EnzConstraintIO>) –> void
- 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
- silent_Es(self: pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilter) pyrosetta.rosetta.utility.vector1_core_io_silent_SilentEnergy ¶
C++: protocols::enzdes::EnzdesScorefileFilter::silent_Es() const –> const class utility::vector1<class core::io::silent::SilentEnergy, class std::allocator<class core::io::silent::SilentEnergy> > &
- class pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilterCreator¶
Bases:
FilterCreator
- assign(self: pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilterCreator, : pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilterCreator) pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilterCreator ¶
C++: protocols::enzdes::EnzdesScorefileFilterCreator::operator=(const class protocols::enzdes::EnzdesScorefileFilterCreator &) –> class protocols::enzdes::EnzdesScorefileFilterCreator &
- create_filter(self: pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilterCreator) pyrosetta.rosetta.protocols.filters.Filter ¶
C++: protocols::enzdes::EnzdesScorefileFilterCreator::create_filter() const –> class std::shared_ptr<class protocols::filters::Filter>
- keyname(self: pyrosetta.rosetta.protocols.enzdes.EnzdesScorefileFilterCreator) str ¶
C++: protocols::enzdes::EnzdesScorefileFilterCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs¶
Bases:
ModifyStoredRBConfs
generates random rbconfs until a total of num_total_rbconfs_ are present in the cacheable observer. The diversifier is used to ensure that all newly generated confs are different. note: no scorefunction used
- apply(self: pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::enzdes::GenerateStoredRBConfs::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs, : pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs) pyrosetta.rosetta.protocols.enzdes.GenerateStoredRBConfs ¶
C++: protocols::enzdes::GenerateStoredRBConfs::operator=(const class protocols::enzdes::GenerateStoredRBConfs &) –> class protocols::enzdes::GenerateStoredRBConfs &
- 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>
- closest_orient_atoms_msd(self: pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs, pose: pyrosetta.rosetta.core.pose.Pose, confs: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) pyrosetta.rosetta.utility.vector1_double ¶
- calculates the closest orient atom (i.e. atoms used in rotamer placement
msd between every conf and the confs coming before it in the pose or in the vector
C++: protocols::enzdes::ModifyStoredRBConfs::closest_orient_atoms_msd(const class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &) const –> class utility::vector1<double, class std::allocator<double> >
- create(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::create() –> class std::shared_ptr<class protocols::moves::Mover>
- 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.enzdes.GenerateStoredRBConfs) str ¶
C++: protocols::enzdes::GenerateStoredRBConfs::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
- swap_coordinates_in_pose(self: pyrosetta.rosetta.protocols.enzdes.ModifyStoredRBConfs, pose: pyrosetta.rosetta.core.pose.Pose, rescoords: pyrosetta.rosetta.core.conformation.Residue) None ¶
- helper function to exchange coordinates in a pose
this function doesn’t actually exchange the residues, but sets all the coords of pose.residue( rescoords.seqpos() ) to what is in rescoords and vice versa
C++: protocols::enzdes::ModifyStoredRBConfs::swap_coordinates_in_pose(class core::pose::Pose &, class core::conformation::Residue &) 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.enzdes.LigBurialFilter¶
Bases:
Filter
- apply(self: pyrosetta.rosetta.protocols.enzdes.LigBurialFilter, pose: pyrosetta.rosetta.core.pose.Pose) bool ¶
C++: protocols::enzdes::LigBurialFilter::apply(const class core::pose::Pose &) const –> bool
- static class_name() str ¶
C++: protocols::enzdes::LigBurialFilter::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.enzdes.LigBurialFilter)