scmin

Bindings for core::pack::scmin namespace

class pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection

Bases: pybind11_object

A collection of ResidueAtomTreeCollection objects for an entire design task.

assign(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection, : pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection) → pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection

C++: core::pack::scmin::AtomTreeCollection::operator=(const class core::pack::scmin::AtomTreeCollection &) –> class core::pack::scmin::AtomTreeCollection &

moltenres_atomtree_collection(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection, moltenresid: int) → pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection

C++: core::pack::scmin::AtomTreeCollection::moltenres_atomtree_collection(unsigned long) –> class core::pack::scmin::ResidueAtomTreeCollection &

residue_atomtree_collection(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection, resid: int) → pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection

C++: core::pack::scmin::AtomTreeCollection::residue_atomtree_collection(unsigned long) –> class core::pack::scmin::ResidueAtomTreeCollection &

residue_atomtree_collection_op(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection, resid: int) → pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection

C++: core::pack::scmin::AtomTreeCollection::residue_atomtree_collection_op(unsigned long) –> class std::shared_ptr<class core::pack::scmin::ResidueAtomTreeCollection>

class pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap

Bases: SCMinMinimizerMap

activate_residue_dofs(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, resindex: int) → None

Activate all the dofs for a particular residue. Ammortized O(1).

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::activate_residue_dofs(unsigned long) –> void

active_residue(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, index: int) → int

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::active_residue(unsigned long) const –> unsigned long

add_atom(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, atom_id: pyrosetta.rosetta.core.id.AtomID, dof_id: pyrosetta.rosetta.core.id.DOF_ID) → None

Invoked during the depth-first traversal through the AtomTree; the atom

tree is indicating that a given atom is controlled by a particular DOF. Record that fact.

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::add_atom(const class core::id::AtomID &, const class core::id::DOF_ID &) –> void

add_torsion(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, new_torsion: pyrosetta.rosetta.core.id.DOF_ID, parent: pyrosetta.rosetta.core.id.DOF_ID) → None

Invoked during the depth-first traversal through the AtomTree. The AtomTree

is indicating that a particular torsion is dependent on another torsion. Record that fact.

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::add_torsion(const class core::id::DOF_ID &, const class core::id::DOF_ID &) –> void

assign(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, : pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap) → pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::operator=(const class core::pack::scmin::AtomTreeSCMinMinimizerMap &) –> class core::pack::scmin::AtomTreeSCMinMinimizerMap &

assign_dofs_to_mobile_residues(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, dofs: pyrosetta.rosetta.utility.vector1_double) → None

Assign the chi values to the residue(s)

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::assign_dofs_to_mobile_residues(const class utility::vector1<double, class std::allocator<double> > &) –> void

atom(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, atid: pyrosetta.rosetta.core.id.AtomID) → pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::atom(const class core::id::AtomID &) const –> const class core::kinematics::tree::Atom &

atom_derivatives(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, resid: int) → pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair

C++: core::pack::scmin::SCMinMinimizerMap::atom_derivatives(unsigned long) –> class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &

clear_active_dofs(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap) → None

Disable the minimization for all residues. Ammortized O(1).

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::clear_active_dofs() –> void

dm(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap) → pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t

Inline accessor

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::dm() const –> const class ObjexxFCL::FArray1D<int> &

dof_node(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, index: int) → pyrosetta.rosetta.core.optimization.DOF_Node

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::dof_node(unsigned long) –> class core::optimization::DOF_Node &

dof_node_for_chi(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, resid: int, chiid: int) → pyrosetta.rosetta.core.optimization.DOF_Node

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::dof_node_for_chi(unsigned long, unsigned long) const –> const class core::optimization::DOF_Node &

domain_map(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap) → pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t

MinimizerMapBase class virtual accessor

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::domain_map() const –> const class ObjexxFCL::FArray1D<int> &

link_torsion_vectors(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap) → None

propagate f1/f2’s up from children to parents

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::link_torsion_vectors() –> void

make_multifunc(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, p: pyrosetta.rosetta.core.pose.Pose, bg_residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, mingraph: core::scoring::MinimizationGraph) → pyrosetta.rosetta.core.optimization.Multifunc

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::make_multifunc(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class core::scoring::ScoreFunction &, class core::scoring::MinimizationGraph &) –> class std::shared_ptr<class core::optimization::Multifunc>

n_dof_nodes(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap) → int

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::n_dof_nodes() const –> unsigned long

nactive_residues(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap) → int

Accessors

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::nactive_residues() const –> unsigned long

residue(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, seqpos: int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::residue(unsigned long) const –> const class core::conformation::Residue &

residue_data(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, seqpos: int) → pyrosetta.rosetta.basic.datacache.BasicDataCache

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::residue_data(unsigned long) const –> class basic::datacache::BasicDataCache &

set_natoms_for_residue(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, resid: int, natoms: int) → None

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::set_natoms_for_residue(unsigned long, unsigned long) –> void

set_nonideal(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, val_in: bool) → None

C++: core::pack::scmin::SCMinMinimizerMap::set_nonideal(bool) –> void

set_total_residue(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, total_residue: int) → None

the AtomTreeSCMinMinimizerMap has to know how many residues are in the pose; this allows

it to do O(1) updates to its DomainMap – this function costs O(N).

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::set_total_residue(unsigned long) –> void

setup(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, trees: pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection) → None

Traverse the atom trees in preparation for minimization to tie together all the

DOFs and the atoms they control.

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::setup(class std::shared_ptr<class core::pack::scmin::AtomTreeCollection>) –> void

starting_dofs(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, dofs: pyrosetta.rosetta.utility.vector1_double) → None

Initialize a multivec with the dofs reflected in the current residue(s)

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::starting_dofs(class utility::vector1<double, class std::allocator<double> > &) const –> void

tor_for_dof(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, dofid: pyrosetta.rosetta.core.id.DOF_ID) → pyrosetta.rosetta.core.id.TorsionID

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::tor_for_dof(const class core::id::DOF_ID &) const –> class core::id::TorsionID

zero_atom_derivative_vectors(self: pyrosetta.rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap) → None

C++: core::pack::scmin::AtomTreeSCMinMinimizerMap::zero_atom_derivative_vectors() –> void

class pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap

Bases: SCMinMinimizerMap

activate_residue_dofs(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, resindex: int) → None

Activate all the dofs for a particular residue. Ammortized O(1).

C++: core::pack::scmin::CartSCMinMinimizerMap::activate_residue_dofs(unsigned long) –> void

active_residue(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, index: int) → int

C++: core::pack::scmin::CartSCMinMinimizerMap::active_residue(unsigned long) const –> unsigned long

add_atom(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, atom_id: pyrosetta.rosetta.core.id.AtomID, dof_id: pyrosetta.rosetta.core.id.DOF_ID) → None

Invoked during the depth-first traversal through the AtomTree; the atom

tree is indicating that a given atom is controlled by a particular DOF. Record that fact.

C++: core::pack::scmin::CartSCMinMinimizerMap::add_atom(const class core::id::AtomID &, const class core::id::DOF_ID &) –> void

add_torsion(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, new_torsion: pyrosetta.rosetta.core.id.DOF_ID, parent: pyrosetta.rosetta.core.id.DOF_ID) → None

Invoked during the depth-first traversal through the AtomTree. The AtomTree

is indicating that a particular torsion is dependent on another torsion. Record that fact.

C++: core::pack::scmin::CartSCMinMinimizerMap::add_torsion(const class core::id::DOF_ID &, const class core::id::DOF_ID &) –> void

assign(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, : pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap) → pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap

C++: core::pack::scmin::CartSCMinMinimizerMap::operator=(const class core::pack::scmin::CartSCMinMinimizerMap &) –> class core::pack::scmin::CartSCMinMinimizerMap &

assign_dofs_to_mobile_residues(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, dofs: pyrosetta.rosetta.utility.vector1_double) → None

Assign the chi values to the residue(s)

C++: core::pack::scmin::CartSCMinMinimizerMap::assign_dofs_to_mobile_residues(const class utility::vector1<double, class std::allocator<double> > &) –> void

atom(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, atid: pyrosetta.rosetta.core.id.AtomID) → pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::pack::scmin::CartSCMinMinimizerMap::atom(const class core::id::AtomID &) const –> const class core::kinematics::tree::Atom &

atom_derivatives(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, resid: int) → pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair

C++: core::pack::scmin::SCMinMinimizerMap::atom_derivatives(unsigned long) –> class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &

clear_active_dofs(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap) → None

Disable the minimization for all residues. Ammortized O(1).

C++: core::pack::scmin::CartSCMinMinimizerMap::clear_active_dofs() –> void

dm(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap) → pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t

Inline accessor

C++: core::pack::scmin::CartSCMinMinimizerMap::dm() const –> const class ObjexxFCL::FArray1D<int> &

dof_node(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, index: int) → pyrosetta.rosetta.core.optimization.DOF_Node

C++: core::pack::scmin::CartSCMinMinimizerMap::dof_node(unsigned long) –> class core::optimization::DOF_Node &

dof_node_for_chi(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, resid: int, chiid: int) → pyrosetta.rosetta.core.optimization.DOF_Node

C++: core::pack::scmin::CartSCMinMinimizerMap::dof_node_for_chi(unsigned long, unsigned long) const –> const class core::optimization::DOF_Node &

domain_map(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap) → pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t

MinimizerMapBase class virtual accessor

C++: core::pack::scmin::CartSCMinMinimizerMap::domain_map() const –> const class ObjexxFCL::FArray1D<int> &

get_atom(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, idx: int) → pyrosetta.rosetta.core.id.AtomID

C++: core::pack::scmin::CartSCMinMinimizerMap::get_atom(unsigned long) –> const class core::id::AtomID &

get_atom_index(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, atm: pyrosetta.rosetta.core.id.AtomID) → int

C++: core::pack::scmin::CartSCMinMinimizerMap::get_atom_index(const class core::id::AtomID &) –> unsigned long

link_torsion_vectors(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap) → None

propagate f1/f2’s up from children to parents

C++: core::pack::scmin::CartSCMinMinimizerMap::link_torsion_vectors() –> void

make_multifunc(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, p: pyrosetta.rosetta.core.pose.Pose, bg_residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, mingraph: core::scoring::MinimizationGraph) → pyrosetta.rosetta.core.optimization.Multifunc

C++: core::pack::scmin::CartSCMinMinimizerMap::make_multifunc(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class core::scoring::ScoreFunction &, class core::scoring::MinimizationGraph &) –> class std::shared_ptr<class core::optimization::Multifunc>

n_dof_nodes(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap) → int

C++: core::pack::scmin::CartSCMinMinimizerMap::n_dof_nodes() const –> unsigned long

nactive_residues(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap) → int

Accessors

C++: core::pack::scmin::CartSCMinMinimizerMap::nactive_residues() const –> unsigned long

residue(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, seqpos: int) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::scmin::CartSCMinMinimizerMap::residue(unsigned long) const –> const class core::conformation::Residue &

residue_data(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, seqpos: int) → pyrosetta.rosetta.basic.datacache.BasicDataCache

C++: core::pack::scmin::CartSCMinMinimizerMap::residue_data(unsigned long) const –> class basic::datacache::BasicDataCache &

set_natoms_for_residue(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, resid: int, natoms: int) → None

C++: core::pack::scmin::CartSCMinMinimizerMap::set_natoms_for_residue(unsigned long, unsigned long) –> void

set_nonideal(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, val_in: bool) → None

C++: core::pack::scmin::SCMinMinimizerMap::set_nonideal(bool) –> void

set_total_residue(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, total_residue: int) → None

the CartSCMinMinimizerMap has to know how many residues are in the pose; this allows

it to do O(1) updates to its DomainMap – this function costs O(N).

C++: core::pack::scmin::CartSCMinMinimizerMap::set_total_residue(unsigned long) –> void

setup(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, trees: pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection) → None

Traverse the atom trees in preparation for minimization to tie together all the

DOFs and the atoms they control.

C++: core::pack::scmin::CartSCMinMinimizerMap::setup(class std::shared_ptr<class core::pack::scmin::AtomTreeCollection>) –> void

starting_dofs(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, dofs: pyrosetta.rosetta.utility.vector1_double) → None

Initialize a multivec with the dofs reflected in the current residue(s)

C++: core::pack::scmin::CartSCMinMinimizerMap::starting_dofs(class utility::vector1<double, class std::allocator<double> > &) const –> void

tor_for_dof(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap, dofid: pyrosetta.rosetta.core.id.DOF_ID) → pyrosetta.rosetta.core.id.TorsionID

C++: core::pack::scmin::CartSCMinMinimizerMap::tor_for_dof(const class core::id::DOF_ID &) const –> class core::id::TorsionID

zero_atom_derivative_vectors(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMinimizerMap) → None

C++: core::pack::scmin::CartSCMinMinimizerMap::zero_atom_derivative_vectors() –> void

class pyrosetta.rosetta.core.pack.scmin.CartSCMinMultifunc

Bases: Multifunc

abort_min(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMultifunc, : pyrosetta.rosetta.utility.vector1_double) → bool

C++: core::pack::scmin::CartSCMinMultifunc::abort_min(const class utility::vector1<double, class std::allocator<double> > &) const –> bool

dfunc(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMultifunc, chi: pyrosetta.rosetta.utility.vector1_double, dE_dchi: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::pack::scmin::CartSCMinMultifunc::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dump(self: pyrosetta.rosetta.core.pack.scmin.CartSCMinMultifunc, : pyrosetta.rosetta.utility.vector1_double, : pyrosetta.rosetta.utility.vector1_double) → None

Error state reached; dump out something corresponding to the

var assignment. Default base class implementation: no_op();

C++: core::pack::scmin::CartSCMinMultifunc::dump(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) const –> void

class pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection

Bases: pybind11_object

The conformation::Residues and kinematics::AtomTrees for a single collection of rotamers (e.g. a RotamerSet). Each chemical::ResidueType gets its own residue/atomtree pair. A particular AtomTree/Residue pair can be set as “active” and manipulated by setter and getters for either the coordinates of the Residues or the chi dihedrals of the AtomTree.

active_atom_tree(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection) → pyrosetta.rosetta.core.kinematics.AtomTree

Inline accessor for the active atom tree.

asserts atom_tree_uptodate_ – make sure that update_atom_tree is called first

C++: core::pack::scmin::ResidueAtomTreeCollection::active_atom_tree() const –> const class core::kinematics::AtomTree &

active_residue(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection) → pyrosetta.rosetta.core.conformation.Residue

Inline accessor for the active residue.

asserts residue_uptodate_ – make sure that update_residue is called first

C++: core::pack::scmin::ResidueAtomTreeCollection::active_residue() const –> const class core::conformation::Residue &

active_residue_cop(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection) → pyrosetta.rosetta.core.conformation.Residue

C++: core::pack::scmin::ResidueAtomTreeCollection::active_residue_cop() const –> class std::shared_ptr<const class core::conformation::Residue>

active_residue_data(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection) → pyrosetta.rosetta.basic.datacache.BasicDataCache

Accessor for the active residue’s data cache

asserts residue_uptodate_ – make sure that update_residue is called first

C++: core::pack::scmin::ResidueAtomTreeCollection::active_residue_data() –> class basic::datacache::BasicDataCache &

active_restype(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection) → pyrosetta.rosetta.core.chemical.ResidueType

C++: core::pack::scmin::ResidueAtomTreeCollection::active_restype() const –> const class core::chemical::ResidueType &

active_restype_index(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection) → int

C++: core::pack::scmin::ResidueAtomTreeCollection::active_restype_index() const –> unsigned long

dof(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, dofid: pyrosetta.rosetta.core.id.DOF_ID) → float

fpd get dof value by DOF_ID

NOTE input resid must be 1

C++: core::pack::scmin::ResidueAtomTreeCollection::dof(const class core::id::DOF_ID &) –> double

save_momento(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, momento: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento) → None

C++: core::pack::scmin::ResidueAtomTreeCollection::save_momento(class core::pack::scmin::ResidueAtomTreeCollectionMomento &) const –> void

set_active_restype_index(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, restype_index: int) → None

C++: core::pack::scmin::ResidueAtomTreeCollection::set_active_restype_index(unsigned long) –> void

set_chi(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, chi_index: int, value: float) → None

Assigns the chi dihedral for the active restype. Must be followed by a call to

update_residue() before the next call to active_residue()

C++: core::pack::scmin::ResidueAtomTreeCollection::set_chi(unsigned long, double) –> void

set_d(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, chi_index: int, value: float) → None

fpd bondlength analog to set_chi

like set_chi, assumes changes propagate to atomtree keyed off of chi#, so we only allow distances corresponding to chi angles to refine distance corresponds to the distance between atoms 3 and 4 defining the chi chino==0 ==> CA-CB distance, which allows us to refine ALA CB position for example

C++: core::pack::scmin::ResidueAtomTreeCollection::set_d(unsigned long, double) –> void

set_rescoords(*args, **kwargs)

Overloaded function.

1. set_rescoords(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, res: pyrosetta.rosetta.core.conformation.Residue) -> None

Assigns the coordinates for a residue. Must be followed by a call to

update_atom_tree() before the next cal to active_atom_tree().

C++: core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(const class core::conformation::Residue &) –> void

2. set_rescoords(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, coords: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) -> None

C++: core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

3. set_rescoords(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, atms: pyrosetta.rosetta.utility.vector1_core_id_AtomID, coords: pyrosetta.rosetta.utility.vector1_numeric_xyzVector_double_t) -> None

C++: core::pack::scmin::ResidueAtomTreeCollection::set_rescoords(const class utility::vector1<class core::id::AtomID, class std::allocator<class core::id::AtomID> > &, const class utility::vector1<class numeric::xyzVector<double>, class std::allocator<class numeric::xyzVector<double> > > &) –> void

set_theta(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, chi_index: int, value: float) → None

fpd bondangle analog to set_chi

same idea as set_d

C++: core::pack::scmin::ResidueAtomTreeCollection::set_theta(unsigned long, double) –> void

update_atom_tree(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection) → None

See comments for update_residue(). After a call to “set_rescoords”, the user must

call update_atomtree() to make sure the atomtree and the residue are in synch.

C++: core::pack::scmin::ResidueAtomTreeCollection::update_atom_tree() –> void

update_from_momento(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection, momento: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento) → None

C++: core::pack::scmin::ResidueAtomTreeCollection::update_from_momento(const class core::pack::scmin::ResidueAtomTreeCollectionMomento &) –> void

update_residue(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollection) → None

The responsibility for making sure that the active residue and the active atomtree

are in synch is offloaded to an external class so that the calls to “active_residue()” and “active_atom_tree()” are as fast as possible (and bitwise const for future multithreaded use). After a round of set_chi() calls, the user for this class must update the residue coordinates.

C++: core::pack::scmin::ResidueAtomTreeCollection::update_residue() –> void

class pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento

Bases: pybind11_object

Class to save the state for a ResidueAtomTreeCollection

assign(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento, : pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento) → pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento

C++: core::pack::scmin::ResidueAtomTreeCollectionMomento::operator=(const class core::pack::scmin::ResidueAtomTreeCollectionMomento &) –> class core::pack::scmin::ResidueAtomTreeCollectionMomento &

coord(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento, ind: int) → pyrosetta.rosetta.numeric.xyzVector_double_t

C++: core::pack::scmin::ResidueAtomTreeCollectionMomento::coord(unsigned long) const –> const class numeric::xyzVector<double> &

copy_coords(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento, : pyrosetta.rosetta.core.conformation.Residue) → None

C++: core::pack::scmin::ResidueAtomTreeCollectionMomento::copy_coords(const class core::conformation::Residue &) –> void

restype_index(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento) → int

C++: core::pack::scmin::ResidueAtomTreeCollectionMomento::restype_index() const –> unsigned long

set_restype_index(self: pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento, setting: int) → None

C++: core::pack::scmin::ResidueAtomTreeCollectionMomento::set_restype_index(unsigned long) –> void

class pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap

Bases: MinimizerMapBase

activate_residue_dofs(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, resindex: int) → None

Activate all the dofs for a particular residue. Ammortized O(1).

C++: core::pack::scmin::SCMinMinimizerMap::activate_residue_dofs(unsigned long) –> void

active_residue(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, index: int) → int

C++: core::pack::scmin::SCMinMinimizerMap::active_residue(unsigned long) const –> unsigned long

add_atom(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, atom_id: pyrosetta.rosetta.core.id.AtomID, dof_id: pyrosetta.rosetta.core.id.DOF_ID) → None

Invoked during the depth-first traversal through the AtomTree; the atom

tree is indicating that a given atom is controlled by a particular DOF. Record that fact.

C++: core::pack::scmin::SCMinMinimizerMap::add_atom(const class core::id::AtomID &, const class core::id::DOF_ID &) –> void

add_torsion(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, new_torsion: pyrosetta.rosetta.core.id.DOF_ID, parent: pyrosetta.rosetta.core.id.DOF_ID) → None

Invoked during the depth-first traversal through the AtomTree. The AtomTree

is indicating that a particular torsion is dependent on another torsion. Record that fact.

C++: core::pack::scmin::SCMinMinimizerMap::add_torsion(const class core::id::DOF_ID &, const class core::id::DOF_ID &) –> void

assign(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, : pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap) → pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap

C++: core::pack::scmin::SCMinMinimizerMap::operator=(const class core::pack::scmin::SCMinMinimizerMap &) –> class core::pack::scmin::SCMinMinimizerMap &

assign_dofs_to_mobile_residues(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, dofs: pyrosetta.rosetta.utility.vector1_double) → None

Assign the chi values to the residue(s)

C++: core::pack::scmin::SCMinMinimizerMap::assign_dofs_to_mobile_residues(const class utility::vector1<double, class std::allocator<double> > &) –> void

atom(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, atid: pyrosetta.rosetta.core.id.AtomID) → pyrosetta.rosetta.core.kinematics.tree.Atom

C++: core::pack::scmin::SCMinMinimizerMap::atom(const class core::id::AtomID &) const –> const class core::kinematics::tree::Atom &

atom_derivatives(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, resid: int) → pyrosetta.rosetta.utility.vector1_core_scoring_DerivVectorPair

C++: core::pack::scmin::SCMinMinimizerMap::atom_derivatives(unsigned long) –> class utility::vector1<class core::scoring::DerivVectorPair, class std::allocator<class core::scoring::DerivVectorPair> > &

clear_active_dofs(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap) → None

Disable the minimization for all residues. Ammortized O(1).

C++: core::pack::scmin::SCMinMinimizerMap::clear_active_dofs() –> void

dm(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap) → pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t

Inline accessor

C++: core::pack::scmin::SCMinMinimizerMap::dm() const –> const class ObjexxFCL::FArray1D<int> &

dof_node(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, index: int) → pyrosetta.rosetta.core.optimization.DOF_Node

C++: core::pack::scmin::SCMinMinimizerMap::dof_node(unsigned long) –> class core::optimization::DOF_Node &

dof_node_for_chi(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, resid: int, chiid: int) → pyrosetta.rosetta.core.optimization.DOF_Node

C++: core::pack::scmin::SCMinMinimizerMap::dof_node_for_chi(unsigned long, unsigned long) const –> const class core::optimization::DOF_Node &

domain_map(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap) → pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t

MinimizerMapBase class virtual accessor

C++: core::pack::scmin::SCMinMinimizerMap::domain_map() const –> const class ObjexxFCL::FArray1D<int> &

link_torsion_vectors(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap) → None

propagate f1/f2’s up from children to parents

C++: core::pack::scmin::SCMinMinimizerMap::link_torsion_vectors() –> void

make_multifunc(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, p: pyrosetta.rosetta.core.pose.Pose, bg_residues: pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, mingraph: core::scoring::MinimizationGraph) → pyrosetta.rosetta.core.optimization.Multifunc

C++: core::pack::scmin::SCMinMinimizerMap::make_multifunc(class core::pose::Pose &, const class utility::vector1<class std::shared_ptr<const class core::conformation::Residue>, class std::allocator<class std::shared_ptr<const class core::conformation::Residue> > > &, const class core::scoring::ScoreFunction &, class core::scoring::MinimizationGraph &) –> class std::shared_ptr<class core::optimization::Multifunc>

n_dof_nodes(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap) → int

C++: core::pack::scmin::SCMinMinimizerMap::n_dof_nodes() const –> unsigned long

nactive_residues(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap) → int

Accessors

C++: core::pack::scmin::SCMinMinimizerMap::nactive_residues() const –> unsigned long

residue(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, seqpos: int) → pyrosetta.rosetta.core.conformation.Residue

Convenience lookup – turns over the request to the AtomTreeCollection

C++: core::pack::scmin::SCMinMinimizerMap::residue(unsigned long) const –> const class core::conformation::Residue &

residue_data(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, seqpos: int) → pyrosetta.rosetta.basic.datacache.BasicDataCache

C++: core::pack::scmin::SCMinMinimizerMap::residue_data(unsigned long) const –> class basic::datacache::BasicDataCache &

set_natoms_for_residue(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, resid: int, natoms: int) → None

C++: core::pack::scmin::SCMinMinimizerMap::set_natoms_for_residue(unsigned long, unsigned long) –> void

set_nonideal(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, val_in: bool) → None

C++: core::pack::scmin::SCMinMinimizerMap::set_nonideal(bool) –> void

set_total_residue(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, total_residue: int) → None

the SCMinMinimizerMap has to know how many residues are in the pose; this allows

it to do O(1) updates to its DomainMap – this function costs O(N).

C++: core::pack::scmin::SCMinMinimizerMap::set_total_residue(unsigned long) –> void

setup(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, trees: pyrosetta.rosetta.core.pack.scmin.AtomTreeCollection) → None

Traverse the atom trees in preparation for minimization to tie together all the

DOFs and the atoms they control.

C++: core::pack::scmin::SCMinMinimizerMap::setup(class std::shared_ptr<class core::pack::scmin::AtomTreeCollection>) –> void

starting_dofs(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, dofs: pyrosetta.rosetta.utility.vector1_double) → None

Initialize a multivec with the dofs reflected in the current residue(s)

C++: core::pack::scmin::SCMinMinimizerMap::starting_dofs(class utility::vector1<double, class std::allocator<double> > &) const –> void

tor_for_dof(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap, dofid: pyrosetta.rosetta.core.id.DOF_ID) → pyrosetta.rosetta.core.id.TorsionID

C++: core::pack::scmin::SCMinMinimizerMap::tor_for_dof(const class core::id::DOF_ID &) const –> class core::id::TorsionID

zero_atom_derivative_vectors(self: pyrosetta.rosetta.core.pack.scmin.SCMinMinimizerMap) → None

C++: core::pack::scmin::SCMinMinimizerMap::zero_atom_derivative_vectors() –> void

class pyrosetta.rosetta.core.pack.scmin.SCMinMultifunc

Bases: Multifunc

abort_min(self: pyrosetta.rosetta.core.pack.scmin.SCMinMultifunc, : pyrosetta.rosetta.utility.vector1_double) → bool

C++: core::pack::scmin::SCMinMultifunc::abort_min(const class utility::vector1<double, class std::allocator<double> > &) const –> bool

dfunc(self: pyrosetta.rosetta.core.pack.scmin.SCMinMultifunc, chi: pyrosetta.rosetta.utility.vector1_double, dE_dchi: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::pack::scmin::SCMinMultifunc::dfunc(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

dump(self: pyrosetta.rosetta.core.pack.scmin.SCMinMultifunc, : pyrosetta.rosetta.utility.vector1_double, : pyrosetta.rosetta.utility.vector1_double) → None

Error state reached; dump out something corresponding to the

var assignment. Default base class implementation: no_op();

C++: core::pack::scmin::SCMinMultifunc::dump(const class utility::vector1<double, class std::allocator<double> > &, const class utility::vector1<double, class std::allocator<double> > &) const –> void

scmin_numerical_derivative_check(self: pyrosetta.rosetta.core.pack.scmin.SCMinMultifunc, start_vars: pyrosetta.rosetta.utility.vector1_double, dE_dvars: pyrosetta.rosetta.utility.vector1_double) → None

C++: core::pack::scmin::SCMinMultifunc::scmin_numerical_derivative_check(const class utility::vector1<double, class std::allocator<double> > &, class utility::vector1<double, class std::allocator<double> > &) const –> void

class pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment

Bases: pybind11_object

A simple class for tracking a network state and its energy where each sidechain’s state is described by a series of chi angles.

any_unassigned(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment) → bool

C++: core::pack::scmin::SidechainStateAssignment::any_unassigned() const –> bool

assign(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment, : pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment) → pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment

C++: core::pack::scmin::SidechainStateAssignment::operator=(const class core::pack::scmin::SidechainStateAssignment &) –> class core::pack::scmin::SidechainStateAssignment &

assign_energy(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment, energy: float) → None

C++: core::pack::scmin::SidechainStateAssignment::assign_energy(double) –> void

assign_state(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment, moltenresid: int, orig_rotid: int) → None

C++: core::pack::scmin::SidechainStateAssignment::assign_state(unsigned long, unsigned long) –> void

energy(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment) → float

C++: core::pack::scmin::SidechainStateAssignment::energy() const –> double

momento_for_moltenres(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment, moltenresid: int) → pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento

C++: core::pack::scmin::SidechainStateAssignment::momento_for_moltenres(unsigned long) const –> const class core::pack::scmin::ResidueAtomTreeCollectionMomento &

n_unassigned(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment) → int

C++: core::pack::scmin::SidechainStateAssignment::n_unassigned() const –> unsigned long

nmoltenres(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment) → int

C++: core::pack::scmin::SidechainStateAssignment::nmoltenres() const –> unsigned long

orig_rotamer_id_for_moltenres(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment, moltenres: int) → int

C++: core::pack::scmin::SidechainStateAssignment::orig_rotamer_id_for_moltenres(unsigned long) const –> unsigned long

state_momento(self: pyrosetta.rosetta.core.pack.scmin.SidechainStateAssignment, moltenresid: int) → pyrosetta.rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento

C++: core::pack::scmin::SidechainStateAssignment::state_momento(unsigned long) –> class core::pack::scmin::ResidueAtomTreeCollectionMomento &