rotamer_set

• symmetry

Bindings for core::pack::rotamer_set namespace

class pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation

Bases: RotamerSetOperation

Adds in rotamers from a list of Residues,

alter_rotamer_set(self: pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, : pyrosetta.rosetta.core.pack.task.PackerTask, : pyrosetta.rosetta.utility.graph.Graph, rotamer_set: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → None

C++: core::pack::rotamer_set::AddResiduesRotamerSetOperation::alter_rotamer_set(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class core::pack::rotamer_set::RotamerSet &) –> void

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation, : pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation) → pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation

C++: core::pack::rotamer_set::AddResiduesRotamerSetOperation::operator=(const class core::pack::rotamer_set::AddResiduesRotamerSetOperation &) –> class core::pack::rotamer_set::AddResiduesRotamerSetOperation &

clone(self: pyrosetta.rosetta.core.pack.rotamer_set.AddResiduesRotamerSetOperation) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

C++: core::pack::rotamer_set::AddResiduesRotamerSetOperation::clone() const –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSetOperation>

increase_packer_residue_radius(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, the_task: pyrosetta.rosetta.core.pack.task.PackerTask, residue_in: int) → float

C++: core::pack::rotamer_set::RotamerSetOperation::increase_packer_residue_radius(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, unsigned long) const –> double

class pyrosetta.rosetta.core.pack.rotamer_set.BumpSelector

Bases: pybind11_object

iterate_bump_selector(self: pyrosetta.rosetta.core.pack.rotamer_set.BumpSelector, bumpenegy: float) → pyrosetta.rosetta.core.pack.rotamer_set.BumpSelectorDecision

run bump filter for current rot

C++: core::pack::rotamer_set::BumpSelector::iterate_bump_selector(double) –> enum core::pack::rotamer_set::BumpSelectorDecision

reset(self: pyrosetta.rosetta.core.pack.rotamer_set.BumpSelector) → None

reset bump selector best energy

C++: core::pack::rotamer_set::BumpSelector::reset() –> void

set_max_rot_bumpenergy(self: pyrosetta.rosetta.core.pack.rotamer_set.BumpSelector, setting: float) → None

C++: core::pack::rotamer_set::BumpSelector::set_max_rot_bumpenergy(double) –> void

class pyrosetta.rosetta.core.pack.rotamer_set.BumpSelectorDecision

Bases: pybind11_object

Members:

KEEP_ROTAMER

DELETE_ROTAMER

DELETE_PREVIOUS_ROTAMER

DELETE_PREVIOUS_ROTAMER = <BumpSelectorDecision.DELETE_PREVIOUS_ROTAMER: 2>

DELETE_ROTAMER = <BumpSelectorDecision.DELETE_ROTAMER: 1>

KEEP_ROTAMER = <BumpSelectorDecision.KEEP_ROTAMER: 0>

property name

property value

class pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet, : pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet) → pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet

C++: core::pack::rotamer_set::ContinuousRotamerSet::operator=(const class core::pack::rotamer_set::ContinuousRotamerSet &) –> class core::pack::rotamer_set::ContinuousRotamerSet &

baserotamer_data(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet, aa_ind: int, rotid_for_aa: int) → pyrosetta.rosetta.core.pack.dunbrack.DunbrackRotamerSampleData

C++: core::pack::rotamer_set::ContinuousRotamerSet::baserotamer_data(unsigned long, unsigned long) const –> const class core::pack::dunbrack::DunbrackRotamerSampleData &

build_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet, pose: pyrosetta.rosetta.core.pose.Pose, resid: int, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::rotamer_set::ContinuousRotamerSet::build_rotamers(const class core::pose::Pose &, unsigned long, const class core::pack::task::PackerTask &) –> void

current_rotamer_coords(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet) → pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t

C++: core::pack::rotamer_set::ContinuousRotamerSet::current_rotamer_coords() const –> const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &

get_n_baserotamers_for_rotblock(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet, which_restype: int) → int

C++: core::pack::rotamer_set::ContinuousRotamerSet::get_n_baserotamers_for_rotblock(unsigned long) const –> unsigned long

get_n_residue_types(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet) → int

C++: core::pack::rotamer_set::ContinuousRotamerSet::get_n_residue_types() const –> unsigned long

get_n_sampling_rotamers_for_rotblock(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet, which_restype: int) → int

C++: core::pack::rotamer_set::ContinuousRotamerSet::get_n_sampling_rotamers_for_rotblock(unsigned long) const –> unsigned long

get_rotblock_index_for_sampling_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet, which_rotamer: int) → int

Rotamers i to i+j of all the same residue type are grouped together.

This function returns the index of the residue type in a contiguous block of rotamers. E.g. rotamers 100 to 120 might all be lysine rotamers, and might be the 8th residue type, with the first 7 residue types spanning rotamers 1 to 99. If new lysine rotamers are appended to the end of the rotamer set, they are considered to be in a separate residue type block. Lysine rotamers 200 to 210 might be block 15 while lysine rotamers 100 to 120 are still block 7.

C++: core::pack::rotamer_set::ContinuousRotamerSet::get_rotblock_index_for_sampling_rotamer(unsigned long) const –> unsigned long

num_base_rotamers_total(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet) → int

C++: core::pack::rotamer_set::ContinuousRotamerSet::num_base_rotamers_total() const –> unsigned long

num_sampling_rotamers_total(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet) → int

C++: core::pack::rotamer_set::ContinuousRotamerSet::num_sampling_rotamers_total() const –> unsigned long

pick_baserotamer_from_rotblock(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet, aa_ind: int, rand_btw_0_and_1: float) → int

C++: core::pack::rotamer_set::ContinuousRotamerSet::pick_baserotamer_from_rotblock(unsigned long, double) const –> unsigned long

resid(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet) → int

C++: core::pack::rotamer_set::ContinuousRotamerSet::resid() const –> unsigned long

restype_for_rotblock(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet, rotblock: int) → pyrosetta.rosetta.core.chemical.ResidueType

C++: core::pack::rotamer_set::ContinuousRotamerSet::restype_for_rotblock(unsigned long) const –> class std::shared_ptr<const class core::chemical::ResidueType>

sampling_id_for_current_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet) → int

C++: core::pack::rotamer_set::ContinuousRotamerSet::sampling_id_for_current_rotamer() const –> unsigned long

class pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets, : pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets) → pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets

C++: core::pack::rotamer_set::ContinuousRotamerSets::operator=(const class core::pack::rotamer_set::ContinuousRotamerSets &) –> class core::pack::rotamer_set::ContinuousRotamerSets &

full_sample_rot_index_2_moltenres_sample_rot_index(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets, sample_rotno: int) → int

C++: core::pack::rotamer_set::ContinuousRotamerSets::full_sample_rot_index_2_moltenres_sample_rot_index(unsigned long) const –> unsigned long

moltenres_for_sample_rot(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets, sample_rotno: int) → int

C++: core::pack::rotamer_set::ContinuousRotamerSets::moltenres_for_sample_rot(unsigned long) const –> unsigned long

moltenresid_2_resid(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets, : int) → int

C++: core::pack::rotamer_set::ContinuousRotamerSets::moltenresid_2_resid(unsigned long) const –> unsigned long

n_sample_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets) → int

C++: core::pack::rotamer_set::ContinuousRotamerSets::n_sample_rotamers() const –> unsigned long

nmoltenres(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets) → int

C++: core::pack::rotamer_set::ContinuousRotamerSets::nmoltenres() const –> unsigned long

resid_2_moltenresid(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets, : int) → int

C++: core::pack::rotamer_set::ContinuousRotamerSets::resid_2_moltenresid(unsigned long) const –> unsigned long

rotamer_set_for_moltenres(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets, : int) → pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet

C++: core::pack::rotamer_set::ContinuousRotamerSets::rotamer_set_for_moltenres(unsigned long) const –> const class core::pack::rotamer_set::ContinuousRotamerSet &

rotamer_set_for_res(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets, : int) → pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSet

C++: core::pack::rotamer_set::ContinuousRotamerSets::rotamer_set_for_res(unsigned long) const –> const class core::pack::rotamer_set::ContinuousRotamerSet &

total_residue(self: pyrosetta.rosetta.core.pack.rotamer_set.ContinuousRotamerSets) → int

C++: core::pack::rotamer_set::ContinuousRotamerSets::total_residue() const –> unsigned long

class pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation

Bases: RotamerSetOperation

Adds in rotamers from a list of Residues,

alter_rotamer_set(self: pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, rotamer_set: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → None

C++: core::pack::rotamer_set::DeleteAllRotamerSetOperation::alter_rotamer_set(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class core::pack::rotamer_set::RotamerSet &) –> void

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation, : pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation) → pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation

C++: core::pack::rotamer_set::DeleteAllRotamerSetOperation::operator=(const class core::pack::rotamer_set::DeleteAllRotamerSetOperation &) –> class core::pack::rotamer_set::DeleteAllRotamerSetOperation &

clone(self: pyrosetta.rosetta.core.pack.rotamer_set.DeleteAllRotamerSetOperation) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

C++: core::pack::rotamer_set::DeleteAllRotamerSetOperation::clone() const –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSetOperation>

increase_packer_residue_radius(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, the_task: pyrosetta.rosetta.core.pack.task.PackerTask, residue_in: int) → float

C++: core::pack::rotamer_set::RotamerSetOperation::increase_packer_residue_radius(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, unsigned long) const –> double

class pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets

Bases: RotamerSetsBase

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets, : pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets) → pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets

C++: core::pack::rotamer_set::FixbbRotamerSets::operator=(const class core::pack::rotamer_set::FixbbRotamerSets &) –> class core::pack::rotamer_set::FixbbRotamerSets &

initialize_pose_for_rotsets_creation(self: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase, pose: pyrosetta.rosetta.core.pose.Pose) → None

Give the pose a chance to stash any data needed by the _rotset_

need nonconst access to pose

C++: core::pack_basic::RotamerSetsBase::initialize_pose_for_rotsets_creation(class core::pose::Pose &) const –> void

moltenres_2_resid(self: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase, : int) → int

C++: core::pack_basic::RotamerSetsBase::moltenres_2_resid(unsigned long) const –> unsigned long

moltenres_2_resid_vector(self: pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::rotamer_set::FixbbRotamerSets::moltenres_2_resid_vector() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

moltenres_for_rotamer(self: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase, : int) → int

C++: core::pack_basic::RotamerSetsBase::moltenres_for_rotamer(unsigned long) const –> unsigned long

moltenres_rotid_2_rotid(self: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase, moltenres: int, moltenresrotid: int) → int

convert moltenres rotid to id in full rotamer enumeration

C++: core::pack_basic::RotamerSetsBase::moltenres_rotid_2_rotid(unsigned long, unsigned long) const –> unsigned long

nmoltenres(self: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) → int

C++: core::pack_basic::RotamerSetsBase::nmoltenres() const –> unsigned long

nrotamer_offset_for_moltenres(self: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase, : int) → int

C++: core::pack_basic::RotamerSetsBase::nrotamer_offset_for_moltenres(unsigned long) const –> unsigned long

nrotamers(self: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) → int

C++: core::pack_basic::RotamerSetsBase::nrotamers() const –> unsigned long

nrotamers_for_moltenres(self: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase, : int) → int

C++: core::pack_basic::RotamerSetsBase::nrotamers_for_moltenres(unsigned long) const –> unsigned long

res_for_rotamer(self: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase, : int) → int

C++: core::pack_basic::RotamerSetsBase::res_for_rotamer(unsigned long) const –> unsigned long

resid_2_moltenres(self: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase, : int) → int

C++: core::pack_basic::RotamerSetsBase::resid_2_moltenres(unsigned long) const –> unsigned long

resid_2_moltenres_vector(self: pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::rotamer_set::FixbbRotamerSets::resid_2_moltenres_vector() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

rotamer(self: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase, : int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack_basic::RotamerSetsBase::rotamer(unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

rotamer_for_moltenres(self: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase, moltenres_id: int, rotamerid: int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack_basic::RotamerSetsBase::rotamer_for_moltenres(unsigned long, unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

rotamer_set_for_moltenresidue(self: pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets, moltenresid: int) → core::pack::rotamer_set::RotamerSet

C++: core::pack::rotamer_set::FixbbRotamerSets::rotamer_set_for_moltenresidue(unsigned long) –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>

rotamer_set_for_residue(self: pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets, resid: int) → core::pack::rotamer_set::RotamerSet

C++: core::pack::rotamer_set::FixbbRotamerSets::rotamer_set_for_residue(unsigned long) –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>

rotid_on_moltenresidue(self: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase, rotid: int) → int

convert rotid in full rotamer enumeration into rotamer id on its source residue

C++: core::pack_basic::RotamerSetsBase::rotid_on_moltenresidue(unsigned long) const –> unsigned long

show(self: pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets, out: pyrosetta.rosetta.std.ostream) → None

C++: core::pack::rotamer_set::FixbbRotamerSets::show(std::ostream &) const –> void

total_residue(self: pyrosetta.rosetta.core.pack_basic.RotamerSetsBase) → int

C++: core::pack_basic::RotamerSetsBase::total_residue() const –> unsigned long

class pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminator

Bases: RotamerSetsOperation

alter_rotamer_sets(self: pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminator, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) → None

C++: core::pack::rotamer_set::PyRotamerEliminator::alter_rotamer_sets(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class core::pack::rotamer_set::RotamerSets &) –> void

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminator, : pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminator) → pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminator

C++: core::pack::rotamer_set::PyRotamerEliminator::operator=(const class core::pack::rotamer_set::PyRotamerEliminator &) –> class core::pack::rotamer_set::PyRotamerEliminator &

clone(self: pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminator) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsOperation

C++: core::pack::rotamer_set::PyRotamerEliminator::clone() const –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSetsOperation>

set_eliminator_function(self: pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminator, f: Callable[[pyrosetta.rosetta.core.pose.Pose, pyrosetta.rosetta.core.scoring.ScoreFunction, pyrosetta.rosetta.core.pack.task.PackerTask, pyrosetta.rosetta.utility.graph.Graph, pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets], pyrosetta.rosetta.utility.vector1_bool]) → None

C++: core::pack::rotamer_set::PyRotamerEliminator::set_eliminator_function(const class std::function<class utility::vector1<bool, class std::allocator<bool> > (const class core::pose::Pose &, class std::shared_ptr<const class core::scoring::ScoreFunction>, class std::shared_ptr<const class core::pack::task::PackerTask>, class std::shared_ptr<const class utility::graph::Graph>, const class core::pack::rotamer_set::RotamerSets &)> &) –> void

class pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminatorTaskOperation

Bases: TaskOperation

apply(self: pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminatorTaskOperation, : pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::rotamer_set::PyRotamerEliminatorTaskOperation::apply(const class core::pose::Pose &, class core::pack::task::PackerTask &) const –> void

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminatorTaskOperation, : pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminatorTaskOperation) → pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminatorTaskOperation

C++: core::pack::rotamer_set::PyRotamerEliminatorTaskOperation::operator=(const class core::pack::rotamer_set::PyRotamerEliminatorTaskOperation &) –> class core::pack::rotamer_set::PyRotamerEliminatorTaskOperation &

clone(self: pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminatorTaskOperation) → pyrosetta.rosetta.core.pack.task.operation.TaskOperation

C++: core::pack::rotamer_set::PyRotamerEliminatorTaskOperation::clone() const –> class std::shared_ptr<class core::pack::task::operation::TaskOperation>

parse_tag(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.utility.tag.Tag, : pyrosetta.rosetta.basic.datacache.DataMap) → None

Used to parse an xml-like tag to load parameters and properties.

C++: core::pack::task::operation::TaskOperation::parse_tag(class std::shared_ptr<const class utility::tag::Tag>, class basic::datacache::DataMap &) –> void

provide_citation_info(self: pyrosetta.rosetta.core.pack.task.operation.TaskOperation, : pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) → None

Provide citations to the passed CitationCollectionList

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by task operations wishing to provide citation information.

C++: core::pack::task::operation::TaskOperation::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

set_eliminator(self: pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminatorTaskOperation, e: pyrosetta.rosetta.core.pack.rotamer_set.PyRotamerEliminator) → None

C++: core::pack::rotamer_set::PyRotamerEliminatorTaskOperation::set_eliminator(class std::shared_ptr<class core::pack::rotamer_set::PyRotamerEliminator>) –> void

class pyrosetta.rosetta.core.pack.rotamer_set.RotamerCouplings

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerCouplings, : pyrosetta.rosetta.core.pack.rotamer_set.RotamerCouplings) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerCouplings

C++: core::pack::rotamer_set::RotamerCouplings::operator=(const class core::pack::rotamer_set::RotamerCouplings &) –> class core::pack::rotamer_set::RotamerCouplings &

resize(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerCouplings, size_in: int) → None

C++: core::pack::rotamer_set::RotamerCouplings::resize(const unsigned long) –> void

class pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks, : pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks

C++: core::pack::rotamer_set::RotamerLinks::operator=(const class core::pack::rotamer_set::RotamerLinks &) –> class core::pack::rotamer_set::RotamerLinks &

get_equiv(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks, index: int) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::rotamer_set::RotamerLinks::get_equiv(const unsigned long) const –> class utility::vector1<unsigned long, class std::allocator<unsigned long> >

get_template(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks, rs: int) → int

C++: core::pack::rotamer_set::RotamerLinks::get_template(unsigned long) const –> unsigned long

has(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks, index: int) → bool

C++: core::pack::rotamer_set::RotamerLinks::has(unsigned long) const –> bool

resize(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks, res: int) → None

C++: core::pack::rotamer_set::RotamerLinks::resize(const unsigned long) –> void

set_equiv(*args, **kwargs)

Overloaded function.

1. set_equiv(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks, rs1: int, rs2: int) -> None

C++: core::pack::rotamer_set::RotamerLinks::set_equiv(const unsigned long, const unsigned long) –> void

2. set_equiv(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks, rs1: int, list: pyrosetta.rosetta.utility.vector1_int) -> None

C++: core::pack::rotamer_set::RotamerLinks::set_equiv(const unsigned long, class utility::vector1<int, class std::allocator<int> >) –> void

set_template(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerLinks, rs1: int, rs2: int) → None

C++: core::pack::rotamer_set::RotamerLinks::set_template(const unsigned long, const unsigned long) –> void

class pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation

Bases: pybind11_object

RotamerSetOperations are able to modify the contents of a RotamerSet within the packer immediately after rotamer creation.

They are handed into the packer through a packer task; each ResidueLevelTask

keeps its own list of rotamer set operations.

Each RotamerSet, within the build_rotamers() method will iterate across

the RotamerSetOperation objects, and call alter_rotamer_set on each element in the ResidueLevelTask’s list of rotamer_set_operations.

RotamerSetOperations are visited in the order in which they are appended

to the ResidueLevelTasks’s operation list.

RotamerSetOperations are unable to correlate changes to rotamer sets across

multiple rotamer sets – they have access to only a single RotamerSet object in their alter_rotamer_set operations. For correlated alterations to rotamer sets, the RotamerSetsOperation class should be used.

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation, : pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerOperation

C++: core::pack::rotamer_set::RotamerOperation::operator=(const class core::pack::rotamer_set::RotamerOperation &) –> class core::pack::rotamer_set::RotamerOperation &

class pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

Bases: RotamerSetBase

add_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, rotamer: pyrosetta.rosetta.core.conformation.Residue) → None

Append a rotamer to the list; it will not be sorted into the same group as other rotamers

of the same group or amino acid unless the last group/amino acid is already the same. Instead it will sit at the end of the list of Rotamers. There are performance implications of using this function instead of add_rotamer_into_existing_group: there are several places in the code which scale quadratically with the number of amino acid groups (but where we assume that this number is small) so if you call this function N times oscilating between ASP and ASN rotamers, you will get O(N^2) performance. If you do not need your rotamers to appear in a particular order, use add_rotamer_into_existing_group instead.

C++: core::pack::rotamer_set::RotamerSet::add_rotamer(const class core::conformation::Residue &) –> void

add_rotamer_into_existing_group(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, rotamer: pyrosetta.rosetta.core.conformation.Residue) → None

Add a rotamer to the RotamerSet where you will group it with other residues of the same type

or barring that, the same group. This will keep the total number of residue type groups down. It will not guarantee (it cannot guarantee) that the newly added rotamer will appear after existing rotamers or at the end of the list of rotamers – if you need that kind of guarantee, use add_rotamer instead.

C++: core::pack::rotamer_set::RotamerSet::add_rotamer_into_existing_group(const class core::conformation::Residue &) –> void

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, : pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

C++: core::pack::rotamer_set::RotamerSet::operator=(const class core::pack::rotamer_set::RotamerSet &) –> class core::pack::rotamer_set::RotamerSet &

build_dependent_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph) → None

C++: core::pack::rotamer_set::RotamerSet::build_dependent_rotamers(const class core::pack::rotamer_set::RotamerSets &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) –> void

build_rotamers(*args, **kwargs)

Overloaded function.

1. build_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, the_pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph) -> None

2. build_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, the_pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, use_neighbor_context: bool) -> None

C++: core::pack::rotamer_set::RotamerSet::build_rotamers(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, bool) –> void

compute_one_and_two_body_energies(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, one_body_energies: pyrosetta.rosetta.utility.vector1_float, two_body_energies: pyrosetta.rosetta.utility.vector1_utility_vector1_float_std_allocator_float_t, packable_neighbors: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: core::pack::rotamer_set::RotamerSet::compute_one_and_two_body_energies(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<float, class std::allocator<float> > &, class utility::vector1<class utility::vector1<float, class std::allocator<float> >, class std::allocator<class utility::vector1<float, class std::allocator<float> > > > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

compute_one_body_energies(*args, **kwargs)

Overloaded function.

1. compute_one_body_energies(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, energies: pyrosetta.rosetta.utility.vector1_float) -> None

2. compute_one_body_energies(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, energies: pyrosetta.rosetta.utility.vector1_float, no_update: bool) -> None

C++: core::pack::rotamer_set::RotamerSet::compute_one_body_energies(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<float, class std::allocator<float> > &, const bool) const –> void

compute_one_body_energy_maps(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, energies: pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector) → None

for OptE

C++: core::pack::rotamer_set::RotamerSet::compute_one_body_energy_maps(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<class core::scoring::EMapVector, class std::allocator<class core::scoring::EMapVector> > &) const –> void

data(self: pyrosetta.rosetta.core.conformation.RotamerSetBase) → pyrosetta.rosetta.basic.datacache.BasicDataCache

BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh

C++: core::conformation::RotamerSetBase::data() –> class basic::datacache::BasicDataCache &

drop_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, rot_id: int) → None

removes a single rotamer and causes a rotamer index update

C++: core::pack::rotamer_set::RotamerSet::drop_rotamer(unsigned long) –> void

drop_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, rotamers_to_delete: pyrosetta.rosetta.utility.vector1_bool) → None

rotamers_to_delete must be of size nrotmaers – each position

in the array that’s “true” is removed from the set of rotamers

C++: core::pack::rotamer_set::RotamerSet::drop_rotamers(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

drop_rotamers_by_index(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, rotamer_indices_to_delete: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

deletes the rotamers in the list with the given indices.

The indices of these rotamers is presumed to be those before any delete operation. e.g. if there are four rotamers, and rotamer_indices_to_delete includes 1 & 3, then the rotamers that will remain are the rotamers originally indexed as 2 and 4, even though their new indices will be 1 & 2.

C++: core::pack::rotamer_set::RotamerSet::drop_rotamers_by_index(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

get_n_residue_groups(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → int

Return the number of different residue groups. Two residue types are considered

to be part of the same block of residues if 1. they have the same address or 2. they have the same “name3” and the same neighbor radius.

C++: core::pack::rotamer_set::RotamerSet::get_n_residue_groups() const –> unsigned long

get_n_residue_types(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → int

Return the number of different residue types; two residue types are considered

different if they have a different address.

C++: core::pack::rotamer_set::RotamerSet::get_n_residue_types() const –> unsigned long

get_n_rotamers_for_residue_group(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, which_resgroup: int) → int

C++: core::pack::rotamer_set::RotamerSet::get_n_rotamers_for_residue_group(unsigned long) const –> unsigned long

get_n_rotamers_for_residue_type(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, which_restype: int) → int

C++: core::pack::rotamer_set::RotamerSet::get_n_rotamers_for_residue_type(unsigned long) const –> unsigned long

get_residue_group_begin(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, which_resgroup: int) → int

Return the first rotamer that belongs to a particular rotamer group

C++: core::pack::rotamer_set::RotamerSet::get_residue_group_begin(unsigned long) const –> unsigned long

get_residue_group_index_for_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, which_rotamer: int) → int

Return the index of the rotamer group for a particular rotamer.

C++: core::pack::rotamer_set::RotamerSet::get_residue_group_index_for_rotamer(unsigned long) const –> unsigned long

get_residue_type_begin(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, which_restype: int) → int

Return the first rotamer of a particular residue type

C++: core::pack::rotamer_set::RotamerSet::get_residue_type_begin(unsigned long) const –> unsigned long

get_residue_type_index_for_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, which_rotamer: int) → int

Rotamers i to i+j of all the same residue type are grouped together.

This function returns the index of the residue type in a contiguous block of rotamers. E.g. rotamers 100 to 120 might all be lysine rotamers, and might be the 8th residue type, with the first 7 residue types spanning rotamers 1 to 99. If new lysine rotamers are appended to the end of the rotamer set, they are considered to be in a separate residue type block. Lysine rotamers 200 to 210 might be block 15 while lysine rotamers 100 to 120 are still block 7.

C++: core::pack::rotamer_set::RotamerSet::get_residue_type_index_for_rotamer(unsigned long) const –> unsigned long

get_trie(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, method_enum_id: int) → pyrosetta.rosetta.core.conformation.AbstractRotamerTrie

C++: core::pack::rotamer_set::RotamerSet::get_trie(unsigned long) const –> class std::shared_ptr<const class core::conformation::AbstractRotamerTrie>

id_for_current_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → int

Return the index in the RotamerSet for the current rotamer

C++: core::pack::rotamer_set::RotamerSet::id_for_current_rotamer() const –> unsigned long

initialize_pose_for_rotset_creation(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, pose: pyrosetta.rosetta.core.pose.Pose) → None

C++: core::pack::rotamer_set::RotamerSet::initialize_pose_for_rotset_creation(class core::pose::Pose &) const –> void

nonconst_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, rot_id: int) → pyrosetta.rosetta.core.conformation.Residue

mutatable access to a single rotamer in the set.

C++: core::pack::rotamer_set::RotamerSet::nonconst_rotamer(unsigned long) –> class std::shared_ptr<class core::conformation::Residue>

num_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → int

C++: core::pack::rotamer_set::RotamerSet::num_rotamers() const –> unsigned long

resid(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → int

C++: core::pack::rotamer_set::RotamerSet::resid() const –> unsigned long

rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, rot_id: int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::RotamerSet::rotamer(unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

rotamer_data_cache(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, rot_id: int) → pyrosetta.rosetta.basic.datacache.BasicDataCache

C++: core::pack::rotamer_set::RotamerSet::rotamer_data_cache(unsigned long) const –> class basic::datacache::BasicDataCache &

rotamer_ref(self: pyrosetta.rosetta.core.conformation.RotamerSetBase, rot_id: int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::conformation::RotamerSetBase::rotamer_ref(unsigned long) const –> const class core::conformation::Residue &

set_resid(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, resid: int) → None

C++: core::pack::rotamer_set::RotamerSet::set_resid(unsigned long) –> void

show(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, out: pyrosetta.rosetta.std.ostream) → None

C++: core::pack::rotamer_set::RotamerSet::show(std::ostream &) const –> void

store_trie(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, method_enum_id: int, trie: pyrosetta.rosetta.core.conformation.AbstractRotamerTrie) → None

C++: core::pack::rotamer_set::RotamerSet::store_trie(unsigned long, class std::shared_ptr<class core::conformation::AbstractRotamerTrie>) –> void

update_rotamer_offsets(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → None

Lazy update of rotamer indices and offsets and integration of those rotamers

in the rotamers_waiting_for_sort_ list.

C++: core::pack::rotamer_set::RotamerSet::update_rotamer_offsets() const –> void

class pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetFactory

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetFactory, : pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetFactory) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetFactory

C++: core::pack::rotamer_set::RotamerSetFactory::operator=(const class core::pack::rotamer_set::RotamerSetFactory &) –> class core::pack::rotamer_set::RotamerSetFactory &

static create_rotamer_set(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

Create a generic RotamerSet object for the pose.

C++: core::pack::rotamer_set::RotamerSetFactory::create_rotamer_set(const class core::pose::Pose &) –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>

class pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

Bases: pybind11_object

alter_rotamer_set(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, rotamer_set: core::pack::rotamer_set::RotamerSet) → None

C++: core::pack::rotamer_set::RotamerSetOperation::alter_rotamer_set(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class core::pack::rotamer_set::RotamerSet &) –> void

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation, : pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

C++: core::pack::rotamer_set::RotamerSetOperation::operator=(const class core::pack::rotamer_set::RotamerSetOperation &) –> class core::pack::rotamer_set::RotamerSetOperation &

clone(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

C++: core::pack::rotamer_set::RotamerSetOperation::clone() const –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSetOperation>

increase_packer_residue_radius(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, the_task: pyrosetta.rosetta.core.pack.task.PackerTask, residue_in: int) → float

C++: core::pack::rotamer_set::RotamerSetOperation::increase_packer_residue_radius(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, unsigned long) const –> double

class pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_

Bases: RotamerSet

Container for a set of rotamers for use in packing. Rotamers are sorted into groups of the same residue type. Offsets into these rotamer groups are maintained by this class, as is information concerning the “original rotamer” – the rotamer present on the input pose before packing began.

add_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rotamer: pyrosetta.rosetta.core.conformation.Residue) → None

C++: core::pack::rotamer_set::RotamerSet_::add_rotamer(const class core::conformation::Residue &) –> void

add_rotamer_into_existing_group(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rotamer: pyrosetta.rosetta.core.conformation.Residue) → None

C++: core::pack::rotamer_set::RotamerSet_::add_rotamer_into_existing_group(const class core::conformation::Residue &) –> void

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, : pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

C++: core::pack::rotamer_set::RotamerSet::operator=(const class core::pack::rotamer_set::RotamerSet &) –> class core::pack::rotamer_set::RotamerSet &

build_dependent_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph) → None

Build rotamers that depend on positions of rotamers built in a previous pass

C++: core::pack::rotamer_set::RotamerSet_::build_dependent_rotamers(const class core::pack::rotamer_set::RotamerSets &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) –> void

build_rotamers(*args, **kwargs)

Overloaded function.

1. build_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, the_pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph) -> None

2. build_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, the_pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, use_neighbor_context: bool) -> None

C++: core::pack::rotamer_set::RotamerSet_::build_rotamers(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, bool) –> void

bump_check(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rotamer: pyrosetta.rosetta.core.conformation.Residue, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph) → float

Computes the “bump energy” of a rotamer: the bump energy is the

sum of rotamer’s interactions with 1) the backbone-and-side chains of neighboring residues that are held fixed during this repacking optimization and 2) the backbones of neighboring residues that are changable during this repacking optimization.

C++: core::pack::rotamer_set::RotamerSet_::bump_check(class std::shared_ptr<const class core::conformation::Residue>, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) const –> float

compute_one_and_two_body_energies(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, one_body_energies: pyrosetta.rosetta.utility.vector1_float, two_body_energies: pyrosetta.rosetta.utility.vector1_utility_vector1_float_std_allocator_float_t, packable_neighbors: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

Computes the packers one body energies for the set of rotamers as well

as two body energies for neighboring positions defined as packable by the task.

C++: core::pack::rotamer_set::RotamerSet_::compute_one_and_two_body_energies(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<float, class std::allocator<float> > &, class utility::vector1<class utility::vector1<float, class std::allocator<float> >, class std::allocator<class utility::vector1<float, class std::allocator<float> > > > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

compute_one_body_energies(*args, **kwargs)

Overloaded function.

1. compute_one_body_energies(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, energies: pyrosetta.rosetta.utility.vector1_float) -> None

2. compute_one_body_energies(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, energies: pyrosetta.rosetta.utility.vector1_float, no_update: bool) -> None

Computes the packers “one body energies” for the set of rotamers.

If no_update is true, we skip the lazy update of rotamers (which is potentially not threadsafe).

C++: core::pack::rotamer_set::RotamerSet_::compute_one_body_energies(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<float, class std::allocator<float> > &, const bool) const –> void

compute_one_body_energy_maps(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, energies: pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector) → None

for OPTE

C++: core::pack::rotamer_set::RotamerSet_::compute_one_body_energy_maps(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<class core::scoring::EMapVector, class std::allocator<class core::scoring::EMapVector> > &) const –> void

data(self: pyrosetta.rosetta.core.conformation.RotamerSetBase) → pyrosetta.rosetta.basic.datacache.BasicDataCache

BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh

C++: core::conformation::RotamerSetBase::data() –> class basic::datacache::BasicDataCache &

drop_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rot_id: int) → None

removes a single rotamer and causes a rotamer index update

C++: core::pack::rotamer_set::RotamerSet_::drop_rotamer(unsigned long) –> void

drop_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rotamers_to_delete: pyrosetta.rosetta.utility.vector1_bool) → None

rotamers_to_delete must be of size nrotmaers – each position

in the array that’s “true” is removed from the set of rotamers

C++: core::pack::rotamer_set::RotamerSet_::drop_rotamers(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

drop_rotamers_by_index(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rotamer_indices_to_delete: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

deletes the rotamers in the list with the given indices.

The indices of these rotamers is presumed to be those before any delete operation. e.g. if there are four rotamers, and rotamer_indices_to_delete includes 1 & 3, then the rotamers that will remain are the rotamers originally indexed as 2 and 4, even though their new indices will be 1 & 2.

C++: core::pack::rotamer_set::RotamerSet_::drop_rotamers_by_index(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

get_n_residue_groups(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_) → int

C++: core::pack::rotamer_set::RotamerSet_::get_n_residue_groups() const –> unsigned long

get_n_residue_types(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_) → int

C++: core::pack::rotamer_set::RotamerSet_::get_n_residue_types() const –> unsigned long

get_n_rotamers_for_residue_group(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, which_resgroup: int) → int

C++: core::pack::rotamer_set::RotamerSet_::get_n_rotamers_for_residue_group(unsigned long) const –> unsigned long

get_n_rotamers_for_residue_type(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, which_resgroup: int) → int

C++: core::pack::rotamer_set::RotamerSet_::get_n_rotamers_for_residue_type(unsigned long) const –> unsigned long

get_residue_group_begin(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, which_resgroup: int) → int

C++: core::pack::rotamer_set::RotamerSet_::get_residue_group_begin(unsigned long) const –> unsigned long

get_residue_group_index_for_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, which_rotamer: int) → int

C++: core::pack::rotamer_set::RotamerSet_::get_residue_group_index_for_rotamer(unsigned long) const –> unsigned long

get_residue_type_begin(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, which_restype: int) → int

C++: core::pack::rotamer_set::RotamerSet_::get_residue_type_begin(unsigned long) const –> unsigned long

get_residue_type_index_for_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, which_rotamer: int) → int

C++: core::pack::rotamer_set::RotamerSet_::get_residue_type_index_for_rotamer(unsigned long) const –> unsigned long

get_trie(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, method_enum_id: int) → pyrosetta.rosetta.core.conformation.AbstractRotamerTrie

C++: core::pack::rotamer_set::RotamerSet_::get_trie(unsigned long) const –> class std::shared_ptr<const class core::conformation::AbstractRotamerTrie>

id_for_current_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_) → int

C++: core::pack::rotamer_set::RotamerSet_::id_for_current_rotamer() const –> unsigned long

initialize_pose_for_rotset_creation(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, : pyrosetta.rosetta.core.pose.Pose) → None

Give the pose a chance to stash any data needed by the _rotset_

need nonconst access to pose

C++: core::pack::rotamer_set::RotamerSet_::initialize_pose_for_rotset_creation(class core::pose::Pose &) const –> void

nonconst_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rot_id: int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::RotamerSet_::nonconst_rotamer(unsigned long) –> class std::shared_ptr<class core::conformation::Residue>

num_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_) → int

C++: core::pack::rotamer_set::RotamerSet_::num_rotamers() const –> unsigned long

resid(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → int

C++: core::pack::rotamer_set::RotamerSet::resid() const –> unsigned long

rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rot_id: int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::RotamerSet_::rotamer(unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

rotamer_data_cache(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rot_id: int) → pyrosetta.rosetta.basic.datacache.BasicDataCache

C++: core::pack::rotamer_set::RotamerSet_::rotamer_data_cache(unsigned long) const –> class basic::datacache::BasicDataCache &

rotamer_ref(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, rot_id: int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::RotamerSet_::rotamer_ref(unsigned long) const –> const class core::conformation::Residue &

set_extra_samples(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, task: pyrosetta.rosetta.core.pack.task.PackerTask, num_10A_neighbors: int, chi: int, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, extra_chi_steps: pyrosetta.rosetta.utility.vector1_double) → None

Pushes standard-deviation multiples that should be sampled

for this residue – if this residue has more neighbors within 10A than the task-specified cutoff for buriedness, then extra rotamer samples are added to the extra_chi_steps vector, otherwise, the vector is not modified.

C++: core::pack::rotamer_set::RotamerSet_::set_extra_samples(const class core::pack::task::PackerTask &, int, int, class std::shared_ptr<const class core::chemical::ResidueType>, class utility::vector1<double, class std::allocator<double> > &) const –> void

set_resid(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, resid: int) → None

C++: core::pack::rotamer_set::RotamerSet::set_resid(unsigned long) –> void

show(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, out: pyrosetta.rosetta.std.ostream) → None

C++: core::pack::rotamer_set::RotamerSet_::show(std::ostream &) const –> void

store_trie(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_, method_enum_id: int, trie: pyrosetta.rosetta.core.conformation.AbstractRotamerTrie) → None

C++: core::pack::rotamer_set::RotamerSet_::store_trie(unsigned long, class std::shared_ptr<class core::conformation::AbstractRotamerTrie>) –> void

update_rotamer_offsets(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet_) → None

Lazy update of rotamer indices and offsets and integration of those rotamers

in the rotamers_waiting_for_sort_ list.

C++: core::pack::rotamer_set::RotamerSet_::update_rotamer_offsets() const –> void

class pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets

Bases: FixbbRotamerSets

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, : pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets

C++: core::pack::rotamer_set::RotamerSets::operator=(const class core::pack::rotamer_set::RotamerSets &) –> class core::pack::rotamer_set::RotamerSets &

build_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph) → None

C++: core::pack::rotamer_set::RotamerSets::build_rotamers(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class utility::graph::Graph>) –> void

compute_energies(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, ig: core::pack::interaction_graph::InteractionGraphBase, threads_to_request: int) → None

Precompute all rotamer pair and rotamer one-body energies, populating

the given interaction graph.

In the multithreaded case, this function requests that work be done in threads. It takes as input the number of threads to request.

C++: core::pack::rotamer_set::RotamerSets::compute_energies(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class utility::graph::Graph>, class std::shared_ptr<class core::pack::interaction_graph::InteractionGraphBase>, const unsigned long) –> void

drop_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, rotamers_to_delete: pyrosetta.rosetta.utility.vector1_bool) → None

rotamers_to_delete must be of size nrotmaers – each position

in the array that’s “true” is removed from the set of rotamers

C++: core::pack::rotamer_set::RotamerSets::drop_rotamers(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

dump_pdb(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, filename: str) → None

C++: core::pack::rotamer_set::RotamerSets::dump_pdb(const class core::pose::Pose &, const std::string &) const –> void

static get_bb_bbE(pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::rotamer_set::RotamerSets::get_bb_bbE(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::conformation::Residue &, const class core::conformation::Residue &) –> float

static get_sc_bbE(pose: pyrosetta.rosetta.core.pose.Pose, scfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue) → float

C++: core::pack::rotamer_set::RotamerSets::get_sc_bbE(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::conformation::Residue &, const class core::conformation::Residue &) –> float

has_rotamer_set_for_residue(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, resid: int) → bool

Does this RotamerSets object store a rotamer set for a residue at position resid

in the pose?

Rotamer sets for non-packable residues aren’t generated, but could conceivably be queried by protocols or energy functions.

Vikram K. Mulligan (vmullig.edu).

C++: core::pack::rotamer_set::RotamerSets::has_rotamer_set_for_residue(const unsigned long) const –> bool

initialize_pose_for_rotsets_creation(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, : pyrosetta.rosetta.core.pose.Pose) → None

Give the pose a chance to stash any data needed by the _rotset_

need nonconst access to pose

C++: core::pack::rotamer_set::RotamerSets::initialize_pose_for_rotsets_creation(class core::pose::Pose &) const –> void

moltenres_2_resid(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, : int) → int

C++: core::pack::rotamer_set::RotamerSets::moltenres_2_resid(unsigned long) const –> unsigned long

moltenres_2_resid_vector(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::rotamer_set::RotamerSets::moltenres_2_resid_vector() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

moltenres_for_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, : int) → int

C++: core::pack::rotamer_set::RotamerSets::moltenres_for_rotamer(unsigned long) const –> unsigned long

moltenres_rotid_2_rotid(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, moltenres: int, moltenresrotid: int) → int

convert moltenres rotid to id in full rotamer enumeration

C++: core::pack::rotamer_set::RotamerSets::moltenres_rotid_2_rotid(unsigned long, unsigned long) const –> unsigned long

nmoltenres(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) → int

C++: core::pack::rotamer_set::RotamerSets::nmoltenres() const –> unsigned long

nrotamer_offset_for_moltenres(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, : int) → int

C++: core::pack::rotamer_set::RotamerSets::nrotamer_offset_for_moltenres(unsigned long) const –> unsigned long

nrotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) → int

C++: core::pack::rotamer_set::RotamerSets::nrotamers() const –> unsigned long

nrotamers_for_moltenres(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, : int) → int

C++: core::pack::rotamer_set::RotamerSets::nrotamers_for_moltenres(unsigned long) const –> unsigned long

offset_data_up_to_date(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) → bool

Used as a debug assert to ensure that RotamerSetsOperations call update_offset_data()

Without this check, rotamer sets operations could potentially introduce very-hard-to-debug

glitches if they don’t call update_offset_data().

C++: core::pack::rotamer_set::RotamerSets::offset_data_up_to_date() –> bool

prepare_sets_for_packing(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::pack::rotamer_set::RotamerSets::prepare_sets_for_packing(const class core::pose::Pose &, const class core::scoring::ScoreFunction &) –> void

res_for_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, : int) → int

C++: core::pack::rotamer_set::RotamerSets::res_for_rotamer(unsigned long) const –> unsigned long

resid_2_moltenres(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, : int) → int

C++: core::pack::rotamer_set::RotamerSets::resid_2_moltenres(unsigned long) const –> unsigned long

resid_2_moltenres_vector(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::rotamer_set::RotamerSets::resid_2_moltenres_vector() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, : int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::RotamerSets::rotamer(unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

rotamer_for_moltenres(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, moltenres_id: int, rotamerid: int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::RotamerSets::rotamer_for_moltenres(unsigned long, unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

rotamer_set_for_moltenresidue(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, moltenresid: int) → core::pack::rotamer_set::RotamerSet

C++: core::pack::rotamer_set::RotamerSets::rotamer_set_for_moltenresidue(unsigned long) –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>

rotamer_set_for_residue(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, resid: int) → core::pack::rotamer_set::RotamerSet

C++: core::pack::rotamer_set::RotamerSets::rotamer_set_for_residue(unsigned long) –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>

rotid_on_moltenresidue(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, rotid: int) → int

convert rotid in full rotamer enumeration into rotamer id on its source residue

C++: core::pack::rotamer_set::RotamerSets::rotid_on_moltenresidue(unsigned long) const –> unsigned long

set_explicit_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, moltenresid: int, rotamers: core::pack::rotamer_set::RotamerSet) → None

C++: core::pack::rotamer_set::RotamerSets::set_explicit_rotamers(unsigned long, class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>) –> void

set_task(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, task: pyrosetta.rosetta.core.pack.task.PackerTask) → None

C++: core::pack::rotamer_set::RotamerSets::set_task(class std::shared_ptr<const class core::pack::task::PackerTask>) –> void

show(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, out: pyrosetta.rosetta.std.ostream) → None

C++: core::pack::rotamer_set::RotamerSets::show(std::ostream &) const –> void

task(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) → pyrosetta.rosetta.core.pack.task.PackerTask

access to packer_task_

C++: core::pack::rotamer_set::RotamerSets::task() const –> class std::shared_ptr<const class core::pack::task::PackerTask>

total_residue(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) → int

C++: core::pack::rotamer_set::RotamerSets::total_residue() const –> unsigned long

update_offset_data(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets) → None

fd: make this public

the reason? we now can update rotamersets interactively from code, so this should be exposed

C++: core::pack::rotamer_set::RotamerSets::update_offset_data() –> void

class pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsFactory

Bases: pybind11_object

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsFactory, : pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsFactory) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsFactory

C++: core::pack::rotamer_set::RotamerSetsFactory::operator=(const class core::pack::rotamer_set::RotamerSetsFactory &) –> class core::pack::rotamer_set::RotamerSetsFactory &

static create_rotamer_sets(pose: pyrosetta.rosetta.core.pose.Pose) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets

Create a generic RotamerSet object for the pose.

C++: core::pack::rotamer_set::RotamerSetsFactory::create_rotamer_sets(const class core::pose::Pose &) –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSets>

class pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsOperation

Bases: pybind11_object

RotamerSetsOperations are able to modify the RotamerSets object

such that changes can be correlated accros multiple rotamer sets.

They are handed into the packer through a packer task; the PackerTask

keeps a list of rotamer sets operations.

The RotamerSets, within the build_rotamers() method will iterate across

the RotamerSetsOperation objects, and call alter_rotamer_sets on itself.

RotamerSetsOperations are visited in the order in which they are appended

to the PackerTask’s operation list.

alter_rotamer_sets(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsOperation, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: utility::graph::Graph, rotamer_sets: core::pack::rotamer_set::RotamerSets) → None

C++: core::pack::rotamer_set::RotamerSetsOperation::alter_rotamer_sets(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class core::pack::rotamer_set::RotamerSets &) –> void

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsOperation, : pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsOperation) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsOperation

C++: core::pack::rotamer_set::RotamerSetsOperation::operator=(const class core::pack::rotamer_set::RotamerSetsOperation &) –> class core::pack::rotamer_set::RotamerSetsOperation &

clone(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsOperation) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetsOperation

C++: core::pack::rotamer_set::RotamerSetsOperation::clone() const –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSetsOperation>

class pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset

Bases: RotamerSet

Container for a subset of rotamers that have been created by another rotamer set. This subset object copies pointers to the rotamers contained in another set, as opposed to cloning the rotamers. It’s main purpose is to manage the bookkeeping involved in packing with a subset of rotamers (when it might be faster to use a subset and to create an interaction graph specifically for that subset than to simply pass an abreviated list of rotamers to the SimAnnealer with the “rot_to_pack” vector).

add_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, rotamer: pyrosetta.rosetta.core.conformation.Residue) → None

C++: core::pack::rotamer_set::RotamerSubset::add_rotamer(const class core::conformation::Residue &) –> void

add_rotamer_into_existing_group(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, rotamer: pyrosetta.rosetta.core.conformation.Residue) → None

C++: core::pack::rotamer_set::RotamerSubset::add_rotamer_into_existing_group(const class core::conformation::Residue &) –> void

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, : pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset

C++: core::pack::rotamer_set::RotamerSubset::operator=(const class core::pack::rotamer_set::RotamerSubset &) –> class core::pack::rotamer_set::RotamerSubset &

build_dependent_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, rotamer_sets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph) → None

C++: core::pack::rotamer_set::RotamerSubset::build_dependent_rotamers(const class core::pack::rotamer_set::RotamerSets &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) –> void

build_pwat_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, pose: pyrosetta.rosetta.core.pose.Pose, resid: int, new_pwat_rotset: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) → None

C++: core::pack::rotamer_set::RotamerSubset::build_pwat_rotamers(const class core::pose::Pose &, unsigned long, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

build_rotamers(*args, **kwargs)

Overloaded function.

1. build_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, the_pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph) -> None

2. build_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, the_pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, use_neighbor_context: bool) -> None

C++: core::pack::rotamer_set::RotamerSubset::build_rotamers(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, bool) –> void

compute_one_and_two_body_energies(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, one_body_energies: pyrosetta.rosetta.utility.vector1_float, two_body_energies: pyrosetta.rosetta.utility.vector1_utility_vector1_float_std_allocator_float_t, packable_neighbors: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

C++: core::pack::rotamer_set::RotamerSubset::compute_one_and_two_body_energies(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<float, class std::allocator<float> > &, class utility::vector1<class utility::vector1<float, class std::allocator<float> >, class std::allocator<class utility::vector1<float, class std::allocator<float> > > > &, class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> void

compute_one_body_energies(*args, **kwargs)

Overloaded function.

1. compute_one_body_energies(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, energies: pyrosetta.rosetta.utility.vector1_float) -> None

2. compute_one_body_energies(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, energies: pyrosetta.rosetta.utility.vector1_float, no_update: bool) -> None

C++: core::pack::rotamer_set::RotamerSubset::compute_one_body_energies(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<float, class std::allocator<float> > &, const bool) const –> void

compute_one_body_energy_maps(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, energies: pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector) → None

for OptE

C++: core::pack::rotamer_set::RotamerSubset::compute_one_body_energy_maps(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<class core::scoring::EMapVector, class std::allocator<class core::scoring::EMapVector> > &) const –> void

data(self: pyrosetta.rosetta.core.conformation.RotamerSetBase) → pyrosetta.rosetta.basic.datacache.BasicDataCache

BasicDataCache indexed by enum in core/pack/rotamer_set/RotamerSetCacheableDataType.hh

C++: core::conformation::RotamerSetBase::data() –> class basic::datacache::BasicDataCache &

drop_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, rot_id: int) → None

removes a single rotamer and causes a rotamer index update

C++: core::pack::rotamer_set::RotamerSubset::drop_rotamer(unsigned long) –> void

drop_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, rotamers_to_delete: pyrosetta.rosetta.utility.vector1_bool) → None

rotamers_to_delete must be of size nrotmaers – each position

in the array that’s “true” is removed from the set of rotamers

C++: core::pack::rotamer_set::RotamerSubset::drop_rotamers(const class utility::vector1<bool, class std::allocator<bool> > &) –> void

drop_rotamers_by_index(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, rotamer_indices_to_delete: pyrosetta.rosetta.utility.vector1_unsigned_long) → None

deletes the rotamers in the list with the given indices.

The indices of these rotamers is presumed to be those before any delete operation. e.g. if there are four rotamers, and rotamer_indices_to_delete includes 1 & 3, then the rotamers that will remain are the rotamers originally indexed as 2 and 4, even though their new indices will be 1 & 2.

C++: core::pack::rotamer_set::RotamerSubset::drop_rotamers_by_index(const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) –> void

get_n_residue_groups(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset) → int

C++: core::pack::rotamer_set::RotamerSubset::get_n_residue_groups() const –> unsigned long

get_n_residue_types(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset) → int

C++: core::pack::rotamer_set::RotamerSubset::get_n_residue_types() const –> unsigned long

get_n_rotamers_for_residue_group(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, which_resgroup: int) → int

C++: core::pack::rotamer_set::RotamerSubset::get_n_rotamers_for_residue_group(unsigned long) const –> unsigned long

get_n_rotamers_for_residue_type(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, which_restype: int) → int

C++: core::pack::rotamer_set::RotamerSubset::get_n_rotamers_for_residue_type(unsigned long) const –> unsigned long

get_residue_group_begin(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, which_resgroup: int) → int

C++: core::pack::rotamer_set::RotamerSubset::get_residue_group_begin(unsigned long) const –> unsigned long

get_residue_group_index_for_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, which_rotamer: int) → int

C++: core::pack::rotamer_set::RotamerSubset::get_residue_group_index_for_rotamer(unsigned long) const –> unsigned long

get_residue_type_begin(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, which_restype: int) → int

C++: core::pack::rotamer_set::RotamerSubset::get_residue_type_begin(unsigned long) const –> unsigned long

get_residue_type_index_for_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, which_rotamer: int) → int

given a rotamer id, return an int which represents a type for this rotamer.

C++: core::pack::rotamer_set::RotamerSubset::get_residue_type_index_for_rotamer(unsigned long) const –> unsigned long

get_trie(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, method_enum_id: int) → pyrosetta.rosetta.core.conformation.AbstractRotamerTrie

C++: core::pack::rotamer_set::RotamerSubset::get_trie(unsigned long) const –> class std::shared_ptr<const class core::conformation::AbstractRotamerTrie>

id_for_current_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset) → int

C++: core::pack::rotamer_set::RotamerSubset::id_for_current_rotamer() const –> unsigned long

initialize_pose_for_rotset_creation(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, : pyrosetta.rosetta.core.pose.Pose) → None

Give the pose a chance to stash any data needed by the _rotset_

need nonconst access to pose

C++: core::pack::rotamer_set::RotamerSubset::initialize_pose_for_rotset_creation(class core::pose::Pose &) const –> void

nonconst_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, rot_id: int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::RotamerSubset::nonconst_rotamer(unsigned long) –> class std::shared_ptr<class core::conformation::Residue>

num_rotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset) → int

C++: core::pack::rotamer_set::RotamerSubset::num_rotamers() const –> unsigned long

resid(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → int

C++: core::pack::rotamer_set::RotamerSet::resid() const –> unsigned long

rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, rot_id: int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::RotamerSubset::rotamer(unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

rotamer_data_cache(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, rot_id: int) → pyrosetta.rosetta.basic.datacache.BasicDataCache

C++: core::pack::rotamer_set::RotamerSubset::rotamer_data_cache(unsigned long) const –> class basic::datacache::BasicDataCache &

rotamer_ref(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, rot_id: int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::RotamerSubset::rotamer_ref(unsigned long) const –> const class core::conformation::Residue &

set_resid(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet, resid: int) → None

C++: core::pack::rotamer_set::RotamerSet::set_resid(unsigned long) –> void

show(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, out: pyrosetta.rosetta.std.ostream) → None

C++: core::pack::rotamer_set::RotamerSubset::show(std::ostream &) const –> void

store_trie(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubset, method_enum_id: int, trie: pyrosetta.rosetta.core.conformation.AbstractRotamerTrie) → None

C++: core::pack::rotamer_set::RotamerSubset::store_trie(unsigned long, class std::shared_ptr<class core::conformation::AbstractRotamerTrie>) –> void

update_rotamer_offsets(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → None

Lazy update of rotamer indices and offsets and integration of those rotamers

in the rotamers_waiting_for_sort_ list.

C++: core::pack::rotamer_set::RotamerSet::update_rotamer_offsets() const –> void

class pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets

Bases: FixbbRotamerSets

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets, : pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets

C++: core::pack::rotamer_set::RotamerSubsets::operator=(const class core::pack::rotamer_set::RotamerSubsets &) –> class core::pack::rotamer_set::RotamerSubsets &

initialize_pose_for_rotsets_creation(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets, : pyrosetta.rosetta.core.pose.Pose) → None

Give the pose a chance to stash any data needed by the _rotset_

need nonconst access to pose

C++: core::pack::rotamer_set::RotamerSubsets::initialize_pose_for_rotsets_creation(class core::pose::Pose &) const –> void

moltenres_2_resid(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets, : int) → int

C++: core::pack::rotamer_set::RotamerSubsets::moltenres_2_resid(unsigned long) const –> unsigned long

moltenres_2_resid_vector(self: pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::rotamer_set::FixbbRotamerSets::moltenres_2_resid_vector() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

moltenres_for_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets, : int) → int

C++: core::pack::rotamer_set::RotamerSubsets::moltenres_for_rotamer(unsigned long) const –> unsigned long

moltenres_rotid_2_rotid(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets, moltenres: int, moltenresrotid: int) → int

convert moltenres rotid to id in full rotamer enumeration

C++: core::pack::rotamer_set::RotamerSubsets::moltenres_rotid_2_rotid(unsigned long, unsigned long) const –> unsigned long

nmoltenres(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets) → int

C++: core::pack::rotamer_set::RotamerSubsets::nmoltenres() const –> unsigned long

nrotamer_offset_for_moltenres(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets, : int) → int

C++: core::pack::rotamer_set::RotamerSubsets::nrotamer_offset_for_moltenres(unsigned long) const –> unsigned long

nrotamers(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets) → int

C++: core::pack::rotamer_set::RotamerSubsets::nrotamers() const –> unsigned long

nrotamers_for_moltenres(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets, : int) → int

C++: core::pack::rotamer_set::RotamerSubsets::nrotamers_for_moltenres(unsigned long) const –> unsigned long

res_for_rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets, : int) → int

C++: core::pack::rotamer_set::RotamerSubsets::res_for_rotamer(unsigned long) const –> unsigned long

resid_2_moltenres(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets, : int) → int

C++: core::pack::rotamer_set::RotamerSubsets::resid_2_moltenres(unsigned long) const –> unsigned long

resid_2_moltenres_vector(self: pyrosetta.rosetta.core.pack.rotamer_set.FixbbRotamerSets) → pyrosetta.rosetta.utility.vector1_unsigned_long

C++: core::pack::rotamer_set::FixbbRotamerSets::resid_2_moltenres_vector() const –> const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &

rotamer(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets, : int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::RotamerSubsets::rotamer(unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

rotamer_for_moltenres(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets, moltenres_id: int, rotamerid: int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::RotamerSubsets::rotamer_for_moltenres(unsigned long, unsigned long) const –> class std::shared_ptr<const class core::conformation::Residue>

rotamer_set_for_moltenresidue(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets, moltenresid: int) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

C++: core::pack::rotamer_set::RotamerSubsets::rotamer_set_for_moltenresidue(unsigned long) –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>

rotamer_set_for_residue(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets, resid: int) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet

C++: core::pack::rotamer_set::RotamerSubsets::rotamer_set_for_residue(unsigned long) –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSet>

rotid_on_moltenresidue(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets, rotid: int) → int

convert rotid in full rotamer enumeration into rotamer id on its source residue

C++: core::pack::rotamer_set::RotamerSubsets::rotid_on_moltenresidue(unsigned long) const –> unsigned long

show(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets, out: pyrosetta.rosetta.std.ostream) → None

C++: core::pack::rotamer_set::RotamerSubsets::show(std::ostream &) const –> void

total_residue(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSubsets) → int

C++: core::pack::rotamer_set::RotamerSubsets::total_residue() const –> unsigned long

class pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation

Bases: RotamerSetOperation

Adds in rotamers from the “unbound” or native structure(s), pulled from one or more PDBs supplied on the command line.

Sequence numbering matters – rotamers will only be added if sequence numbers match AND the ResidueType is allowed by the PackerTask. By itself, this class does NOT grant a Dunbrack energy bonus to the native rotamer(s).

add_pose(self: pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation, pose: pyrosetta.rosetta.core.pose.Pose) → None

Adds rotamers from the specified pose to the unbound collection.

C++: core::pack::rotamer_set::UnboundRotamersOperation::add_pose(class std::shared_ptr<const class core::pose::Pose>) –> void

alter_rotamer_set(self: pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation, pose: pyrosetta.rosetta.core.pose.Pose, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, ptask: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, rotamer_set: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSet) → None

C++: core::pack::rotamer_set::UnboundRotamersOperation::alter_rotamer_set(const class core::pose::Pose &, const class core::scoring::ScoreFunction &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, class core::pack::rotamer_set::RotamerSet &) –> void

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation, : pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation) → pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation

C++: core::pack::rotamer_set::UnboundRotamersOperation::operator=(const class core::pack::rotamer_set::UnboundRotamersOperation &) –> class core::pack::rotamer_set::UnboundRotamersOperation &

clone(self: pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation) → pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation

C++: core::pack::rotamer_set::UnboundRotamersOperation::clone() const –> class std::shared_ptr<class core::pack::rotamer_set::RotamerSetOperation>

increase_packer_residue_radius(self: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSetOperation, pose: pyrosetta.rosetta.core.pose.Pose, the_task: pyrosetta.rosetta.core.pack.task.PackerTask, residue_in: int) → float

C++: core::pack::rotamer_set::RotamerSetOperation::increase_packer_residue_radius(const class core::pose::Pose &, class std::shared_ptr<const class core::pack::task::PackerTask>, unsigned long) const –> double

initialize_from_command_line(self: pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation) → None

Loads poses from the -unboundrot flag.

C++: core::pack::rotamer_set::UnboundRotamersOperation::initialize_from_command_line() –> void

is_initialized(self: pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation) → bool

Has this object been initialized?

C++: core::pack::rotamer_set::UnboundRotamersOperation::is_initialized() const –> bool

total_residue(self: pyrosetta.rosetta.core.pack.rotamer_set.UnboundRotamersOperation) → int

C++: core::pack::rotamer_set::UnboundRotamersOperation::total_residue() –> unsigned long

class pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo

Bases: pybind11_object

aa(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo, aa_in: pyrosetta.rosetta.core.chemical.AA) → None

C++: core::pack::rotamer_set::WaterAnchorInfo::aa(const enum core::chemical::AA &) –> void

anchor_atom(*args, **kwargs)

Overloaded function.

1. anchor_atom(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo, type: pyrosetta.rosetta.core.chemical.ResidueType) -> int

C++: core::pack::rotamer_set::WaterAnchorInfo::anchor_atom(const class core::chemical::ResidueType &) const –> unsigned long

2. anchor_atom(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo, name: str) -> None

C++: core::pack::rotamer_set::WaterAnchorInfo::anchor_atom(const std::string &) –> void

3. anchor_atom(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo) -> str

C++: core::pack::rotamer_set::WaterAnchorInfo::anchor_atom() const –> std::string

anchor_residue(*args, **kwargs)

Overloaded function.

1. anchor_residue(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo) -> int

C++: core::pack::rotamer_set::WaterAnchorInfo::anchor_residue() const –> unsigned long

2. anchor_residue(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo, rsd: int) -> None

C++: core::pack::rotamer_set::WaterAnchorInfo::anchor_residue(const unsigned long) –> void

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo, : pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo) → pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo

C++: core::pack::rotamer_set::WaterAnchorInfo::operator=(const class core::pack::rotamer_set::WaterAnchorInfo &) –> class core::pack::rotamer_set::WaterAnchorInfo &

attaches_to_residue_type(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo, type: pyrosetta.rosetta.core.chemical.ResidueType) → bool

C++: core::pack::rotamer_set::WaterAnchorInfo::attaches_to_residue_type(const class core::chemical::ResidueType &) const –> bool

design_anchor_index(*args, **kwargs)

Overloaded function.

1. design_anchor_index(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo, ii: int) -> None

C++: core::pack::rotamer_set::WaterAnchorInfo::design_anchor_index(const unsigned long &) –> void

2. design_anchor_index(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo) -> int

C++: core::pack::rotamer_set::WaterAnchorInfo::design_anchor_index() const –> unsigned long

enforced(*args, **kwargs)

Overloaded function.

1. enforced(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo) -> bool

C++: core::pack::rotamer_set::WaterAnchorInfo::enforced() const –> bool

2. enforced(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo, enf: bool) -> None

C++: core::pack::rotamer_set::WaterAnchorInfo::enforced(bool) –> void

nstep(*args, **kwargs)

Overloaded function.

1. nstep(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo) -> int

C++: core::pack::rotamer_set::WaterAnchorInfo::nstep() const –> unsigned long

2. nstep(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo, nstep_in: int) -> None

C++: core::pack::rotamer_set::WaterAnchorInfo::nstep(const unsigned long) –> void

rotamer_bonds(*args, **kwargs)

Overloaded function.

1. rotamer_bonds(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo) -> str

C++: core::pack::rotamer_set::WaterAnchorInfo::rotamer_bonds() const –> std::string

2. rotamer_bonds(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterAnchorInfo, bonds: str) -> None

C++: core::pack::rotamer_set::WaterAnchorInfo::rotamer_bonds(std::string) –> void

class pyrosetta.rosetta.core.pack.rotamer_set.WaterPackingInfo

Bases: CacheableData

assign(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterPackingInfo, : pyrosetta.rosetta.core.pack.rotamer_set.WaterPackingInfo) → pyrosetta.rosetta.core.pack.rotamer_set.WaterPackingInfo

C++: core::pack::rotamer_set::WaterPackingInfo::operator=(const class core::pack::rotamer_set::WaterPackingInfo &) –> class core::pack::rotamer_set::WaterPackingInfo &

clear(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterPackingInfo) → None

C++: core::pack::rotamer_set::WaterPackingInfo::clear() –> void

clone(self: pyrosetta.rosetta.core.pack.rotamer_set.WaterPackingInfo) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: core::pack::rotamer_set::WaterPackingInfo::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) → pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

pyrosetta.rosetta.core.pack.rotamer_set.bb_independent_rotamers(*args, **kwargs)

Overloaded function.

1. bb_independent_rotamers(rot_restype: pyrosetta.rosetta.core.chemical.ResidueType) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t

2. bb_independent_rotamers(rot_restype: pyrosetta.rosetta.core.chemical.ResidueType, ignore_cmdline: bool) -> pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t

a crude function to spit out a list of rotamers

given the residue type only, independent of backbone currently there is no proper way of doing this, since the Dunbrack bbind library is not implemented in rosetta. this function tries to circumvent that by constructing a one residue pose and then using the regular dunbrack library, which will use neutral phi/psi for the only residue in the pose the bool ignore_cmdline can be used if someone only wants base inverse rotamers but use the full set in packing

C++: core::pack::rotamer_set::bb_independent_rotamers(class std::shared_ptr<const class core::chemical::ResidueType>, bool) –> class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > >

pyrosetta.rosetta.core.pack.rotamer_set.build_anchorless_water_rotamers(seqpos: int, h2o_type: pyrosetta.rosetta.core.chemical.ResidueType, pose: pyrosetta.rosetta.core.pose.Pose, new_rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, score_fxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

builds water molecule rotamers on top of cubic lattice in hydrate/SPaDES protocol

C++: core::pack::rotamer_set::build_anchorless_water_rotamers(const unsigned long, const class core::chemical::ResidueType &, const class core::pose::Pose &, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>, const class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.core.pack.rotamer_set.build_dependent_water_rotamers(rotsets: pyrosetta.rosetta.core.pack.rotamer_set.RotamerSets, seqpos_water: int, h2o_type: pyrosetta.rosetta.core.chemical.ResidueType, task: pyrosetta.rosetta.core.pack.task.PackerTask, pose: pyrosetta.rosetta.core.pose.Pose, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, new_rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::pack::rotamer_set::build_dependent_water_rotamers(const class core::pack::rotamer_set::RotamerSets &, const unsigned long, const class core::chemical::ResidueType &, const class core::pack::task::PackerTask &, const class core::pose::Pose &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, const class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.core.pack.rotamer_set.build_dna_rotamers(resid: int, pose: pyrosetta.rosetta.core.pose.Pose, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, task: pyrosetta.rosetta.core.pack.task.PackerTask, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::rotamer_set::build_dna_rotamers(const unsigned long, const class core::pose::Pose &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::pack::task::PackerTask &, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) –> void

pyrosetta.rosetta.core.pack.rotamer_set.build_independent_water_rotamers(seqpos_water: int, h2o_type: pyrosetta.rosetta.core.chemical.ResidueType, task: pyrosetta.rosetta.core.pack.task.PackerTask, pose: pyrosetta.rosetta.core.pose.Pose, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, new_rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) → None

C++: core::pack::rotamer_set::build_independent_water_rotamers(const unsigned long, const class core::chemical::ResidueType &, const class core::pack::task::PackerTask &, const class core::pose::Pose &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, const class core::scoring::ScoreFunction &) –> void

pyrosetta.rosetta.core.pack.rotamer_set.build_random_dna_rotamers(resid: int, pose: pyrosetta.rosetta.core.pose.Pose, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, level: pyrosetta.rosetta.core.pack.task.ExtraRotSample, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::rotamer_set::build_random_dna_rotamers(const unsigned long, const class core::pose::Pose &, class std::shared_ptr<const class core::chemical::ResidueType>, const enum core::pack::task::ExtraRotSample &, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) –> void

pyrosetta.rosetta.core.pack.rotamer_set.build_rna_rotamers(resid: int, pose: pyrosetta.rosetta.core.pose.Pose, concrete_residue: pyrosetta.rosetta.core.chemical.ResidueType, task: pyrosetta.rosetta.core.pack.task.PackerTask, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, id_for_current_rotamer: int) → None

C++: core::pack::rotamer_set::build_rna_rotamers(const unsigned long, const class core::pose::Pose &, class std::shared_ptr<const class core::chemical::ResidueType>, const class core::pack::task::PackerTask &, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long &) –> void

pyrosetta.rosetta.core.pack.rotamer_set.build_rotamers_from_rotamer_bins(residue: pyrosetta.rosetta.core.conformation.Residue, rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

Make a rotamer (Residue) for every combination of torsion angle in the rotamer bins listed in the params

file for the given Residue.

C++: core::pack::rotamer_set::build_rotamers_from_rotamer_bins(const class core::conformation::Residue &, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) –> void

pyrosetta.rosetta.core.pack.rotamer_set.build_rotated_water_rotamers(seqpos_water: int, task: pyrosetta.rosetta.core.pack.task.PackerTask, pose: pyrosetta.rosetta.core.pose.Pose, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph, new_rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, incl_vrt: bool) → None

C++: core::pack::rotamer_set::build_rotated_water_rotamers(const unsigned long, const class core::pack::task::PackerTask &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class std::shared_ptr<const class utility::graph::Graph>, class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, bool) –> void

pyrosetta.rosetta.core.pack.rotamer_set.bump_check(rotamer: pyrosetta.rosetta.core.conformation.Residue, resid: int, sf: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask, packer_neighbor_graph: pyrosetta.rosetta.utility.graph.Graph) → float

C++: core::pack::rotamer_set::bump_check(class std::shared_ptr<const class core::conformation::Residue>, unsigned long, const class core::scoring::ScoreFunction &, const class core::pose::Pose &, const class core::pack::task::PackerTask &, class std::shared_ptr<const class utility::graph::Graph>) –> float

pyrosetta.rosetta.core.pack.rotamer_set.create_oriented_water_rotamer(h2o_type: pyrosetta.rosetta.core.chemical.ResidueType, xyz_atom1: pyrosetta.rosetta.numeric.xyzVector_double_t, xyz_O: pyrosetta.rosetta.numeric.xyzVector_double_t, xyz_atom2: pyrosetta.rosetta.numeric.xyzVector_double_t, name1: str, name2: str, tp5: pyrosetta.rosetta.core.conformation.Residue) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::rotamer_set::create_oriented_water_rotamer(const class core::chemical::ResidueType &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const class numeric::xyzVector<double> &, const std::string &, const std::string &, const class core::conformation::Residue &) –> class std::shared_ptr<class core::conformation::Residue>

pyrosetta.rosetta.core.pack.rotamer_set.debug_dump_rotamers(rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) → None

C++: core::pack::rotamer_set::debug_dump_rotamers(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &) –> void

pyrosetta.rosetta.core.pack.rotamer_set.different_resgroup(rt1: pyrosetta.rosetta.core.chemical.ResidueType, rt2: pyrosetta.rosetta.core.chemical.ResidueType) → bool

should two residue types be considered to belong to the same residue-type group?

C++: core::pack::rotamer_set::different_resgroup(const class core::chemical::ResidueType &, const class core::chemical::ResidueType &) –> bool

pyrosetta.rosetta.core.pack.rotamer_set.different_restype(rt1: pyrosetta.rosetta.core.chemical.ResidueType, rt2: pyrosetta.rosetta.core.chemical.ResidueType) → bool

should two residue types be considered the same residue type?

C++: core::pack::rotamer_set::different_restype(const class core::chemical::ResidueType &, const class core::chemical::ResidueType &) –> bool

pyrosetta.rosetta.core.pack.rotamer_set.sort_new_rotamers_into_rotset_vector(rotamers: pyrosetta.rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, rotamers_waiting_for_sort: pyrosetta.rosetta.std.list_std_shared_ptr_core_conformation_Residue_t, id_for_current_rotamer: int) → None

C++: core::pack::rotamer_set::sort_new_rotamers_into_rotset_vector(class utility::vector1<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, class std::list<class std::shared_ptr<class core::conformation::Residue>, class std::allocator<class std::shared_ptr<class core::conformation::Residue> > > &, unsigned long &) –> void