select¶

Bindings for core::select namespace

class pyrosetta.rosetta.core.select.Enumerate1WithSelector¶

Bases: pybind11_object

dereference(self: pyrosetta.rosetta.core.select.Enumerate1WithSelector) → int¶: C++: core::select::Enumerate1WithSelector::operator*() –> unsigned long &

pre_increment(self: pyrosetta.rosetta.core.select.Enumerate1WithSelector) → None¶: C++: core::select::Enumerate1WithSelector::operator++() –> void

class pyrosetta.rosetta.core.select.PreSelectedResidRange¶

Bases: pybind11_object

begin(self: pyrosetta.rosetta.core.select.PreSelectedResidRange) → pyrosetta.rosetta.core.select.Enumerate1WithSelector¶: C++: core::select::PreSelectedResidRange::begin() –> class core::select::Enumerate1WithSelector

end(self: pyrosetta.rosetta.core.select.PreSelectedResidRange) → pyrosetta.rosetta.core.select.Enumerate1WithSelector¶: C++: core::select::PreSelectedResidRange::end() –> class core::select::Enumerate1WithSelector

pyrosetta.rosetta.core.select.fill_neighbor_residues(*args, **kwargs)¶

Overloaded function.

fill_neighbor_residues(pose: pyrosetta.rosetta.core.pose.Pose, residue_positions: pyrosetta.rosetta.utility.vector1_bool) -> None
fill_neighbor_residues(pose: pyrosetta.rosetta.core.pose.Pose, residue_positions: pyrosetta.rosetta.utility.vector1_bool, neighbor_dis: float) -> None

Fill a boolean vector of residues with neighboring residues.

Uses 10A neighbor graph for neighbors, THEN takes distance from selection to neighbors to trim neighbors. residue_positions includes positions and neighbors. Use a NOT selector to get only the neighbors.

C++: core::select::fill_neighbor_residues(const class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> > &, double) –> void

pyrosetta.rosetta.core.select.fill_tenA_neighbor_residues(pose: pyrosetta.rosetta.core.pose.Pose, residue_positions: pyrosetta.rosetta.utility.vector1_bool) → None¶

Fill neighbor residues within 10 A CB distance cutoff using the 10 A neighbor graph in energies into the boolean vector.

C++: core::select::fill_tenA_neighbor_residues(const class core::pose::Pose &, class utility::vector1<bool, class std::allocator<bool> > &) –> void

pyrosetta.rosetta.core.select.filter_neighbors_by_distance(pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, selection_and_neighbors: pyrosetta.rosetta.utility.vector1_bool, dist_cutoff: float) → None¶

filter neighbors to a certain CB distance.: Takes distance from selection to neighbors to trim neighbors.

C++: core::select::filter_neighbors_by_distance(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, class utility::vector1<bool, class std::allocator<bool> > &, double &) –> void

pyrosetta.rosetta.core.select.get_master_subunit_selection(pose: pyrosetta.rosetta.core.pose.Pose, full_subset: pyrosetta.rosetta.utility.vector1_bool) → pyrosetta.rosetta.utility.vector1_bool¶

Turns off all residues that are not part of the master subunit.

C++: core::select::get_master_subunit_selection(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) –> class utility::vector1<bool, class std::allocator<bool> >

pyrosetta.rosetta.core.select.get_neighbor_residues(pose: pyrosetta.rosetta.core.pose.Pose, residue_positions: pyrosetta.rosetta.utility.vector1_bool, neighbor_dis: float) → pyrosetta.rosetta.utility.vector1_bool¶

Get a boolean vector of neighbor residues given some distance < 10A

C++: core::select::get_neighbor_residues(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, double) –> class utility::vector1<bool, class std::allocator<bool> >

pyrosetta.rosetta.core.select.get_pymol_selection_for_atoms(*args, **kwargs)¶

Overloaded function.

get_pymol_selection_for_atoms(pose: pyrosetta.rosetta.core.pose.Pose, atoms: pyrosetta.rosetta.utility.vector1_core_id_AtomID, sele_name: str) -> str
get_pymol_selection_for_atoms(pose: pyrosetta.rosetta.core.pose.Pose, atoms: pyrosetta.rosetta.utility.vector1_core_id_AtomID, sele_name: str, skip_virts: bool) -> str

Return a pymol selection of a set of atoms.

C++: core::select::get_pymol_selection_for_atoms(const class core::pose::Pose &, const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &, const std::string &, bool) –> std::string

pyrosetta.rosetta.core.select.get_residue_selector_from_subset(subset: pyrosetta.rosetta.utility.vector1_bool) → pyrosetta.rosetta.core.select.residue_selector.ResidueSelector¶

Convert a residue subset back into a residue selector.

Not only does this allow one to go from a residue subset back to a selector,
but by applying a selector to a pose and using this to go back to a selector, one can turn context-dependent residue selectors into context-independent residue selectors

C++: core::select::get_residue_selector_from_subset(class utility::vector1<bool, class std::allocator<bool> >) –> class std::shared_ptr<class core::select::residue_selector::ResidueSelector>

pyrosetta.rosetta.core.select.get_residue_set_from_subset(*args, **kwargs)¶

Overloaded function.

get_residue_set_from_subset(subset: pyrosetta.rosetta.utility.vector1_bool) -> pyrosetta.rosetta.std.set_unsigned_long_t
get_residue_set_from_subset(subset: pyrosetta.rosetta.utility.vector1_bool, select: bool) -> pyrosetta.rosetta.std.set_unsigned_long_t

Get a std::set of the indexes which are the same value as ‘select’ in the ResidueSubset.

C++: core::select::get_residue_set_from_subset(const class utility::vector1<bool, class std::allocator<bool> > &, bool) –> class std::set<unsigned long, struct std::less<unsigned long>, class std::allocator<unsigned long> >

pyrosetta.rosetta.core.select.get_residues_from_subset(*args, **kwargs)¶

Overloaded function.

get_residues_from_subset(subset: pyrosetta.rosetta.utility.vector1_bool) -> pyrosetta.rosetta.utility.vector1_unsigned_long
get_residues_from_subset(subset: pyrosetta.rosetta.utility.vector1_bool, select: bool) -> pyrosetta.rosetta.utility.vector1_unsigned_long

Get a vector1 of the indexes which are the same value as ‘select’ in the ResidueSubset.

C++: core::select::get_residues_from_subset(const class utility::vector1<bool, class std::allocator<bool> > &, bool) –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

pyrosetta.rosetta.core.select.get_subset_from_residues(*args, **kwargs)¶

Overloaded function.

get_subset_from_residues(selection: pyrosetta.rosetta.utility.vector1_unsigned_long, total_nres: int) -> pyrosetta.rosetta.utility.vector1_bool
get_subset_from_residues(selection: pyrosetta.rosetta.utility.vector1_unsigned_long, total_nres: int, invert: bool) -> pyrosetta.rosetta.utility.vector1_bool

Get a vector1 of true/false (a ResidueSubset) from a list of residue numbers.

If invert is true, residues not in the selection are true in the returned vector.

C++: core::select::get_subset_from_residues(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, unsigned long, bool) –> class utility::vector1<bool, class std::allocator<bool> >

pyrosetta.rosetta.core.select.get_tenA_neighbor_residues(pose: pyrosetta.rosetta.core.pose.Pose, residue_positions: pyrosetta.rosetta.utility.vector1_bool) → pyrosetta.rosetta.utility.vector1_bool¶

Get neighbor residues within 10 A CB distance cutoff using the 10 A neighbor graph in energies.: Returns ONLY the neighbor residues.

C++: core::select::get_tenA_neighbor_residues(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) –> class utility::vector1<bool, class std::allocator<bool> >

pyrosetta.rosetta.core.select.resids(*args, **kwargs)¶

Overloaded function.

resids(pose: pyrosetta.rosetta.core.pose.Pose) -> pyrosetta.rosetta.utility.SimpleRange1

USAGE: for( core::Size const resid : resids( pose ) )

C++: core::select::resids(const class core::pose::Pose &) –> class utility::SimpleRange1

resids(pose: pyrosetta.rosetta.core.pose.Pose, selectors: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_select_residue_selector_ResidueSelector_t) -> pyrosetta.rosetta.core.select.PreSelectedResidRange

USAGES: for( core::Size const resid : resids( pose, {s1, s2} ) )

C++: core::select::resids(const class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<const class core::select::residue_selector::ResidueSelector>, class std::allocator<class std::shared_ptr<const class core::select::residue_selector::ResidueSelector> > > &) –> class core::select::PreSelectedResidRange

pyrosetta.rosetta.core.select.trim_neighbors_by_distance(pose: pyrosetta.rosetta.core.pose.Pose, selection: pyrosetta.rosetta.utility.vector1_bool, selection_and_neighbors: pyrosetta.rosetta.utility.vector1_bool, dist_cutoff: float) → pyrosetta.rosetta.utility.vector1_bool¶

filter neighbors to a certain CB distance.: Takes distance from selection to neighbors to trim neighbors.

C++: core::select::trim_neighbors_by_distance(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &, double &) –> class utility::vector1<bool, class std::allocator<bool> >