Bindings for core::pack::scmin namespace

Classes
		builtins.object AtomTreeCollection ResidueAtomTreeCollection ResidueAtomTreeCollectionMomento SidechainStateAssignment rosetta.core.kinematics.MinimizerMapBase(builtins.object) SCMinMinimizerMap AtomTreeSCMinMinimizerMap CartSCMinMinimizerMap rosetta.core.optimization.Multifunc(builtins.object) CartSCMinMultifunc SCMinMultifunc   class AtomTreeCollection(builtins.object)     A collection of ResidueAtomTreeCollection objects for an entire design task.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.core.pack.scmin.AtomTreeCollection, pose : rosetta.core.pose.Pose,  : rosetta.core.pack.rotamer_set.RotamerSets) -> NoneType   2. __init__(self : rosetta.core.pack.scmin.AtomTreeCollection, pose : rosetta.core.pose.Pose,  : rosetta.core.pack.task.PackerTask) -> NoneType   3. __init__(self : rosetta.core.pack.scmin.AtomTreeCollection, pose : rosetta.core.pose.Pose, rset : rosetta.core.pack.rotamer_set.RotamerSet, resid : int) -> NoneType   4. __init__(self : rosetta.core.pack.scmin.AtomTreeCollection, pose : rosetta.core.pose.Pose, rltask : rosetta.core.pack.task.ResidueLevelTask, resid : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.scmin.AtomTreeCollection,  : rosetta.core.pack.scmin.AtomTreeCollection) -> rosetta.core.pack.scmin.AtomTreeCollection moltenres_atomtree_collection(...) from builtins.PyCapsule moltenres_atomtree_collection(self : rosetta.core.pack.scmin.AtomTreeCollection, moltenresid : int) -> rosetta.core.pack.scmin.ResidueAtomTreeCollection residue_atomtree_collection(...) from builtins.PyCapsule residue_atomtree_collection(self : rosetta.core.pack.scmin.AtomTreeCollection, resid : int) -> rosetta.core.pack.scmin.ResidueAtomTreeCollection residue_atomtree_collection_op(...) from builtins.PyCapsule residue_atomtree_collection_op(self : rosetta.core.pack.scmin.AtomTreeCollection, resid : int) -> rosetta.core.pack.scmin.ResidueAtomTreeCollection   class AtomTreeSCMinMinimizerMap(SCMinMinimizerMap)       Method resolution order: AtomTreeSCMinMinimizerMap SCMinMinimizerMap rosetta.core.kinematics.MinimizerMapBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. activate_residue_dofs(...) from builtins.PyCapsule activate_residue_dofs(self : rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, resindex : int) -> NoneType   Activate all the dofs for a particular residue.  Ammortized O(1). active_residue(...) from builtins.PyCapsule active_residue(self : rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, index : int) -> int add_atom(...) from builtins.PyCapsule add_atom(self : rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, atom_id : rosetta.core.id.AtomID, dof_id : rosetta.core.id.DOF_ID) -> NoneType   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. add_torsion(...) from builtins.PyCapsule add_torsion(self : rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, new_torsion : rosetta.core.id.DOF_ID, parent : rosetta.core.id.DOF_ID) -> NoneType   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. assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap,  : rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap) -> rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap assign_dofs_to_mobile_residues(...) from builtins.PyCapsule assign_dofs_to_mobile_residues(self : rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, dofs : rosetta.utility.vector1_double) -> NoneType   Assign the chi values to the residue(s) atom(...) from builtins.PyCapsule atom(self : rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, atid : rosetta.core.id.AtomID) -> rosetta.core.kinematics.tree.Atom clear_active_dofs(...) from builtins.PyCapsule clear_active_dofs(rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap) -> NoneType   Disable the minimization for all residues.  Ammortized O(1). dm(...) from builtins.PyCapsule dm(rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap) -> ObjexxFCL::FArray1D<int>   Inline accessor dof_node(...) from builtins.PyCapsule dof_node(self : rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, index : int) -> rosetta.core.optimization.DOF_Node dof_node_for_chi(...) from builtins.PyCapsule dof_node_for_chi(self : rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, resid : int, chiid : int) -> rosetta.core.optimization.DOF_Node domain_map(...) from builtins.PyCapsule domain_map(rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap) -> ObjexxFCL::FArray1D<int>   MinimizerMapBase class virtual accessor link_torsion_vectors(...) from builtins.PyCapsule link_torsion_vectors(rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap) -> NoneType   propagate f1/f2's up from children to parents make_multifunc(...) from builtins.PyCapsule make_multifunc(self : rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, p : rosetta.core.pose.Pose, bg_residues : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, sfxn : rosetta.core.scoring.ScoreFunction, mingraph : core::scoring::MinimizationGraph) -> rosetta.core.optimization.Multifunc n_dof_nodes(...) from builtins.PyCapsule n_dof_nodes(rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap) -> int nactive_residues(...) from builtins.PyCapsule nactive_residues(rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap) -> int   Accessors residue(...) from builtins.PyCapsule residue(self : rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, seqpos : int) -> rosetta.core.conformation.Residue set_natoms_for_residue(...) from builtins.PyCapsule set_natoms_for_residue(self : rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, resid : int, natoms : int) -> NoneType set_total_residue(...) from builtins.PyCapsule set_total_residue(self : rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, total_residue : int) -> NoneType   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). setup(...) from builtins.PyCapsule setup(self : rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, trees : rosetta.core.pack.scmin.AtomTreeCollection) -> NoneType   Traverse the atom trees in preparation for minimization to tie together all the  DOFs and the atoms they control. starting_dofs(...) from builtins.PyCapsule starting_dofs(self : rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, dofs : rosetta.utility.vector1_double) -> NoneType   Initialize a multivec with the dofs reflected in the current residue(s) tor_for_dof(...) from builtins.PyCapsule tor_for_dof(self : rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap, dofid : rosetta.core.id.DOF_ID) -> rosetta.core.id.TorsionID zero_atom_derivative_vectors(...) from builtins.PyCapsule zero_atom_derivative_vectors(rosetta.core.pack.scmin.AtomTreeSCMinMinimizerMap) -> NoneType Methods inherited from SCMinMinimizerMap: atom_derivatives(...) from builtins.PyCapsule atom_derivatives(self : rosetta.core.pack.scmin.SCMinMinimizerMap, resid : int) -> rosetta.utility.vector1_core_scoring_DerivVectorPair set_nonideal(...) from builtins.PyCapsule set_nonideal(self : rosetta.core.pack.scmin.SCMinMinimizerMap, val_in : bool) -> NoneType   class CartSCMinMinimizerMap(SCMinMinimizerMap)       Method resolution order: CartSCMinMinimizerMap SCMinMinimizerMap rosetta.core.kinematics.MinimizerMapBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.pack.scmin.CartSCMinMinimizerMap) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. activate_residue_dofs(...) from builtins.PyCapsule activate_residue_dofs(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap, resindex : int) -> NoneType   Activate all the dofs for a particular residue.  Ammortized O(1). active_residue(...) from builtins.PyCapsule active_residue(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap, index : int) -> int add_atom(...) from builtins.PyCapsule add_atom(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap, atom_id : rosetta.core.id.AtomID, dof_id : rosetta.core.id.DOF_ID) -> NoneType   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. add_torsion(...) from builtins.PyCapsule add_torsion(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap, new_torsion : rosetta.core.id.DOF_ID, parent : rosetta.core.id.DOF_ID) -> NoneType   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. assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap,  : rosetta.core.pack.scmin.CartSCMinMinimizerMap) -> rosetta.core.pack.scmin.CartSCMinMinimizerMap assign_dofs_to_mobile_residues(...) from builtins.PyCapsule assign_dofs_to_mobile_residues(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap, dofs : rosetta.utility.vector1_double) -> NoneType   Assign the chi values to the residue(s) atom(...) from builtins.PyCapsule atom(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap, atid : rosetta.core.id.AtomID) -> rosetta.core.kinematics.tree.Atom clear_active_dofs(...) from builtins.PyCapsule clear_active_dofs(rosetta.core.pack.scmin.CartSCMinMinimizerMap) -> NoneType   Disable the minimization for all residues.  Ammortized O(1). dm(...) from builtins.PyCapsule dm(rosetta.core.pack.scmin.CartSCMinMinimizerMap) -> ObjexxFCL::FArray1D<int>   Inline accessor dof_node(...) from builtins.PyCapsule dof_node(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap, index : int) -> rosetta.core.optimization.DOF_Node dof_node_for_chi(...) from builtins.PyCapsule dof_node_for_chi(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap, resid : int, chiid : int) -> rosetta.core.optimization.DOF_Node domain_map(...) from builtins.PyCapsule domain_map(rosetta.core.pack.scmin.CartSCMinMinimizerMap) -> ObjexxFCL::FArray1D<int>   MinimizerMapBase class virtual accessor get_atom(...) from builtins.PyCapsule get_atom(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap, idx : int) -> rosetta.core.id.AtomID get_atom_index(...) from builtins.PyCapsule get_atom_index(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap, atm : rosetta.core.id.AtomID) -> int link_torsion_vectors(...) from builtins.PyCapsule link_torsion_vectors(rosetta.core.pack.scmin.CartSCMinMinimizerMap) -> NoneType   propagate f1/f2's up from children to parents make_multifunc(...) from builtins.PyCapsule make_multifunc(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap, p : rosetta.core.pose.Pose, bg_residues : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, sfxn : rosetta.core.scoring.ScoreFunction, mingraph : core::scoring::MinimizationGraph) -> rosetta.core.optimization.Multifunc n_dof_nodes(...) from builtins.PyCapsule n_dof_nodes(rosetta.core.pack.scmin.CartSCMinMinimizerMap) -> int nactive_residues(...) from builtins.PyCapsule nactive_residues(rosetta.core.pack.scmin.CartSCMinMinimizerMap) -> int   Accessors residue(...) from builtins.PyCapsule residue(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap, seqpos : int) -> rosetta.core.conformation.Residue set_natoms_for_residue(...) from builtins.PyCapsule set_natoms_for_residue(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap, resid : int, natoms : int) -> NoneType set_total_residue(...) from builtins.PyCapsule set_total_residue(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap, total_residue : int) -> NoneType   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). setup(...) from builtins.PyCapsule setup(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap, trees : rosetta.core.pack.scmin.AtomTreeCollection) -> NoneType   Traverse the atom trees in preparation for minimization to tie together all the  DOFs and the atoms they control. starting_dofs(...) from builtins.PyCapsule starting_dofs(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap, dofs : rosetta.utility.vector1_double) -> NoneType   Initialize a multivec with the dofs reflected in the current residue(s) tor_for_dof(...) from builtins.PyCapsule tor_for_dof(self : rosetta.core.pack.scmin.CartSCMinMinimizerMap, dofid : rosetta.core.id.DOF_ID) -> rosetta.core.id.TorsionID zero_atom_derivative_vectors(...) from builtins.PyCapsule zero_atom_derivative_vectors(rosetta.core.pack.scmin.CartSCMinMinimizerMap) -> NoneType Methods inherited from SCMinMinimizerMap: atom_derivatives(...) from builtins.PyCapsule atom_derivatives(self : rosetta.core.pack.scmin.SCMinMinimizerMap, resid : int) -> rosetta.utility.vector1_core_scoring_DerivVectorPair set_nonideal(...) from builtins.PyCapsule set_nonideal(self : rosetta.core.pack.scmin.SCMinMinimizerMap, val_in : bool) -> NoneType   class CartSCMinMultifunc(rosetta.core.optimization.Multifunc)       Method resolution order: CartSCMinMultifunc rosetta.core.optimization.Multifunc builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.core.pack.scmin.CartSCMinMultifunc, chi : rosetta.utility.vector1_double) -> float __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, p : rosetta.core.pose.Pose, bg_residues : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, sfxn : rosetta.core.scoring.ScoreFunction, mingraph : core::scoring::MinimizationGraph, scminmap : rosetta.core.pack.scmin.SCMinMinimizerMap) -> NoneType   2. __init__(handle, rosetta.core.pack.scmin.CartSCMinMultifunc) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. abort_min(...) from builtins.PyCapsule abort_min(self : rosetta.core.pack.scmin.CartSCMinMultifunc,  : rosetta.utility.vector1_double) -> bool dfunc(...) from builtins.PyCapsule dfunc(self : rosetta.core.pack.scmin.CartSCMinMultifunc, chi : rosetta.utility.vector1_double, dE_dchi : rosetta.utility.vector1_double) -> NoneType dump(...) from builtins.PyCapsule dump(self : rosetta.core.pack.scmin.CartSCMinMultifunc,  : rosetta.utility.vector1_double,  : rosetta.utility.vector1_double) -> NoneType   Error state reached; dump out something corresponding to the  var assignment.  Default base class implementation: no_op();   class ResidueAtomTreeCollection(builtins.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.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.core.pack.scmin.ResidueAtomTreeCollection, rltask : rosetta.core.pack.task.ResidueLevelTask, conformation : rosetta.core.conformation.Conformation, orig_res : rosetta.core.conformation.Residue) -> NoneType   2. __init__(self : rosetta.core.pack.scmin.ResidueAtomTreeCollection, rset : rosetta.core.pack.rotamer_set.RotamerSet, resid : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. active_atom_tree(...) from builtins.PyCapsule active_atom_tree(rosetta.core.pack.scmin.ResidueAtomTreeCollection) -> rosetta.core.kinematics.AtomTree   Inline accessor for the active atom tree.  asserts atom_tree_uptodate_ -- make sure that update_atom_tree is called first active_residue(...) from builtins.PyCapsule active_residue(rosetta.core.pack.scmin.ResidueAtomTreeCollection) -> rosetta.core.conformation.Residue   Inline accessor for the active residue.  asserts residue_uptodate_ -- make sure that update_residue is called first active_residue_cop(...) from builtins.PyCapsule active_residue_cop(rosetta.core.pack.scmin.ResidueAtomTreeCollection) -> rosetta.core.conformation.Residue active_restype(...) from builtins.PyCapsule active_restype(rosetta.core.pack.scmin.ResidueAtomTreeCollection) -> rosetta.core.chemical.ResidueType active_restype_index(...) from builtins.PyCapsule active_restype_index(rosetta.core.pack.scmin.ResidueAtomTreeCollection) -> int dof(...) from builtins.PyCapsule dof(self : rosetta.core.pack.scmin.ResidueAtomTreeCollection, dofid : rosetta.core.id.DOF_ID) -> float   fpd  get dof value by DOF_ID      NOTE input resid must be 1 save_momento(...) from builtins.PyCapsule save_momento(self : rosetta.core.pack.scmin.ResidueAtomTreeCollection, momento : rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento) -> NoneType set_active_restype_index(...) from builtins.PyCapsule set_active_restype_index(self : rosetta.core.pack.scmin.ResidueAtomTreeCollection, restype_index : int) -> NoneType set_chi(...) from builtins.PyCapsule set_chi(self : rosetta.core.pack.scmin.ResidueAtomTreeCollection, chi_index : int, value : float) -> NoneType   Assigns the chi dihedral for the active restype.  Must be followed by a call to  update_residue() before the next call to active_residue() set_d(...) from builtins.PyCapsule set_d(self : rosetta.core.pack.scmin.ResidueAtomTreeCollection, chi_index : int, value : float) -> NoneType   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 set_rescoords(...) from builtins.PyCapsule set_rescoords(*args, **kwargs) Overloaded function.   1. set_rescoords(self : rosetta.core.pack.scmin.ResidueAtomTreeCollection, res : rosetta.core.conformation.Residue) -> NoneType   Assigns the coordinates for a residue.  Must be followed by a call to  update_atom_tree() before the next cal to active_atom_tree().   2. set_rescoords(self : rosetta.core.pack.scmin.ResidueAtomTreeCollection, coords : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType   3. set_rescoords(self : rosetta.core.pack.scmin.ResidueAtomTreeCollection, atms : rosetta.utility.vector1_core_id_AtomID, coords : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType set_theta(...) from builtins.PyCapsule set_theta(self : rosetta.core.pack.scmin.ResidueAtomTreeCollection, chi_index : int, value : float) -> NoneType   fpd bondangle analog to set_chi     same idea as set_d update_atom_tree(...) from builtins.PyCapsule update_atom_tree(rosetta.core.pack.scmin.ResidueAtomTreeCollection) -> NoneType   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. update_from_momento(...) from builtins.PyCapsule update_from_momento(self : rosetta.core.pack.scmin.ResidueAtomTreeCollection, momento : rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento) -> NoneType update_residue(...) from builtins.PyCapsule update_residue(rosetta.core.pack.scmin.ResidueAtomTreeCollection) -> NoneType   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.   class ResidueAtomTreeCollectionMomento(builtins.object)     Class to save the state for a ResidueAtomTreeCollection     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento) -> NoneType   2. __init__(self : rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento,  : rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento,  : rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento) -> rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento coord(...) from builtins.PyCapsule coord(self : rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento, ind : int) -> rosetta.numeric.xyzVector_double_t copy_coords(...) from builtins.PyCapsule copy_coords(self : rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento,  : rosetta.core.conformation.Residue) -> NoneType restype_index(...) from builtins.PyCapsule restype_index(rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento) -> int set_restype_index(...) from builtins.PyCapsule set_restype_index(self : rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento, setting : int) -> NoneType   class SCMinMinimizerMap(rosetta.core.kinematics.MinimizerMapBase)       Method resolution order: SCMinMinimizerMap rosetta.core.kinematics.MinimizerMapBase builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.pack.scmin.SCMinMinimizerMap) -> NoneType   2. __init__(rosetta.core.pack.scmin.SCMinMinimizerMap, rosetta.core.pack.scmin.SCMinMinimizerMap) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. activate_residue_dofs(...) from builtins.PyCapsule activate_residue_dofs(self : rosetta.core.pack.scmin.SCMinMinimizerMap, resindex : int) -> NoneType   Activate all the dofs for a particular residue.  Ammortized O(1). active_residue(...) from builtins.PyCapsule active_residue(self : rosetta.core.pack.scmin.SCMinMinimizerMap, index : int) -> int add_atom(...) from builtins.PyCapsule add_atom(self : rosetta.core.pack.scmin.SCMinMinimizerMap, atom_id : rosetta.core.id.AtomID, dof_id : rosetta.core.id.DOF_ID) -> NoneType   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. add_torsion(...) from builtins.PyCapsule add_torsion(self : rosetta.core.pack.scmin.SCMinMinimizerMap, new_torsion : rosetta.core.id.DOF_ID, parent : rosetta.core.id.DOF_ID) -> NoneType   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. assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.scmin.SCMinMinimizerMap,  : rosetta.core.pack.scmin.SCMinMinimizerMap) -> rosetta.core.pack.scmin.SCMinMinimizerMap assign_dofs_to_mobile_residues(...) from builtins.PyCapsule assign_dofs_to_mobile_residues(self : rosetta.core.pack.scmin.SCMinMinimizerMap, dofs : rosetta.utility.vector1_double) -> NoneType   Assign the chi values to the residue(s) atom(...) from builtins.PyCapsule atom(self : rosetta.core.pack.scmin.SCMinMinimizerMap, atid : rosetta.core.id.AtomID) -> rosetta.core.kinematics.tree.Atom atom_derivatives(...) from builtins.PyCapsule atom_derivatives(self : rosetta.core.pack.scmin.SCMinMinimizerMap, resid : int) -> rosetta.utility.vector1_core_scoring_DerivVectorPair clear_active_dofs(...) from builtins.PyCapsule clear_active_dofs(rosetta.core.pack.scmin.SCMinMinimizerMap) -> NoneType   Disable the minimization for all residues.  Ammortized O(1). dm(...) from builtins.PyCapsule dm(rosetta.core.pack.scmin.SCMinMinimizerMap) -> ObjexxFCL::FArray1D<int>   Inline accessor dof_node(...) from builtins.PyCapsule dof_node(self : rosetta.core.pack.scmin.SCMinMinimizerMap, index : int) -> rosetta.core.optimization.DOF_Node dof_node_for_chi(...) from builtins.PyCapsule dof_node_for_chi(self : rosetta.core.pack.scmin.SCMinMinimizerMap, resid : int, chiid : int) -> rosetta.core.optimization.DOF_Node domain_map(...) from builtins.PyCapsule domain_map(rosetta.core.pack.scmin.SCMinMinimizerMap) -> ObjexxFCL::FArray1D<int>   MinimizerMapBase class virtual accessor link_torsion_vectors(...) from builtins.PyCapsule link_torsion_vectors(rosetta.core.pack.scmin.SCMinMinimizerMap) -> NoneType   propagate f1/f2's up from children to parents make_multifunc(...) from builtins.PyCapsule make_multifunc(self : rosetta.core.pack.scmin.SCMinMinimizerMap, p : rosetta.core.pose.Pose, bg_residues : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, sfxn : rosetta.core.scoring.ScoreFunction, mingraph : core::scoring::MinimizationGraph) -> rosetta.core.optimization.Multifunc n_dof_nodes(...) from builtins.PyCapsule n_dof_nodes(rosetta.core.pack.scmin.SCMinMinimizerMap) -> int nactive_residues(...) from builtins.PyCapsule nactive_residues(rosetta.core.pack.scmin.SCMinMinimizerMap) -> int   Accessors residue(...) from builtins.PyCapsule residue(self : rosetta.core.pack.scmin.SCMinMinimizerMap, seqpos : int) -> rosetta.core.conformation.Residue   Convenience lookup -- turns over the request to the AtomTreeCollection set_natoms_for_residue(...) from builtins.PyCapsule set_natoms_for_residue(self : rosetta.core.pack.scmin.SCMinMinimizerMap, resid : int, natoms : int) -> NoneType set_nonideal(...) from builtins.PyCapsule set_nonideal(self : rosetta.core.pack.scmin.SCMinMinimizerMap, val_in : bool) -> NoneType set_total_residue(...) from builtins.PyCapsule set_total_residue(self : rosetta.core.pack.scmin.SCMinMinimizerMap, total_residue : int) -> NoneType   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). setup(...) from builtins.PyCapsule setup(self : rosetta.core.pack.scmin.SCMinMinimizerMap, trees : rosetta.core.pack.scmin.AtomTreeCollection) -> NoneType   Traverse the atom trees in preparation for minimization to tie together all the  DOFs and the atoms they control. starting_dofs(...) from builtins.PyCapsule starting_dofs(self : rosetta.core.pack.scmin.SCMinMinimizerMap, dofs : rosetta.utility.vector1_double) -> NoneType   Initialize a multivec with the dofs reflected in the current residue(s) tor_for_dof(...) from builtins.PyCapsule tor_for_dof(self : rosetta.core.pack.scmin.SCMinMinimizerMap, dofid : rosetta.core.id.DOF_ID) -> rosetta.core.id.TorsionID zero_atom_derivative_vectors(...) from builtins.PyCapsule zero_atom_derivative_vectors(rosetta.core.pack.scmin.SCMinMinimizerMap) -> NoneType   class SCMinMultifunc(rosetta.core.optimization.Multifunc)       Method resolution order: SCMinMultifunc rosetta.core.optimization.Multifunc builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.core.pack.scmin.SCMinMultifunc, chi : rosetta.utility.vector1_double) -> float __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, p : rosetta.core.pose.Pose, bg_residues : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, sfxn : rosetta.core.scoring.ScoreFunction, mingraph : core::scoring::MinimizationGraph, scminmap : core::pack::scmin::SCMinMinimizerMap) -> NoneType   2. __init__(handle, rosetta.core.pack.scmin.SCMinMultifunc) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. abort_min(...) from builtins.PyCapsule abort_min(self : rosetta.core.pack.scmin.SCMinMultifunc,  : rosetta.utility.vector1_double) -> bool dfunc(...) from builtins.PyCapsule dfunc(self : rosetta.core.pack.scmin.SCMinMultifunc, chi : rosetta.utility.vector1_double, dE_dchi : rosetta.utility.vector1_double) -> NoneType dump(...) from builtins.PyCapsule dump(self : rosetta.core.pack.scmin.SCMinMultifunc,  : rosetta.utility.vector1_double,  : rosetta.utility.vector1_double) -> NoneType   Error state reached; dump out something corresponding to the  var assignment.  Default base class implementation: no_op(); scmin_numerical_derivative_check(...) from builtins.PyCapsule scmin_numerical_derivative_check(self : rosetta.core.pack.scmin.SCMinMultifunc, start_vars : rosetta.utility.vector1_double, dE_dvars : rosetta.utility.vector1_double) -> NoneType   class SidechainStateAssignment(builtins.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.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.core.pack.scmin.SidechainStateAssignment, nmoltenres : int) -> NoneType   2. __init__(self : rosetta.core.pack.scmin.SidechainStateAssignment,  : rosetta.core.pack.scmin.SidechainStateAssignment) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. any_unassigned(...) from builtins.PyCapsule any_unassigned(rosetta.core.pack.scmin.SidechainStateAssignment) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.core.pack.scmin.SidechainStateAssignment,  : rosetta.core.pack.scmin.SidechainStateAssignment) -> rosetta.core.pack.scmin.SidechainStateAssignment assign_energy(...) from builtins.PyCapsule assign_energy(self : rosetta.core.pack.scmin.SidechainStateAssignment, energy : float) -> NoneType assign_state(...) from builtins.PyCapsule assign_state(self : rosetta.core.pack.scmin.SidechainStateAssignment, moltenresid : int, orig_rotid : int) -> NoneType energy(...) from builtins.PyCapsule energy(rosetta.core.pack.scmin.SidechainStateAssignment) -> float momento_for_moltenres(...) from builtins.PyCapsule momento_for_moltenres(self : rosetta.core.pack.scmin.SidechainStateAssignment, moltenresid : int) -> rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento n_unassigned(...) from builtins.PyCapsule n_unassigned(rosetta.core.pack.scmin.SidechainStateAssignment) -> int nmoltenres(...) from builtins.PyCapsule nmoltenres(rosetta.core.pack.scmin.SidechainStateAssignment) -> int orig_rotamer_id_for_moltenres(...) from builtins.PyCapsule orig_rotamer_id_for_moltenres(self : rosetta.core.pack.scmin.SidechainStateAssignment, moltenres : int) -> int state_momento(...) from builtins.PyCapsule state_momento(self : rosetta.core.pack.scmin.SidechainStateAssignment, moltenresid : int) -> rosetta.core.pack.scmin.ResidueAtomTreeCollectionMomento