denovo_design¶
Bindings for protocols::denovo_design namespace
- class pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover¶
Bases:
MultiplePoseMover
- apply(self: pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
C++: protocols::rosetta_scripts::MultiplePoseMover::apply(class core::pose::Pose &) –> void
- assign(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::operator=(const class protocols::moves::Mover &) –> class protocols::moves::Mover &
- build_and_score_disulfide(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, blank_pose: pyrosetta.rosetta.core.pose.Pose, sfxn_disulfonly: pyrosetta.rosetta.core.scoring.ScoreFunction, sfxn_full: pyrosetta.rosetta.core.scoring.ScoreFunction, relax_bb: bool, res1: int, res2: int) float ¶
temporarily tries building a disulfide between the given positions, scores, and restores the pose
C++: protocols::denovo_design::DisulfidizeMover::build_and_score_disulfide(class core::pose::Pose &, class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class core::scoring::ScoreFunction>, const bool, const unsigned long, const unsigned long) const –> double
- check_disulfide_cb_distance(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, pose: pyrosetta.rosetta.core.pose.Pose, res1: int, res2: int) bool ¶
checks disulfide CB-CB distance
C++: protocols::denovo_design::DisulfidizeMover::check_disulfide_cb_distance(const class core::pose::Pose &, const unsigned long, const unsigned long) const –> bool
- check_disulfide_match_rt(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, pose: pyrosetta.rosetta.core.pose.Pose, res1: int, res2: int, disulfPot: pyrosetta.rosetta.core.scoring.disulfides.DisulfideMatchingPotential, mirror: bool) bool ¶
checks disulfide match rt
C++: protocols::denovo_design::DisulfidizeMover::check_disulfide_match_rt(const class core::pose::Pose &, const unsigned long, const unsigned long, const class core::scoring::disulfides::DisulfideMatchingPotential &, const bool) const –> bool
- check_disulfide_score(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, pose: pyrosetta.rosetta.core.pose.Pose, res1: int, res2: int, sfxn_disulfonly: pyrosetta.rosetta.core.scoring.ScoreFunction, sfxn_full: pyrosetta.rosetta.core.scoring.ScoreFunction) bool ¶
checks disulfide rosetta score
C++: protocols::denovo_design::DisulfidizeMover::check_disulfide_score(class core::pose::Pose &, const unsigned long, const unsigned long, class std::shared_ptr<class core::scoring::ScoreFunction>, class std::shared_ptr<class core::scoring::ScoreFunction>) const –> bool
- check_disulfide_seqpos(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, res1: int, res2: int) bool ¶
checks seqpos to ensure that min_loop is satisfied
C++: protocols::denovo_design::DisulfidizeMover::check_disulfide_seqpos(const unsigned long, const unsigned long) const –> bool
- check_residue_type(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, pose: pyrosetta.rosetta.core.pose.Pose, res: int) bool ¶
checks seqpos to ensure that min_loop is satisfied
C++: protocols::denovo_design::DisulfidizeMover::check_residue_type(const class core::pose::Pose &, const unsigned long) const –> bool
- clear_info(self: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
clear_info is called by jd2 before calling apply
C++: protocols::moves::Mover::clear_info() –> void
- clone(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover) pyrosetta.rosetta.protocols.moves.Mover ¶
return a fresh instance of this class in an owning pointer
C++: protocols::denovo_design::DisulfidizeMover::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>
- find_current_disulfides(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, pose: pyrosetta.rosetta.core.pose.Pose, subset1: pyrosetta.rosetta.utility.vector1_bool, subset2: pyrosetta.rosetta.utility.vector1_bool) pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t ¶
finds disulfides within a pose subset
C++: protocols::denovo_design::DisulfidizeMover::find_current_disulfides(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >
- find_possible_disulfides(*args, **kwargs)¶
Overloaded function.
find_possible_disulfides(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, pose: pyrosetta.rosetta.core.pose.Pose, residueset1: pyrosetta.rosetta.utility.vector1_bool, residueset2: pyrosetta.rosetta.utility.vector1_bool, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t
find disulfides in the given neighborhood
C++: protocols::denovo_design::DisulfidizeMover::find_possible_disulfides(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &, class std::shared_ptr<class core::scoring::ScoreFunction>) const –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >
find_possible_disulfides(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, pose: pyrosetta.rosetta.core.pose.Pose, set1: pyrosetta.rosetta.std.set_unsigned_long_t, set2: pyrosetta.rosetta.std.set_unsigned_long_t, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) -> pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t
find disulfides in the given neighborhood between residues in set 1 and residues in set 2
C++: protocols::denovo_design::DisulfidizeMover::find_possible_disulfides(const class core::pose::Pose &, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, class std::shared_ptr<class core::scoring::ScoreFunction>) const –> class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >
- fresh_instance(self: pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::rosetta_scripts::MultiplePoseMover::fresh_instance() const –> class std::shared_ptr<class protocols::moves::Mover>
- get_additional_output(self: pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::rosetta_scripts::MultiplePoseMover::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.denovo_design.DisulfidizeMover) str ¶
C++: protocols::denovo_design::DisulfidizeMover::get_name() const –> std::string
- get_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.core.pose.Pose ¶
C++: protocols::moves::Mover::get_native_pose() const –> class std::shared_ptr<const class core::pose::Pose>
- get_self_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::moves::Mover::get_self_ptr() –> class std::shared_ptr<class protocols::moves::Mover>
- get_self_weak_ptr(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.weak_ptr_protocols_moves_Mover_t ¶
C++: protocols::moves::Mover::get_self_weak_ptr() –> class std::weak_ptr<class protocols::moves::Mover>
- get_type(self: pyrosetta.rosetta.protocols.moves.Mover) str ¶
C++: protocols::moves::Mover::get_type() const –> std::string
- info(self: pyrosetta.rosetta.protocols.moves.Mover) pyrosetta.rosetta.std.list_std_string_t ¶
non-const accessor
C++: protocols::moves::Mover::info() –> class std::list<std::string, class std::allocator<std::string > > &
- last_proposal_density_ratio(self: pyrosetta.rosetta.protocols.moves.Mover) float ¶
C++: protocols::moves::Mover::last_proposal_density_ratio() –> double
- make_disulfide(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, pose: pyrosetta.rosetta.core.pose.Pose, res1: int, res2: int, relax_bb: bool, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
forms a disulfide between res1 and res2, optionally allowing backbone movement
C++: protocols::denovo_design::DisulfidizeMover::make_disulfide(class core::pose::Pose &, const unsigned long, const unsigned long, const bool, class std::shared_ptr<class core::scoring::ScoreFunction>) const –> void
- make_disulfides(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, pose: pyrosetta.rosetta.core.pose.Pose, disulf: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, relax_bb: bool, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
creates disulfides given the list of pairs given
C++: protocols::denovo_design::DisulfidizeMover::make_disulfides(class core::pose::Pose &, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &, const bool, class std::shared_ptr<class core::scoring::ScoreFunction>) const –> void
- mixed_disulfide(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, pose: pyrosetta.rosetta.core.pose.Pose, res1: int, res2: int) bool ¶
Returns true if this is a mixed D/L disulfide, false otherwise.
C++: protocols::denovo_design::DisulfidizeMover::mixed_disulfide(const class core::pose::Pose &, const unsigned long, const unsigned long) const –> bool
- static mover_name() str ¶
C++: protocols::denovo_design::DisulfidizeMover::mover_name() –> std::string
- mutate_disulfides_to_ala(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, pose: pyrosetta.rosetta.core.pose.Pose, current_ds: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) None ¶
mutates the given disulfides to ALA
C++: protocols::denovo_design::DisulfidizeMover::mutate_disulfides_to_ala(class core::pose::Pose &, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) const –> void
- static name() str ¶
C++: protocols::moves::Mover::name() –> std::string
- noncanonical_disulfide(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, pose: pyrosetta.rosetta.core.pose.Pose, res1: int, res2: int) bool ¶
- Returns true if at least one of the partners in this disulfide is NOT
D-cysteine or L-cysteine. Returns false otherwise.
C++: protocols::denovo_design::DisulfidizeMover::noncanonical_disulfide(const class core::pose::Pose &, const unsigned long, const unsigned long) const –> bool
- parse_my_tag(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, tag: pyrosetta.rosetta.utility.tag.Tag, data: pyrosetta.rosetta.basic.datacache.DataMap) None ¶
Parses the DisulfidizerMoverTags
C++: protocols::denovo_design::DisulfidizeMover::parse_my_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void
- provide_citation_info(self: pyrosetta.rosetta.protocols.moves.Mover, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None ¶
- Provide citations to the passed CitationCollectionList
Subclasses should add the info for themselves and any other classes they use.
The default implementation of this function does nothing. It may be overriden by movers wishing to provide citation information.
C++: protocols::moves::Mover::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void
- static provide_xml_schema(xsd: utility::tag::XMLSchemaDefinition) None ¶
C++: protocols::denovo_design::DisulfidizeMover::provide_xml_schema(class utility::tag::XMLSchemaDefinition &) –> void
- recursive_multiple_disulfide_former(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, disulfides_formed: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t, disulfides_possible: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) pyrosetta.rosetta.utility.vector1_utility_vector1_std_pair_unsigned_long_unsigned_long_std_allocator_std_pair_unsigned_long_unsigned_long_t ¶
Function for recursively creating multiple disulfides
C++: protocols::denovo_design::DisulfidizeMover::recursive_multiple_disulfide_former(const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) const –> class utility::vector1<class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > >, class std::allocator<class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > > >
- 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_cys_types(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, lcys: bool, dcys: bool, beta_cys: bool) None ¶
Set the types of cysteines that we design with:
By default, we use only L-cysteine (not D-cysteine or beta-3-cysteine).
C++: protocols::denovo_design::DisulfidizeMover::set_cys_types(const bool, const bool, const bool) –> void
- set_include_current_ds(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, include_current: bool) None ¶
If set, the current disulfides in the pose will be included in the set of possible disulfide configurations that are returned
C++: protocols::denovo_design::DisulfidizeMover::set_include_current_ds(const bool) –> void
- set_input_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for poses contained for rms
C++: protocols::moves::Mover::set_input_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_keep_current_ds(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, keep_current: bool) None ¶
If set, the current disulfides in the pose will be kept as-is
C++: protocols::denovo_design::DisulfidizeMover::set_keep_current_ds(const bool) –> void
- set_match_rt_limit(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, matchrtval: float) None ¶
sets the maximum allowed “match-rt-limit” (default=1.0)
Changed from default=2.0 by VKM on 19 Aug 2015 after fixing major bug in DisulfideMatchPotential.
C++: protocols::denovo_design::DisulfidizeMover::set_match_rt_limit(const double) –> void
- set_max_dist(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, dist: float) None ¶
sets the maximum distance to have an allowed disulfide
C++: protocols::denovo_design::DisulfidizeMover::set_max_dist(const double) –> void
- set_max_disulf_score(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, maxscoreval: float) None ¶
sets the maximum allowed per-disulfide dslf_fa13 score (default=0.0)
C++: protocols::denovo_design::DisulfidizeMover::set_max_disulf_score(const double) –> void
- set_max_disulfides(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, max_disulf: int) None ¶
sets maximum number of disulfides
C++: protocols::denovo_design::DisulfidizeMover::set_max_disulfides(const unsigned long) –> void
- set_min_disulfides(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, min_disulf: int) None ¶
sets minimum number of disulfides
C++: protocols::denovo_design::DisulfidizeMover::set_min_disulfides(const unsigned long) –> void
- set_min_loop(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, minloopval: int) None ¶
sets the min_loop value (number of residues between disulfide-joined residues) (default=8)
C++: protocols::denovo_design::DisulfidizeMover::set_min_loop(const unsigned long) –> void
- set_mutate_gly(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, mutate_gly: bool) None ¶
If true, GLY –> CYS mutations will be allowed. Default=false
C++: protocols::denovo_design::DisulfidizeMover::set_mutate_gly(const bool) –> void
- set_mutate_pro(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, mutate_pro: bool) None ¶
If true, PRO –> CYS mutations will be allowed. Default=false
C++: protocols::denovo_design::DisulfidizeMover::set_mutate_pro(const bool) –> void
- set_native_pose(self: pyrosetta.rosetta.protocols.moves.Mover, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
setter for native poses contained for rms —- we should get rid of this method? it is widely used, but a bit unsafe
C++: protocols::moves::Mover::set_native_pose(class std::shared_ptr<const class core::pose::Pose>) –> void
- set_previous_mover(self: pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover, m: pyrosetta.rosetta.protocols.moves.Mover) None ¶
Used by RosettaScripts to set the previous mover to pull poses from
C++: protocols::rosetta_scripts::MultiplePoseMover::set_previous_mover(const class std::shared_ptr<class protocols::moves::Mover>) –> void
- set_rosetta_scripts_tag(self: pyrosetta.rosetta.protocols.rosetta_scripts.MultiplePoseMover, tag: pyrosetta.rosetta.utility.tag.Tag) None ¶
sets rosettascripts tag
C++: protocols::rosetta_scripts::MultiplePoseMover::set_rosetta_scripts_tag(class std::shared_ptr<const class utility::tag::Tag>) –> void
- set_score_or_matchrt(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, score_or_match: bool) None ¶
If true, the disulfide score OR the match_rt score can indicate that a disulfide is reasonable. If false, both the disulfide score AND the match_rt score are needed
C++: protocols::denovo_design::DisulfidizeMover::set_score_or_matchrt(const bool) –> void
- set_scorefxn(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, sfxn_in: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
Set the scorefunction to use for scoring disulfides, minimizing, and repacking.
Clones the input scorefunction; does not copy it.
C++: protocols::denovo_design::DisulfidizeMover::set_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- set_set1_selector(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None ¶
sets the selector for set 1 – disulfides will connect residues in set 1 to residues in set 2
C++: protocols::denovo_design::DisulfidizeMover::set_set1_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void
- set_set2_selector(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, selector: pyrosetta.rosetta.core.select.residue_selector.ResidueSelector) None ¶
sets the selector for set 2 – disulfides will connect residues in set 1 to residues in set 2
C++: protocols::denovo_design::DisulfidizeMover::set_set2_selector(class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>) –> void
- set_sort_scorefxn(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, sort_scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
Set the scorefunction to use for sorting the final results.
Clones the input scorefunction; does not copy it.
C++: protocols::denovo_design::DisulfidizeMover::set_sort_scorefxn(class std::shared_ptr<const class core::scoring::ScoreFunction>) –> void
- set_type(self: pyrosetta.rosetta.protocols.moves.Mover, setting: str) None ¶
Set the ‘type’ string
C++: protocols::moves::Mover::set_type(const std::string &) –> void
- 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
- tag_disulfide(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, pose: pyrosetta.rosetta.core.pose.Pose, res1: int, res2: int) None ¶
creates a residue tags on disulfides to inform users that this disulfide was created by disulfidize
C++: protocols::denovo_design::DisulfidizeMover::tag_disulfide(class core::pose::Pose &, const unsigned long, const unsigned long) const –> void
- tag_disulfides(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMover, pose: pyrosetta.rosetta.core.pose.Pose, disulf: pyrosetta.rosetta.utility.vector1_std_pair_unsigned_long_unsigned_long_t) None ¶
creates a residue tags on disulfides to inform users that this disulfide was created by disulfidize
C++: protocols::denovo_design::DisulfidizeMover::tag_disulfides(class core::pose::Pose &, const class utility::vector1<struct std::pair<unsigned long, unsigned long>, class std::allocator<struct std::pair<unsigned long, unsigned long> > > &) 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.denovo_design.DisulfidizeMoverCreator¶
Bases:
MoverCreator
- assign(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMoverCreator, : pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMoverCreator) pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMoverCreator ¶
C++: protocols::denovo_design::DisulfidizeMoverCreator::operator=(const class protocols::denovo_design::DisulfidizeMoverCreator &) –> class protocols::denovo_design::DisulfidizeMoverCreator &
- create_mover(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMoverCreator) pyrosetta.rosetta.protocols.moves.Mover ¶
C++: protocols::denovo_design::DisulfidizeMoverCreator::create_mover() const –> class std::shared_ptr<class protocols::moves::Mover>
- keyname(self: pyrosetta.rosetta.protocols.denovo_design.DisulfidizeMoverCreator) str ¶
C++: protocols::denovo_design::DisulfidizeMoverCreator::keyname() const –> std::string
- pyrosetta.rosetta.protocols.denovo_design.abego_str(abego: pyrosetta.rosetta.utility.vector1_std_string) str ¶
C++: protocols::denovo_design::abego_str(const class utility::vector1<std::string, class std::allocator<std::string > > &) –> std::string
- pyrosetta.rosetta.protocols.denovo_design.abego_vector(ab: str) pyrosetta.rosetta.utility.vector1_std_string ¶
C++: protocols::denovo_design::abego_vector(const std::string &) –> class utility::vector1<std::string, class std::allocator<std::string > >
- pyrosetta.rosetta.protocols.denovo_design.add_chain_from_pose(to_add: pyrosetta.rosetta.core.pose.Pose, combined: pyrosetta.rosetta.core.pose.Pose) None ¶
dumps a pose into another pose as a new chain
C++: protocols::denovo_design::add_chain_from_pose(class std::shared_ptr<const class core::pose::Pose>, class std::shared_ptr<class core::pose::Pose>) –> void
- pyrosetta.rosetta.protocols.denovo_design.add_cutpoints(pose: pyrosetta.rosetta.core.pose.Pose, sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData) None ¶
C++: protocols::denovo_design::add_cutpoints(class core::pose::Pose &, const class protocols::denovo_design::components::StructureData &) –> void
- pyrosetta.rosetta.protocols.denovo_design.add_remark(remarks: pyrosetta.rosetta.core.io.Remarks, num: int, str_val: str) None ¶
adds a remark to a Remarks object, splitting it into multiple remarks if it is too long
C++: protocols::denovo_design::add_remark(class core::io::Remarks &, const unsigned long, const std::string &) –> void
- pyrosetta.rosetta.protocols.denovo_design.add_residues_to_pose(pose: pyrosetta.rosetta.core.pose.Pose, template_pose: pyrosetta.rosetta.core.pose.Pose, new_chain: bool) None ¶
adds residues from template_pose to pose. If new_chain == true, creates covalent bond
C++: protocols::denovo_design::add_residues_to_pose(class core::pose::Pose &, const class core::pose::Pose &, const bool) –> void
- pyrosetta.rosetta.protocols.denovo_design.construct_dummy_pose(*args, **kwargs)¶
Overloaded function.
construct_dummy_pose(restype_name: str) -> pyrosetta.rosetta.core.pose.Pose
builds an extended-conformation poly-XXX pose
C++: protocols::denovo_design::construct_dummy_pose(const std::string &) –> class std::shared_ptr<class core::pose::Pose>
construct_dummy_pose(restype_name: str, length: int) -> pyrosetta.rosetta.core.pose.Pose
C++: protocols::denovo_design::construct_dummy_pose(const std::string &, const unsigned long) –> class std::shared_ptr<class core::pose::Pose>
construct_dummy_pose(restype: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.core.pose.Pose
C++: protocols::denovo_design::construct_dummy_pose(const class core::chemical::ResidueType &) –> class std::shared_ptr<class core::pose::Pose>
construct_dummy_pose(restype: pyrosetta.rosetta.core.chemical.ResidueType, length: int) -> pyrosetta.rosetta.core.pose.Pose
C++: protocols::denovo_design::construct_dummy_pose(const class core::chemical::ResidueType &, const unsigned long) –> class std::shared_ptr<class core::pose::Pose>
- pyrosetta.rosetta.protocols.denovo_design.construct_poly_ala_pose(*args, **kwargs)¶
Overloaded function.
construct_poly_ala_pose(pose: pyrosetta.rosetta.core.pose.Pose, keep_disulf: bool, set1: pyrosetta.rosetta.utility.vector1_bool, set2: pyrosetta.rosetta.utility.vector1_bool) -> None
construct_poly_ala_pose(pose: pyrosetta.rosetta.core.pose.Pose, keep_disulf: bool, set1: pyrosetta.rosetta.utility.vector1_bool, set2: pyrosetta.rosetta.utility.vector1_bool, keep_chirality: bool) -> None
creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine
If keep_chirality is true, the D-amino acids are mutated to D-alanine.
C++: protocols::denovo_design::construct_poly_ala_pose(class core::pose::Pose &, const bool, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &, const bool) –> void
construct_poly_ala_pose(pose: pyrosetta.rosetta.core.pose.Pose, keep_disulf: bool, res_set: pyrosetta.rosetta.std.set_unsigned_long_t) -> None
construct_poly_ala_pose(pose: pyrosetta.rosetta.core.pose.Pose, keep_disulf: bool, res_set: pyrosetta.rosetta.std.set_unsigned_long_t, keep_chirality: bool) -> None
creates a poly-ala pose where every non-gly, non-cyd, protein residue except those in the given set are converted to alanine
If keep_chirality is true, the D-amino acids are mutated to D-alanine.
C++: protocols::denovo_design::construct_poly_ala_pose(class core::pose::Pose &, const bool, const class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> > &, const bool) –> void
- pyrosetta.rosetta.protocols.denovo_design.count_bulges(perm: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, segment: str) int ¶
counts the beta-bulges in the given segment. This simply counts all abego A’s in the segment
C++: protocols::denovo_design::count_bulges(const class protocols::denovo_design::components::StructureData &, const std::string &) –> unsigned long
- pyrosetta.rosetta.protocols.denovo_design.extract_int(num: float, m: int, n: int) int ¶
- given a number 0 <= x < 1, calculate an integer M <= x <= N
NOTE THAT THIS FUNCTION MODIFIES THE PARAMETER
C++: protocols::denovo_design::extract_int(double &, const unsigned long, const unsigned long) –> unsigned long
- pyrosetta.rosetta.protocols.denovo_design.find_jump_rec(ft: pyrosetta.rosetta.core.kinematics.FoldTree, residue: int) int ¶
helper function that looks for the given residue in a fold tree and returns the jump that controls its 6D-DoFs
C++: protocols::denovo_design::find_jump_rec(const class core::kinematics::FoldTree &, const unsigned long) –> int
- pyrosetta.rosetta.protocols.denovo_design.get_resid(sd: pyrosetta.rosetta.protocols.denovo_design.components.StructureData, resid_str: str) int ¶
C++: protocols::denovo_design::get_resid(const class protocols::denovo_design::components::StructureData &, const std::string &) –> unsigned long
- pyrosetta.rosetta.protocols.denovo_design.get_residue_selector(data: pyrosetta.rosetta.basic.datacache.DataMap, name: str) pyrosetta.rosetta.core.select.residue_selector.ResidueSelector ¶
C++: protocols::denovo_design::get_residue_selector(const class basic::datacache::DataMap &, const std::string &) –> class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>
- pyrosetta.rosetta.protocols.denovo_design.insert_peptide_edges(ft: pyrosetta.rosetta.core.kinematics.FoldTree, jedge: pyrosetta.rosetta.core.kinematics.Edge) None ¶
inserts the peptide edges to accomodate the new jump edge given
C++: protocols::denovo_design::insert_peptide_edges(class core::kinematics::FoldTree &, const class core::kinematics::Edge &) –> void
- pyrosetta.rosetta.protocols.denovo_design.linear_chainbreak(pose: pyrosetta.rosetta.core.pose.Pose, pos: int) float ¶
evaluate linear chainbreak at a position
- If necessary, will evaluate using a copy of the Pose with a cut
fold tree. If cutpoint variants are present at chainbreak, will use existing variants and not modify them. If cutpoint variants are not found will add them and then remove them once calculation is finished. Eventually this should be merged into protocols/forge/methods/linear_chainbreak.cc However, the changes I needed to make to that file break certain parts of remodel
C++: protocols::denovo_design::linear_chainbreak(const class core::pose::Pose &, const unsigned long) –> double
- pyrosetta.rosetta.protocols.denovo_design.loop_start_without_overlap(pose: pyrosetta.rosetta.core.pose.Pose, startres: int, overlap: int) int ¶
C++: protocols::denovo_design::loop_start_without_overlap(const class core::pose::Pose &, unsigned long, const unsigned long) –> unsigned long
- pyrosetta.rosetta.protocols.denovo_design.loop_stop_without_overlap(pose: pyrosetta.rosetta.core.pose.Pose, stopres: int, overlap: int) int ¶
C++: protocols::denovo_design::loop_stop_without_overlap(const class core::pose::Pose &, unsigned long, const unsigned long) –> unsigned long
- pyrosetta.rosetta.protocols.denovo_design.parse_motif_string(motif_str: str, secstruct: str, abego: str) None ¶
Computes secondary structure string from the given motifs
Motif string to be parsed (e.g. “5EB-2LG-5EB”)
Secondary structure string to be cleared and filled
ABEGO string to be cleared and filled
C++: protocols::denovo_design::parse_motif_string(const std::string &, std::string &, std::string &) –> void
- pyrosetta.rosetta.protocols.denovo_design.rebuild_missing_atoms(pose: pyrosetta.rosetta.core.pose.Pose, resi: int) None ¶
given a residue, rebuilds all missing atoms
C++: protocols::denovo_design::rebuild_missing_atoms(class core::pose::Pose &, const unsigned long) –> void
- pyrosetta.rosetta.protocols.denovo_design.remove_all_jump_atoms(orig: pyrosetta.rosetta.core.kinematics.FoldTree) pyrosetta.rosetta.core.kinematics.FoldTree ¶
C++: protocols::denovo_design::remove_all_jump_atoms(const class core::kinematics::FoldTree &) –> class core::kinematics::FoldTree
- pyrosetta.rosetta.protocols.denovo_design.remove_missing_jump_atoms(pose: pyrosetta.rosetta.core.pose.Pose, orig: pyrosetta.rosetta.core.kinematics.FoldTree) pyrosetta.rosetta.core.kinematics.FoldTree ¶
C++: protocols::denovo_design::remove_missing_jump_atoms(const class core::pose::Pose &, const class core::kinematics::FoldTree &) –> class core::kinematics::FoldTree
- pyrosetta.rosetta.protocols.denovo_design.same_pose(pose1: pyrosetta.rosetta.core.pose.Pose, pose2: pyrosetta.rosetta.core.pose.Pose) bool ¶
Tells whether the two given poses are identical based on # resides and dihedrals
C++: protocols::denovo_design::same_pose(const class core::pose::Pose &, const class core::pose::Pose &) –> bool
- pyrosetta.rosetta.protocols.denovo_design.slide_jump(ft_orig: pyrosetta.rosetta.core.kinematics.FoldTree, jump_idx: int, new_start: int, new_stop: int) pyrosetta.rosetta.core.kinematics.FoldTree ¶
C++: protocols::denovo_design::slide_jump(const class core::kinematics::FoldTree &, const unsigned long, const unsigned long, const unsigned long) –> class core::kinematics::FoldTree
- pyrosetta.rosetta.protocols.denovo_design.symmetric_fold_tree(pose: pyrosetta.rosetta.core.pose.Pose, asymm_ft: pyrosetta.rosetta.core.kinematics.FoldTree) pyrosetta.rosetta.core.kinematics.FoldTree ¶
- Given a symmetric pose, and a fold tree for the asymmetric unit, constructs and
returns a symmetric fold tree while preserving the topology of the aysmmetric unit’s fold tree
C++: protocols::denovo_design::symmetric_fold_tree(const class core::pose::Pose &, const class core::kinematics::FoldTree &) –> class core::kinematics::FoldTree
- pyrosetta.rosetta.protocols.denovo_design.symmetric_residue_subset(pose: pyrosetta.rosetta.core.pose.Pose, subset: pyrosetta.rosetta.utility.vector1_bool) pyrosetta.rosetta.utility.vector1_bool ¶
- Given a symmetric pose and a ResidueSubset for the asymmetric unit, constructs
and returns a residue subset compatible with the symmetric pose based on the given asymmetric unit residue subset
C++: protocols::denovo_design::symmetric_residue_subset(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) –> class utility::vector1<bool, class std::allocator<bool> >
- pyrosetta.rosetta.protocols.denovo_design.symmetric_secstruct(pose: pyrosetta.rosetta.core.pose.Pose, asymm_secstruct: str) str ¶
- Given a symmetric pose and a secstruct for the asymmetric unit, constructs and
returns a secondary structure string compatible with the symmetric pose based on the secondary structure of the asymmetric unit
C++: protocols::denovo_design::symmetric_secstruct(const class core::pose::Pose &, const std::string &) –> std::string