carbohydrates¶
Bindings for protocols::carbohydrates namespace
- class pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover¶
Bases:
Mover
Mutates residues to create a potential glycosylation site using known sequence motifs of N- or C- linked glycans. Includes options for Enhanced Sequons for N-linked glycans that have been shown to have higher rates of glycosylation
as well as other positions that have been shown to influence the glycosylation chemistry.
Creates the glycan sequence motif around (and including) the potential glycosylation site. If the site could not be created due to the position being too close to the beginning or end of the sequence, Will set the mover status to fail, do not retry.
Creates an N-Linked Sequence Motif by default using the non-enhanced motif. This can be changed in options.
- apply(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Apply the mover
If the sequon could not be created (for example the length of the sequon is longer than the protein/etc. It will set mover_failed_do_not retry. It is your responsiblity to catch this and do whatever you wish with it.
C++: protocols::carbohydrates::CreateGlycanSequonMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover, : pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover) pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover ¶
C++: protocols::carbohydrates::CreateGlycanSequonMover::operator=(const class protocols::carbohydrates::CreateGlycanSequonMover &) –> class protocols::carbohydrates::CreateGlycanSequonMover &
- 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.carbohydrates.CreateGlycanSequonMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::carbohydrates::CreateGlycanSequonMover::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.carbohydrates.CreateGlycanSequonMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::carbohydrates::CreateGlycanSequonMover::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.carbohydrates.CreateGlycanSequonMover) str ¶
C++: protocols::carbohydrates::CreateGlycanSequonMover::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::carbohydrates::CreateGlycanSequonMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::carbohydrates::CreateGlycanSequonMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
Provide the citation.
C++: protocols::carbohydrates::CreateGlycanSequonMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::carbohydrates::CreateGlycanSequonMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_design_neighbors(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover, design_neighbors: bool) None ¶
Should we design neighbors of the motif? Default is False.
C++: protocols::carbohydrates::CreateGlycanSequonMover::set_design_neighbors(const bool) –> void
- set_design_x_positions(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover, design_x_positions: bool) None ¶
- If there is an X in the motif, should we design it or leave it alone.
Default is to leave it alone.
C++: protocols::carbohydrates::CreateGlycanSequonMover::set_design_x_positions(const bool) –> void
- set_glycan_sequon_type(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover, sequon: pyrosetta.rosetta.protocols.carbohydrates.GlycanSequon) None ¶
Set any sequon type
C++: protocols::carbohydrates::CreateGlycanSequonMover::set_glycan_sequon_type(enum protocols::carbohydrates::GlycanSequon) –> void
- set_glycosylation_position(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover, position: int, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- Set the target glycosylation position for which the sequence motif will be created around.
If this is in beginning or end of protein and could not be created, will set fail do not retry mover status.
C++: protocols::carbohydrates::CreateGlycanSequonMover::set_glycosylation_position(unsigned long, const class core::pose::Pose &) –> 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_pack_distance(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover, pack_distance: float) None ¶
Set the neighbor detection distance for any packing/design of neighbors.
C++: protocols::carbohydrates::CreateGlycanSequonMover::set_pack_distance(const double) –> void
- set_pack_neighbors(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover, pack_neighbors: bool) None ¶
Should we pack neighbors of the motif? Default is True
C++: protocols::carbohydrates::CreateGlycanSequonMover::set_pack_neighbors(const bool) –> void
- set_pack_rounds(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover, pack_rounds: int) None ¶
Number of rounds to run packing/design. Default is 5
C++: protocols::carbohydrates::CreateGlycanSequonMover::set_pack_rounds(unsigned long) –> void
- set_positions_as_start_of_sequon(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover, positions_as_start: bool) None ¶
- Instead of having each position be the glycosylation position, have each position be the start of the sequon.
This just makes using ResidueSelectors with this class a bit easier if needed.
This only effects the basic_enhanced and best_enhanced sequons!
C++: protocols::carbohydrates::CreateGlycanSequonMover::set_positions_as_start_of_sequon(bool) –> void
- set_residue_selector(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None ¶
- Set a number of positions using a residue selector.
The positions are where glycosylation is intended to occur.
C++: protocols::carbohydrates::CreateGlycanSequonMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void
- set_score_function(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
C++: protocols::carbohydrates::CreateGlycanSequonMover::set_score_function(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
- set_use_basic_enhanced_n_linked_sequon(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover, enhanced: bool) None ¶
Set to use the enhanced sequon which has been shown to result in higher rates of glycosylation and slightly lower complex types as the glycan site. (Aromatics at n+2)
DEFAULT: False
- REFS:
- “Enhanced Aromatic Sequons Increase Oligosaccharyltransferase Glycosylation Efficiency and Glycan Homogeneity”
Murray et al., 2015, Chemistry & Biology 22, 1052–1062 http://dx.doi.org/10.1016/j.chembiol.2015.06.017
- “Residues Comprising the Enhanced Aromatic Sequon Influence Protein N‐Glycosylation Efficiency”
Yen-Wen Huang, J. Am. Chem. Soc. 2017, 139, 12947−12955 DOI: 10.1021/jacs.7b03868
C++: protocols::carbohydrates::CreateGlycanSequonMover::set_use_basic_enhanced_n_linked_sequon(bool) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover) -> None
show(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::carbohydrates::CreateGlycanSequonMover::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.carbohydrates.CreateGlycanSequonMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMoverCreator, : pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMoverCreator) pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMoverCreator ¶
C++: protocols::carbohydrates::CreateGlycanSequonMoverCreator::operator=(const class protocols::carbohydrates::CreateGlycanSequonMoverCreator &) –> class protocols::carbohydrates::CreateGlycanSequonMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::carbohydrates::CreateGlycanSequonMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.carbohydrates.CreateGlycanSequonMoverCreator) str ¶
C++: protocols::carbohydrates::CreateGlycanSequonMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler¶
Bases:
Mover
Main mover for Glycan Relax, which optimizes glycans in a pose. Each round optimizes either one residue for BB sampling, linkage, or multiple for minimization. Currently uses a random sampler with a set of weights to each mover for sampling.
- Weights are currently as follows:
.40 Phi/Psi Sugar BB Sampling .20 Linkage Conformer Sampling .30 Small BB Sampling - equal weight to phi, psi, or omega
-> .17 +/- 15 degrees -> .086 +/- 45 degrees -> .044 +/- 90 degrees
.05 GlycanTreeMinMover .05 PackRotamersMover
Supports Symmetry
- apply(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::carbohydrates::GlycanSampler::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, : pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler) pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler ¶
C++: protocols::carbohydrates::GlycanSampler::operator=(const class protocols::carbohydrates::GlycanSampler &) –> class protocols::carbohydrates::GlycanSampler &
- 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.carbohydrates.GlycanSampler) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::carbohydrates::GlycanSampler::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>
- force_total_rounds(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, total_rounds: int) None ¶
This allows us to force a number of rounds instead of doing rounds*glycan residues
C++: protocols::carbohydrates::GlycanSampler::force_total_rounds(unsigned long) –> void
- fresh_instance(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::carbohydrates::GlycanSampler::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_glycan_sampler_rounds(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler) int ¶
Get the number of glycan sampler rounds this class is set to run.
C++: protocols::carbohydrates::GlycanSampler::get_glycan_sampler_rounds() –> unsigned long
- 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.carbohydrates.GlycanSampler) str ¶
C++: protocols::carbohydrates::GlycanSampler::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
- idealize_glycan_residues(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, pose: pyrosetta.rosetta.core.pose.Pose, tree_subset: pyrosetta.rosetta.utility.vector1_unsigned_long) None ¶
Attempt to idealize all residues in of a set of trees. Experimental!
C++: protocols::carbohydrates::GlycanSampler::idealize_glycan_residues(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- static mover_name() str ¶
C++: protocols::carbohydrates::GlycanSampler::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::carbohydrates::GlycanSampler::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
Provide the citation.
C++: protocols::carbohydrates::GlycanSampler::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::carbohydrates::GlycanSampler::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- randomize_glycan_torsions(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, pose: pyrosetta.rosetta.core.pose.Pose, subset: pyrosetta.rosetta.utility.vector1_bool) None ¶
Randomize all torsions of the subset. Used to start the protocol.
C++: protocols::carbohydrates::GlycanSampler::randomize_glycan_torsions(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) 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.carbohydrates.GlycanSampler) bool ¶
C++: protocols::carbohydrates::GlycanSampler::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_defaults(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler) None ¶
C++: protocols::carbohydrates::GlycanSampler::set_defaults() –> void
- set_inner_bb_cycles(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, inner_bb_cycles: int) None ¶
- Set the number of inner cycles for BB sampling through small/sugarBB.
This is multiplied by the number of glycan residues Default 1
C++: protocols::carbohydrates::GlycanSampler::set_inner_bb_cycles(unsigned long) –> 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_kt(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, kt: float) None ¶
C++: protocols::carbohydrates::GlycanSampler::set_kt(double) –> void
- set_min_rings(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, min_rings: bool) None ¶
set to minimize ring torsions during minimzation. Default false.
C++: protocols::carbohydrates::GlycanSampler::set_min_rings(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_population_based_conformer_sampling(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, pop_based_sampling: bool) None ¶
Set how our Conformer mover samples. Default is to do uniform sampling on the conformers instead of using the population as probabilities.
C++: protocols::carbohydrates::GlycanSampler::set_population_based_conformer_sampling(bool) –> void
- set_protein_linkage_prob_sampling(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, root_probs: bool) None ¶
Set Conformer Sampling through probabilities at the linkage to the protein only
C++: protocols::carbohydrates::GlycanSampler::set_protein_linkage_prob_sampling(bool) –> void
- set_randomize_first(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, randomize_first: bool) None ¶
- Set the protocol to randomize torsions before beginning.
This actually helps get to lower energy models. Default True. If doing refinement, this is automatically turned off.
C++: protocols::carbohydrates::GlycanSampler::set_randomize_first(bool) –> void
- set_refine(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, refine: bool) None ¶
Set refinement mode instead of denovo modeling mode.
C++: protocols::carbohydrates::GlycanSampler::set_refine(bool) –> void
- set_residue_selector(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None ¶
Set the Movemap
C++: protocols::carbohydrates::GlycanSampler::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void
- set_rounds(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, rounds: int) None ¶
- Each round applys a random mover to pose.
This setting is multiplied by the number of glycan residues in the movemap for the total number of rounds
C++: protocols::carbohydrates::GlycanSampler::set_rounds(unsigned long) –> void
- set_scorefunction(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
Set the ScoreFunction
C++: protocols::carbohydrates::GlycanSampler::set_scorefunction(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- set_selector(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None ¶
Set a ResidueSelector for glycan residue selection, instead of the typical movemap.
C++: protocols::carbohydrates::GlycanSampler::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void
- set_taskfactory(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, tf: pyrosetta.rosetta.core.pack.task.TaskFactory) None ¶
Set the TaskFactory to control side-chain packing of surrounding amino acids and the OH groups of the glycans.
C++: protocols::carbohydrates::GlycanSampler::set_taskfactory(class std::shared_ptr<const class core::pack::task::TaskFactory>) –> 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
- set_use_gaussian_sampling(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, use_gaussian_sampling: bool) None ¶
- Set whether if we are sampling torsions uniformly within an SD for the LinkageConformerMover (false)
or sampling the gaussian (true). Default false
C++: protocols::carbohydrates::GlycanSampler::set_use_gaussian_sampling(bool) –> void
- set_use_shear(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, use_shear: bool) None ¶
- Set the protocol to use the refactored Shear Mover for glycan torsions at 10 % probability.
Default false.
C++: protocols::carbohydrates::GlycanSampler::set_use_shear(bool) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler) -> None
show(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::carbohydrates::GlycanSampler::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 &
- use_cartmin(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSampler, use_cartmin: bool) None ¶
- Use Cartesian minimization instead of Dihedral minimization.
Default (for now) is dihedral.
C++: protocols::carbohydrates::GlycanSampler::use_cartmin(bool) –> void
- class pyrosetta.rosetta.protocols.carbohydrates.GlycanSamplerCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSamplerCreator, : pyrosetta.rosetta.protocols.carbohydrates.GlycanSamplerCreator) pyrosetta.rosetta.protocols.carbohydrates.GlycanSamplerCreator ¶
C++: protocols::carbohydrates::GlycanSamplerCreator::operator=(const class protocols::carbohydrates::GlycanSamplerCreator &) –> class protocols::carbohydrates::GlycanSamplerCreator &
- create_mover(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSamplerCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::carbohydrates::GlycanSamplerCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanSamplerCreator) str ¶
C++: protocols::carbohydrates::GlycanSamplerCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.carbohydrates.GlycanSequon¶
Bases:
pybind11_object
Members:
n_linked_typical
n_linked_basic_enhanced
n_linked_best_enhanced
c_linked_NxC
c_linked_WxxW
c_linked_WSTxC
- c_linked_NxC = <GlycanSequon.c_linked_NxC: 4>¶
- c_linked_WSTxC = <GlycanSequon.c_linked_WSTxC: 6>¶
- c_linked_WxxW = <GlycanSequon.c_linked_WxxW: 5>¶
- n_linked_basic_enhanced = <GlycanSequon.n_linked_basic_enhanced: 2>¶
- n_linked_best_enhanced = <GlycanSequon.n_linked_best_enhanced: 3>¶
- n_linked_typical = <GlycanSequon.n_linked_typical: 1>¶
- property name¶
- property value¶
- class pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover¶
Bases:
Mover
A class that selects the downstream branch from residues in a movemap/selector, and minimizes those residues if on in the primary glycan movemap. Multiple Applies randomly select a different residue in the movemap/selector
Supports Symmetry
- apply(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Apply the mover
C++: protocols::carbohydrates::GlycanTreeMinMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover, : pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover) pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover ¶
C++: protocols::carbohydrates::GlycanTreeMinMover::operator=(const class protocols::carbohydrates::GlycanTreeMinMover &) –> class protocols::carbohydrates::GlycanTreeMinMover &
- static class_name() str ¶
Show the contents of the Mover
C++: protocols::carbohydrates::GlycanTreeMinMover::class_name() –> std::string
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::carbohydrates::GlycanTreeMinMover::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.carbohydrates.GlycanTreeMinMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::carbohydrates::GlycanTreeMinMover::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.carbohydrates.GlycanTreeMinMover) str ¶
Get the name of the Mover
C++: protocols::carbohydrates::GlycanTreeMinMover::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.carbohydrates.GlycanTreeMinMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::carbohydrates::GlycanTreeMinMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
Provide the citation.
C++: protocols::carbohydrates::GlycanTreeMinMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::carbohydrates::GlycanTreeMinMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_min_bb(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover, min_bb: bool) None ¶
Minimize BB? Default True
C++: protocols::carbohydrates::GlycanTreeMinMover::set_min_bb(bool) –> void
- set_min_chi(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover, min_chi: bool) None ¶
Minimize Chi? Default True
C++: protocols::carbohydrates::GlycanTreeMinMover::set_min_chi(bool) –> void
- set_min_rings(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover, min_rings: bool) None ¶
Minimize Rings? Default False
C++: protocols::carbohydrates::GlycanTreeMinMover::set_min_rings(bool) –> void
- set_minmover(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover, min_mover: protocols::minimization_packing::MinMover) None ¶
- Set a pre-configured MinMover for this class.
Will OVERRIDE movemap settings.
C++: protocols::carbohydrates::GlycanTreeMinMover::set_minmover(class std::shared_ptr<const class protocols::minimization_packing::MinMover>) –> 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_residue_selector(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None ¶
C++: protocols::carbohydrates::GlycanTreeMinMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> 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.carbohydrates.GlycanTreeMinMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMoverCreator, : pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMoverCreator) pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMoverCreator ¶
C++: protocols::carbohydrates::GlycanTreeMinMoverCreator::operator=(const class protocols::carbohydrates::GlycanTreeMinMoverCreator &) –> class protocols::carbohydrates::GlycanTreeMinMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::carbohydrates::GlycanTreeMinMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeMinMoverCreator) str ¶
C++: protocols::carbohydrates::GlycanTreeMinMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler¶
Bases:
Mover
A protocol for optimizing glycan trees using the GlycanSampler from the base of the tree out to the leaves.
Works by making all other residues virtual except the ones it is working on (current Layer). A virtual residue is not scored. It will start at the first glycan residues, and then move out to the edges.
GENERAL ALGORITHM
We start at the roots, and make all other glycan residues virtual. We first model towards the leaves and this is considered the forward direction. the GlycanSampler is used for the actual modeling, we only model a layer at a time, until we reach the tips. If more than one round is set, the protocol will move backwards on the next round, from the leafs to the roots. A third round will involve relaxation again in the forward direction. So we go forward, back, forward, etc. for how ever many rounds you set.
QUECHING
By default, we model all glycans simultaneously. First, all glycan roots (the start of the tree), and slowly unvirtualize all glycan residues, while only modeling each layer. Alternatively, we can choose a particular glycan tree, run the algorithm, and then choose another glycan tree randomly until all glycan trees have been optimized. Here, we call this quenching.
GLYCAN LAYERS
Draw a tree on a paper. We start with the beginning N residues, and work our way out towards the leaves. Layers are defined by the glycan residue distance to the rooot. This enables branching residues to be considered the same layer conceptually and computationally, and allows them to be modeled together.
- --LAYER SIZE–
The distance that make up a layer. If we have a distance of 2, we first model all glycans that are equal to or less than 2 residue distance to the root. We then slide this layer up. So we take all residues that have a distance between 3 and 1, and so on.
–WINDOW SIZE–
The layers are slid down throught the tree of the glycan. The window size represents the overlap in the layers. A window size of 1, means that the last residue (or residues of layer 1) from the last modeling effort, will be used again as part of the next layer. A window size of 0, means that no residues will be re-modeled. Typically, we would want at least a window size of 1.
- apply(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Apply the mover
C++: protocols::carbohydrates::GlycanTreeModeler::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, : pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler) pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler ¶
C++: protocols::carbohydrates::GlycanTreeModeler::operator=(const class protocols::carbohydrates::GlycanTreeModeler &) –> class protocols::carbohydrates::GlycanTreeModeler &
- 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.carbohydrates.GlycanTreeModeler) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::carbohydrates::GlycanTreeModeler::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.carbohydrates.GlycanTreeModeler) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::carbohydrates::GlycanTreeModeler::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.carbohydrates.GlycanTreeModeler) str ¶
C++: protocols::carbohydrates::GlycanTreeModeler::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::carbohydrates::GlycanTreeModeler::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::carbohydrates::GlycanTreeModeler::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
Provide the citation.
C++: protocols::carbohydrates::GlycanTreeModeler::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::carbohydrates::GlycanTreeModeler::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_final_min_pack_min(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, minpackmin: bool) None ¶
- Change the setting to do a final min/pack/min of all glycan residues or glycan residues set by the selector
at the end of the protocol.
C++: protocols::carbohydrates::GlycanTreeModeler::set_final_min_pack_min(const bool) –> void
- set_force_virts_for_refinement(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, force_virts: bool) None ¶
- Refinement now models layers in the context of the full glycan tree.
- Turn this option on to use non-scored residues (virtuals) at the ends of the tree that are not being modeled.
This is how the de-novo protocol works.
C++: protocols::carbohydrates::GlycanTreeModeler::set_force_virts_for_refinement(bool) –> void
- set_glycan_sampler_kt(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, kT: float) None ¶
Override the GlycanSampler KT
C++: protocols::carbohydrates::GlycanTreeModeler::set_glycan_sampler_kt(double) –> void
- set_glycan_sampler_rounds(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, glycan_sampler_rounds: int) None ¶
Override Glycan Relax rounds.
C++: protocols::carbohydrates::GlycanTreeModeler::set_glycan_sampler_rounds(unsigned long) –> void
- set_hybrid_protocol(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, hybrid_protocol: bool) None ¶
- Set to use an experimental protocol where we build out the glycans, but re-model the full tree during the building process
Default false
C++: protocols::carbohydrates::GlycanTreeModeler::set_hybrid_protocol(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_layer_size(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, layer_size: int) None ¶
- Set the layer size we will be using. A layer is a set of glycan residues that we will be optimizing.
We work our way through the layers, while the rest of the (downstream) residues are virtual (not scored).
The distance that make up a layer. If we have a distance of 2, we first model all glycans that are equal to or less than 2 residue distance to the root. We then slide this layer up. So we take all residues that have a distance between 3 and 1, and so on.
C++: protocols::carbohydrates::GlycanTreeModeler::set_layer_size(const unsigned long) –> 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_protein_linkage_prob_sampling(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, root_probs: bool) None ¶
Set Conformer Sampling through probabilities at the linkage to the protein only
C++: protocols::carbohydrates::GlycanTreeModeler::set_protein_linkage_prob_sampling(bool) –> void
- set_quench_mode(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, quench_mode: bool) None ¶
- Set the protocol to use a quench-like algorithm, where we work on a single glycan tree at a time until
all are modeled.
C++: protocols::carbohydrates::GlycanTreeModeler::set_quench_mode(bool) –> void
- set_refine(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, refine: bool) None ¶
- Set a boolean that we will be refining instead of de-novo modeling.
This also makes it so that modeling is done in the context of the full glycan tree and no virtual residues are used.
If you would like to change this behavior, use the function set_force_virts_for_refinement.
C++: protocols::carbohydrates::GlycanTreeModeler::set_refine(const bool) –> void
- set_rounds(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, rounds: int) None ¶
C++: protocols::carbohydrates::GlycanTreeModeler::set_rounds(const unsigned long) –> void
- set_scorefxn(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
Set the scorefunction used for modeling.
C++: protocols::carbohydrates::GlycanTreeModeler::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- set_selector(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None ¶
- Set a residue selector to limit the residues we will be modeling.
If you are using quench mode, the selector will limit the trees to model. So the residues that are true should correspond to the start of the trees you wish to model.
If you wish to limit further, this is not currently supported. So email me and I can add it.
C++: protocols::carbohydrates::GlycanTreeModeler::set_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> 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
- set_use_conformer_probabilities(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, conformer_probs: bool) None ¶
Set the LinkageConformer to use probabilites.
C++: protocols::carbohydrates::GlycanTreeModeler::set_use_conformer_probabilities(bool) –> void
- set_use_gaussian_sampling(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, gaussian_sampling: bool) None ¶
- Set whether if we are sampling torsions uniformly within an SD for the LinkageConformerMover (false)
or sampling the gaussian (true). Default false
C++: protocols::carbohydrates::GlycanTreeModeler::set_use_gaussian_sampling(bool) –> void
- set_use_shear(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, use_shear: bool) None ¶
C++: protocols::carbohydrates::GlycanTreeModeler::set_use_shear(bool) –> void
- set_window_size(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, window_size: int) None ¶
Set the window size. This is the overlap of the layers during modeling.
The layers are slid down throught the tree of the glycan. The window size represents the overlap in the layers. A window size of 1, means that the last residue (or residues of layer 1) from the last modeling effort, will be used again as part of the next layer. A window size of 0, means that no residues will be re-modeled. Typically, we would want at least a window size of 1.
C++: protocols::carbohydrates::GlycanTreeModeler::set_window_size(const unsigned long) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler) -> None
show(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModeler, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::carbohydrates::GlycanTreeModeler::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.carbohydrates.GlycanTreeModelerCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModelerCreator, : pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModelerCreator) pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModelerCreator ¶
C++: protocols::carbohydrates::GlycanTreeModelerCreator::operator=(const class protocols::carbohydrates::GlycanTreeModelerCreator &) –> class protocols::carbohydrates::GlycanTreeModelerCreator &
- create_mover(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModelerCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::carbohydrates::GlycanTreeModelerCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.carbohydrates.GlycanTreeModelerCreator) str ¶
C++: protocols::carbohydrates::GlycanTreeModelerCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens¶
Bases:
Mover
This code sets all the anomeric hydrogen positions based on the input structure
- apply(self: pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::carbohydrates::IdealizeAnomericHydrogens::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens, : pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens) pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens ¶
C++: protocols::carbohydrates::IdealizeAnomericHydrogens::operator=(const class protocols::carbohydrates::IdealizeAnomericHydrogens &) –> class protocols::carbohydrates::IdealizeAnomericHydrogens &
- 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.carbohydrates.IdealizeAnomericHydrogens) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::carbohydrates::IdealizeAnomericHydrogens::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.carbohydrates.IdealizeAnomericHydrogens) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::carbohydrates::IdealizeAnomericHydrogens::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.carbohydrates.IdealizeAnomericHydrogens) str ¶
C++: protocols::carbohydrates::IdealizeAnomericHydrogens::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::carbohydrates::IdealizeAnomericHydrogens::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::carbohydrates::IdealizeAnomericHydrogens::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogens, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
Provide the citation.
C++: protocols::carbohydrates::IdealizeAnomericHydrogens::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::carbohydrates::IdealizeAnomericHydrogens::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.moves.Mover) -> None
show(self: pyrosetta.rosetta.protocols.moves.Mover, output: pyrosetta.rosetta.std.ostream) -> None
Outputs details about the Mover, including current settings.
C++: protocols::moves::Mover::show(std::ostream &) const –> void
- test_move(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
- : Unit test support function. Apply one move to a given pose.
Allows extra test specific functions to be called before applying
C++: protocols::moves::Mover::test_move(class core::pose::Pose &) –> void
- type(*args, **kwargs)¶
Overloaded function.
type(self: pyrosetta.rosetta.protocols.moves.Mover, type_in: str) -> None
Set the ‘type’ string
C++: protocols::moves::Mover::type(const std::string &) –> void
type(self: pyrosetta.rosetta.protocols.moves.Mover) -> str
Get the set ‘type’ string
C++: protocols::moves::Mover::type() const –> const std::string &
- class pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogensCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogensCreator, : pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogensCreator) pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogensCreator ¶
C++: protocols::carbohydrates::IdealizeAnomericHydrogensCreator::operator=(const class protocols::carbohydrates::IdealizeAnomericHydrogensCreator &) –> class protocols::carbohydrates::IdealizeAnomericHydrogensCreator &
- create_mover(self: pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogensCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::carbohydrates::IdealizeAnomericHydrogensCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.carbohydrates.IdealizeAnomericHydrogensCreator) str ¶
C++: protocols::carbohydrates::IdealizeAnomericHydrogensCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover¶
Bases:
Mover
- This code changes all of the dihedrals of a particular glycosidic linkage based on database info,
esentially sampling carbohydrate dihedral conformers of two residues. Randomly samples on any set selector at each apply or (default) samples a linkage conformer for each residue set.
The linkage conformers are carbohydrate residue type and (and linkage oxygen) dependant ie MAN-MAN If data is not known here, by default we sample from restype-independant data. If there are multiple conformers for a given linkage, will randomly select from them.
3 Main Conformer Sampling Strategies:
/ 1) Mean + uniform in X standard deviations (Default) / ->Build conformers using the means of dihedrals + or - some amount within X standard deviations of the mean. / / See Also: / LinkageConformerMover.set_x_standard_deviations / / 2) Mean + probability in X standard deviations / / 3) Idealize / -> Use only means when building linkage conformers. / / See: / LinkageConformerMover.set_idealize_torsions //
- apply(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::carbohydrates::LinkageConformerMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover, : pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover) pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover ¶
C++: protocols::carbohydrates::LinkageConformerMover::operator=(const class protocols::carbohydrates::LinkageConformerMover &) –> class protocols::carbohydrates::LinkageConformerMover &
- 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.carbohydrates.LinkageConformerMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::carbohydrates::LinkageConformerMover::clone() const –> class std::shared_ptr<class protocols::moves::Mover>
- conformer_found(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover) bool ¶
Boolean for if the restype-dependant conformer was found at apply. Resets at successive applies.
C++: protocols::carbohydrates::LinkageConformerMover::conformer_found() const –> bool
- 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.carbohydrates.LinkageConformerMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::carbohydrates::LinkageConformerMover::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.carbohydrates.LinkageConformerMover) str ¶
C++: protocols::carbohydrates::LinkageConformerMover::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::carbohydrates::LinkageConformerMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::carbohydrates::LinkageConformerMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
Provide the citation.
C++: protocols::carbohydrates::LinkageConformerMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::carbohydrates::LinkageConformerMover::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.carbohydrates.LinkageConformerMover) bool ¶
C++: protocols::carbohydrates::LinkageConformerMover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover) bool ¶
C++: protocols::carbohydrates::LinkageConformerMover::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_defaults(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover) None ¶
Set everything to default values, including linkage pairs.
C++: protocols::carbohydrates::LinkageConformerMover::set_defaults() –> void
- set_idealize_torsions(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover, idealize_torsions: bool) None ¶
- Idealize the torsion angles instead of sampling from SD.
Default FALSE
C++: protocols::carbohydrates::LinkageConformerMover::set_idealize_torsions(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_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_residue_selector(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None ¶
- Set the Selector. Each apply will randomly sample Selector.
If the conformer is not found, will set move status to false. Will optimize the linkage between the residue and the parent residue.
C++: protocols::carbohydrates::LinkageConformerMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void
- set_root_prob_sampling(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover, root_prob_sampling: bool) None ¶
- Set the LCM to use probabilities for the ASN (or other residue) linkage.
Default False
C++: protocols::carbohydrates::LinkageConformerMover::set_root_prob_sampling(bool) –> void
- set_single_resnum(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover, pose: pyrosetta.rosetta.core.pose.Pose, resnum: int) None ¶
Set a single resnum to sample on instead of a movemap.
C++: protocols::carbohydrates::LinkageConformerMover::set_single_resnum(const class core::pose::Pose &, unsigned long) –> 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
- set_use_conformer_population_stats(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover, setting: bool) None ¶
Use conformer population data to weight sampling. Default TRUE.
C++: protocols::carbohydrates::LinkageConformerMover::set_use_conformer_population_stats(const bool) –> void
- set_use_gaussian_sampling(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover, prob_sd_sample: bool) None ¶
- Set whether if we are sampling uniformly within 1 SD or by sampling on the full gaussian directly.
Default FALSE
C++: protocols::carbohydrates::LinkageConformerMover::set_use_gaussian_sampling(bool) –> void
- set_use_sugar_bb_data_if_needed(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover, use_sugar_bb: bool) None ¶
- Use phi/psi data if restype-dependant conformer data unavailable.
Will set phi/psi to lowest energy values if idealize is true. Default FALSE
C++: protocols::carbohydrates::LinkageConformerMover::set_use_sugar_bb_data_if_needed(bool) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover) -> None
show(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::carbohydrates::LinkageConformerMover::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.carbohydrates.LinkageConformerMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMoverCreator, : pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMoverCreator) pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMoverCreator ¶
C++: protocols::carbohydrates::LinkageConformerMoverCreator::operator=(const class protocols::carbohydrates::LinkageConformerMoverCreator &) –> class protocols::carbohydrates::LinkageConformerMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::carbohydrates::LinkageConformerMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.carbohydrates.LinkageConformerMoverCreator) str ¶
C++: protocols::carbohydrates::LinkageConformerMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.carbohydrates.QuenchDirection¶
Bases:
pybind11_object
Members:
forward
backward
- backward = <QuenchDirection.backward: 2>¶
- forward = <QuenchDirection.forward: 1>¶
- property name¶
- property value¶
- class pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover¶
Bases:
Mover
A Mover class for flipping the plane of a carbohydrate pyranose ring 180 degrees about its anomeric bond.
Based on a given ResidueSelector and limited by a MoveMap, this mover selects applicable cyclic residues
and performs a 180-degree shearing move in which the anomeric bond and the main-chain bond on the opposite side of the ring are moved in opposite directions. An “applicable” residue is limited to 1,4-linked aldopyranoses or 2,5- linked ketopyranoses for which both the anomeric bond and the glycosidic linkage bond are equatorial.
- apply(self: pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover, input_pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Apply the corresponding move to <input_pose>.
C++: protocols::carbohydrates::RingPlaneFlipMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover, object_to_copy: pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover) pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover ¶
C++: protocols::carbohydrates::RingPlaneFlipMover::operator=(const class protocols::carbohydrates::RingPlaneFlipMover &) –> class protocols::carbohydrates::RingPlaneFlipMover &
- 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.carbohydrates.RingPlaneFlipMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::carbohydrates::RingPlaneFlipMover::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.carbohydrates.RingPlaneFlipMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::carbohydrates::RingPlaneFlipMover::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.carbohydrates.RingPlaneFlipMover) str ¶
Return the name of the Mover.
C++: protocols::carbohydrates::RingPlaneFlipMover::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
- movemap(*args, **kwargs)¶
Overloaded function.
movemap(self: pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover, pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.core.kinematics.MoveMap
Get the current MoveMap, creating it if needed.
C++: protocols::carbohydrates::RingPlaneFlipMover::movemap(const class core::pose::Pose &) const –> class std::shared_ptr<const class core::kinematics::MoveMap>
movemap(self: pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover, new_movemap: pyrosetta.rosetta.core.kinematics.MoveMap) -> None
Set the MoveMap.
C++: protocols::carbohydrates::RingPlaneFlipMover::movemap(class std::shared_ptr<class core::kinematics::MoveMap>) –> void
- movemap_factory(self: pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover, new_movemap_factory: pyrosetta.rosetta.core.select.movemap.MoveMapFactory) None ¶
Set the MoveMapFactory.
C++: protocols::carbohydrates::RingPlaneFlipMover::movemap_factory(class std::shared_ptr<const class core::select::movemap::MoveMapFactory>) –> void
- static mover_name() str ¶
C++: protocols::carbohydrates::RingPlaneFlipMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::carbohydrates::RingPlaneFlipMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
Provide the citation.
C++: protocols::carbohydrates::RingPlaneFlipMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::carbohydrates::RingPlaneFlipMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Register options with the option system.
C++: protocols::carbohydrates::RingPlaneFlipMover::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
- selector(*args, **kwargs)¶
Overloaded function.
selector(self: pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector
Get the current ResidueSelector.
C++: protocols::carbohydrates::RingPlaneFlipMover::selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>
selector(self: pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover, new_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None
Set the ResidueSelector.
C++: protocols::carbohydrates::RingPlaneFlipMover::selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> 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.carbohydrates.RingPlaneFlipMover) -> None
show(self: pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMover, output: pyrosetta.rosetta.std.ostream) -> None
Generate string representation of RingPlaneFlipMover for debugging purposes.
C++: protocols::carbohydrates::RingPlaneFlipMover::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.carbohydrates.RingPlaneFlipMoverCreator¶
Bases:
MoverCreator
MoverCreator allowing the MoverFactory to create a RingConformationMover
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMoverCreator, : pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMoverCreator) pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMoverCreator ¶
C++: protocols::carbohydrates::RingPlaneFlipMoverCreator::operator=(const class protocols::carbohydrates::RingPlaneFlipMoverCreator &) –> class protocols::carbohydrates::RingPlaneFlipMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
Return an up-casted owning pointer (MoverOP) to the mover.
C++: protocols::carbohydrates::RingPlaneFlipMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.carbohydrates.RingPlaneFlipMoverCreator) str ¶
Return the key name for the associated Mover (RingPlaneFlipMoverCreator).
C++: protocols::carbohydrates::RingPlaneFlipMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover¶
Bases:
Mover
A mover for glycosylation of biological glycosylations. Currently glysolylation is done based on string, not from PDB. Use the GlycanSampler to model the resulting glycosylation!.
- Single Glycosylation:
If a single glycosylation is passed, it will glycosylate all positions set with this glycan.
- Multiple Glycosylations:
If multiple glycosylations are passed, will randomly select from these on apply to sample glycan hetergenecity. see glyco.set_weights to set weights for these glycans to sample non-random heterogenecity in the glycoform.
- The site should be ASN for N-linked glycosylations OR SER/THR for O-linked glycosylations
If a glycan already exists, will strip off the current glycan by default. set glyco.set_strip_existing_glycans( false ) to branch off existing glycans instead of deleting them.
see CreateGlycoSiteMover to create glyco sites (as N-linked glycosylations will need a specific motif to be biological)
Will randomly select from set positions and glycosylate all positions set.
- Glycosylations:
If your name ends with .iupac or .gws (GlycoWorkBench), will try to load the file
Next, it will check the short names in the Rosetta database for your string. If the string is in common_names.txt, will load the paired iupac sequence. See database/chemical/carbohydrates/common_glycans/common_names.txt for accepted short names.
Names include man3, man5, and man9.
If the name is not found, will attempt to build the glycan as an iupac sequence from the string.
- TODO JAB: Add Glycosylate from pdb/cif files in addition to IUPAC and short names.
No current RosettaCarbohydrate functionality to load from PDB/CIF and attach to an existing pose..
- apply(self: pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::carbohydrates::SimpleGlycosylateMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover, : pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover) pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover ¶
C++: protocols::carbohydrates::SimpleGlycosylateMover::operator=(const class protocols::carbohydrates::SimpleGlycosylateMover &) –> class protocols::carbohydrates::SimpleGlycosylateMover &
- 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.carbohydrates.SimpleGlycosylateMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::carbohydrates::SimpleGlycosylateMover::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.carbohydrates.SimpleGlycosylateMover) pyrosetta.rosetta.protocols.moves.Mover ¶
required in the context of the parser/scripting scheme
C++: protocols::carbohydrates::SimpleGlycosylateMover::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.carbohydrates.SimpleGlycosylateMover) str ¶
C++: protocols::carbohydrates::SimpleGlycosylateMover::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::carbohydrates::SimpleGlycosylateMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
parse XML tag (to use this Mover in Rosetta Scripts)
C++: protocols::carbohydrates::SimpleGlycosylateMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
Provide the citation.
C++: protocols::carbohydrates::SimpleGlycosylateMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::carbohydrates::SimpleGlycosylateMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Overload this static method if you access options within the mover.
These options will end up in -help of your application if users of this mover call register_options. Do this recursively! If you use movers within your mover, call their register_options in your register_options() method.
C++: protocols::moves::Mover::register_options() –> void
- reinitialize_for_each_job(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be freshly regenerated on
each use.
C++: protocols::moves::Mover::reinitialize_for_each_job() const –> bool
- reinitialize_for_new_input(self: pyrosetta.rosetta.protocols.moves.Mover) bool ¶
- Inform the Job Distributor (August ‘08 vintage) whether this object needs to be regenerated when the input
pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for that one input pose).
C++: protocols::moves::Mover::reinitialize_for_new_input() const –> bool
- reset_status(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
resets status to SUCCESS, meant to be used before an apply(). The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
C++: protocols::moves::Mover::reset_status() –> void
- set_current_job(self: pyrosetta.rosetta.protocols.moves.Mover, job: protocols::jobdist::BasicJob) None ¶
C++: protocols::moves::Mover::set_current_job(class std::shared_ptr<const class protocols::jobdist::BasicJob>) –> void
- set_current_tag(self: pyrosetta.rosetta.protocols.moves.Mover, new_tag: str) None ¶
C++: protocols::moves::Mover::set_current_tag(const std::string &) –> void
- set_glycosylation(self: pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover, iupac_or_common_string: str) None ¶
- Set the glycosylation that will happen.
See database/chemical/carbohydrates/common_glycans for common names. Names include man3, man5, and man9.
Can also use full iupac names.
See also: glycosylate.set_glycosylation_weights
C++: protocols::carbohydrates::SimpleGlycosylateMover::set_glycosylation(const std::string &) –> void
- set_glycosylation_weights(self: pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover, weights: pyrosetta.rosetta.utility.vector1_double) None ¶
Set weights for potential glycosylation if more than one is set.
C++: protocols::carbohydrates::SimpleGlycosylateMover::set_glycosylation_weights(const class utility::vector1<double, class std::allocator<double> > &) –> void
- set_glycosylations(self: pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover, iupac_or_common_strings: pyrosetta.rosetta.utility.vector1_std_string) None ¶
- Set possible glycosylations - the mover will randomly pick these on apply
See database/chemical/carbohydrates/common_glycans for accepted names. Names include man3, man5, and man9.
Can also use full iupac names.
See also: glycosylate.set_glycosylation_weights
C++: protocols::carbohydrates::SimpleGlycosylateMover::set_glycosylations(const class utility::vector1<std::string, class std::allocator<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_position(self: pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover, position: int) None ¶
Set a single resnum position
C++: protocols::carbohydrates::SimpleGlycosylateMover::set_position(unsigned long) –> void
- set_residue_selector(self: pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None ¶
Set positions from a Residue Selector.
C++: protocols::carbohydrates::SimpleGlycosylateMover::set_residue_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void
- set_strip_existing_glycans(self: pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover, strip_existing: bool) None ¶
- This sets whether if we already have a glycan at a position, whether to extend it or delete the existing glycan.
- Advanced functionality - use with caution.
Not yet work.
C++: protocols::carbohydrates::SimpleGlycosylateMover::set_strip_existing_glycans(bool) –> 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.carbohydrates.SimpleGlycosylateMover) -> None
show(self: pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMover, output: pyrosetta.rosetta.std.ostream) -> None
C++: protocols::carbohydrates::SimpleGlycosylateMover::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.carbohydrates.SimpleGlycosylateMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMoverCreator, : pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMoverCreator) pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMoverCreator ¶
C++: protocols::carbohydrates::SimpleGlycosylateMoverCreator::operator=(const class protocols::carbohydrates::SimpleGlycosylateMoverCreator &) –> class protocols::carbohydrates::SimpleGlycosylateMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::carbohydrates::SimpleGlycosylateMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.carbohydrates.SimpleGlycosylateMoverCreator) str ¶
C++: protocols::carbohydrates::SimpleGlycosylateMoverCreator::keyname() const –> std::string
- class pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover¶
Bases:
Mover
A Mover class for tautomerizing from one anomer to another at a reducing end.
This carbohydrate-specific Mover randomly selects a free reducing end (not a glycoside) and inverts the
stereochemistry, swapping alpha anomers for beta and beta for alpha. (This could be considered an extremely limited design case; however, reducing ends readily tautomerize in solution, in contrast to other cases, in which residues do not readily mutate into others!) It is generally not certain which form is preferred (if any) in sugar-binding proteins, and crystal structures sometimes arbitrarily assign one anomer over another when fitting density, so this Mover can assure that each anomer is sampled. If a ResidueSelector is set, the Mover will select from the subset at random; it will not guarantee tautomerization of every Residue in the subset.
This Mover assumes that, any time a new saccharide .params file is added to the Rosetta database, its
anomer is also added.
- apply(self: pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover, input_pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Apply the corresponding move to <input_pose>.
C++: protocols::carbohydrates::TautomerizeAnomerMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover, object_to_copy: pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover) pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover ¶
C++: protocols::carbohydrates::TautomerizeAnomerMover::operator=(const class protocols::carbohydrates::TautomerizeAnomerMover &) –> class protocols::carbohydrates::TautomerizeAnomerMover &
- 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.carbohydrates.TautomerizeAnomerMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::carbohydrates::TautomerizeAnomerMover::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.carbohydrates.TautomerizeAnomerMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::carbohydrates::TautomerizeAnomerMover::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.carbohydrates.TautomerizeAnomerMover) str ¶
Return the name of the Mover.
C++: protocols::carbohydrates::TautomerizeAnomerMover::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::carbohydrates::TautomerizeAnomerMover::mover_name() –> std::string
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- parse_my_tag(self: pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
C++: protocols::carbohydrates::TautomerizeAnomerMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
Provide the citation.
C++: protocols::carbohydrates::TautomerizeAnomerMover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::carbohydrates::TautomerizeAnomerMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- static register_options() None ¶
Register options with the option system.
C++: protocols::carbohydrates::TautomerizeAnomerMover::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
- selector(*args, **kwargs)¶
Overloaded function.
selector(self: pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover) -> pyrosetta.rosetta.core.select.residue_selector.ResidueSelector
Get the current ResidueSelector.
C++: protocols::carbohydrates::TautomerizeAnomerMover::selector() const –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>
selector(self: pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover, new_selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) -> None
Set the ResidueSelector.
C++: protocols::carbohydrates::TautomerizeAnomerMover::selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> 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.carbohydrates.TautomerizeAnomerMover) -> None
show(self: pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMover, output: pyrosetta.rosetta.std.ostream) -> None
Generate string representation of TautomerizeAnomerMover for debugging purposes.
C++: protocols::carbohydrates::TautomerizeAnomerMover::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.carbohydrates.TautomerizeAnomerMoverCreator¶
Bases:
MoverCreator
MoverCreator allowing the MoverFactory to create a TautomerizeAnomerMover.
- assign(self: pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMoverCreator, : pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMoverCreator) pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMoverCreator ¶
C++: protocols::carbohydrates::TautomerizeAnomerMoverCreator::operator=(const class protocols::carbohydrates::TautomerizeAnomerMoverCreator &) –> class protocols::carbohydrates::TautomerizeAnomerMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
Return an up-casted owning pointer (MoverOP) to the mover.
C++: protocols::carbohydrates::TautomerizeAnomerMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.carbohydrates.TautomerizeAnomerMoverCreator) str ¶
Return the key name for the associated Mover (TautomerizeAnomerMoverCreator).
C++: protocols::carbohydrates::TautomerizeAnomerMoverCreator::keyname() const –> std::string
- pyrosetta.rosetta.protocols.carbohydrates.create_sequons() pyrosetta.rosetta.std.map_protocols_carbohydrates_GlycanSequon_std_string ¶
Create a map of the name and full sequon
C++: protocols::carbohydrates::create_sequons() –> class std::map<enum protocols::carbohydrates::GlycanSequon, std::string, struct std::less<enum protocols::carbohydrates::GlycanSequon>, class std::allocator<struct std::pair<const enum protocols::carbohydrates::GlycanSequon, std::string > > >
- pyrosetta.rosetta.protocols.carbohydrates.get_all_glycans_and_neighbor_res_task_factory(*args, **kwargs)¶
Overloaded function.
get_all_glycans_and_neighbor_res_task_factory(subset: pyrosetta.rosetta.utility.vector1_bool) -> pyrosetta.rosetta.core.pack.task.TaskFactory
get_all_glycans_and_neighbor_res_task_factory(subset: pyrosetta.rosetta.utility.vector1_bool, pack_distance: float) -> pyrosetta.rosetta.core.pack.task.TaskFactory
get_all_glycans_and_neighbor_res_task_factory(subset: pyrosetta.rosetta.utility.vector1_bool, pack_distance: float, read_resfile: bool) -> pyrosetta.rosetta.core.pack.task.TaskFactory
Get a TaskFactory of all residues in the subset and neighboring residues.
- Operations:
InitializeFromCommandline ReadResFile? If option given on cmd-line, returns TF up to this. NeighborhoodResidueSelector/OperateOnResidueSubset RestrictRepacking/PreventRepacking
C++: protocols::carbohydrates::get_all_glycans_and_neighbor_res_task_factory(const class utility::vector1<bool, class std::allocator<bool> > &, double, bool) –> class std::shared_ptr<class core::pack::task::TaskFactory>
- pyrosetta.rosetta.protocols.carbohydrates.get_total_rounds_for_overlap_one_layer_two(pose: pyrosetta.rosetta.core.pose.Pose, residue_subset: pyrosetta.rosetta.utility.vector1_bool, sampler_rounds: int) int ¶
- Used for benchmarking to test even sampling of different kinematic protocols
Get the total number of sampling rounds for the GlycanTreeModeler protocol with previous default settings.
C++: protocols::carbohydrates::get_total_rounds_for_overlap_one_layer_two(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, unsigned long) –> unsigned long
- pyrosetta.rosetta.protocols.carbohydrates.run_shear_min_pack(*args, **kwargs)¶
Overloaded function.
run_shear_min_pack(min_mover: protocols::minimization_packing::MinMover, packer: protocols::minimization_packing::PackRotamersMover, shear: protocols::simple_moves::ShearMover, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo, n_glycan_residues: int, pose: pyrosetta.rosetta.core.pose.Pose) -> None
run_shear_min_pack(min_mover: protocols::minimization_packing::MinMover, packer: protocols::minimization_packing::PackRotamersMover, shear: protocols::simple_moves::ShearMover, mc: pyrosetta.rosetta.protocols.moves.MonteCarlo, n_glycan_residues: int, pose: pyrosetta.rosetta.core.pose.Pose, use_shear: bool) -> None
Run a shear/min/pack on all residues set to move.
C++: protocols::carbohydrates::run_shear_min_pack(class protocols::minimization_packing::MinMover &, class protocols::minimization_packing::PackRotamersMover &, class protocols::simple_moves::ShearMover &, class protocols::moves::MonteCarlo &, unsigned long, class core::pose::Pose &, bool) –> void