Bindings for core::scoring namespace

Modules
		rosetta.core.scoring.EnergiesCacheableDataType rosetta.core.scoring.aa_composition_energy rosetta.core.scoring.aa_repeat_energy rosetta.core.scoring.annealing rosetta.core.scoring.bin_transitions rosetta.core.scoring.carbohydrates rosetta.core.scoring.carbon_hbonds rosetta.core.scoring.constraints rosetta.core.scoring.cryst rosetta.core.scoring.custom_pair_distance rosetta.core.scoring.disulfides rosetta.core.scoring.dna rosetta.core.scoring.dssp rosetta.core.scoring.elec rosetta.core.scoring.electron_density rosetta.core.scoring.electron_density_atomwise rosetta.core.scoring.etable rosetta.core.scoring.fiber_diffraction rosetta.core.scoring.func rosetta.core.scoring.geometric_solvation rosetta.core.scoring.hackaro rosetta.core.scoring.hbonds rosetta.core.scoring.interface_ rosetta.core.scoring.lkball rosetta.core.scoring.loop_graph rosetta.core.scoring.magnesium rosetta.core.scoring.membrane rosetta.core.scoring.methods rosetta.core.scoring.mm rosetta.core.scoring.motif rosetta.core.scoring.nv rosetta.core.scoring.orbitals rosetta.core.scoring.packing rosetta.core.scoring.packstat rosetta.core.scoring.power_diagram rosetta.core.scoring.rna rosetta.core.scoring.sasa rosetta.core.scoring.saxs rosetta.core.scoring.sc rosetta.core.scoring.solid_surface rosetta.core.scoring.sym_e rosetta.core.scoring.symmetry rosetta.core.scoring.trie rosetta.core.scoring.vdwaals

Classes
		builtins.object APBSConfig APBSResult APBSWrapper AtomNeighbor AtomVDW BB_Pos CSA CenHBPotential CenRotEnvPairPotential ContextGraphFactory ContextGraphType DC DerivVectorPair EMapVector Energies EnvPairPotential MembranePotential Membrane_FAPotential FACTSPotential FACTSResidueInfo FACTSRsdTypeInfo GenBornPotential GenBornResidueInfo Hairpin Hairpins Helices LREnergyContainer DenseEnergyContainer OneToAllEnergyContainer PolymerBondedEnergyContainer MultipoleAxisType MultipoleElecPotential MultipoleParameter NeighborList OmegaTether PDatom PDinter PDvertex PQR P_AA P_AA_ss PairEPotential PoissonBoltzmannPotential Predicate ExcludedResPredicate IsProteinCAPredicate ResRangePredicate SelectedResPredicate ProQPotential ProteinTorsion RDC RDC_Rohl RamaPrePro Rama_Table_Type Ramachandran Ramachandran2B ResPairMinimizationData ResSingleMinimizationData ResidueNeighborConstIterator DenseNeighborConstIterator OneToAllNeighborConstIterator PolymerBondedNeighborConstIterator ResidueNeighborIterator DenseNeighborIterator OneToAllNeighborIterator PolymerBondedNeighborIterator SASAPotential SAnode ScoreFunction DockingScoreFunction MinScoreScoreFunction ScoreFunctionFactory ScoreFunctionInfo ScoreType ScoreTypeManager SecondaryStructurePotential SecondaryStructureWeights SmallAtNb SmoothEnvPairPotential SmoothScoreTermCoeffs SplitUnfoldedTwoBodyPotential Strands TMscore TMscoreStore UnfoldedStatePotential VdWTinkerPotential WaterAdductHBondPotential min_pair_data min_single_data rosetta.basic.datacache.CacheableData(builtins.object) CenListInfo ChemicalShiftAnisotropy DipolarCoupling FACTSPoseInfo FACTSRotamerSetInfo GenBornPoseInfo GenBornRotamerSetInfo MembraneEmbed MembraneTopology Membrane_FAEmbed MultipoleElecPoseInfo MultipoleElecResidueInfo MultipoleElecRotamerSetInfo ResidualDipolarCoupling ResidualDipolarCoupling_Rohl ResidueNblistData ResiduePairNeighborList SS_Info SS_Killhairpins_Info VdWTinkerPoseInfo VdWTinkerResidueInfo VdWTinkerRotamerSetInfo rosetta.core.graph.Edge(builtins.object) EnergyEdge MinimizationEdge TenANeighborEdge TwelveANeighborEdge rosetta.core.graph.Graph(builtins.object) ContextGraph TenANeighborGraph TwelveANeighborGraph EnergyGraph MinimizationGraph rosetta.core.graph.Node(builtins.object) EnergyNode MinimizationNode TenANeighborNode TwelveANeighborNode rosetta.utility.SingletonBase_core_scoring_ScoringManager_t(builtins.object) ScoringManager   class APBSConfig(builtins.object)     ------------------------------------------------------------------------------------- APBSConfig     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.core.scoring.APBSConfig, pose : rosetta.core.pose.Pose, natoms : int, dbg : int, calcenergy : bool) -> NoneType   2. __init__(self : rosetta.core.scoring.APBSConfig,  : rosetta.core.scoring.APBSConfig) -> 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.scoring.APBSConfig,  : rosetta.core.scoring.APBSConfig) -> rosetta.core.scoring.APBSConfig Data descriptors defined here: calcenergy cfac dbg fadd i_param natoms nsims ofrac r_param space   class APBSResult(builtins.object)     ------------------------------------------------------------------------------------- APBSResult     Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __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.scoring.APBSResult,  : rosetta.core.scoring.APBSResult) -> rosetta.core.scoring.APBSResult Data descriptors defined here: dbx dby dbz dx dy dz esEnergy grid_data ibx iby ibz npEnergy npx npy npz nwrites qfx qfy qfz   class APBSWrapper(builtins.object)     ------------------------------------------------------------------------------------- APBS wrapper     Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.scoring.APBSWrapper, pose : rosetta.core.pose.Pose, charged_residues : rosetta.std.map_std_string_bool, dbg : int, calcenergy : bool) -> 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.scoring.APBSWrapper,  : rosetta.core.scoring.APBSWrapper) -> rosetta.core.scoring.APBSWrapper exec(...) from builtins.PyCapsule exec(rosetta.core.scoring.APBSWrapper) -> core::scoring::APBSResult   class AtomNeighbor(builtins.object)     The neighborlist is used during minimization to speed atom-atom energy calculations. It stores a list of potentially interacting neighbor atoms for each atom in the system.   The logic for using the nblist is tricky.   Tentative scheme: turn on nblist scoring at start of minimization   // at this point, want pose to be fully scored // so perhaps a call to scorefxn(pose) ?? // Real const start_score( scorefxn( pose ) );   pose.energies().setup_use_nblist( true );   Real const start_func( func( vars ) ); // nblist setup inside this call   now require that all energy evaluations have an identical set of moving dofs (guaranteed if all energy calculations are inside function evaluations). This is checked inside each scorecaln using the nblist.   when using the nblist, the rsd-rsd neighbor information is not updated. This will probably be a good thing in that it will smooth the energy landscape during minimization...   in a nblist score calculation, we do two things: recover cached energies for non-pair-moved positions, and get atom-atom energies for the pairs that are on the nblist. We don't cache 2d energies for moving positions, since we are not looping over rsd nbr links for that score calculation so the caching would be pretty time- consuming I think.   The nblist has the count_pair weights stored, so no calls to count_pair !!   turn off nblist scoring at the end of minimization. Since we have not been updating rsd-pair energies for moving pairs, and the rsd-rsd nblist is potentially out of data, we reset the neighborgraph at this point to ensure a complete score calculation next time.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.AtomNeighbor) -> NoneType   2. __init__(rosetta.core.scoring.AtomNeighbor, int, int, int, float) -> NoneType   doc   3. __init__(self : rosetta.core.scoring.AtomNeighbor, rsd_in : int, atomno_in : int, path_dist_in : int, weight_in : float, weight_func_in : float) -> NoneType   4. __init__(self : rosetta.core.scoring.AtomNeighbor,  : rosetta.core.scoring.AtomNeighbor) -> 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.scoring.AtomNeighbor,  : rosetta.core.scoring.AtomNeighbor) -> rosetta.core.scoring.AtomNeighbor atomno(...) from builtins.PyCapsule atomno(rosetta.core.scoring.AtomNeighbor) -> int path_dist(...) from builtins.PyCapsule path_dist(rosetta.core.scoring.AtomNeighbor) -> int rsd(...) from builtins.PyCapsule rsd(rosetta.core.scoring.AtomNeighbor) -> int temp1(...) from builtins.PyCapsule temp1(rosetta.core.scoring.AtomNeighbor) -> float temp2(...) from builtins.PyCapsule temp2(rosetta.core.scoring.AtomNeighbor) -> float temp3(...) from builtins.PyCapsule temp3(rosetta.core.scoring.AtomNeighbor) -> float temp4(...) from builtins.PyCapsule temp4(rosetta.core.scoring.AtomNeighbor) -> float weight(...) from builtins.PyCapsule weight(rosetta.core.scoring.AtomNeighbor) -> float weight_func(...) from builtins.PyCapsule weight_func(rosetta.core.scoring.AtomNeighbor) -> float   fpd   class AtomVDW(builtins.object)       Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.core.scoring.AtomVDW, atom_type_index : int) -> rosetta.utility.vector1_double __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.core.scoring.AtomVDW, atom_type_set_name : str) -> NoneType   2. __init__(self : rosetta.core.scoring.AtomVDW,  : rosetta.core.scoring.AtomVDW) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. approximate_vdw_radius(...) from builtins.PyCapsule approximate_vdw_radius(self : rosetta.core.scoring.AtomVDW, atom_type_index : int) -> float assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.AtomVDW,  : rosetta.core.scoring.AtomVDW) -> rosetta.core.scoring.AtomVDW atom_type_set_name(...) from builtins.PyCapsule atom_type_set_name(rosetta.core.scoring.AtomVDW) -> str   class BB_Pos(builtins.object)     ///////////////////////////////////////////////////////////////////////////////////////////////////     Methods defined here: C(...) from builtins.PyCapsule C(self : rosetta.core.scoring.BB_Pos, i : int) -> rosetta.numeric.xyzVector_double_t   accessor for C's coordinate on residue i, requires take_coordinates_from_pose have been recently called. CA(...) from builtins.PyCapsule CA(self : rosetta.core.scoring.BB_Pos, i : int) -> rosetta.numeric.xyzVector_double_t   accessor for CA's coordinate on residue i, requires take_coordinates_from_pose have been recently called. CB(...) from builtins.PyCapsule CB(self : rosetta.core.scoring.BB_Pos, i : int) -> rosetta.numeric.xyzVector_double_t   accessor for CB's coordinate on residue i, requires take_coordinates_from_pose have been recently called. N(...) from builtins.PyCapsule N(self : rosetta.core.scoring.BB_Pos, i : int) -> rosetta.numeric.xyzVector_double_t   accessor for N's coordinate on residue i, requires take_coordinates_from_pose have been recently called. O(...) from builtins.PyCapsule O(self : rosetta.core.scoring.BB_Pos, i : int) -> rosetta.numeric.xyzVector_double_t   accessor for O's coordinate on residue i, requires take_coordinates_from_pose have been recently called. __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.core.scoring.BB_Pos,  : rosetta.core.scoring.BB_Pos) -> NoneType   2. __init__(rosetta.core.scoring.BB_Pos) -> 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.scoring.BB_Pos,  : rosetta.core.scoring.BB_Pos) -> rosetta.core.scoring.BB_Pos resize(...) from builtins.PyCapsule resize(self : rosetta.core.scoring.BB_Pos, nres : int) -> NoneType take_coordinates_from_pose(...) from builtins.PyCapsule take_coordinates_from_pose(self : rosetta.core.scoring.BB_Pos, pose : rosetta.core.pose.Pose) -> NoneType   class CSA(builtins.object)     //////////////////////////////////////////////     Methods defined here: CSAcomputed(...) from builtins.PyCapsule CSAcomputed(*args, **kwargs) Overloaded function.   1. CSAcomputed(rosetta.core.scoring.CSA) -> float   2. CSAcomputed(rosetta.core.scoring.CSA) -> float CSAerr(...) from builtins.PyCapsule CSAerr(rosetta.core.scoring.CSA) -> float CSAval(...) from builtins.PyCapsule CSAval(rosetta.core.scoring.CSA) -> float __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.CSA) -> NoneType   2. __init__(self : rosetta.core.scoring.CSA, res1 : int, atom1 : str, sigma1 : float, sigma2 : float, sigma3 : float, CSAval : float, CSAerr : float, weight : float) -> NoneType   3. __init__(self : rosetta.core.scoring.CSA,  : rosetta.core.scoring.CSA) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.scoring.CSA) -> str alpha(...) from builtins.PyCapsule alpha(rosetta.core.scoring.CSA) -> float assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.CSA,  : rosetta.core.scoring.CSA) -> rosetta.core.scoring.CSA atom1(...) from builtins.PyCapsule atom1(rosetta.core.scoring.CSA) -> str atom2(...) from builtins.PyCapsule atom2(rosetta.core.scoring.CSA) -> str atom3(...) from builtins.PyCapsule atom3(rosetta.core.scoring.CSA) -> str beta(...) from builtins.PyCapsule beta(rosetta.core.scoring.CSA) -> float f1ij(...) from builtins.PyCapsule f1ij(rosetta.core.scoring.CSA) -> rosetta.numeric.xyzVector_double_t f2ij(...) from builtins.PyCapsule f2ij(rosetta.core.scoring.CSA) -> rosetta.numeric.xyzVector_double_t f3ij(...) from builtins.PyCapsule f3ij(rosetta.core.scoring.CSA) -> rosetta.numeric.xyzVector_double_t gamma(...) from builtins.PyCapsule gamma(rosetta.core.scoring.CSA) -> float res1(...) from builtins.PyCapsule res1(rosetta.core.scoring.CSA) -> int res2(...) from builtins.PyCapsule res2(rosetta.core.scoring.CSA) -> int res3(...) from builtins.PyCapsule res3(rosetta.core.scoring.CSA) -> int set_weight(...) from builtins.PyCapsule set_weight(self : rosetta.core.scoring.CSA, w_in : float) -> NoneType sigma1(...) from builtins.PyCapsule sigma1(rosetta.core.scoring.CSA) -> float sigma2(...) from builtins.PyCapsule sigma2(rosetta.core.scoring.CSA) -> float sigma3(...) from builtins.PyCapsule sigma3(rosetta.core.scoring.CSA) -> float weight(...) from builtins.PyCapsule weight(rosetta.core.scoring.CSA) -> float Data descriptors defined here: CSAval_computed_ f1ij_ f2ij_ f3ij_   class CenHBPotential(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.CenHBPotential) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_lr_gaussian(...) from builtins.PyCapsule add_lr_gaussian(self : rosetta.core.scoring.CenHBPotential, A_in : float, mu_in : rosetta.numeric.xyzVector_double_t, sigma_in : rosetta.numeric.xyzVector_double_t) -> NoneType add_sr_gaussian(...) from builtins.PyCapsule add_sr_gaussian(self : rosetta.core.scoring.CenHBPotential, A_in : float, mu_in : rosetta.numeric.xyzVector_double_t, sigma_in : rosetta.numeric.xyzVector_double_t) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.CenHBPotential,  : rosetta.core.scoring.CenHBPotential) -> rosetta.core.scoring.CenHBPotential clear(...) from builtins.PyCapsule clear(rosetta.core.scoring.CenHBPotential) -> NoneType cutoff(...) from builtins.PyCapsule cutoff(self : rosetta.core.scoring.CenHBPotential, seqsep : int) -> float dfunc(...) from builtins.PyCapsule dfunc(self : rosetta.core.scoring.CenHBPotential, seqsep : int, d : float, xd : float, xh : float) -> rosetta.numeric.xyzVector_double_t dfunc_soft(...) from builtins.PyCapsule dfunc_soft(self : rosetta.core.scoring.CenHBPotential, a1 : rosetta.numeric.xyzVector_double_t, a2 : rosetta.numeric.xyzVector_double_t, b1 : rosetta.numeric.xyzVector_double_t, b2 : rosetta.numeric.xyzVector_double_t, dv : rosetta.numeric.xyzVector_double_t, df_dABNC_1 : rosetta.utility.vector1_numeric_xyzVector_double_t, df_dABNC_2 : rosetta.utility.vector1_numeric_xyzVector_double_t) -> NoneType func(...) from builtins.PyCapsule func(self : rosetta.core.scoring.CenHBPotential, seqsep : int, d : float, xd : float, xh : float) -> float func_soft(...) from builtins.PyCapsule func_soft(self : rosetta.core.scoring.CenHBPotential, a1 : rosetta.numeric.xyzVector_double_t, a2 : rosetta.numeric.xyzVector_double_t, b1 : rosetta.numeric.xyzVector_double_t, b2 : rosetta.numeric.xyzVector_double_t, dv : rosetta.numeric.xyzVector_double_t) -> float nlr_gaussians(...) from builtins.PyCapsule nlr_gaussians(rosetta.core.scoring.CenHBPotential) -> int nsr_gaussians(...) from builtins.PyCapsule nsr_gaussians(rosetta.core.scoring.CenHBPotential) -> int set_cutoff_lr(...) from builtins.PyCapsule set_cutoff_lr(self : rosetta.core.scoring.CenHBPotential, cut_in : float) -> NoneType set_cutoff_sr(...) from builtins.PyCapsule set_cutoff_sr(self : rosetta.core.scoring.CenHBPotential, cut_in : float) -> NoneType   class CenListInfo(rosetta.basic.datacache.CacheableData)     /////////////////////////////////////////////////////////////////////////////////////////////////     Keep track of the cenlist information     Method resolution order: CenListInfo rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.scoring.CenListInfo) -> 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.scoring.CenListInfo,  : rosetta.core.scoring.CenListInfo) -> rosetta.core.scoring.CenListInfo calculated(...) from builtins.PyCapsule calculated(*args, **kwargs) Overloaded function.   1. calculated(rosetta.core.scoring.CenListInfo) -> bool   2. calculated(rosetta.core.scoring.CenListInfo) -> bool clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.CenListInfo) -> rosetta.basic.datacache.CacheableData fcen10(...) from builtins.PyCapsule fcen10(*args, **kwargs) Overloaded function.   1. fcen10(self : rosetta.core.scoring.CenListInfo, seqpos : int) -> float   2. fcen10(self : rosetta.core.scoring.CenListInfo, seqpos : int) -> float fcen12(...) from builtins.PyCapsule fcen12(*args, **kwargs) Overloaded function.   1. fcen12(self : rosetta.core.scoring.CenListInfo, seqpos : int) -> float   2. fcen12(self : rosetta.core.scoring.CenListInfo, seqpos : int) -> float fcen6(...) from builtins.PyCapsule fcen6(*args, **kwargs) Overloaded function.   1. fcen6(self : rosetta.core.scoring.CenListInfo, seqpos : int) -> float   2. fcen6(self : rosetta.core.scoring.CenListInfo, seqpos : int) -> float initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.scoring.CenListInfo, pose : rosetta.core.pose.Pose) -> NoneType set_fcen10(...) from builtins.PyCapsule set_fcen10(self : rosetta.core.scoring.CenListInfo, seqpos : int, value : float) -> NoneType set_fcen12(...) from builtins.PyCapsule set_fcen12(self : rosetta.core.scoring.CenListInfo, seqpos : int, value : float) -> NoneType set_fcen6(...) from builtins.PyCapsule set_fcen6(self : rosetta.core.scoring.CenListInfo, seqpos : int, value : float) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.scoring.CenListInfo) -> int Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class CenRotEnvPairPotential(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.CenRotEnvPairPotential) -> 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.scoring.CenRotEnvPairPotential,  : rosetta.core.scoring.CenRotEnvPairPotential) -> rosetta.core.scoring.CenRotEnvPairPotential compute_centroid_environment(...) from builtins.PyCapsule compute_centroid_environment(self : rosetta.core.scoring.CenRotEnvPairPotential, pose : rosetta.core.pose.Pose) -> NoneType compute_dcentroid_environment(...) from builtins.PyCapsule compute_dcentroid_environment(self : rosetta.core.scoring.CenRotEnvPairPotential, pose : rosetta.core.pose.Pose) -> NoneType evaluate_cen_rot_env_and_cbeta_deriv(...) from builtins.PyCapsule evaluate_cen_rot_env_and_cbeta_deriv(self : rosetta.core.scoring.CenRotEnvPairPotential, pose : rosetta.core.pose.Pose, rsd : rosetta.core.conformation.Residue, f2_cen_env : rosetta.numeric.xyzVector_double_t, f2_cen_cb6 : rosetta.numeric.xyzVector_double_t, f2_cen_cb12 : rosetta.numeric.xyzVector_double_t, f2_cb_env : rosetta.numeric.xyzVector_double_t, f2_cb_cb6 : rosetta.numeric.xyzVector_double_t, f2_cb_cb12 : rosetta.numeric.xyzVector_double_t) -> NoneType evaluate_cen_rot_env_and_cbeta_score(...) from builtins.PyCapsule evaluate_cen_rot_env_and_cbeta_score(self : rosetta.core.scoring.CenRotEnvPairPotential, pose : rosetta.core.pose.Pose, rsd : rosetta.core.conformation.Residue, env_contribution : float, cbeta6_contribution : float, cbeta12_contribution : float) -> NoneType   env evaluate_cen_rot_pair_deriv(...) from builtins.PyCapsule evaluate_cen_rot_pair_deriv(self : rosetta.core.scoring.CenRotEnvPairPotential, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, cendist : float, d_pair : float) -> NoneType evaluate_cen_rot_pair_orientation_deriv(...) from builtins.PyCapsule evaluate_cen_rot_pair_orientation_deriv(self : rosetta.core.scoring.CenRotEnvPairPotential, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, cendist : float, ang : float, dE_dr : float, dE_d_ang : float, dE_d_dih : float) -> NoneType evaluate_cen_rot_pair_orientation_score(...) from builtins.PyCapsule evaluate_cen_rot_pair_orientation_score(self : rosetta.core.scoring.CenRotEnvPairPotential, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, cendist : float, ang1_contribution : float, ang2_contribution : float, dih_contribution : float) -> NoneType evaluate_cen_rot_pair_score(...) from builtins.PyCapsule evaluate_cen_rot_pair_score(self : rosetta.core.scoring.CenRotEnvPairPotential, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, cendist : float, pair_contribution : float) -> NoneType   pair finalize(...) from builtins.PyCapsule finalize(self : rosetta.core.scoring.CenRotEnvPairPotential, pose : rosetta.core.pose.Pose) -> NoneType   class ChemicalShiftAnisotropy(rosetta.basic.datacache.CacheableData)     ChemicalShiftAnisotropys are mainly handled by this class     related classed: CSA --- a single line in an CSA file - representing a single csa coupling                         ChemicalShiftAnisotropyEnergy -- an energy method which triggers computations handled by this class.     Method resolution order: ChemicalShiftAnisotropy rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   doc   2. __init__(self : handle, filename : str) -> NoneType   3. __init__(handle, rosetta.core.scoring.ChemicalShiftAnisotropy) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.scoring.ChemicalShiftAnisotropy) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.ChemicalShiftAnisotropy, other : rosetta.core.scoring.ChemicalShiftAnisotropy) -> rosetta.core.scoring.ChemicalShiftAnisotropy clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.ChemicalShiftAnisotropy) -> rosetta.basic.datacache.CacheableData compute_csascore(...) from builtins.PyCapsule compute_csascore(self : rosetta.core.scoring.ChemicalShiftAnisotropy, pose : rosetta.core.pose.Pose) -> float   compute csa score for given pose (non-constant due to membrane) get_CSA_data(...) from builtins.PyCapsule get_CSA_data(rosetta.core.scoring.ChemicalShiftAnisotropy) -> rosetta.utility.vector1_core_scoring_CSA   get the raw CSA data Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class ContextGraph(rosetta.core.graph.Graph)       Method resolution order: ContextGraph rosetta.core.graph.Graph builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.ContextGraph) -> NoneType   2. __init__(self : rosetta.core.scoring.ContextGraph, num_nodes : int) -> NoneType   3. __init__(rosetta.core.scoring.ContextGraph, rosetta.core.scoring.ContextGraph) -> 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.scoring.ContextGraph, source : rosetta.core.scoring.ContextGraph) -> rosetta.core.scoring.ContextGraph clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.ContextGraph) -> rosetta.core.scoring.ContextGraph conditionally_add_edge(...) from builtins.PyCapsule conditionally_add_edge(self : rosetta.core.scoring.ContextGraph, lower_node_id : int, upper_node_id : int, dsq : float) -> NoneType neighbor_cutoff(...) from builtins.PyCapsule neighbor_cutoff(rosetta.core.scoring.ContextGraph) -> float update_from_pose(...) from builtins.PyCapsule update_from_pose(self : rosetta.core.scoring.ContextGraph, pose : rosetta.core.pose.Pose) -> NoneType Methods inherited from rosetta.core.graph.Graph: add_edge(...) from builtins.PyCapsule add_edge(*args, **kwargs) Overloaded function.   1. add_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   add an edge between two vertices.  Invokes "create_edge" from the derived class.  Returns a pointer to the edge after its been added, allowing the calling function  to immediately set data for this edge.   2. add_edge(self : rosetta.core.graph.Graph, example_edge : rosetta.core.graph.Edge) -> rosetta.core.graph.Edge   add an edge to this graph copying the data from an edge in another graph.  Returns a pointer to the edge after its been added, allowing the calling function  to immediately set data for this edge. all_pairs_shortest_paths(...) from builtins.PyCapsule all_pairs_shortest_paths(rosetta.core.graph.Graph) -> ObjexxFCL::FArray2D<int>   O(V^3).  Computes all pairs shortest paths using Warshall's algorithm  and writes all the path distances to the two-dimensional table. const_edge_list_begin(...) from builtins.PyCapsule const_edge_list_begin(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex const_edge_list_end(...) from builtins.PyCapsule const_edge_list_end(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex copy_connectivity(...) from builtins.PyCapsule copy_connectivity(self : rosetta.core.graph.Graph, source : rosetta.core.graph.Graph) -> NoneType   copy the edge connectivity from a source graph with a potentially  unknown type. delete_edge(...) from builtins.PyCapsule delete_edge(self : rosetta.core.graph.Graph, edge : rosetta.core.graph.Edge) -> NoneType   remove an edge from the graph. (NEW AS OF 12/9/07) Never call C++'s  "delete" function on an edge pointer directly.  Derived classes must implement this function.  If they wish to use unordered_object_pools to manage their memory drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.graph.Graph) -> NoneType   delete all the edges present in the graph drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.graph.Graph, node : int) -> NoneType   delete all the edges for a single vertex in the graph edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   returns a pointer to the edge connecting nodes node1 and node2, if that edge exists  in the graph, o.w. returns 0.  Focuses the graph on this edge for fast subsequent retrieval.   2. find_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   returns a const pointer to the edge connecting nodes node1 and node2, if that edge exists  in the graph, o.w. returns 0.  Focuses the graph on this edge for fast subsequent retrieval. focused_edge(...) from builtins.PyCapsule focused_edge(*args, **kwargs) Overloaded function.   1. focused_edge(rosetta.core.graph.Graph) -> rosetta.core.graph.Edge   returns a pointer to the focused edge   2. focused_edge(rosetta.core.graph.Graph) -> rosetta.core.graph.Edge   returns a const-pointer to the focused edge getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.graph.Graph) -> int   returns a count of all the memory used by every vertex and edge in a graph  by invoking the polymorphic count_static_memory and count_dynamic_memory of each  (possibly derived) node and edge object as well as for the (possibly derived) graph  class. get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> bool   is an edge already present in the graph? O(V) worst case.  O(1) iff all vertices have O(1) edges get_node(...) from builtins.PyCapsule get_node(*args, **kwargs) Overloaded function.   1. get_node(self : rosetta.core.graph.Graph, index : int) -> rosetta.core.graph.Node   2. get_node(self : rosetta.core.graph.Graph, index : int) -> rosetta.core.graph.Node get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.graph.Graph) -> rosetta.core.graph.Graph   self pointers   2. get_self_ptr(rosetta.core.graph.Graph) -> rosetta.core.graph.Graph num_edges(...) from builtins.PyCapsule num_edges(rosetta.core.graph.Graph) -> int num_nodes(...) from builtins.PyCapsule num_nodes(rosetta.core.graph.Graph) -> int   the number of nodes in the graph print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.graph.Graph) -> NoneType   send summary information to the screen for all vertices in the graph set_num_nodes(...) from builtins.PyCapsule set_num_nodes(self : rosetta.core.graph.Graph, num_nodes : int) -> NoneType   set the number of nodes in the graph -- deletes any existing edges in the graph   class ContextGraphFactory(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.ContextGraphFactory) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. create_context_graph(...) from builtins.PyCapsule create_context_graph(type : rosetta.core.scoring.ContextGraphType) -> rosetta.core.scoring.ContextGraph   class ContextGraphType(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.core.scoring.ContextGraphType, rosetta.core.scoring.ContextGraphType) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.core.scoring.ContextGraphType) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.ContextGraphType, int) -> NoneType   2. __init__(rosetta.core.scoring.ContextGraphType, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.core.scoring.ContextGraphType) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.core.scoring.ContextGraphType, rosetta.core.scoring.ContextGraphType) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.core.scoring.ContextGraphType) -> str Data and other attributes defined here: centroid_neighbor_graph = ContextGraphType.num_context_graph_types num_context_graph_types = ContextGraphType.num_context_graph_types ten_A_neighbor_graph = ContextGraphType.ten_A_neighbor_graph twelve_A_neighbor_graph = ContextGraphType.twelve_A_neighbor_graph   class DC(builtins.object)     //////////////////////////////////////////////     Methods defined here: DCcomputed(...) from builtins.PyCapsule DCcomputed(*args, **kwargs) Overloaded function.   1. DCcomputed(rosetta.core.scoring.DC) -> float   2. DCcomputed(rosetta.core.scoring.DC) -> float DCerr(...) from builtins.PyCapsule DCerr(rosetta.core.scoring.DC) -> float DCval(...) from builtins.PyCapsule DCval(rosetta.core.scoring.DC) -> float Dconst(...) from builtins.PyCapsule Dconst(rosetta.core.scoring.DC) -> float __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.DC) -> NoneType   2. __init__(self : rosetta.core.scoring.DC, res1 : int, atom1 : str, res2 : int, atom2 : str, DCval : float, DCerr : float, weight : float) -> NoneType   3. __init__(self : rosetta.core.scoring.DC,  : rosetta.core.scoring.DC) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.scoring.DC) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.DC,  : rosetta.core.scoring.DC) -> rosetta.core.scoring.DC atom1(...) from builtins.PyCapsule atom1(rosetta.core.scoring.DC) -> str atom2(...) from builtins.PyCapsule atom2(rosetta.core.scoring.DC) -> str f1ij(...) from builtins.PyCapsule f1ij(rosetta.core.scoring.DC) -> rosetta.numeric.xyzVector_double_t f2ij(...) from builtins.PyCapsule f2ij(rosetta.core.scoring.DC) -> rosetta.numeric.xyzVector_double_t get_DC_data_type(...) from builtins.PyCapsule get_DC_data_type(self : rosetta.core.scoring.DC, atom1 : str, atom2 : str) -> rosetta.core.scoring.DC_TYPE res1(...) from builtins.PyCapsule res1(rosetta.core.scoring.DC) -> int res2(...) from builtins.PyCapsule res2(rosetta.core.scoring.DC) -> int set_weight(...) from builtins.PyCapsule set_weight(self : rosetta.core.scoring.DC, w_in : float) -> NoneType type(...) from builtins.PyCapsule type(rosetta.core.scoring.DC) -> rosetta.core.scoring.DC_TYPE weight(...) from builtins.PyCapsule weight(rosetta.core.scoring.DC) -> float Data descriptors defined here: DCval_computed_ f1ij_ f2ij_ Data and other attributes defined here: DC_TYPE = <class 'rosetta.core.scoring.DC.DC_TYPE'> DC_TYPE_CC = DC_TYPE.DC_TYPE_CC DC_TYPE_CH = DC_TYPE.DC_TYPE_CH DC_TYPE_NC = DC_TYPE.DC_TYPE_NC DC_TYPE_NH = DC_TYPE.DC_TYPE_NH   class DenseEnergyContainer(LREnergyContainer)     ////////////////////////////////////////////////////////////////////////     Method resolution order: DenseEnergyContainer LREnergyContainer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, size_in : int, score_type_in : rosetta.core.scoring.ScoreType) -> NoneType   2. __init__(handle, rosetta.core.scoring.DenseEnergyContainer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. any_neighbors_for_residue(...) from builtins.PyCapsule any_neighbors_for_residue(self : rosetta.core.scoring.DenseEnergyContainer,  : int) -> bool any_upper_neighbors_for_residue(...) from builtins.PyCapsule any_upper_neighbors_for_residue(self : rosetta.core.scoring.DenseEnergyContainer, resid : int) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.DenseEnergyContainer,  : rosetta.core.scoring.DenseEnergyContainer) -> rosetta.core.scoring.DenseEnergyContainer clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.DenseEnergyContainer) -> rosetta.core.scoring.LREnergyContainer const_neighbor_iterator_begin(...) from builtins.PyCapsule const_neighbor_iterator_begin(self : rosetta.core.scoring.DenseEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborConstIterator   ///////////////// const versions const_neighbor_iterator_end(...) from builtins.PyCapsule const_neighbor_iterator_end(self : rosetta.core.scoring.DenseEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborConstIterator const_upper_neighbor_iterator_begin(...) from builtins.PyCapsule const_upper_neighbor_iterator_begin(self : rosetta.core.scoring.DenseEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborConstIterator const_upper_neighbor_iterator_end(...) from builtins.PyCapsule const_upper_neighbor_iterator_end(self : rosetta.core.scoring.DenseEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborConstIterator empty(...) from builtins.PyCapsule empty(rosetta.core.scoring.DenseEnergyContainer) -> bool neighbor_iterator_begin(...) from builtins.PyCapsule neighbor_iterator_begin(self : rosetta.core.scoring.DenseEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborIterator   ///////////////// non-const versions neighbor_iterator_end(...) from builtins.PyCapsule neighbor_iterator_end(self : rosetta.core.scoring.DenseEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborIterator set_num_nodes(...) from builtins.PyCapsule set_num_nodes(self : rosetta.core.scoring.DenseEnergyContainer, size_in : int) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.scoring.DenseEnergyContainer) -> int upper_neighbor_iterator_begin(...) from builtins.PyCapsule upper_neighbor_iterator_begin(self : rosetta.core.scoring.DenseEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborIterator upper_neighbor_iterator_end(...) from builtins.PyCapsule upper_neighbor_iterator_end(self : rosetta.core.scoring.DenseEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborIterator   class DenseNeighborConstIterator(ResidueNeighborConstIterator)     ////////////////////////////////////////////////////     Method resolution order: DenseNeighborConstIterator ResidueNeighborConstIterator builtins.object Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.scoring.DenseNeighborConstIterator, other : rosetta.core.scoring.ResidueNeighborConstIterator) -> bool __init__(...) from builtins.PyCapsule __init__(self : handle, pos1_in : int, pos2_in : int, st : rosetta.core.scoring.ScoreType, table_in : ObjexxFCL::FArray2D<double>, computed_in : ObjexxFCL::FArray2D<bool>) -> NoneType __ne__(...) from builtins.PyCapsule __ne__(self : rosetta.core.scoring.DenseNeighborConstIterator, other : rosetta.core.scoring.ResidueNeighborConstIterator) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. accumulate_energy(...) from builtins.PyCapsule accumulate_energy(self : rosetta.core.scoring.DenseNeighborConstIterator, emap : rosetta.core.scoring.EMapVector) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.DenseNeighborConstIterator, src : rosetta.core.scoring.ResidueNeighborConstIterator) -> rosetta.core.scoring.ResidueNeighborConstIterator energy_computed(...) from builtins.PyCapsule energy_computed(rosetta.core.scoring.DenseNeighborConstIterator) -> bool lower_neighbor_id(...) from builtins.PyCapsule lower_neighbor_id(rosetta.core.scoring.DenseNeighborConstIterator) -> int neighbor_id(...) from builtins.PyCapsule neighbor_id(rosetta.core.scoring.DenseNeighborConstIterator) -> int plus_plus(...) from builtins.PyCapsule plus_plus(rosetta.core.scoring.DenseNeighborConstIterator) -> rosetta.core.scoring.ResidueNeighborConstIterator residue_iterated_on(...) from builtins.PyCapsule residue_iterated_on(rosetta.core.scoring.DenseNeighborConstIterator) -> int retrieve_energy(...) from builtins.PyCapsule retrieve_energy(self : rosetta.core.scoring.DenseNeighborConstIterator, emap : rosetta.core.scoring.EMapVector) -> NoneType upper_neighbor_id(...) from builtins.PyCapsule upper_neighbor_id(rosetta.core.scoring.DenseNeighborConstIterator) -> int   class DenseNeighborIterator(ResidueNeighborIterator)     ////////////////////////////////////////////////////     Method resolution order: DenseNeighborIterator ResidueNeighborIterator builtins.object Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.scoring.DenseNeighborIterator, other : rosetta.core.scoring.ResidueNeighborIterator) -> bool __init__(...) from builtins.PyCapsule __init__(self : handle, pos1_in : int, pos2_in : int, st : rosetta.core.scoring.ScoreType, table_in : ObjexxFCL::FArray2D<double>, computed_in : ObjexxFCL::FArray2D<bool>) -> NoneType __ne__(...) from builtins.PyCapsule __ne__(self : rosetta.core.scoring.DenseNeighborIterator, other : rosetta.core.scoring.ResidueNeighborIterator) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. accumulate_energy(...) from builtins.PyCapsule accumulate_energy(self : rosetta.core.scoring.DenseNeighborIterator, emap : rosetta.core.scoring.EMapVector) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.DenseNeighborIterator, src : rosetta.core.scoring.ResidueNeighborIterator) -> rosetta.core.scoring.ResidueNeighborIterator energy_computed(...) from builtins.PyCapsule energy_computed(rosetta.core.scoring.DenseNeighborIterator) -> bool lower_neighbor_id(...) from builtins.PyCapsule lower_neighbor_id(rosetta.core.scoring.DenseNeighborIterator) -> int mark_energy_computed(...) from builtins.PyCapsule mark_energy_computed(rosetta.core.scoring.DenseNeighborIterator) -> NoneType mark_energy_uncomputed(...) from builtins.PyCapsule mark_energy_uncomputed(rosetta.core.scoring.DenseNeighborIterator) -> NoneType neighbor_id(...) from builtins.PyCapsule neighbor_id(rosetta.core.scoring.DenseNeighborIterator) -> int plus_plus(...) from builtins.PyCapsule plus_plus(rosetta.core.scoring.DenseNeighborIterator) -> rosetta.core.scoring.ResidueNeighborIterator residue_iterated_on(...) from builtins.PyCapsule residue_iterated_on(rosetta.core.scoring.DenseNeighborIterator) -> int retrieve_energy(...) from builtins.PyCapsule retrieve_energy(self : rosetta.core.scoring.DenseNeighborIterator, emap : rosetta.core.scoring.EMapVector) -> NoneType save_energy(...) from builtins.PyCapsule save_energy(self : rosetta.core.scoring.DenseNeighborIterator, emap : rosetta.core.scoring.EMapVector) -> NoneType upper_neighbor_id(...) from builtins.PyCapsule upper_neighbor_id(rosetta.core.scoring.DenseNeighborIterator) -> int   class DerivVectorPair(builtins.object)     A glorified struct for holding f1/f2 vectors used to represent the derivatives in our internal-geometry based minimization algorithms.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.DerivVectorPair) -> NoneType   2. __init__(self : rosetta.core.scoring.DerivVectorPair,  : rosetta.core.scoring.DerivVectorPair) -> 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.scoring.DerivVectorPair,  : rosetta.core.scoring.DerivVectorPair) -> rosetta.core.scoring.DerivVectorPair f1(...) from builtins.PyCapsule f1(*args, **kwargs) Overloaded function.   1. f1(rosetta.core.scoring.DerivVectorPair) -> rosetta.numeric.xyzVector_double_t   2. f1(rosetta.core.scoring.DerivVectorPair) -> rosetta.numeric.xyzVector_double_t f2(...) from builtins.PyCapsule f2(*args, **kwargs) Overloaded function.   1. f2(rosetta.core.scoring.DerivVectorPair) -> rosetta.numeric.xyzVector_double_t   2. f2(rosetta.core.scoring.DerivVectorPair) -> rosetta.numeric.xyzVector_double_t   class DipolarCoupling(rosetta.basic.datacache.CacheableData)     DipolarCouplings are mainly handled by this class     related classed: DC --- a single line in an DC file - representing a single dc coupling                         DipolarCouplingEnergy -- an energy method which triggers computations handled by this class.     Method resolution order: DipolarCoupling rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   doc   2. __init__(self : handle, filename : str) -> NoneType   3. __init__(handle, rosetta.core.scoring.DipolarCoupling) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.scoring.DipolarCoupling) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.DipolarCoupling, other : rosetta.core.scoring.DipolarCoupling) -> rosetta.core.scoring.DipolarCoupling clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.DipolarCoupling) -> rosetta.basic.datacache.CacheableData compute_dcscore(...) from builtins.PyCapsule compute_dcscore(self : rosetta.core.scoring.DipolarCoupling, pose : rosetta.core.pose.Pose) -> float   compute dc score for given pose (non-constant due to membrane) get_DC_data(...) from builtins.PyCapsule get_DC_data(rosetta.core.scoring.DipolarCoupling) -> rosetta.utility.vector1_core_scoring_DC   get the raw DC data Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class DockingScoreFunction(ScoreFunction)       Method resolution order: DockingScoreFunction ScoreFunction builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.core.scoring.DockingScoreFunction, pose : rosetta.core.pose.Pose) -> float   ////////////////////////////////////////////////////////////////////////// __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(*args, **kwargs) Overloaded function.   1. assign(self : rosetta.core.scoring.DockingScoreFunction, src : rosetta.core.scoring.ScoreFunction) -> NoneType   INTERNAL USE ONLY   2. assign(self : rosetta.core.scoring.DockingScoreFunction, src : rosetta.core.scoring.DockingScoreFunction) -> NoneType   INTERNAL USE ONLY clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.DockingScoreFunction) -> rosetta.core.scoring.ScoreFunction Methods inherited from ScoreFunction: __getitem__(...) from builtins.PyCapsule __getitem__(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType) -> float   Returns the weight of the ScoreType  <t>    example(s):      scorefxn[fa_sol]  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.set_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name __str__(...) from builtins.PyCapsule __str__(rosetta.core.scoring.ScoreFunction) -> str add_extra_method(...) from builtins.PyCapsule add_extra_method(*args, **kwargs) Overloaded function.   1. add_extra_method(self : rosetta.core.scoring.ScoreFunction, new_type : rosetta.core.scoring.ScoreType, new_weight : float, new_method : core::scoring::methods::EnergyMethod) -> NoneType   Adds a scoring method that is not necessarily included in  the core library   2. add_extra_method(self : rosetta.core.scoring.ScoreFunction, new_weights : rosetta.std.map_core_scoring_ScoreType_double, new_method : core::scoring::methods::EnergyMethod) -> NoneType   Adds a scoring method that is not necessarily included in  the core library add_weights_from_file(...) from builtins.PyCapsule add_weights_from_file(self : rosetta.core.scoring.ScoreFunction, filename : str) -> NoneType   Initializes this ScoreFunction from the given  <filename> all_energies_begin(...) from builtins.PyCapsule all_energies_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::EnergyMethod const> const*, std::vector<std::shared_ptr<core::scoring::methods::EnergyMethod const>, std::allocator<std::shared_ptr<core::scoring::methods::EnergyMethod const> > > > all_energies_end(...) from builtins.PyCapsule all_energies_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::EnergyMethod const> const*, std::vector<std::shared_ptr<core::scoring::methods::EnergyMethod const>, std::allocator<std::shared_ptr<core::scoring::methods::EnergyMethod const> > > > all_methods(...) from builtins.PyCapsule all_methods(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t any_lr_residue_pair_energy(...) from builtins.PyCapsule any_lr_residue_pair_energy(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, res1 : int, res2 : int) -> bool apply_patch_from_file(...) from builtins.PyCapsule apply_patch_from_file(self : rosetta.core.scoring.ScoreFunction, filename : str) -> NoneType   Applies a patch from the given  <filename> are_they_neighbors(...) from builtins.PyCapsule are_they_neighbors(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, pos1 : int, pos2 : int) -> bool   Returns true if the  <pose>  positions  <pos1>  and  <pos2>  are neighbors bump_check_backbone(...) from builtins.PyCapsule bump_check_backbone(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Scores the sidechain from  <pose>  Residue  <rsd1>  against the  backbone of Residue  <rsd2> bump_check_full(...) from builtins.PyCapsule bump_check_full(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType cd_1b_types(...) from builtins.PyCapsule cd_1b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType   convenience access to all cd 1b score types cd_2b_begin(...) from builtins.PyCapsule cd_2b_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy> > > > cd_2b_end(...) from builtins.PyCapsule cd_2b_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy> > > > cd_2b_intrares_begin(...) from builtins.PyCapsule cd_2b_intrares_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> > > > cd_2b_intrares_end(...) from builtins.PyCapsule cd_2b_intrares_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> > > > cd_2b_types(...) from builtins.PyCapsule cd_2b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType   convenience access to all cd 2b score types cd_lr_2b_methods_begin(...) from builtins.PyCapsule cd_lr_2b_methods_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy> > > > cd_lr_2b_methods_end(...) from builtins.PyCapsule cd_lr_2b_methods_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy> > > > cd_lr_2b_types(...) from builtins.PyCapsule cd_lr_2b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType check_methods_in_right_order(...) from builtins.PyCapsule check_methods_in_right_order(self : rosetta.core.scoring.ScoreFunction, score_type_in_first_method : rosetta.core.scoring.ScoreType, score_type_in_second_method : rosetta.core.scoring.ScoreType) -> bool   check order of methods ci_1b_types(...) from builtins.PyCapsule ci_1b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType   convenience access to all ci 1b score types ci_2b_begin(...) from builtins.PyCapsule ci_2b_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy> > > > ci_2b_end(...) from builtins.PyCapsule ci_2b_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy> > > > ci_2b_intrares_begin(...) from builtins.PyCapsule ci_2b_intrares_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> > > > ci_2b_intrares_end(...) from builtins.PyCapsule ci_2b_intrares_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> > > > ci_2b_types(...) from builtins.PyCapsule ci_2b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType   convenience access to all ci 2b score types ci_lr_2b_methods_begin(...) from builtins.PyCapsule ci_lr_2b_methods_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy> > > > ci_lr_2b_methods_end(...) from builtins.PyCapsule ci_lr_2b_methods_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy> > > > ci_lr_2b_types(...) from builtins.PyCapsule ci_lr_2b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType clone_as_base_class(...) from builtins.PyCapsule clone_as_base_class(rosetta.core.scoring.ScoreFunction) -> rosetta.core.scoring.ScoreFunction   If you *want* to discard subclass information, the following function is availible energy_method_options(...) from builtins.PyCapsule energy_method_options(rosetta.core.scoring.ScoreFunction) -> core::scoring::methods::EnergyMethodOptions   Returns the EnergyMethodOptions object contained in this  ScoreFunction (const access) eval_cd_1b(...) from builtins.PyCapsule eval_cd_1b(self : rosetta.core.scoring.ScoreFunction, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted one body energies of all context  dependent one body energies for  <pose>  Residue  <rsd>  into  EnergyMap  <emap>     : EnergyMap is an EMapVector eval_cd_2b(...) from builtins.PyCapsule eval_cd_2b(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulate the unweighted short range context dependent two body  interaction energies of  <pose>  between Residue  <rsd1>  and Residue  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_cd_2b_bb_bb(...) from builtins.PyCapsule eval_cd_2b_bb_bb(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted short ranged context dependent two body  interaction energies of  <pose>  between the backbones of Residue  <rsd1>  and  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_cd_2b_bb_sc(...) from builtins.PyCapsule eval_cd_2b_bb_sc(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted short ranged context dependent two body  interaction energies of  <pose>  between the backbone of Residue  <rsd1>  and the sidechain of Residue  <rsd2>  into EnergyMap <emap>     : EnergyMap is an EMapVector eval_cd_2b_sc_sc(...) from builtins.PyCapsule eval_cd_2b_sc_sc(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted short ranged context dependent two body  interaction energies of  <pose>  between the sidechains of Residue  <rsd1>  and Residue  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_cd_intrares_energy(...) from builtins.PyCapsule eval_cd_intrares_energy(self : rosetta.core.scoring.ScoreFunction, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted intra-residue one body energies for all  context dependent two body terms that define intra-residue energies of  <pose>  Residue  <rsd>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_ci_1b(...) from builtins.PyCapsule eval_ci_1b(self : rosetta.core.scoring.ScoreFunction, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType eval_ci_2b(...) from builtins.PyCapsule eval_ci_2b(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted context independent two body  interaction energies of  <pose>  between Residue  <rsd1>  and Residue  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_ci_2b_bb_bb(...) from builtins.PyCapsule eval_ci_2b_bb_bb(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted context independent two body  interaction energies of  <pose>  between the backbones of Residue  <rsd1>  and Residue  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_ci_2b_bb_sc(...) from builtins.PyCapsule eval_ci_2b_bb_sc(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted short range context independent two  body interaction energies of  <pose>  between the backbone of Residue  <rsd1>  and the sidechain of Residue  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_ci_2b_sc_sc(...) from builtins.PyCapsule eval_ci_2b_sc_sc(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted short range context dependent two body  interaction energies of  <pose>  between the sidechains of Residue  <rsd1>  and Residue  <rsd2>  into Energymap  <emap>     : EnergyMap is an EMapVector eval_ci_intrares_energy(...) from builtins.PyCapsule eval_ci_intrares_energy(self : rosetta.core.scoring.ScoreFunction, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted intra-residue one body energies for all  context independent two body terms that define intra-residue energies of  <pose>  Residue  <rsd>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_dof_derivative(...) from builtins.PyCapsule eval_dof_derivative(self : rosetta.core.scoring.ScoreFunction, dof_id : rosetta.core.id.DOF_ID, torsion_id : core::id::TorsionID, pose : rosetta.core.pose.Pose) -> float eval_intrares_energy(...) from builtins.PyCapsule eval_intrares_energy(self : rosetta.core.scoring.ScoreFunction, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates for rsd the unweighted intra-residue one body energies  for all context dependent and context independent two body terms that  define intra-residue energies     : EnergyMap is an EMapVector eval_long_range_twobody_energies(...) from builtins.PyCapsule eval_long_range_twobody_energies(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType eval_npd_atom_derivative(...) from builtins.PyCapsule eval_npd_atom_derivative(self : rosetta.core.scoring.ScoreFunction, atom_id : rosetta.core.id.AtomID, pose : rosetta.core.pose.Pose, domain_map : ObjexxFCL::FArray1D<int>, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t) -> NoneType eval_onebody_energies(...) from builtins.PyCapsule eval_onebody_energies(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType eval_twobody_neighbor_energies(...) from builtins.PyCapsule eval_twobody_neighbor_energies(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType evaluate_rotamer_background_energies(...) from builtins.PyCapsule evaluate_rotamer_background_energies(self : rosetta.core.scoring.ScoreFunction, set1 : rosetta.core.conformation.RotamerSetBase, residue2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, energy_vector : rosetta.utility.vector1_float) -> NoneType evaluate_rotamer_intrares_energies(...) from builtins.PyCapsule evaluate_rotamer_intrares_energies(self : rosetta.core.scoring.ScoreFunction, set : rosetta.core.conformation.RotamerSetBase, pose : rosetta.core.pose.Pose, energies : rosetta.utility.vector1_float) -> NoneType evaluate_rotamer_intrares_energy_maps(...) from builtins.PyCapsule evaluate_rotamer_intrares_energy_maps(self : rosetta.core.scoring.ScoreFunction, set : rosetta.core.conformation.RotamerSetBase, pose : rosetta.core.pose.Pose, emaps : rosetta.utility.vector1_core_scoring_EMapVector) -> NoneType evaluate_rotamer_pair_energies(...) from builtins.PyCapsule evaluate_rotamer_pair_energies(self : rosetta.core.scoring.ScoreFunction, set1 : rosetta.core.conformation.RotamerSetBase, set2 : rosetta.core.conformation.RotamerSetBase, pose : rosetta.core.pose.Pose, energy_table : ObjexxFCL::FArray2D<float>) -> NoneType finalize_after_derivatives(...) from builtins.PyCapsule finalize_after_derivatives(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType get_name(...) from builtins.PyCapsule get_name(rosetta.core.scoring.ScoreFunction) -> str get_nonzero_weighted_scoretypes(...) from builtins.PyCapsule get_nonzero_weighted_scoretypes(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType   Returns a list of the ScoreTypes which are non-zero with  their current weights    example(s):      scorefxn.get_nonzero_weighted_scoretypes()  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.set_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.scoring.ScoreFunction) -> rosetta.core.scoring.ScoreFunction   self pointers   2. get_self_ptr(rosetta.core.scoring.ScoreFunction) -> rosetta.core.scoring.ScoreFunction get_sub_score(...) from builtins.PyCapsule get_sub_score(*args, **kwargs) Overloaded function.   1. get_sub_score(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, residue_mask : rosetta.utility.vector1_bool) -> float   Compute the score for subset of residues   2. get_sub_score(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, residue_mask : rosetta.utility.vector1_bool, emap : rosetta.core.scoring.EMapVector) -> NoneType   Compute the score for subset of residues   3. get_sub_score(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, residue_mask : rosetta.utility.vector1_bool) -> float   Compute the score for subset of residues   4. get_sub_score(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, residue_mask : rosetta.utility.vector1_bool, emap : rosetta.core.scoring.EMapVector) -> NoneType   Compute the score for subset of residues get_sub_score_exclude_res(...) from builtins.PyCapsule get_sub_score_exclude_res(*args, **kwargs) Overloaded function.   1. get_sub_score_exclude_res(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, exclude_list : rosetta.utility.vector1_unsigned_long) -> float   Compute the score for subset of residues   2. get_sub_score_exclude_res(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, exclude_list : rosetta.utility.vector1_unsigned_long, emap : rosetta.core.scoring.EMapVector) -> NoneType   Compute the score for subset of residues   3. get_sub_score_exclude_res(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, exclude_list : rosetta.utility.vector1_unsigned_long) -> float   Compute the score for subset of residues   4. get_sub_score_exclude_res(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, exclude_list : rosetta.utility.vector1_unsigned_long, emap : rosetta.core.scoring.EMapVector) -> NoneType   Compute the score for subset of residues get_weight(...) from builtins.PyCapsule get_weight(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType) -> float   Returns the weight for ScoreType  <t>    examples(s):      scorefxn.get_weight(fa_sol)  See also:      ScoreFunction      ScoreFunction.set_weight      ScoreType      create_score_function      name_from_score_type      score_type_from_name has_nonzero_weight(...) from builtins.PyCapsule has_nonzero_weight(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType) -> bool   Returns true if the ScoreType  <t>  has a non-zero weight    example(s):      scorefxn.has_nonzero_weight(fa_sol)  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.has_zero_weight      ScoreFunction.set_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name has_zero_weight(...) from builtins.PyCapsule has_zero_weight(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType) -> bool   Returns true if the ScoreType  <t>  has a weight of zero,    example(s):      scorefxn.has_zero_weight(fa_sol)  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.has_nonzero_weight      ScoreFunction.set_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name indicate_required_context_graphs(...) from builtins.PyCapsule indicate_required_context_graphs(self : rosetta.core.scoring.ScoreFunction, context_graphs_required : rosetta.utility.vector1_bool) -> NoneType   find which context graphs the energy methods require info(...) from builtins.PyCapsule info(rosetta.core.scoring.ScoreFunction) -> core::scoring::ScoreFunctionInfo   return an object to describe abstractly the methods contained in this  ScoreFunction so that class Energies can ensure that the ScoreFunction is  properly evaluated (ie, no obsolete cashed data is used ) initialize_from_file(...) from builtins.PyCapsule initialize_from_file(self : rosetta.core.scoring.ScoreFunction, filename : str) -> NoneType   Resets everything before reading the  <filename> long_range_energies_begin(...) from builtins.PyCapsule long_range_energies_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const> > > > long_range_energies_end(...) from builtins.PyCapsule long_range_energies_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const> > > > max_atomic_interaction_cutoff(...) from builtins.PyCapsule max_atomic_interaction_cutoff(rosetta.core.scoring.ScoreFunction) -> float   Returns the largest atomic interaction cutoff required by the  EnergyMethods merge(...) from builtins.PyCapsule merge(self : rosetta.core.scoring.ScoreFunction, scorefxn_to_be_merged : rosetta.core.scoring.ScoreFunction) -> NoneType   Merges in the weights of another score function    example(s):      scorefxn.merge(scorefxn2)  See also:      ScoreFunction      ScoreFunction.weights      Energies      create_score_function name(...) from builtins.PyCapsule name(self : rosetta.core.scoring.ScoreFunction, weights_tag : str) -> NoneType   Accumulates the unweighted one body energies of all context  independent one body energies for  <pose>  Residue  <rsd>  into  EnergyMap  <emap>     : EnergyMap is an EMapVector perturb_weights(...) from builtins.PyCapsule perturb_weights(rosetta.core.scoring.ScoreFunction) -> NoneType   Randomly perturbs non-zero score function weights prepare_rotamers_for_packing(...) from builtins.PyCapsule prepare_rotamers_for_packing(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, set : rosetta.core.conformation.RotamerSetBase) -> NoneType   Lets the scoring functions cache anything they need to rapidly  calculate rotamer pair energies used in packing (like a trie, e.g.) ready_for_nonideal_scoring(...) from builtins.PyCapsule ready_for_nonideal_scoring(rosetta.core.scoring.ScoreFunction) -> bool reinitialize_minnode_for_residue(...) from builtins.PyCapsule reinitialize_minnode_for_residue(self : rosetta.core.scoring.ScoreFunction, min_node : core::scoring::MinimizationNode, rsd : rosetta.core.conformation.Residue, min_map : core::kinematics::MinimizerMapBase, pose : rosetta.core.pose.Pose) -> NoneType reset(...) from builtins.PyCapsule reset(rosetta.core.scoring.ScoreFunction) -> NoneType   Resets the ScoreFunction to default values reset_energy_methods(...) from builtins.PyCapsule reset_energy_methods(rosetta.core.scoring.ScoreFunction) -> NoneType score(...) from builtins.PyCapsule score(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> float   Scores the given  <pose>  using this ScoreFunction. Alters the  Energies object within  <pose>, but does not alter this ScoreFunction     : Synonym for () operator. Makes code look a little nicer. Doesn't  do anything but call () operator. score_by_scoretype(...) from builtins.PyCapsule score_by_scoretype(*args, **kwargs) Overloaded function.   1. score_by_scoretype(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, t : rosetta.core.scoring.ScoreType) -> float   Returns the score of the ScoreType  <t>   2. score_by_scoretype(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, t : rosetta.core.scoring.ScoreType, weighted : bool) -> float   Returns the score of the ScoreType  <t> score_types_by_method_type(...) from builtins.PyCapsule score_types_by_method_type(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.methods.EnergyMethodType) -> rosetta.utility.vector1_core_scoring_ScoreType serialize_weights(...) from builtins.PyCapsule serialize_weights(rosetta.core.scoring.ScoreFunction) -> str   Serializes the non-zero score function term weights  Format: { term : weight, ... } set_energy_method_options(...) from builtins.PyCapsule set_energy_method_options(self : rosetta.core.scoring.ScoreFunction, energy_method_options_in : core::scoring::methods::EnergyMethodOptions) -> NoneType   Sets the EnergyMethodOptions object contained in this ScoreFunction.  with appropriate update of all the energy methods. set_etable(...) from builtins.PyCapsule set_etable(self : rosetta.core.scoring.ScoreFunction, etable_name : str) -> NoneType   Given a  <filename> (represented by a std::string), set the  e_table for this ScoreFunction. set_method_weights(...) from builtins.PyCapsule set_method_weights(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType, wts : rosetta.utility.vector1_double) -> NoneType set_weight(...) from builtins.PyCapsule set_weight(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType, setting : float) -> NoneType   Sets the weight for ScoreType  <t>  to  <setting>    example(s):      scorefxn.set_weight(fa_sol,.5)  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name set_weight_if_zero(...) from builtins.PyCapsule set_weight_if_zero(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType, setting : float) -> NoneType   Sets the weight for ScoreType  <t>  to  <setting> if weight is originally zero    example(s):      scorefxn.set_weight_if_zero(fa_sol,.5)  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.set_weight      ScoreType      create_score_function      name_from_score_type      score_type_from_name setup_for_derivatives(...) from builtins.PyCapsule setup_for_derivatives(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType setup_for_lr2benmeth_minimization_for_respair(...) from builtins.PyCapsule setup_for_lr2benmeth_minimization_for_respair(*args, **kwargs) Overloaded function.   1. setup_for_lr2benmeth_minimization_for_respair(self : rosetta.core.scoring.ScoreFunction, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, lr2benergy : core::scoring::methods::LongRangeTwoBodyEnergy, g : core::scoring::MinimizationGraph, min_map : core::kinematics::MinimizerMapBase, p : rosetta.core.pose.Pose, res_moving_wrt_eachother : bool, accumulate_fixed_energies : bool, rni : core::scoring::ResidueNeighborConstIterator, fixed_energies : rosetta.core.scoring.EMapVector) -> NoneType   Initialize an edge in the MinimizationGraph with a particular long-range two body   2. setup_for_lr2benmeth_minimization_for_respair(self : rosetta.core.scoring.ScoreFunction, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, lr2benergy : core::scoring::methods::LongRangeTwoBodyEnergy, g : core::scoring::MinimizationGraph, min_map : core::kinematics::MinimizerMapBase, p : rosetta.core.pose.Pose, res_moving_wrt_eachother : bool, accumulate_fixed_energies : bool, rni : core::scoring::ResidueNeighborConstIterator, fixed_energies : rosetta.core.scoring.EMapVector, edge_weight : float) -> NoneType   Initialize an edge in the MinimizationGraph with a particular long-range two body   3. setup_for_lr2benmeth_minimization_for_respair(self : rosetta.core.scoring.ScoreFunction, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, lr2benergy : core::scoring::methods::LongRangeTwoBodyEnergy, g : core::scoring::MinimizationGraph, min_map : core::kinematics::MinimizerMapBase, p : rosetta.core.pose.Pose, res_moving_wrt_eachother : bool, accumulate_fixed_energies : bool, rni : core::scoring::ResidueNeighborConstIterator, fixed_energies : rosetta.core.scoring.EMapVector, edge_weight : float, edge_dweight : float) -> NoneType   Initialize an edge in the MinimizationGraph with a particular long-range two body setup_for_minimizing(...) from builtins.PyCapsule setup_for_minimizing(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, min_map : core::kinematics::MinimizerMapBase) -> NoneType   Initializes a MinimizationGraph and caches it in  Energies object of  <pose>     : for use during minimization setup_for_minimizing_for_node(...) from builtins.PyCapsule setup_for_minimizing_for_node(self : rosetta.core.scoring.ScoreFunction, min_node : core::scoring::MinimizationNode, rsd : rosetta.core.conformation.Residue, min_map : core::kinematics::MinimizerMapBase, pose : rosetta.core.pose.Pose, accumulate_fixed_energies : bool, fixed_energies : rosetta.core.scoring.EMapVector) -> NoneType   Initialize a single node of a MinimizationGraph with the one-body and two-body  energy methods that are held within this ScoreFunction object. setup_for_minimizing_sr2b_enmeths_for_minedge(...) from builtins.PyCapsule setup_for_minimizing_sr2b_enmeths_for_minedge(*args, **kwargs) Overloaded function.   1. setup_for_minimizing_sr2b_enmeths_for_minedge(self : rosetta.core.scoring.ScoreFunction, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, min_edge : core::scoring::MinimizationEdge, min_map : core::kinematics::MinimizerMapBase, pose : rosetta.core.pose.Pose, res_moving_wrt_eachother : bool, accumulate_fixed_energies : bool, energy_edge : core::scoring::EnergyEdge, fixed_energies : rosetta.core.scoring.EMapVector) -> NoneType   Initialize a single MinimizationEdge for a particular part of residues, storing  sr2b energy method pointers on the edge for those sr2b energy methods in this ScoreFunction   2. setup_for_minimizing_sr2b_enmeths_for_minedge(self : rosetta.core.scoring.ScoreFunction, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, min_edge : core::scoring::MinimizationEdge, min_map : core::kinematics::MinimizerMapBase, pose : rosetta.core.pose.Pose, res_moving_wrt_eachother : bool, accumulate_fixed_energies : bool, energy_edge : core::scoring::EnergyEdge, fixed_energies : rosetta.core.scoring.EMapVector, edge_weight : float) -> NoneType   Initialize a single MinimizationEdge for a particular part of residues, storing  sr2b energy method pointers on the edge for those sr2b energy methods in this ScoreFunction setup_for_packing(...) from builtins.PyCapsule setup_for_packing(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, residues_repacking : rosetta.utility.vector1_bool, residues_designing : rosetta.utility.vector1_bool) -> NoneType   Lets the scoring functions cache anything they need to calculate  energies in a packing step (rotamer_trials or pack_rotamers)     : the Etable caches tries for each of the residues, the  hydrogen bond function caches backbone/backbone hydrogen bonds setup_for_scoring(...) from builtins.PyCapsule setup_for_scoring(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType   For external scorers: Let the energy methods prepare for  evaluating their scores on a particular structure     : invoked during scoring. show(...) from builtins.PyCapsule show(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType   Scores  <pose>  and shows the raw and weighted scores for each  non-zero ScoreType     : this function is mostly for convenience in PyRosetta    example(s):      scorefxn.show(pose)  See also:      ScoreFunction      ScoreFunction.weights      Energies      create_score_function update_residue_for_packing(...) from builtins.PyCapsule update_residue_for_packing(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, resid : int) -> NoneType   If inside packing, the pose changes conformation, inform the  scoring functions that any data they have cached in the Energies object  is out of date. In particular, this is to update the trie(s) during  rotamer trials. weights(...) from builtins.PyCapsule weights(rosetta.core.scoring.ScoreFunction) -> rosetta.core.scoring.EMapVector   Returns an EnergyMap of the current set of weights    example(s):      scorefxn.weights()  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.set_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name whole_structure_types(...) from builtins.PyCapsule whole_structure_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType ws_methods_begin(...) from builtins.PyCapsule ws_methods_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::WholeStructureEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::WholeStructureEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::WholeStructureEnergy> > > > ws_methods_end(...) from builtins.PyCapsule ws_methods_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::WholeStructureEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::WholeStructureEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::WholeStructureEnergy> > > >   class EMapVector(builtins.object)     A vector for storing energy data, initially all values are 0     : several methods using EMapVector objects add in values,  be sure to use the zero method between uses    Common Methods:      EMapVector.zero     Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.scoring.EMapVector, src : rosetta.core.scoring.EMapVector) -> bool   == operator for comparing two energy maps element by element __getitem__(...) from builtins.PyCapsule __getitem__(*args, **kwargs) Overloaded function.   1. __getitem__(self : rosetta.core.scoring.EMapVector, st : rosetta.core.scoring.ScoreType) -> float   [] operator for getting a non-const reference to the energy for a ScoreType   2. __getitem__(self : rosetta.core.scoring.EMapVector, st : rosetta.core.scoring.ScoreType) -> float   [] operator for getting the value for a ScoreType __imul__(...) from builtins.PyCapsule __imul__(*args, **kwargs) Overloaded function.   1. __imul__(self : rosetta.core.scoring.EMapVector, scalar : float) -> NoneType   *= operator, for performing multiplication of a vector by a scalar   2. __imul__(self : rosetta.core.scoring.EMapVector, src : rosetta.core.scoring.EMapVector) -> NoneType   *= operator, for performing element-by-element multiplication of two vectors __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.EMapVector) -> NoneType   2. __init__(self : rosetta.core.scoring.EMapVector, src : rosetta.core.scoring.EMapVector) -> NoneType __ne__(...) from builtins.PyCapsule __ne__(self : rosetta.core.scoring.EMapVector, src : rosetta.core.scoring.EMapVector) -> bool   != operator for comparing two energy maps element by element __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.scoring.EMapVector) -> str accumulate(...) from builtins.PyCapsule accumulate(*args, **kwargs) Overloaded function.   1. accumulate(self : rosetta.core.scoring.EMapVector, src : rosetta.core.scoring.EMapVector, l : rosetta.utility.vector1_core_scoring_ScoreType) -> NoneType   accumulate a subset of the positions   2. accumulate(self : rosetta.core.scoring.EMapVector, src : rosetta.core.scoring.EMapVector, l : rosetta.utility.vector1_core_scoring_ScoreType, wt : float) -> NoneType   accumulate a subset of the positions with a common weight factor assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.EMapVector, rhs : rosetta.core.scoring.EMapVector) -> rosetta.core.scoring.EMapVector begin(...) from builtins.PyCapsule begin(*args, **kwargs) Overloaded function.   1. begin(rosetta.core.scoring.EMapVector) -> float   const-iterator to the begining of the vector of energies   2. begin(rosetta.core.scoring.EMapVector) -> float   non-const-iterator to the begining of the vector of energies clear(...) from builtins.PyCapsule clear(rosetta.core.scoring.EMapVector) -> NoneType   Set every value to zero    example(s):      emap.zero()  See also:      EMapVector      EMapVector.get      EMapVector.set      ScoreFunction      create_score_function dot(...) from builtins.PyCapsule dot(*args, **kwargs) Overloaded function.   1. dot(self : rosetta.core.scoring.EMapVector, src : rosetta.core.scoring.EMapVector) -> float   Returns the dot product of this object with EMapVector  <src>     : useful for multiplying weights with scores    example(s):      we = scorefxn.weights()      emap.dot(we)  See also:      EMapVector      ScoreFunction      ScoreFunction.weights      create_score_function   2. dot(self : rosetta.core.scoring.EMapVector, src : rosetta.core.scoring.EMapVector, l : rosetta.utility.vector1_core_scoring_ScoreType) -> float   dot product of two EMapVectors  over a subset of the score types end(...) from builtins.PyCapsule end(*args, **kwargs) Overloaded function.   1. end(rosetta.core.scoring.EMapVector) -> float   const-iterator to the end of the vector of energies   2. end(rosetta.core.scoring.EMapVector) -> float   non-const-iterator to the end of the vector of energies get(...) from builtins.PyCapsule get(self : rosetta.core.scoring.EMapVector, st : rosetta.core.scoring.ScoreType) -> float   Returns the value for ScoreType  <st>    example(s):      emap.get(fa_sol)  See also:      EMapVector      EMapVector.set      ScoreFunction      create_score_function norm_squared(...) from builtins.PyCapsule norm_squared(self : rosetta.core.scoring.EMapVector, l : rosetta.utility.vector1_core_scoring_ScoreType) -> float   accumulate the squared values of a subset of the positions print(...) from builtins.PyCapsule print(rosetta.core.scoring.EMapVector) -> NoneType   print the contents of an emap vector to standard out set(...) from builtins.PyCapsule set(self : rosetta.core.scoring.EMapVector, st : rosetta.core.scoring.ScoreType, val : float) -> float   Sets the value for ScoreType  <st>  to  <val>    example(s):      emap.set(fa_sol,13.37)  See also:      EMapVector      EMapVector.get      ScoreFunction      create_score_function show_nonzero(...) from builtins.PyCapsule show_nonzero(rosetta.core.scoring.EMapVector) -> str   convert the non-zero positions of the energy map to a string sum(...) from builtins.PyCapsule sum(rosetta.core.scoring.EMapVector) -> float   Returns the sum of this vector    example(s):      emap.sum()  See also:      EMapVector      EMapVector.get      EMapVector.set      ScoreFunction      create_score_function weighted_string_of(...) from builtins.PyCapsule weighted_string_of(self : rosetta.core.scoring.EMapVector, weights : rosetta.core.scoring.EMapVector) -> str   convert the weighted energies in this energy map to a string  for those score types that have non-zero values in the "weights" energy map. zero(...) from builtins.PyCapsule zero(*args, **kwargs) Overloaded function.   1. zero(self : rosetta.core.scoring.EMapVector, l : rosetta.utility.vector1_core_scoring_ScoreType) -> NoneType   Zero a subset of the positions, as in calibrating a scale   2. zero(rosetta.core.scoring.EMapVector) -> NoneType   Set every value to zero    example(s):      emap.zero()  See also:      EMapVector      EMapVector.get      EMapVector.set      ScoreFunction      create_score_function   class Energies(builtins.object)     Stores total, residue, and residue-pair energies, as well as residue neighbor information.     Meant to replace fullatom_energies:: namespace.     Stores residue neighbor information as well as cached residue pair energies in O(N) space using a graph.     Also stores a DomainMap object which is used during scoring to know which rsd pairs have changed relative orientation and which residues have changed internally     We distinguish between two kinds of per-residue (1D) energy: onebody residue energies and twobody residue energies. Onebody residue energies are things like dunbrack, intrares, Paa, which depend only on the state of the residue in question. Twobody residue energies (like the residue atr energy) are summations of twobody interactions involving a single residue. The onebody energies can be reused at positions whose internal phi/psi/chi conformation hasn't changed. Twobody residue energies, on the other hand must be invalidated if the structure has changed at all.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.scoring.Energies) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.scoring.Energies) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.Energies, rhs : rosetta.core.scoring.Energies) -> rosetta.core.scoring.Energies clear(...) from builtins.PyCapsule clear(rosetta.core.scoring.Energies) -> NoneType   kill everything (that nobody forgot about) clear_energies(...) from builtins.PyCapsule clear_energies(rosetta.core.scoring.Energies) -> NoneType   for debugging -- forget all stored energies, does not change size clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.Energies) -> rosetta.core.scoring.Energies context_graph(...) from builtins.PyCapsule context_graph(*args, **kwargs) Overloaded function.   1. context_graph(self : rosetta.core.scoring.Energies, type : rosetta.core.scoring.ContextGraphType) -> core::scoring::ContextGraph   2. context_graph(self : rosetta.core.scoring.Energies, type : rosetta.core.scoring.ContextGraphType) -> core::scoring::ContextGraph data(...) from builtins.PyCapsule data(*args, **kwargs) Overloaded function.   1. data(rosetta.core.scoring.Energies) -> rosetta.basic.datacache.BasicDataCache   BasicDataCache indexed by enum in core/scoring/EnergiesCacheableDataType.hh   2. data(rosetta.core.scoring.Energies) -> rosetta.basic.datacache.BasicDataCache   BasicDataCache indexed by enum in core/scoring/EnergiesCacheableDataType.hh discard_conformation_domain_map(...) from builtins.PyCapsule discard_conformation_domain_map(rosetta.core.scoring.Energies) -> bool   instructs Pose whether the domain map info in the Conformation object should be discarded domain_map(...) from builtins.PyCapsule domain_map(*args, **kwargs) Overloaded function.   1. domain_map(self : rosetta.core.scoring.Energies, pos : int) -> int   Return the color assigned to a particular residue (index = pos) as held in the  domain map describing how this residue has moved with respect to the other residues in the  pose.    CAUTION new behavior: domain_map may not return 0 for residues that have undergone internal  degree of freedom changes since the last scoring.  Ask the res_moved() method for that information   2. domain_map(rosetta.core.scoring.Energies) -> ObjexxFCL::FArray1D<int>   Read access for the domain map. energies_updated(...) from builtins.PyCapsule energies_updated(rosetta.core.scoring.Energies) -> bool   Returns true if the score is up-to-date    example(s):      pose.energies().energies_updated()  See also:      Energies      Energies.residue_total_energy      Energies.residue_total_energies      Pose      ScoreFunction      ScoreFunction.show      create_score_function energy_graph(...) from builtins.PyCapsule energy_graph(*args, **kwargs) Overloaded function.   1. energy_graph(rosetta.core.scoring.Energies) -> core::scoring::EnergyGraph   Read access to the EnergyGraph.   2. energy_graph(rosetta.core.scoring.Energies) -> core::scoring::EnergyGraph   Write access to the EnergyGraph. finalized_energies(...) from builtins.PyCapsule finalized_energies(*args, **kwargs) Overloaded function.   1. finalized_energies(rosetta.core.scoring.Energies) -> rosetta.core.scoring.EMapVector   Read access to the components of the "finalized" energies;  These will include any score component calculated in the finalize  phase of score function evaluation.  These energies are copied  between Energies objects, and are not evaluated during the component-  energy update.   2. finalized_energies(rosetta.core.scoring.Energies) -> rosetta.core.scoring.EMapVector   Write access to the components of the "finalized" energies.  This access is intended only for the ScoreFunction. get_scorefxn_info(...) from builtins.PyCapsule get_scorefxn_info(rosetta.core.scoring.Energies) -> core::scoring::ScoreFunctionInfo   get scorefxn info long_range_container(...) from builtins.PyCapsule long_range_container(self : rosetta.core.scoring.Energies,  : rosetta.core.scoring.methods.LongRangeEnergyType) -> core::scoring::LREnergyContainer minimization_graph(...) from builtins.PyCapsule minimization_graph(*args, **kwargs) Overloaded function.   1. minimization_graph(rosetta.core.scoring.Energies) -> core::scoring::MinimizationGraph   2. minimization_graph(rosetta.core.scoring.Energies) -> core::scoring::MinimizationGraph nblist(...) from builtins.PyCapsule nblist(self : rosetta.core.scoring.Energies, type : rosetta.core.scoring.EnergiesCacheableDataType.Enum) -> core::scoring::NeighborList nonconst_long_range_container(...) from builtins.PyCapsule nonconst_long_range_container(self : rosetta.core.scoring.Energies,  : rosetta.core.scoring.methods.LongRangeEnergyType) -> core::scoring::LREnergyContainer onebody_energies(...) from builtins.PyCapsule onebody_energies(*args, **kwargs) Overloaded function.   1. onebody_energies(self : rosetta.core.scoring.Energies, seqpos : int) -> rosetta.core.scoring.EMapVector   Read access to the components of the one-body energies.   2. onebody_energies(self : rosetta.core.scoring.Energies, seqpos : int) -> rosetta.core.scoring.EMapVector   Write access to the components of the one-body energies.  This access is intended only for the ScoreFunction. require_context_graph(...) from builtins.PyCapsule require_context_graph(self : rosetta.core.scoring.Energies,  : rosetta.core.scoring.ContextGraphType) -> NoneType   Allows non-scorefunction components of Rosetta to impose requirements on  the context graphs that this object maintains. res_moved(...) from builtins.PyCapsule res_moved(self : rosetta.core.scoring.Energies, seqpos : int) -> bool   check if rsd has changed internal conformation, necessitating,  recomputation of 1d energies like dun,intra,prob,etc reset_nblist(...) from builtins.PyCapsule reset_nblist(rosetta.core.scoring.Energies) -> NoneType reset_res_moved(...) from builtins.PyCapsule reset_res_moved(self : rosetta.core.scoring.Energies, seqpos : int) -> NoneType residue_neighbors_updated(...) from builtins.PyCapsule residue_neighbors_updated(rosetta.core.scoring.Energies) -> bool residue_total_energies(...) from builtins.PyCapsule residue_total_energies(self : rosetta.core.scoring.Energies, seqpos : int) -> rosetta.core.scoring.EMapVector   Returns the unweighted total_energies EnergyMap for  Residue  <seqpos>     : only evaluated when requested (lazy!), inaccessible during  minimization, EnergyMap is an EMapVector    example(s):      r3 = pose.energies().residue_total_energies(3)      r3[fa_sol]  See also:      Energies      Energies.residue_total_energy      Pose      ScoreFunction      ScoreFunction.show      create_score_function      EMapVector residue_total_energy(...) from builtins.PyCapsule residue_total_energy(self : rosetta.core.scoring.Energies, seqpos : int) -> float   Returns the weighted total energy of residue  <seqpos>    example(s):      pose.energies().residue_total_energy(3)  See also:      Energies      Energies.residue_total_energies      Pose      ScoreFunction      ScoreFunction.show      create_score_function same_type_as_me(...) from builtins.PyCapsule same_type_as_me(*args, **kwargs) Overloaded function.   1. same_type_as_me(self : rosetta.core.scoring.Energies, other : rosetta.core.scoring.Energies) -> bool   determine whether my type is the same as another Conformation's   2. same_type_as_me(self : rosetta.core.scoring.Energies, other : rosetta.core.scoring.Energies, recurse : bool) -> bool   determine whether my type is the same as another Conformation's scoring(...) from builtins.PyCapsule scoring(rosetta.core.scoring.Energies) -> bool   are we in the midst of a scoring calculation? scoring_begin(...) from builtins.PyCapsule scoring_begin(self : rosetta.core.scoring.Energies, sfxn : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType   Notification of the start of a scoring calculation. scoring_end(...) from builtins.PyCapsule scoring_end(self : rosetta.core.scoring.Energies, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   signal from the scorefxn that scoring is over set_long_range_container(...) from builtins.PyCapsule set_long_range_container(self : rosetta.core.scoring.Energies,  : rosetta.core.scoring.methods.LongRangeEnergyType,  : core::scoring::LREnergyContainer) -> NoneType set_minimization_graph(...) from builtins.PyCapsule set_minimization_graph(self : rosetta.core.scoring.Energies,  : core::scoring::MinimizationGraph) -> NoneType set_nblist(...) from builtins.PyCapsule set_nblist(self : rosetta.core.scoring.Energies, type : rosetta.core.scoring.EnergiesCacheableDataType.Enum, nblist_in : core::scoring::NeighborList) -> NoneType set_owner(...) from builtins.PyCapsule set_owner(self : rosetta.core.scoring.Energies, owner : rosetta.core.pose.Pose) -> NoneType   Pose must claim its Energies object; this should happen once,  at the time the Pose is allocated.  Future copying of the Energies object  will not change ownership.  The purpose of ownership is to allow lazy context-graph  creation.  When context graphs are requested that have not been created, they  must be created and their edges must be updated to represent the current conformation  of the pose. set_use_nblist(...) from builtins.PyCapsule set_use_nblist(self : rosetta.core.scoring.Energies, pose : rosetta.core.pose.Pose, domain_map_in : ObjexxFCL::FArray1D<int>, use_nblist_auto_update : bool) -> NoneType show(...) from builtins.PyCapsule show(*args, **kwargs) Overloaded function.   1. show(rosetta.core.scoring.Energies) -> NoneType   2. show(self : rosetta.core.scoring.Energies, res : int) -> NoneType   Shows the energy information of residue  <seqpos>     : wrapper function of energies.show(Size) for Pyrosetta    example(s):      pose.energies().show(3)  See also:      Energies      Energies.residue_total_energies      Energies.residue_total_energy      Pose      ScoreFunction      ScoreFunction.show      create_score_function size(...) from builtins.PyCapsule size(rosetta.core.scoring.Energies) -> int   Returns the number of held residue energies    example(s):      r3 = pose.energies().residue_total_energies(3)      r3[fa_sol]  See also:      Energies      Energies.residue_total_energies      Energies.residue_total_energy      Pose      ScoreFunction      ScoreFunction.show      create_score_function structure_has_moved(...) from builtins.PyCapsule structure_has_moved(self : rosetta.core.scoring.Energies, nres : int) -> NoneType   called (eg by pose) to notify us of a change to the structure           Triggers clearing of the total energies and the twobody rsd energies         PHIL -- should also mark the neighbor links as invalid somehow...         Called by pose when someone tries to access us, if the Conformation         indicates that the structure has moved since the last score evaluation           const b/c called inside const access methods tenA_neighbor_graph(...) from builtins.PyCapsule tenA_neighbor_graph(*args, **kwargs) Overloaded function.   1. tenA_neighbor_graph(rosetta.core.scoring.Energies) -> core::scoring::TenANeighborGraph   get the graph encoding # neighbors within 10 Angstroms  If the graph has not been requested up until this point, then it will  be instantiated and filled.  If the pose has changed size since the last  score function evaluation (or if the pose has never been scored) this  function will exit.   2. tenA_neighbor_graph(rosetta.core.scoring.Energies) -> core::scoring::TenANeighborGraph   Write access to the graph encoding # neighbors within 10 Angstroms  If the graph has not been requested up until this point, then it will  be instantiated and filled.  If the pose has changed size since the last  score function evaluation (or if the pose has never been scored) this  function will exit. total_energies(...) from builtins.PyCapsule total_energies(*args, **kwargs) Overloaded function.   1. total_energies(rosetta.core.scoring.Energies) -> rosetta.core.scoring.EMapVector   Returns the total_energies EnergyMap after first computing the  component energies if they are not up-to-date   2. total_energies(rosetta.core.scoring.Energies) -> rosetta.core.scoring.EMapVector   Returns a non-const reference to the total_energies EnergyMap  so that external sources may append additional information to the Energies  object.  This is primarily useful for outputting score data with structures  when those terms are not part of the energy function.  This function will update the component energies if they are not up-to-date. total_energy(...) from builtins.PyCapsule total_energy(*args, **kwargs) Overloaded function.   1. total_energy(rosetta.core.scoring.Energies) -> float   Returns the total score    example(s):      pose.energies().total_energy()  See also:      Energies      Energies.residue_total_energy      Energies.residue_total_energies      Pose      ScoreFunction      ScoreFunction.show      create_score_function   2. total_energy(rosetta.core.scoring.Energies) -> float twelveA_neighbor_graph(...) from builtins.PyCapsule twelveA_neighbor_graph(*args, **kwargs) Overloaded function.   1. twelveA_neighbor_graph(rosetta.core.scoring.Energies) -> core::scoring::TwelveANeighborGraph   get the graph encoding # neighbors within 12 Angstroms   2. twelveA_neighbor_graph(rosetta.core.scoring.Energies) -> core::scoring::TwelveANeighborGraph update_residue_neighbors(...) from builtins.PyCapsule update_residue_neighbors(self : rosetta.core.scoring.Energies, domain_map_in : ObjexxFCL::FArray1D<int>, pose : rosetta.core.pose.Pose) -> NoneType   update the residue neighbors use_nblist(...) from builtins.PyCapsule use_nblist(rosetta.core.scoring.Energies) -> bool use_nblist_auto_update(...) from builtins.PyCapsule use_nblist_auto_update(rosetta.core.scoring.Energies) -> bool use_nblist_of_type(...) from builtins.PyCapsule use_nblist_of_type(self : rosetta.core.scoring.Energies, type : rosetta.core.scoring.EnergiesCacheableDataType.Enum) -> bool weights(...) from builtins.PyCapsule weights(*args, **kwargs) Overloaded function.   1. weights(rosetta.core.scoring.Energies) -> rosetta.core.scoring.EMapVector   Returns an EnergyMap of the ScoreFunction weights from the last  scoring    example(s):      we = pose.energies().weights()      we[fa_atr]  See also:      Energies      Energies.residue_total_energies      Energies.residue_total_energy      Pose      ScoreFunction      ScoreFunction.show      create_score_function      EMapVector   2. weights(self : rosetta.core.scoring.Energies, new_weights : rosetta.core.scoring.EMapVector) -> NoneType   Setter for the weights in this Energies object.   class EnergyEdge(rosetta.core.graph.Edge)     Class EnergyEdge holds scores for pair interactions for short-ranged energy functions.  It also records whether or not it has been scored -- when an edge is added to the graph, it sets "energies_computed_" as false, and the ScoreFunction class marks edges as having their energies computed once it computes them.     Method resolution order: EnergyEdge rosetta.core.graph.Edge builtins.object Methods defined here: __getitem__(...) from builtins.PyCapsule __getitem__(self : rosetta.core.scoring.EnergyEdge, st : rosetta.core.scoring.ScoreType) -> float   Read the value stored on this edge for a particular score type. __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, owner : core::scoring::EnergyGraph, n1 : int, n2 : int) -> NoneType   2. __init__(self : handle, owner : core::scoring::EnergyGraph, example_edge : rosetta.core.scoring.EnergyEdge) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_to_energy_map(...) from builtins.PyCapsule add_to_energy_map(*args, **kwargs) Overloaded function.   1. add_to_energy_map(self : rosetta.core.scoring.EnergyEdge, emap : rosetta.core.scoring.EMapVector) -> NoneType   Add the non-zero elements into the energy map   2. add_to_energy_map(self : rosetta.core.scoring.EnergyEdge, emap : rosetta.core.scoring.EMapVector, subset : rosetta.utility.vector1_core_scoring_ScoreType) -> NoneType   Add the non-zero elements into the energy map copy_from(...) from builtins.PyCapsule copy_from(self : rosetta.core.scoring.EnergyEdge, source : rosetta.core.graph.Edge) -> NoneType   Copy the data held on the example edge, source.  The source edge must be castable to class EnergyEdge. count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.scoring.EnergyEdge) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.scoring.EnergyEdge) -> int dot(...) from builtins.PyCapsule dot(self : rosetta.core.scoring.EnergyEdge, weights : rosetta.core.scoring.EMapVector) -> float   Compute the weighted energy for the components stored on this edge energies_not_yet_computed(...) from builtins.PyCapsule energies_not_yet_computed(rosetta.core.scoring.EnergyEdge) -> bool fill_energy_map(...) from builtins.PyCapsule fill_energy_map(rosetta.core.scoring.EnergyEdge) -> rosetta.core.scoring.EMapVector   Load an energy map with the non-zero mark_energies_computed(...) from builtins.PyCapsule mark_energies_computed(rosetta.core.scoring.EnergyEdge) -> NoneType mark_energies_uncomputed(...) from builtins.PyCapsule mark_energies_uncomputed(rosetta.core.scoring.EnergyEdge) -> NoneType square_distance(...) from builtins.PyCapsule square_distance(*args, **kwargs) Overloaded function.   1. square_distance(rosetta.core.scoring.EnergyEdge) -> float   2. square_distance(self : rosetta.core.scoring.EnergyEdge, dsqr : float) -> NoneType store_active_energies(...) from builtins.PyCapsule store_active_energies(*args, **kwargs) Overloaded function.   1. store_active_energies(self : rosetta.core.scoring.EnergyEdge, emap : rosetta.core.scoring.EMapVector) -> NoneType   Store the energies held in the input emap on this edge; only  those ScoreTypes which are active are stored.   2. store_active_energies(self : rosetta.core.scoring.EnergyEdge, emap : rosetta.core.scoring.EMapVector, subset : rosetta.utility.vector1_core_scoring_ScoreType) -> NoneType   Store the intersection of the energies held in the input emap on this edge:  The intersection is between the set of active ScoreTypes and the ScoreTypes given  in the input "subset" list.  subset need not be sorted. Methods inherited from rosetta.core.graph.Edge: get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.graph.Edge) -> int   returns the index of the lower node get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.graph.Edge, node_index : int) -> int   returns the index of the one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon. get_other_node(...) from builtins.PyCapsule get_other_node(*args, **kwargs) Overloaded function.   1. get_other_node(self : rosetta.core.graph.Edge, node_index : int) -> rosetta.core.graph.Node   returns a const pointer to one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon.   2. get_other_node(self : rosetta.core.graph.Edge, node_index : int) -> rosetta.core.graph.Node   returns a non-const pointer to one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon. get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.graph.Edge) -> int   returns the index of the upper node is_loop(...) from builtins.PyCapsule is_loop(rosetta.core.graph.Edge) -> bool   Is this edge a loop? In Pseudographs, loop edges are incident twice on a single vertex. same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.graph.Edge, node1 : int, node2 : int) -> bool   Is this the same edge as another edge (node1,node2)?  Note:  this graph does not work for multi-graphs.  Edges must be unique. set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.graph.Edge, edge_iterator : rosetta.core.graph.EdgeListIterator) -> NoneType   called only by class Graph, this function gives the Edge the data it needs  to later delete itself from its owner's edge list in constant time.   class EnergyGraph(rosetta.core.graph.Graph)     Class to hold the component energies between pairs of residues. Each node represents a residue in its corresponding structure. Each edge in the graph holds a two-body energy map representing the unweighted components of the energy function for those terms with non-zero weight.  The EnergyGraph may be accessed from the pose's Energies object, but at a price of an extra score evaluation.  This second score evaluation may be avoided if you use the ScoreFunction::score_components( pose ) method.     Method resolution order: EnergyGraph rosetta.core.graph.Graph builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, num_nodes : int) -> NoneType   2. __init__(handle) -> NoneType   3. __init__(handle, rosetta.core.scoring.EnergyGraph) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. active_2b_score_types(...) from builtins.PyCapsule active_2b_score_types(rosetta.core.scoring.EnergyGraph) -> rosetta.utility.vector1_core_scoring_ScoreType active_score_types(...) from builtins.PyCapsule active_score_types(self : rosetta.core.scoring.EnergyGraph, active : rosetta.utility.vector1_core_scoring_ScoreType) -> bool   Set the active score types, and return true if the new score types  are the same as the old score types and the graph state is still good.  Returns false if the score types have changed, indicating that the graph  has dropped all of its edges; add_energy_edge(...) from builtins.PyCapsule add_energy_edge(self : rosetta.core.scoring.EnergyGraph, index1 : int, index2 : int, dsq : float) -> NoneType   Add an energy edge to the graph and store the square distance array_pool(...) from builtins.PyCapsule array_pool(rosetta.core.scoring.EnergyGraph) -> rosetta.core.graph.ArrayPool_double_t   Give non-const access to the array pool -- this function should only  be called by class EnergyEdge.  I wish C++ let me declare this function private  and that EnergyEdge could be a "friend" of this function. assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.EnergyGraph, rhs : rosetta.core.scoring.EnergyGraph) -> rosetta.core.scoring.EnergyGraph deallocate_arraypoolelement(...) from builtins.PyCapsule deallocate_arraypoolelement(self : rosetta.core.scoring.EnergyGraph, element : rosetta.core.graph.ArrayPoolElement_double_t) -> NoneType   As an edge is deleted from the graph, it must reliquish hold over its  array-pool element so that the element may be reused by new edges. delete_edge(...) from builtins.PyCapsule delete_edge(self : rosetta.core.scoring.EnergyGraph, edge : rosetta.core.graph.Edge) -> NoneType find_energy_edge(...) from builtins.PyCapsule find_energy_edge(*args, **kwargs) Overloaded function.   1. find_energy_edge(self : rosetta.core.scoring.EnergyGraph, n1 : int, n2 : int) -> rosetta.core.scoring.EnergyEdge   2. find_energy_edge(self : rosetta.core.scoring.EnergyGraph, n1 : int, n2 : int) -> rosetta.core.scoring.EnergyEdge get_energy_node(...) from builtins.PyCapsule get_energy_node(*args, **kwargs) Overloaded function.   1. get_energy_node(self : rosetta.core.scoring.EnergyGraph, index : int) -> rosetta.core.scoring.EnergyNode   Add an energy edge to the graph and set the energies  for the non-zero-weighted components of the input emap.  void  add_energy_edge( Size index1, Size index2, EnergyMap const & emap );   2. get_energy_node(self : rosetta.core.scoring.EnergyGraph, index : int) -> rosetta.core.scoring.EnergyNode n_active_score_types(...) from builtins.PyCapsule n_active_score_types(rosetta.core.scoring.EnergyGraph) -> int score_type_2_active(...) from builtins.PyCapsule score_type_2_active(rosetta.core.scoring.EnergyGraph) -> rosetta.utility.vector1_int Methods inherited from rosetta.core.graph.Graph: add_edge(...) from builtins.PyCapsule add_edge(*args, **kwargs) Overloaded function.   1. add_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   add an edge between two vertices.  Invokes "create_edge" from the derived class.  Returns a pointer to the edge after its been added, allowing the calling function  to immediately set data for this edge.   2. add_edge(self : rosetta.core.graph.Graph, example_edge : rosetta.core.graph.Edge) -> rosetta.core.graph.Edge   add an edge to this graph copying the data from an edge in another graph.  Returns a pointer to the edge after its been added, allowing the calling function  to immediately set data for this edge. all_pairs_shortest_paths(...) from builtins.PyCapsule all_pairs_shortest_paths(rosetta.core.graph.Graph) -> ObjexxFCL::FArray2D<int>   O(V^3).  Computes all pairs shortest paths using Warshall's algorithm  and writes all the path distances to the two-dimensional table. const_edge_list_begin(...) from builtins.PyCapsule const_edge_list_begin(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex const_edge_list_end(...) from builtins.PyCapsule const_edge_list_end(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex copy_connectivity(...) from builtins.PyCapsule copy_connectivity(self : rosetta.core.graph.Graph, source : rosetta.core.graph.Graph) -> NoneType   copy the edge connectivity from a source graph with a potentially  unknown type. drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.graph.Graph) -> NoneType   delete all the edges present in the graph drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.graph.Graph, node : int) -> NoneType   delete all the edges for a single vertex in the graph edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   returns a pointer to the edge connecting nodes node1 and node2, if that edge exists  in the graph, o.w. returns 0.  Focuses the graph on this edge for fast subsequent retrieval.   2. find_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   returns a const pointer to the edge connecting nodes node1 and node2, if that edge exists  in the graph, o.w. returns 0.  Focuses the graph on this edge for fast subsequent retrieval. focused_edge(...) from builtins.PyCapsule focused_edge(*args, **kwargs) Overloaded function.   1. focused_edge(rosetta.core.graph.Graph) -> rosetta.core.graph.Edge   returns a pointer to the focused edge   2. focused_edge(rosetta.core.graph.Graph) -> rosetta.core.graph.Edge   returns a const-pointer to the focused edge getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.graph.Graph) -> int   returns a count of all the memory used by every vertex and edge in a graph  by invoking the polymorphic count_static_memory and count_dynamic_memory of each  (possibly derived) node and edge object as well as for the (possibly derived) graph  class. get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> bool   is an edge already present in the graph? O(V) worst case.  O(1) iff all vertices have O(1) edges get_node(...) from builtins.PyCapsule get_node(*args, **kwargs) Overloaded function.   1. get_node(self : rosetta.core.graph.Graph, index : int) -> rosetta.core.graph.Node   2. get_node(self : rosetta.core.graph.Graph, index : int) -> rosetta.core.graph.Node get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.graph.Graph) -> rosetta.core.graph.Graph   self pointers   2. get_self_ptr(rosetta.core.graph.Graph) -> rosetta.core.graph.Graph num_edges(...) from builtins.PyCapsule num_edges(rosetta.core.graph.Graph) -> int num_nodes(...) from builtins.PyCapsule num_nodes(rosetta.core.graph.Graph) -> int   the number of nodes in the graph print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.graph.Graph) -> NoneType   send summary information to the screen for all vertices in the graph set_num_nodes(...) from builtins.PyCapsule set_num_nodes(self : rosetta.core.graph.Graph, num_nodes : int) -> NoneType   set the number of nodes in the graph -- deletes any existing edges in the graph   class EnergyNode(rosetta.core.graph.Node)     Class EnergyNode holds the result of a domainmap update from the Conformation object held by a pose; if the internal degrees of freedom for a residue (corresponding to a node in this graph) have changed (and are marked with color "0" in the domainmap), then the EnergyNode object will hold that information for the ScoringFunction to retrieve     Method resolution order: EnergyNode rosetta.core.graph.Node builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.graph.Graph, index : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. copy_from(...) from builtins.PyCapsule copy_from(self : rosetta.core.scoring.EnergyNode, source : rosetta.core.graph.Node) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.scoring.EnergyNode) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.scoring.EnergyNode) -> int moved(...) from builtins.PyCapsule moved(*args, **kwargs) Overloaded function.   1. moved(rosetta.core.scoring.EnergyNode) -> bool   2. moved(self : rosetta.core.scoring.EnergyNode,  : bool) -> NoneType print(...) from builtins.PyCapsule print(rosetta.core.scoring.EnergyNode) -> NoneType Methods inherited from rosetta.core.graph.Node: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.graph.Node, edge_ptr : core::graph::Edge,  : rosetta.core.graph.EdgeListIterator) -> NoneType   adds edge pointer to edge list; returns an iterator to the new  list element const_edge_list_begin(...) from builtins.PyCapsule const_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its edge list const_edge_list_end(...) from builtins.PyCapsule const_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its edge list const_lower_edge_list_begin(...) from builtins.PyCapsule const_lower_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its lower-edge list const_lower_edge_list_end(...) from builtins.PyCapsule const_lower_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its lower-edge list const_upper_edge_list_begin(...) from builtins.PyCapsule const_upper_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its upper-edge list const_upper_edge_list_end(...) from builtins.PyCapsule const_upper_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its upper-edge list drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.graph.Node) -> NoneType   deletes all edges incident upon this node drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.graph.Node, edge_iterator : rosetta.core.graph.EdgeListIterator) -> NoneType   removes an edge iterator from the node's edge list.  Only called by Edge class. edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its edge list edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its edge list find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.graph.Node, other_node_index : int) -> core::graph::Edge   a "slow" (linear) search for an edge.   2. find_edge(self : rosetta.core.graph.Node, other_node_index : int) -> core::graph::Edge get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.graph.Node) -> int   the index for this node get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.graph.Node) -> int   the number of upper neighbors -- which "self" neighborness is counted if a loop edge  is present get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.graph.Node) -> int   the number of lower neighbors loop_incident(...) from builtins.PyCapsule loop_incident(rosetta.core.graph.Node) -> bool   NOTE TO SELF: remove loop support lower_edge_list_begin(...) from builtins.PyCapsule lower_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its lower-edge list lower_edge_list_end(...) from builtins.PyCapsule lower_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its lower-edge list num_edges(...) from builtins.PyCapsule num_edges(rosetta.core.graph.Node) -> int   the number of edges incident on this node, which may include a loop edge num_neighbors_counting_self(...) from builtins.PyCapsule num_neighbors_counting_self(rosetta.core.graph.Node) -> int   the number of neighbors counting "self" as a neighbor. num_neighbors_counting_self_static(...) from builtins.PyCapsule num_neighbors_counting_self_static(rosetta.core.graph.Node) -> int   the number of neighbors counting "self" as neighbor. Defaults to  num_neighbors_counting_self() but can be set to other values as well.  Useful in calculation of symmetrical structures. set_num_neighbors_counting_self_static(...) from builtins.PyCapsule set_num_neighbors_counting_self_static(self : rosetta.core.graph.Node, neighbor : int) -> NoneType   manually change the number of neighbors for a Node. Used  for symmetry scoring upper_edge_list_begin(...) from builtins.PyCapsule upper_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its upper-edge list upper_edge_list_end(...) from builtins.PyCapsule upper_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its upper-edge list   class EnvPairPotential(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.EnvPairPotential) -> NoneType   2. __init__(self : rosetta.core.scoring.EnvPairPotential,  : rosetta.core.scoring.EnvPairPotential) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. cenlist_from_pose(...) from builtins.PyCapsule cenlist_from_pose( : rosetta.core.pose.Pose) -> rosetta.core.scoring.CenListInfo compute_centroid_environment(...) from builtins.PyCapsule compute_centroid_environment(self : rosetta.core.scoring.EnvPairPotential, pose : rosetta.core.pose.Pose) -> NoneType evaluate_env_and_cbeta_scores(...) from builtins.PyCapsule evaluate_env_and_cbeta_scores(self : rosetta.core.scoring.EnvPairPotential, pose : rosetta.core.pose.Pose, rsd : rosetta.core.conformation.Residue, env_score : float, cb_score6 : float, cb_score12 : float) -> NoneType evaluate_pair_and_cenpack_score(...) from builtins.PyCapsule evaluate_pair_and_cenpack_score(self : rosetta.core.scoring.EnvPairPotential, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, cendist : float, pair_contribution : float, cenpack_contribution : float) -> NoneType finalize(...) from builtins.PyCapsule finalize(self : rosetta.core.scoring.EnvPairPotential, pose : rosetta.core.pose.Pose) -> NoneType nonconst_cenlist_from_pose(...) from builtins.PyCapsule nonconst_cenlist_from_pose( : rosetta.core.pose.Pose) -> rosetta.core.scoring.CenListInfo   class ExcludedResPredicate(Predicate)       Method resolution order: ExcludedResPredicate Predicate builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.core.scoring.ExcludedResPredicate, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, resno : int, atomno : int) -> bool __init__(...) from builtins.PyCapsule __init__(self : handle, excluded : rosetta.utility.vector1_unsigned_long, predicate : rosetta.core.scoring.Predicate) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. Methods inherited from Predicate: assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.Predicate,  : rosetta.core.scoring.Predicate) -> rosetta.core.scoring.Predicate   class FACTSPoseInfo(rosetta.basic.datacache.CacheableData)     /////////////////////////////////////////////////////////////////////////////////////////////////     Method resolution order: FACTSPoseInfo rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.scoring.FACTSPoseInfo) -> 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.scoring.FACTSPoseInfo,  : rosetta.core.scoring.FACTSPoseInfo) -> rosetta.core.scoring.FACTSPoseInfo being_packed(...) from builtins.PyCapsule being_packed(self : rosetta.core.scoring.FACTSPoseInfo, seqpos : int) -> bool clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.FACTSPoseInfo) -> rosetta.basic.datacache.CacheableData context_derivative_empty(...) from builtins.PyCapsule context_derivative_empty(rosetta.core.scoring.FACTSPoseInfo) -> bool initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.scoring.FACTSPoseInfo, pose : rosetta.core.pose.Pose, rsdtypemap : rosetta.std.map_const_core_chemical_ResidueType_*_std_shared_ptr_const_core_scoring_FACTSRsdTypeInfo_t) -> NoneType is_changed(...) from builtins.PyCapsule is_changed(self : rosetta.core.scoring.FACTSPoseInfo, pose : rosetta.core.pose.Pose) -> bool placeholder_info(...) from builtins.PyCapsule placeholder_info(self : rosetta.core.scoring.FACTSPoseInfo, seqpos : int) -> rosetta.core.scoring.FACTSResidueInfo placeholder_residue(...) from builtins.PyCapsule placeholder_residue(self : rosetta.core.scoring.FACTSPoseInfo, seqpos : int) -> rosetta.core.conformation.Residue residue_info(...) from builtins.PyCapsule residue_info(*args, **kwargs) Overloaded function.   1. residue_info(self : rosetta.core.scoring.FACTSPoseInfo, i : int) -> rosetta.core.scoring.FACTSResidueInfo   2. residue_info(self : rosetta.core.scoring.FACTSPoseInfo, i : int) -> rosetta.core.scoring.FACTSResidueInfo set_placeholder(...) from builtins.PyCapsule set_placeholder(self : rosetta.core.scoring.FACTSPoseInfo, i : int, rsd : rosetta.core.conformation.Residue, info : rosetta.core.scoring.FACTSResidueInfo) -> NoneType set_repack_list(...) from builtins.PyCapsule set_repack_list(self : rosetta.core.scoring.FACTSPoseInfo, repacking_residues : rosetta.utility.vector1_bool) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.scoring.FACTSPoseInfo) -> int update_enumeration_shell(...) from builtins.PyCapsule update_enumeration_shell(*args, **kwargs) Overloaded function.   1. update_enumeration_shell(self : rosetta.core.scoring.FACTSPoseInfo, pose : rosetta.core.pose.Pose) -> NoneType   2. update_enumeration_shell(self : rosetta.core.scoring.FACTSPoseInfo, pose : rosetta.core.pose.Pose, enumerate_second_shell : bool) -> NoneType Data descriptors defined here: being_packed_ context_derivative_empty_ placeholder_info_ placeholder_residue_ residue_info_ Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class FACTSPotential(builtins.object)     ***********************************************************************************************     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.FACTSPotential) -> NoneType   2. __init__(self : rosetta.core.scoring.FACTSPotential,  : rosetta.core.scoring.FACTSPotential) -> 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.scoring.FACTSPotential,  : rosetta.core.scoring.FACTSPotential) -> rosetta.core.scoring.FACTSPotential eval_atom_nonpolar_derivative(...) from builtins.PyCapsule eval_atom_nonpolar_derivative(self : rosetta.core.scoring.FACTSPotential, id : rosetta.core.id.AtomID, weight : float, pose : rosetta.core.pose.Pose,  : ObjexxFCL::FArray1D<int>,  : bool, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t) -> NoneType eval_atom_polar_derivative(...) from builtins.PyCapsule eval_atom_polar_derivative(self : rosetta.core.scoring.FACTSPotential, id : rosetta.core.id.AtomID, weight_elec : float, weight_solv : float, pose : rosetta.core.pose.Pose,  : ObjexxFCL::FArray1D<int>,  : bool, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t) -> NoneType evaluate_nonpolar_energy(...) from builtins.PyCapsule evaluate_nonpolar_energy(self : rosetta.core.scoring.FACTSPotential, rsd1 : rosetta.core.conformation.Residue, facts1 : rosetta.core.scoring.FACTSResidueInfo, rsd2 : rosetta.core.conformation.Residue) -> float evaluate_polar_energy(...) from builtins.PyCapsule evaluate_polar_energy(self : rosetta.core.scoring.FACTSPotential, rsd1 : rosetta.core.conformation.Residue, facts1 : rosetta.core.scoring.FACTSResidueInfo, rsd2 : rosetta.core.conformation.Residue, E_elec : float, E_solv_self : float, E_solv_pair : float) -> NoneType evaluate_polar_otf_energy(...) from builtins.PyCapsule evaluate_polar_otf_energy(self : rosetta.core.scoring.FACTSPotential, rsd1 : rosetta.core.conformation.Residue, facts1 : rosetta.core.scoring.FACTSResidueInfo, rsd2 : rosetta.core.conformation.Residue, facts2 : rosetta.core.scoring.FACTSResidueInfo, E_elec : float, E_solv_self : float, E_solv_pair : float) -> NoneType get_rotamers_born_radii(...) from builtins.PyCapsule get_rotamers_born_radii(self : rosetta.core.scoring.FACTSPotential, pose : rosetta.core.pose.Pose, rotamer_set : rosetta.core.conformation.RotamerSetBase) -> NoneType get_single_rotamer_born_radii(...) from builtins.PyCapsule get_single_rotamer_born_radii(self : rosetta.core.scoring.FACTSPotential, rsd1 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, facts_info : rosetta.core.scoring.FACTSPoseInfo, facts1 : rosetta.core.scoring.FACTSResidueInfo) -> NoneType set_default(...) from builtins.PyCapsule set_default(rosetta.core.scoring.FACTSPotential) -> NoneType setup_for_derivatives(...) from builtins.PyCapsule setup_for_derivatives(self : rosetta.core.scoring.FACTSPotential, pose : rosetta.core.pose.Pose) -> NoneType setup_for_packing(...) from builtins.PyCapsule setup_for_packing(self : rosetta.core.scoring.FACTSPotential, pose : rosetta.core.pose.Pose, repacking_residues : rosetta.utility.vector1_bool) -> NoneType setup_for_scoring(...) from builtins.PyCapsule setup_for_scoring(self : rosetta.core.scoring.FACTSPotential, pose : rosetta.core.pose.Pose, packing : bool) -> NoneType update_residue_for_packing(...) from builtins.PyCapsule update_residue_for_packing(self : rosetta.core.scoring.FACTSPotential, pose : rosetta.core.pose.Pose, seqpos : int) -> NoneType   class FACTSResidueInfo(builtins.object)     ***********************************************************************************************     Methods defined here: Ai(...) from builtins.PyCapsule Ai(*args, **kwargs) Overloaded function.   1. Ai(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> float   2. Ai(rosetta.core.scoring.FACTSResidueInfo) -> rosetta.utility.vector1_double BR(...) from builtins.PyCapsule BR(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> float Bi(...) from builtins.PyCapsule Bi(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> float Ci(...) from builtins.PyCapsule Ci(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> float Di(...) from builtins.PyCapsule Di(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> float E_elec(...) from builtins.PyCapsule E_elec(self : rosetta.core.scoring.FACTSResidueInfo, res : int) -> float E_solv(...) from builtins.PyCapsule E_solv(self : rosetta.core.scoring.FACTSResidueInfo, res : int) -> float E_solv_pair(...) from builtins.PyCapsule E_solv_pair(self : rosetta.core.scoring.FACTSResidueInfo, res : int) -> float E_solv_self(...) from builtins.PyCapsule E_solv_self(self : rosetta.core.scoring.FACTSResidueInfo, res : int) -> float Ei(...) from builtins.PyCapsule Ei(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> float __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.FACTSResidueInfo) -> NoneType   2. __init__(rosetta.core.scoring.FACTSResidueInfo, rosetta.core.conformation.Residue, rosetta.core.scoring.FACTSRsdTypeInfo) -> NoneType   doc   3. __init__(self : rosetta.core.scoring.FACTSResidueInfo, rsd : rosetta.core.conformation.Residue, restypeinfo : rosetta.core.scoring.FACTSRsdTypeInfo, is_rotamer : bool) -> NoneType   4. __init__(self : rosetta.core.scoring.FACTSResidueInfo,  : rosetta.core.scoring.FACTSResidueInfo) -> 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.scoring.FACTSResidueInfo,  : rosetta.core.scoring.FACTSResidueInfo) -> rosetta.core.scoring.FACTSResidueInfo changed(...) from builtins.PyCapsule changed(rosetta.core.scoring.FACTSResidueInfo) -> bool clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.FACTSResidueInfo) -> rosetta.core.scoring.FACTSResidueInfo dBR_dG(...) from builtins.PyCapsule dBR_dG(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> float dB_dBdnmtr(...) from builtins.PyCapsule dB_dBdnmtr(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> float dB_dBnmtr(...) from builtins.PyCapsule dB_dBnmtr(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> float dG_dCi(...) from builtins.PyCapsule dG_dCi(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> float dSA_dDi(...) from builtins.PyCapsule dSA_dDi(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> float dnmtr(...) from builtins.PyCapsule dnmtr(*args, **kwargs) Overloaded function.   1. dnmtr(rosetta.core.scoring.FACTSResidueInfo) -> rosetta.utility.vector1_double   2. dnmtr(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> float dsolv_dBR(...) from builtins.PyCapsule dsolv_dBR(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> float elecF2(...) from builtins.PyCapsule elecF2(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t enumeration_shell(...) from builtins.PyCapsule enumeration_shell(rosetta.core.scoring.FACTSResidueInfo) -> bool esolvE(...) from builtins.PyCapsule esolvE(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> float flag_for_calculation(...) from builtins.PyCapsule flag_for_calculation(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> bool initialize(...) from builtins.PyCapsule initialize(*args, **kwargs) Overloaded function.   1. initialize(self : rosetta.core.scoring.FACTSResidueInfo, rsd : rosetta.core.conformation.Residue, restypeinfo : rosetta.core.scoring.FACTSRsdTypeInfo) -> NoneType   2. initialize(self : rosetta.core.scoring.FACTSResidueInfo, rsd : rosetta.core.conformation.Residue, restypeinfo : rosetta.core.scoring.FACTSRsdTypeInfo, is_rotamer : bool) -> NoneType natoms(...) from builtins.PyCapsule natoms(rosetta.core.scoring.FACTSResidueInfo) -> int nmtr(...) from builtins.PyCapsule nmtr(*args, **kwargs) Overloaded function.   1. nmtr(rosetta.core.scoring.FACTSResidueInfo) -> rosetta.utility.vector1_numeric_xyzVector_double_t   2. nmtr(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t refresh_energy_cache(...) from builtins.PyCapsule refresh_energy_cache(self : rosetta.core.scoring.FACTSResidueInfo, nres : int) -> NoneType restypeinfo(...) from builtins.PyCapsule restypeinfo(rosetta.core.scoring.FACTSResidueInfo) -> rosetta.core.scoring.FACTSRsdTypeInfo sasa(...) from builtins.PyCapsule sasa(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> float sasaF2(...) from builtins.PyCapsule sasaF2(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t set_changed(...) from builtins.PyCapsule set_changed(self : rosetta.core.scoring.FACTSResidueInfo, value : bool) -> NoneType set_enumeration_shell(...) from builtins.PyCapsule set_enumeration_shell(self : rosetta.core.scoring.FACTSResidueInfo, value : bool) -> NoneType solvF2BR(...) from builtins.PyCapsule solvF2BR(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t solvF2d(...) from builtins.PyCapsule solvF2d(self : rosetta.core.scoring.FACTSResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t store_xyz(...) from builtins.PyCapsule store_xyz(self : rosetta.core.scoring.FACTSResidueInfo, rsd : rosetta.core.conformation.Residue) -> NoneType xyz(...) from builtins.PyCapsule xyz(rosetta.core.scoring.FACTSResidueInfo) -> rosetta.utility.vector1_numeric_xyzVector_double_t Data descriptors defined here: Ai_ BR_ Bi_ Ci_ Di_ E_elec_ E_solv_ E_solv_pair_ E_solv_self_ Ei_ changed_ dBR_dG_ dB_dBdnmtr_ dB_dBnmtr_ dG_dCi_ dSA_dDi_ dnmtr_ dsolv_dBR_ elecF2_ enumeration_shell_ esolvE_ flag_for_calculation_ natoms_ nmtr_ sasaF2_ sasa_ solvF2BR_ solvF2d_ xyz_   class FACTSRotamerSetInfo(rosetta.basic.datacache.CacheableData)     /////////////////////////////////////////////////////////////////////////////////////////////////     Method resolution order: FACTSRotamerSetInfo rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle, rosetta.core.scoring.FACTSRotamerSetInfo) -> NoneType   2. __init__(self : handle, rotamer_set : rosetta.core.conformation.RotamerSetBase, rsdtypemap : rosetta.std.map_const_core_chemical_ResidueType_*_std_shared_ptr_const_core_scoring_FACTSRsdTypeInfo_t) -> 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.scoring.FACTSRotamerSetInfo,  : rosetta.core.scoring.FACTSRotamerSetInfo) -> rosetta.core.scoring.FACTSRotamerSetInfo clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.FACTSRotamerSetInfo) -> rosetta.basic.datacache.CacheableData initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.scoring.FACTSRotamerSetInfo, rotamer_set : rosetta.core.conformation.RotamerSetBase, rsdtypemap : rosetta.std.map_const_core_chemical_ResidueType_*_std_shared_ptr_const_core_scoring_FACTSRsdTypeInfo_t) -> NoneType   dont forget to 0 the born_radii residue_info(...) from builtins.PyCapsule residue_info(*args, **kwargs) Overloaded function.   1. residue_info(self : rosetta.core.scoring.FACTSRotamerSetInfo, i : int) -> rosetta.core.scoring.FACTSResidueInfo   2. residue_info(self : rosetta.core.scoring.FACTSRotamerSetInfo, i : int) -> rosetta.core.scoring.FACTSResidueInfo size(...) from builtins.PyCapsule size(rosetta.core.scoring.FACTSRotamerSetInfo) -> int Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class FACTSRsdTypeInfo(builtins.object)     ***********************************************************************************************     Methods defined here: COradius2(...) from builtins.PyCapsule COradius2(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> float __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.FACTSRsdTypeInfo) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. a0(...) from builtins.PyCapsule a0(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> float a1(...) from builtins.PyCapsule a1(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> float a2(...) from builtins.PyCapsule a2(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> float a3(...) from builtins.PyCapsule a3(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> float alpha(...) from builtins.PyCapsule alpha(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> float assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.FACTSRsdTypeInfo,  : rosetta.core.scoring.FACTSRsdTypeInfo) -> rosetta.core.scoring.FACTSRsdTypeInfo b1(...) from builtins.PyCapsule b1(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> float b2(...) from builtins.PyCapsule b2(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> float c0(...) from builtins.PyCapsule c0(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> float c1(...) from builtins.PyCapsule c1(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> float c2(...) from builtins.PyCapsule c2(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> float c3(...) from builtins.PyCapsule c3(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> float charged(...) from builtins.PyCapsule charged(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> bool create_info(...) from builtins.PyCapsule create_info(self : rosetta.core.scoring.FACTSRsdTypeInfo, rsd : rosetta.core.chemical.ResidueType) -> NoneType d1(...) from builtins.PyCapsule d1(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> float d2(...) from builtins.PyCapsule d2(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> float intra_elec_scale(...) from builtins.PyCapsule intra_elec_scale(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm1 : int, atm2 : int) -> float intra_solv_scale(...) from builtins.PyCapsule intra_solv_scale(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm1 : int, atm2 : int) -> float is_chargedH(...) from builtins.PyCapsule is_chargedH(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm1 : int) -> bool is_freedof(...) from builtins.PyCapsule is_freedof(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm1 : int) -> bool natoms(...) from builtins.PyCapsule natoms(rosetta.core.scoring.FACTSRsdTypeInfo) -> int not_using(...) from builtins.PyCapsule not_using(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> bool q(...) from builtins.PyCapsule q(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> float volume(...) from builtins.PyCapsule volume(self : rosetta.core.scoring.FACTSRsdTypeInfo, atm : int) -> float   class GenBornPoseInfo(rosetta.basic.datacache.CacheableData)     ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////     Method resolution order: GenBornPoseInfo rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.scoring.GenBornPoseInfo) -> 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.scoring.GenBornPoseInfo,  : rosetta.core.scoring.GenBornPoseInfo) -> rosetta.core.scoring.GenBornPoseInfo being_packed(...) from builtins.PyCapsule being_packed(self : rosetta.core.scoring.GenBornPoseInfo, seqpos : int) -> bool clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.GenBornPoseInfo) -> rosetta.basic.datacache.CacheableData initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.scoring.GenBornPoseInfo, pose : rosetta.core.pose.Pose) -> NoneType placeholder_info(...) from builtins.PyCapsule placeholder_info(self : rosetta.core.scoring.GenBornPoseInfo, seqpos : int) -> rosetta.core.scoring.GenBornResidueInfo placeholder_residue(...) from builtins.PyCapsule placeholder_residue(self : rosetta.core.scoring.GenBornPoseInfo, seqpos : int) -> rosetta.core.conformation.Residue residue_info(...) from builtins.PyCapsule residue_info(*args, **kwargs) Overloaded function.   1. residue_info(self : rosetta.core.scoring.GenBornPoseInfo, i : int) -> rosetta.core.scoring.GenBornResidueInfo   2. residue_info(self : rosetta.core.scoring.GenBornPoseInfo, i : int) -> rosetta.core.scoring.GenBornResidueInfo set_placeholder(...) from builtins.PyCapsule set_placeholder(self : rosetta.core.scoring.GenBornPoseInfo, i : int, rsd : rosetta.core.conformation.Residue, info : rosetta.core.scoring.GenBornResidueInfo) -> NoneType set_repack_list(...) from builtins.PyCapsule set_repack_list(self : rosetta.core.scoring.GenBornPoseInfo, repacking_residues : rosetta.utility.vector1_bool) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.scoring.GenBornPoseInfo) -> int Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class GenBornPotential(builtins.object)     ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.GenBornPotential) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. eval_atom_derivative(...) from builtins.PyCapsule eval_atom_derivative(self : rosetta.core.scoring.GenBornPotential, id : rosetta.core.id.AtomID, weight : float, pose : rosetta.core.pose.Pose, domain_map : ObjexxFCL::FArray1D<int>, exclude_DNA_DNA : bool, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t) -> NoneType get_all_born_radii(...) from builtins.PyCapsule get_all_born_radii(self : rosetta.core.scoring.GenBornPotential, pose : rosetta.core.pose.Pose) -> NoneType   called prior to scoring, eg get_res_res_elecE(...) from builtins.PyCapsule get_res_res_elecE(self : rosetta.core.scoring.GenBornPotential, rsd1 : rosetta.core.conformation.Residue, gb1 : rosetta.core.scoring.GenBornResidueInfo, rsd2 : rosetta.core.conformation.Residue, gb2 : rosetta.core.scoring.GenBornResidueInfo) -> float get_rotamers_born_radii(...) from builtins.PyCapsule get_rotamers_born_radii(self : rosetta.core.scoring.GenBornPotential, pose : rosetta.core.pose.Pose, rotamer_set : rosetta.core.conformation.RotamerSetBase) -> NoneType setup_for_packing(...) from builtins.PyCapsule setup_for_packing(self : rosetta.core.scoring.GenBornPotential, pose : rosetta.core.pose.Pose, repacking_residues : rosetta.utility.vector1_bool) -> NoneType update_residue_for_packing(...) from builtins.PyCapsule update_residue_for_packing(self : rosetta.core.scoring.GenBornPotential, pose : rosetta.core.pose.Pose, seqpos : int) -> NoneType   class GenBornResidueInfo(builtins.object)     ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.core.scoring.GenBornResidueInfo, rsd : rosetta.core.conformation.Residue) -> NoneType   2. __init__(self : rosetta.core.scoring.GenBornResidueInfo,  : rosetta.core.scoring.GenBornResidueInfo) -> 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.scoring.GenBornResidueInfo,  : rosetta.core.scoring.GenBornResidueInfo) -> rosetta.core.scoring.GenBornResidueInfo atomic_radius(...) from builtins.PyCapsule atomic_radius(*args, **kwargs) Overloaded function.   1. atomic_radius(self : rosetta.core.scoring.GenBornResidueInfo, atm : int) -> float   2. atomic_radius(self : rosetta.core.scoring.GenBornResidueInfo, atm : int) -> float born_radius(...) from builtins.PyCapsule born_radius(*args, **kwargs) Overloaded function.   1. born_radius(self : rosetta.core.scoring.GenBornResidueInfo, atm : int) -> float   2. born_radius(self : rosetta.core.scoring.GenBornResidueInfo, atm : int) -> float clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.GenBornResidueInfo) -> rosetta.core.scoring.GenBornResidueInfo initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.scoring.GenBornResidueInfo, rsd : rosetta.core.conformation.Residue) -> NoneType scale_factor(...) from builtins.PyCapsule scale_factor(*args, **kwargs) Overloaded function.   1. scale_factor(self : rosetta.core.scoring.GenBornResidueInfo, atm : int) -> float   2. scale_factor(self : rosetta.core.scoring.GenBornResidueInfo, atm : int) -> float size(...) from builtins.PyCapsule size(rosetta.core.scoring.GenBornResidueInfo) -> int   class GenBornRotamerSetInfo(rosetta.basic.datacache.CacheableData)     ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////     Method resolution order: GenBornRotamerSetInfo rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle, rosetta.core.scoring.GenBornRotamerSetInfo) -> NoneType   2. __init__(self : handle, rotamer_set : rosetta.core.conformation.RotamerSetBase) -> 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.scoring.GenBornRotamerSetInfo,  : rosetta.core.scoring.GenBornRotamerSetInfo) -> rosetta.core.scoring.GenBornRotamerSetInfo clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.GenBornRotamerSetInfo) -> rosetta.basic.datacache.CacheableData initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.scoring.GenBornRotamerSetInfo, rotamer_set : rosetta.core.conformation.RotamerSetBase) -> NoneType   dont forget to 0 the born_radii residue_info(...) from builtins.PyCapsule residue_info(*args, **kwargs) Overloaded function.   1. residue_info(self : rosetta.core.scoring.GenBornRotamerSetInfo, i : int) -> rosetta.core.scoring.GenBornResidueInfo   2. residue_info(self : rosetta.core.scoring.GenBornRotamerSetInfo, i : int) -> rosetta.core.scoring.GenBornResidueInfo size(...) from builtins.PyCapsule size(rosetta.core.scoring.GenBornRotamerSetInfo) -> int Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class Hairpin(builtins.object)     ///////////////////////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.Hairpin) -> NoneType   2. __init__(self : rosetta.core.scoring.Hairpin, s1_1 : int, s1_2 : int, s2_1 : int, s2_2 : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.scoring.Hairpin) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.Hairpin, s : rosetta.core.scoring.Hairpin) -> rosetta.core.scoring.Hairpin   copy assignment s1_end(...) from builtins.PyCapsule s1_end(rosetta.core.scoring.Hairpin) -> int s1_start(...) from builtins.PyCapsule s1_start(rosetta.core.scoring.Hairpin) -> int s2_end(...) from builtins.PyCapsule s2_end(rosetta.core.scoring.Hairpin) -> int s2_start(...) from builtins.PyCapsule s2_start(rosetta.core.scoring.Hairpin) -> int Data descriptors defined here: range_pair_   class Hairpins(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.Hairpins) -> NoneType   2. __init__(self : rosetta.core.scoring.Hairpins, s : rosetta.core.scoring.Hairpins) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.scoring.Hairpins) -> str append_hairpin(...) from builtins.PyCapsule append_hairpin(self : rosetta.core.scoring.Hairpins, s1_1 : int, s1_2 : int, s2_1 : int, s2_2 : int) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.Hairpins, s : rosetta.core.scoring.Hairpins) -> rosetta.core.scoring.Hairpins   copy assignment clear(...) from builtins.PyCapsule clear(rosetta.core.scoring.Hairpins) -> NoneType list(...) from builtins.PyCapsule list(rosetta.core.scoring.Hairpins) -> rosetta.utility.vector1_core_scoring_Hairpin size(...) from builtins.PyCapsule size(rosetta.core.scoring.Hairpins) -> int Data descriptors defined here: hairpin_list_   class Helices(builtins.object)     ///////////////////////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.Helices) -> NoneType   2. __init__(self : rosetta.core.scoring.Helices, total_residue : int) -> NoneType   3. __init__(self : rosetta.core.scoring.Helices, h : rosetta.core.scoring.Helices) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.scoring.Helices) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.Helices, h : rosetta.core.scoring.Helices) -> rosetta.core.scoring.Helices   copy assignment resize(...) from builtins.PyCapsule resize(self : rosetta.core.scoring.Helices, nres : int) -> NoneType Data descriptors defined here: HH_helix_end HH_resnum total_HH_dimer total_helices   class IsProteinCAPredicate(Predicate)       Method resolution order: IsProteinCAPredicate Predicate builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.core.scoring.IsProteinCAPredicate, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, resno : int, atomno : int) -> bool __init__(...) from builtins.PyCapsule __init__(handle) -> 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.scoring.IsProteinCAPredicate,  : rosetta.core.scoring.IsProteinCAPredicate) -> rosetta.core.scoring.IsProteinCAPredicate   class LREnergyContainer(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.LREnergyContainer) -> NoneType   2. __init__(rosetta.core.scoring.LREnergyContainer, rosetta.core.scoring.LREnergyContainer) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. any_neighbors_for_residue(...) from builtins.PyCapsule any_neighbors_for_residue(self : rosetta.core.scoring.LREnergyContainer, resid : int) -> bool any_upper_neighbors_for_residue(...) from builtins.PyCapsule any_upper_neighbors_for_residue(self : rosetta.core.scoring.LREnergyContainer, resid : int) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.LREnergyContainer,  : rosetta.core.scoring.LREnergyContainer) -> rosetta.core.scoring.LREnergyContainer clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.LREnergyContainer) -> rosetta.core.scoring.LREnergyContainer const_neighbor_iterator_begin(...) from builtins.PyCapsule const_neighbor_iterator_begin(self : rosetta.core.scoring.LREnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborConstIterator const_neighbor_iterator_end(...) from builtins.PyCapsule const_neighbor_iterator_end(self : rosetta.core.scoring.LREnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborConstIterator const_upper_neighbor_iterator_begin(...) from builtins.PyCapsule const_upper_neighbor_iterator_begin(self : rosetta.core.scoring.LREnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborConstIterator const_upper_neighbor_iterator_end(...) from builtins.PyCapsule const_upper_neighbor_iterator_end(self : rosetta.core.scoring.LREnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborConstIterator empty(...) from builtins.PyCapsule empty(rosetta.core.scoring.LREnergyContainer) -> bool neighbor_iterator_begin(...) from builtins.PyCapsule neighbor_iterator_begin(self : rosetta.core.scoring.LREnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborIterator neighbor_iterator_end(...) from builtins.PyCapsule neighbor_iterator_end(self : rosetta.core.scoring.LREnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborIterator set_num_nodes(...) from builtins.PyCapsule set_num_nodes(self : rosetta.core.scoring.LREnergyContainer,  : int) -> NoneType upper_neighbor_iterator_begin(...) from builtins.PyCapsule upper_neighbor_iterator_begin(self : rosetta.core.scoring.LREnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborIterator upper_neighbor_iterator_end(...) from builtins.PyCapsule upper_neighbor_iterator_end(self : rosetta.core.scoring.LREnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborIterator   class MembraneEmbed(rosetta.basic.datacache.CacheableData)     Whole Pose Membrane Embedding     Define the embedding of the membrane pose based on computed    normal and center parameters. These are initialzed in the membrane protein    framework and then recomputed based upon the structured and stored in MP residues    (see MP Framework code)     Method resolution order: MembraneEmbed rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.scoring.MembraneEmbed) -> 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.scoring.MembraneEmbed,  : rosetta.core.scoring.MembraneEmbed) -> rosetta.core.scoring.MembraneEmbed calculated(...) from builtins.PyCapsule calculated(*args, **kwargs) Overloaded function.   1. calculated(rosetta.core.scoring.MembraneEmbed) -> bool   Return Calculated (no idea what this does)   2. calculated(rosetta.core.scoring.MembraneEmbed) -> bool   Return Non_Ref Calculated (no idea what this does - maybe observer) center(...) from builtins.PyCapsule center(rosetta.core.scoring.MembraneEmbed) -> rosetta.numeric.xyzVector_double_t   Get Center Parameter clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.MembraneEmbed) -> rosetta.basic.datacache.CacheableData   Clone Cacheable Data depth(...) from builtins.PyCapsule depth(*args, **kwargs) Overloaded function.   1. depth(self : rosetta.core.scoring.MembraneEmbed, seqpos : int) -> float   Compute depth of residue in the membrane   2. depth(self : rosetta.core.scoring.MembraneEmbed, seqpos : int) -> float   Get NonConst Depth initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.scoring.MembraneEmbed, pose : rosetta.core.pose.Pose) -> NoneType   Initialize Membrane Embedding From Pose?? normal(...) from builtins.PyCapsule normal(rosetta.core.scoring.MembraneEmbed) -> rosetta.numeric.xyzVector_double_t   Get Normal Parameter penalty(...) from builtins.PyCapsule penalty(rosetta.core.scoring.MembraneEmbed) -> float   Get MP Penalty set_center(...) from builtins.PyCapsule set_center(self : rosetta.core.scoring.MembraneEmbed, v : rosetta.numeric.xyzVector_double_t) -> NoneType   Set Pose Embedding Center (should not use this method, deprecated 3/11/14) set_normal(...) from builtins.PyCapsule set_normal(self : rosetta.core.scoring.MembraneEmbed, v : rosetta.numeric.xyzVector_double_t) -> NoneType   Set Pose Embedding Normal (should not use this method, deprecated 3/11/14) set_penalty(...) from builtins.PyCapsule set_penalty(self : rosetta.core.scoring.MembraneEmbed, p : float) -> NoneType   Set Penalty size(...) from builtins.PyCapsule size(rosetta.core.scoring.MembraneEmbed) -> int   Compute Size of MP (] spanning(...) from builtins.PyCapsule spanning(*args, **kwargs) Overloaded function.   1. spanning(rosetta.core.scoring.MembraneEmbed) -> bool   Return Ref Spanning Parameter   2. spanning(rosetta.core.scoring.MembraneEmbed) -> bool   Return Non_Ref Spanning Parameter Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class MembranePotential(EnvPairPotential)     Rosetta Membrane Low Resolution Scoring Methods     Compute scoring terms part of the Membrane Low resolution energy function. Developed    by Vladmir Yarov-Yaravoy et al. 2006. Includes Menv, MPair, MCBeta, and membrane    alpha helical specific penalties. Framework tied.     Method resolution order: MembranePotential EnvPairPotential builtins.object Methods defined here: Membed_init(...) from builtins.PyCapsule Membed_init(rosetta.core.scoring.MembranePotential) -> bool   Initialize Membrane Embedding Menv_penalties(...) from builtins.PyCapsule Menv_penalties(rosetta.core.scoring.MembranePotential) -> bool   User Specified use penalties __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.scoring.MembranePotential) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. compute_membrane_embedding(...) from builtins.PyCapsule compute_membrane_embedding(self : rosetta.core.scoring.MembranePotential, pose : rosetta.core.pose.Pose) -> NoneType   Compute Membrane Embedding from pose and add Membed to Pose Cache evaluate_cbeta(...) from builtins.PyCapsule evaluate_cbeta(self : rosetta.core.scoring.MembranePotential, pose : rosetta.core.pose.Pose, rsd : rosetta.core.conformation.Residue, membrane_cb_score : float) -> NoneType   Evaluate CBeta Score (no idea...?) evaluate_env(...) from builtins.PyCapsule evaluate_env(*args, **kwargs) Overloaded function.   1. evaluate_env(self : rosetta.core.scoring.MembranePotential, pose : rosetta.core.pose.Pose, rsd : rosetta.core.conformation.Residue, MembraneDepth : float, membrane_env_score : float) -> NoneType   Evalaute Membrane Environment   2. evaluate_env(self : rosetta.core.scoring.MembranePotential, pose : rosetta.core.pose.Pose, rsd : rosetta.core.conformation.Residue, membrane_env_score : float) -> NoneType evaluate_pair(...) from builtins.PyCapsule evaluate_pair(self : rosetta.core.scoring.MembranePotential, pose : rosetta.core.pose.Pose, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, cendist : float, membrane_pair_score : float) -> NoneType   Evaluate Energy For Two Residues finalize(...) from builtins.PyCapsule finalize(self : rosetta.core.scoring.MembranePotential, pose : rosetta.core.pose.Pose) -> NoneType   Finalize Setup of MP Potential Class init_membrane_center_normal(...) from builtins.PyCapsule init_membrane_center_normal(self : rosetta.core.scoring.MembranePotential, pose : rosetta.core.pose.Pose, normal : rosetta.numeric.xyzVector_double_t, center : rosetta.numeric.xyzVector_double_t) -> NoneType   Initialize Membrane Center/Normal non_helix_in_membrane_penalty(...) from builtins.PyCapsule non_helix_in_membrane_penalty(*args, **kwargs) Overloaded function.   1. non_helix_in_membrane_penalty(self : rosetta.core.scoring.MembranePotential, pose : rosetta.core.pose.Pose, non_helix_in_membrane_penalty : float) -> NoneType   Compute penaly for alpha helices that are not tm spanning   2. non_helix_in_membrane_penalty(self : rosetta.core.scoring.MembranePotential, pose : rosetta.core.pose.Pose, normal : rosetta.numeric.xyzVector_double_t, center : rosetta.numeric.xyzVector_double_t, non_helix_in_membrane_penalty : float) -> NoneType termini_penalty(...) from builtins.PyCapsule termini_penalty(*args, **kwargs) Overloaded function.   1. termini_penalty(self : rosetta.core.scoring.MembranePotential, pose : rosetta.core.pose.Pose, termini_penalty : float) -> NoneType   Compute penalty for ???   2. termini_penalty(self : rosetta.core.scoring.MembranePotential, pose : rosetta.core.pose.Pose, normal : rosetta.numeric.xyzVector_double_t, center : rosetta.numeric.xyzVector_double_t, termin_penalty : float) -> NoneType tm_projection_penalty(...) from builtins.PyCapsule tm_projection_penalty(*args, **kwargs) Overloaded function.   1. tm_projection_penalty(self : rosetta.core.scoring.MembranePotential, pose : rosetta.core.pose.Pose, tm_proj : float) -> NoneType   Compute Transmembrane Spanning Projection Penalty (documentation for what this is - se MP potential from refactor)   2. tm_projection_penalty(self : rosetta.core.scoring.MembranePotential, pose : rosetta.core.pose.Pose, normal : rosetta.numeric.xyzVector_double_t, center : rosetta.numeric.xyzVector_double_t, tm_proj : float) -> NoneType Methods inherited from EnvPairPotential: cenlist_from_pose(...) from builtins.PyCapsule cenlist_from_pose( : rosetta.core.pose.Pose) -> rosetta.core.scoring.CenListInfo compute_centroid_environment(...) from builtins.PyCapsule compute_centroid_environment(self : rosetta.core.scoring.EnvPairPotential, pose : rosetta.core.pose.Pose) -> NoneType evaluate_env_and_cbeta_scores(...) from builtins.PyCapsule evaluate_env_and_cbeta_scores(self : rosetta.core.scoring.EnvPairPotential, pose : rosetta.core.pose.Pose, rsd : rosetta.core.conformation.Residue, env_score : float, cb_score6 : float, cb_score12 : float) -> NoneType evaluate_pair_and_cenpack_score(...) from builtins.PyCapsule evaluate_pair_and_cenpack_score(self : rosetta.core.scoring.EnvPairPotential, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, cendist : float, pair_contribution : float, cenpack_contribution : float) -> NoneType nonconst_cenlist_from_pose(...) from builtins.PyCapsule nonconst_cenlist_from_pose( : rosetta.core.pose.Pose) -> rosetta.core.scoring.CenListInfo   class MembraneTopology(rosetta.basic.datacache.CacheableData)       Method resolution order: MembraneTopology rosetta.basic.datacache.CacheableData builtins.object Methods defined here: LipidBurial(...) from builtins.PyCapsule LipidBurial(self : rosetta.core.scoring.MembraneTopology, n : int) -> float LipidExposure(...) from builtins.PyCapsule LipidExposure(self : rosetta.core.scoring.MembraneTopology, n : int) -> float LipoDefined(...) from builtins.PyCapsule LipoDefined(rosetta.core.scoring.MembraneTopology) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.scoring.MembraneTopology) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. allow_scoring(...) from builtins.PyCapsule allow_scoring(self : rosetta.core.scoring.MembraneTopology, seqpos : int) -> bool allow_tmh_scoring(...) from builtins.PyCapsule allow_tmh_scoring(self : rosetta.core.scoring.MembraneTopology, tmh : int) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.MembraneTopology,  : rosetta.core.scoring.MembraneTopology) -> rosetta.core.scoring.MembraneTopology clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.MembraneTopology) -> rosetta.basic.datacache.CacheableData depth(...) from builtins.PyCapsule depth(*args, **kwargs) Overloaded function.   1. depth(self : rosetta.core.scoring.MembraneTopology, seqpos : int) -> float   2. depth(rosetta.core.scoring.MembraneTopology) -> rosetta.utility.vector1_double get_subset(...) from builtins.PyCapsule get_subset(self : rosetta.core.scoring.MembraneTopology, TMH_list : rosetta.utility.vector1_unsigned_long, src : rosetta.core.scoring.MembraneTopology) -> NoneType helix_id(...) from builtins.PyCapsule helix_id(self : rosetta.core.scoring.MembraneTopology, n : int) -> int initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.scoring.MembraneTopology, spanfile : str) -> NoneType initialized(...) from builtins.PyCapsule initialized(*args, **kwargs) Overloaded function.   1. initialized(rosetta.core.scoring.MembraneTopology) -> bool   2. initialized(rosetta.core.scoring.MembraneTopology) -> bool print(...) from builtins.PyCapsule print(rosetta.core.scoring.MembraneTopology) -> NoneType read_in_spanfile(...) from builtins.PyCapsule read_in_spanfile(rosetta.core.scoring.MembraneTopology) -> str reset_allowed_scoring(...) from builtins.PyCapsule reset_allowed_scoring(rosetta.core.scoring.MembraneTopology) -> NoneType reset_tmh_insert(...) from builtins.PyCapsule reset_tmh_insert(rosetta.core.scoring.MembraneTopology) -> NoneType set_allow_scoring(...) from builtins.PyCapsule set_allow_scoring(self : rosetta.core.scoring.MembraneTopology, pos : int, setting : bool) -> NoneType set_allow_tmh_scoring(...) from builtins.PyCapsule set_allow_tmh_scoring(self : rosetta.core.scoring.MembraneTopology, tmh : int, setting : bool) -> NoneType set_tmh_inserted(...) from builtins.PyCapsule set_tmh_inserted(self : rosetta.core.scoring.MembraneTopology, tmh_inserted : int) -> NoneType shift_span(...) from builtins.PyCapsule shift_span(self : rosetta.core.scoring.MembraneTopology, shift : int) -> NoneType span_begin(...) from builtins.PyCapsule span_begin(self : rosetta.core.scoring.MembraneTopology, n : int) -> int span_end(...) from builtins.PyCapsule span_end(self : rosetta.core.scoring.MembraneTopology, n : int) -> int tmh_inserted(...) from builtins.PyCapsule tmh_inserted(rosetta.core.scoring.MembraneTopology) -> int tmhelix(...) from builtins.PyCapsule tmhelix(rosetta.core.scoring.MembraneTopology) -> int tmregion(...) from builtins.PyCapsule tmregion(self : rosetta.core.scoring.MembraneTopology, pos : int) -> bool Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class Membrane_FAEmbed(rosetta.basic.datacache.CacheableData)     Membrane Fullatom embedding info     Cacheable Data - Stores Full atom embedding information including    projection from z axis, fa depth, center, penalty, membrane thicnkess    steepness and normal     Method resolution order: Membrane_FAEmbed rosetta.basic.datacache.CacheableData builtins.object Methods defined here: Fa_Membed_update(...) from builtins.PyCapsule Fa_Membed_update(*args, **kwargs) Overloaded function.   1. Fa_Membed_update(rosetta.core.scoring.Membrane_FAEmbed) -> bool   2. Fa_Membed_update(rosetta.core.scoring.Membrane_FAEmbed) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.scoring.Membrane_FAEmbed) -> 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.scoring.Membrane_FAEmbed,  : rosetta.core.scoring.Membrane_FAEmbed) -> rosetta.core.scoring.Membrane_FAEmbed calculated(...) from builtins.PyCapsule calculated(*args, **kwargs) Overloaded function.   1. calculated(rosetta.core.scoring.Membrane_FAEmbed) -> bool   2. calculated(rosetta.core.scoring.Membrane_FAEmbed) -> bool clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.Membrane_FAEmbed) -> rosetta.basic.datacache.CacheableData   Cacheable Data base Mehtod - Clone Object fa_center(...) from builtins.PyCapsule fa_center(*args, **kwargs) Overloaded function.   1. fa_center(rosetta.core.scoring.Membrane_FAEmbed) -> float   Compute Fullatom Center   2. fa_center(rosetta.core.scoring.Membrane_FAEmbed) -> float fa_depth(...) from builtins.PyCapsule fa_depth(*args, **kwargs) Overloaded function.   1. fa_depth(self : rosetta.core.scoring.Membrane_FAEmbed, seqpos : int, atom : int) -> float   Compute Depth of Position in Membrane   2. fa_depth(self : rosetta.core.scoring.Membrane_FAEmbed, seqpos : int, atom : int) -> float fa_penalty(...) from builtins.PyCapsule fa_penalty(*args, **kwargs) Overloaded function.   1. fa_penalty(rosetta.core.scoring.Membrane_FAEmbed) -> float   2. fa_penalty(rosetta.core.scoring.Membrane_FAEmbed) -> float fa_proj(...) from builtins.PyCapsule fa_proj(*args, **kwargs) Overloaded function.   1. fa_proj(self : rosetta.core.scoring.Membrane_FAEmbed, seqpos : int, atom : int) -> float   Compute FA Proj to Z Axis   2. fa_proj(self : rosetta.core.scoring.Membrane_FAEmbed, seqpos : int, atom : int) -> float fa_proj_coord(...) from builtins.PyCapsule fa_proj_coord(*args, **kwargs) Overloaded function.   1. fa_proj_coord(self : rosetta.core.scoring.Membrane_FAEmbed, seqpos : int, atom : int) -> rosetta.numeric.xyzVector_double_t   Get Coordinates (I think it is storing these)   2. fa_proj_coord(self : rosetta.core.scoring.Membrane_FAEmbed, seqpos : int, atom : int) -> rosetta.numeric.xyzVector_double_t fa_proj_deriv(...) from builtins.PyCapsule fa_proj_deriv(*args, **kwargs) Overloaded function.   1. fa_proj_deriv(self : rosetta.core.scoring.Membrane_FAEmbed, seqpos : int, atom : int) -> float   Compute Derivative of Fa Proj.   2. fa_proj_deriv(self : rosetta.core.scoring.Membrane_FAEmbed, seqpos : int, atom : int) -> float initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.scoring.Membrane_FAEmbed, pose : rosetta.core.pose.Pose) -> NoneType steepness(...) from builtins.PyCapsule steepness(*args, **kwargs) Overloaded function.   1. steepness(rosetta.core.scoring.Membrane_FAEmbed) -> float   2. steepness(rosetta.core.scoring.Membrane_FAEmbed) -> float thickness(...) from builtins.PyCapsule thickness(*args, **kwargs) Overloaded function.   1. thickness(rosetta.core.scoring.Membrane_FAEmbed) -> float   2. thickness(rosetta.core.scoring.Membrane_FAEmbed) -> float Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class Membrane_FAPotential(EnvPairPotential)     Mmebrane Fullatom Potential - Scoring Class     Helper methods for computing fullatom energy terms    in the membrane scoring function     Method resolution order: Membrane_FAPotential EnvPairPotential builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.scoring.Membrane_FAPotential) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. compute_fa_projection(...) from builtins.PyCapsule compute_fa_projection(self : rosetta.core.scoring.Membrane_FAPotential, pose : rosetta.core.pose.Pose) -> NoneType finalize(...) from builtins.PyCapsule finalize(self : rosetta.core.scoring.Membrane_FAPotential, pose : rosetta.core.pose.Pose) -> NoneType   Base Class Method - Finalize Scoring Setup Methods inherited from EnvPairPotential: cenlist_from_pose(...) from builtins.PyCapsule cenlist_from_pose( : rosetta.core.pose.Pose) -> rosetta.core.scoring.CenListInfo compute_centroid_environment(...) from builtins.PyCapsule compute_centroid_environment(self : rosetta.core.scoring.EnvPairPotential, pose : rosetta.core.pose.Pose) -> NoneType evaluate_env_and_cbeta_scores(...) from builtins.PyCapsule evaluate_env_and_cbeta_scores(self : rosetta.core.scoring.EnvPairPotential, pose : rosetta.core.pose.Pose, rsd : rosetta.core.conformation.Residue, env_score : float, cb_score6 : float, cb_score12 : float) -> NoneType evaluate_pair_and_cenpack_score(...) from builtins.PyCapsule evaluate_pair_and_cenpack_score(self : rosetta.core.scoring.EnvPairPotential, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, cendist : float, pair_contribution : float, cenpack_contribution : float) -> NoneType nonconst_cenlist_from_pose(...) from builtins.PyCapsule nonconst_cenlist_from_pose( : rosetta.core.pose.Pose) -> rosetta.core.scoring.CenListInfo   class MinScoreScoreFunction(ScoreFunction)       Method resolution order: MinScoreScoreFunction ScoreFunction builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.core.scoring.MinScoreScoreFunction, pose : rosetta.core.pose.Pose) -> float   ////////////////////////////////////////////////////////////////////////// __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, src : rosetta.core.scoring.ScoreFunction,  : float) -> NoneType   3. __init__(self : handle,  : float) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(*args, **kwargs) Overloaded function.   1. assign(self : rosetta.core.scoring.MinScoreScoreFunction, src : rosetta.core.scoring.ScoreFunction) -> NoneType   INTERNAL USE ONLY   2. assign(self : rosetta.core.scoring.MinScoreScoreFunction, src : rosetta.core.scoring.MinScoreScoreFunction) -> NoneType   INTERNAL USE ONLY clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.MinScoreScoreFunction) -> rosetta.core.scoring.ScoreFunction Methods inherited from ScoreFunction: __getitem__(...) from builtins.PyCapsule __getitem__(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType) -> float   Returns the weight of the ScoreType  <t>    example(s):      scorefxn[fa_sol]  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.set_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name __str__(...) from builtins.PyCapsule __str__(rosetta.core.scoring.ScoreFunction) -> str add_extra_method(...) from builtins.PyCapsule add_extra_method(*args, **kwargs) Overloaded function.   1. add_extra_method(self : rosetta.core.scoring.ScoreFunction, new_type : rosetta.core.scoring.ScoreType, new_weight : float, new_method : core::scoring::methods::EnergyMethod) -> NoneType   Adds a scoring method that is not necessarily included in  the core library   2. add_extra_method(self : rosetta.core.scoring.ScoreFunction, new_weights : rosetta.std.map_core_scoring_ScoreType_double, new_method : core::scoring::methods::EnergyMethod) -> NoneType   Adds a scoring method that is not necessarily included in  the core library add_weights_from_file(...) from builtins.PyCapsule add_weights_from_file(self : rosetta.core.scoring.ScoreFunction, filename : str) -> NoneType   Initializes this ScoreFunction from the given  <filename> all_energies_begin(...) from builtins.PyCapsule all_energies_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::EnergyMethod const> const*, std::vector<std::shared_ptr<core::scoring::methods::EnergyMethod const>, std::allocator<std::shared_ptr<core::scoring::methods::EnergyMethod const> > > > all_energies_end(...) from builtins.PyCapsule all_energies_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::EnergyMethod const> const*, std::vector<std::shared_ptr<core::scoring::methods::EnergyMethod const>, std::allocator<std::shared_ptr<core::scoring::methods::EnergyMethod const> > > > all_methods(...) from builtins.PyCapsule all_methods(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t any_lr_residue_pair_energy(...) from builtins.PyCapsule any_lr_residue_pair_energy(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, res1 : int, res2 : int) -> bool apply_patch_from_file(...) from builtins.PyCapsule apply_patch_from_file(self : rosetta.core.scoring.ScoreFunction, filename : str) -> NoneType   Applies a patch from the given  <filename> are_they_neighbors(...) from builtins.PyCapsule are_they_neighbors(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, pos1 : int, pos2 : int) -> bool   Returns true if the  <pose>  positions  <pos1>  and  <pos2>  are neighbors bump_check_backbone(...) from builtins.PyCapsule bump_check_backbone(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Scores the sidechain from  <pose>  Residue  <rsd1>  against the  backbone of Residue  <rsd2> bump_check_full(...) from builtins.PyCapsule bump_check_full(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType cd_1b_types(...) from builtins.PyCapsule cd_1b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType   convenience access to all cd 1b score types cd_2b_begin(...) from builtins.PyCapsule cd_2b_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy> > > > cd_2b_end(...) from builtins.PyCapsule cd_2b_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy> > > > cd_2b_intrares_begin(...) from builtins.PyCapsule cd_2b_intrares_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> > > > cd_2b_intrares_end(...) from builtins.PyCapsule cd_2b_intrares_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> > > > cd_2b_types(...) from builtins.PyCapsule cd_2b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType   convenience access to all cd 2b score types cd_lr_2b_methods_begin(...) from builtins.PyCapsule cd_lr_2b_methods_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy> > > > cd_lr_2b_methods_end(...) from builtins.PyCapsule cd_lr_2b_methods_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy> > > > cd_lr_2b_types(...) from builtins.PyCapsule cd_lr_2b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType check_methods_in_right_order(...) from builtins.PyCapsule check_methods_in_right_order(self : rosetta.core.scoring.ScoreFunction, score_type_in_first_method : rosetta.core.scoring.ScoreType, score_type_in_second_method : rosetta.core.scoring.ScoreType) -> bool   check order of methods ci_1b_types(...) from builtins.PyCapsule ci_1b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType   convenience access to all ci 1b score types ci_2b_begin(...) from builtins.PyCapsule ci_2b_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy> > > > ci_2b_end(...) from builtins.PyCapsule ci_2b_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy> > > > ci_2b_intrares_begin(...) from builtins.PyCapsule ci_2b_intrares_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> > > > ci_2b_intrares_end(...) from builtins.PyCapsule ci_2b_intrares_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> > > > ci_2b_types(...) from builtins.PyCapsule ci_2b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType   convenience access to all ci 2b score types ci_lr_2b_methods_begin(...) from builtins.PyCapsule ci_lr_2b_methods_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy> > > > ci_lr_2b_methods_end(...) from builtins.PyCapsule ci_lr_2b_methods_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy> > > > ci_lr_2b_types(...) from builtins.PyCapsule ci_lr_2b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType clone_as_base_class(...) from builtins.PyCapsule clone_as_base_class(rosetta.core.scoring.ScoreFunction) -> rosetta.core.scoring.ScoreFunction   If you *want* to discard subclass information, the following function is availible energy_method_options(...) from builtins.PyCapsule energy_method_options(rosetta.core.scoring.ScoreFunction) -> core::scoring::methods::EnergyMethodOptions   Returns the EnergyMethodOptions object contained in this  ScoreFunction (const access) eval_cd_1b(...) from builtins.PyCapsule eval_cd_1b(self : rosetta.core.scoring.ScoreFunction, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted one body energies of all context  dependent one body energies for  <pose>  Residue  <rsd>  into  EnergyMap  <emap>     : EnergyMap is an EMapVector eval_cd_2b(...) from builtins.PyCapsule eval_cd_2b(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulate the unweighted short range context dependent two body  interaction energies of  <pose>  between Residue  <rsd1>  and Residue  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_cd_2b_bb_bb(...) from builtins.PyCapsule eval_cd_2b_bb_bb(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted short ranged context dependent two body  interaction energies of  <pose>  between the backbones of Residue  <rsd1>  and  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_cd_2b_bb_sc(...) from builtins.PyCapsule eval_cd_2b_bb_sc(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted short ranged context dependent two body  interaction energies of  <pose>  between the backbone of Residue  <rsd1>  and the sidechain of Residue  <rsd2>  into EnergyMap <emap>     : EnergyMap is an EMapVector eval_cd_2b_sc_sc(...) from builtins.PyCapsule eval_cd_2b_sc_sc(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted short ranged context dependent two body  interaction energies of  <pose>  between the sidechains of Residue  <rsd1>  and Residue  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_cd_intrares_energy(...) from builtins.PyCapsule eval_cd_intrares_energy(self : rosetta.core.scoring.ScoreFunction, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted intra-residue one body energies for all  context dependent two body terms that define intra-residue energies of  <pose>  Residue  <rsd>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_ci_1b(...) from builtins.PyCapsule eval_ci_1b(self : rosetta.core.scoring.ScoreFunction, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType eval_ci_2b(...) from builtins.PyCapsule eval_ci_2b(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted context independent two body  interaction energies of  <pose>  between Residue  <rsd1>  and Residue  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_ci_2b_bb_bb(...) from builtins.PyCapsule eval_ci_2b_bb_bb(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted context independent two body  interaction energies of  <pose>  between the backbones of Residue  <rsd1>  and Residue  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_ci_2b_bb_sc(...) from builtins.PyCapsule eval_ci_2b_bb_sc(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted short range context independent two  body interaction energies of  <pose>  between the backbone of Residue  <rsd1>  and the sidechain of Residue  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_ci_2b_sc_sc(...) from builtins.PyCapsule eval_ci_2b_sc_sc(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted short range context dependent two body  interaction energies of  <pose>  between the sidechains of Residue  <rsd1>  and Residue  <rsd2>  into Energymap  <emap>     : EnergyMap is an EMapVector eval_ci_intrares_energy(...) from builtins.PyCapsule eval_ci_intrares_energy(self : rosetta.core.scoring.ScoreFunction, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted intra-residue one body energies for all  context independent two body terms that define intra-residue energies of  <pose>  Residue  <rsd>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_dof_derivative(...) from builtins.PyCapsule eval_dof_derivative(self : rosetta.core.scoring.ScoreFunction, dof_id : rosetta.core.id.DOF_ID, torsion_id : core::id::TorsionID, pose : rosetta.core.pose.Pose) -> float eval_intrares_energy(...) from builtins.PyCapsule eval_intrares_energy(self : rosetta.core.scoring.ScoreFunction, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates for rsd the unweighted intra-residue one body energies  for all context dependent and context independent two body terms that  define intra-residue energies     : EnergyMap is an EMapVector eval_long_range_twobody_energies(...) from builtins.PyCapsule eval_long_range_twobody_energies(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType eval_npd_atom_derivative(...) from builtins.PyCapsule eval_npd_atom_derivative(self : rosetta.core.scoring.ScoreFunction, atom_id : rosetta.core.id.AtomID, pose : rosetta.core.pose.Pose, domain_map : ObjexxFCL::FArray1D<int>, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t) -> NoneType eval_onebody_energies(...) from builtins.PyCapsule eval_onebody_energies(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType eval_twobody_neighbor_energies(...) from builtins.PyCapsule eval_twobody_neighbor_energies(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType evaluate_rotamer_background_energies(...) from builtins.PyCapsule evaluate_rotamer_background_energies(self : rosetta.core.scoring.ScoreFunction, set1 : rosetta.core.conformation.RotamerSetBase, residue2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, energy_vector : rosetta.utility.vector1_float) -> NoneType evaluate_rotamer_intrares_energies(...) from builtins.PyCapsule evaluate_rotamer_intrares_energies(self : rosetta.core.scoring.ScoreFunction, set : rosetta.core.conformation.RotamerSetBase, pose : rosetta.core.pose.Pose, energies : rosetta.utility.vector1_float) -> NoneType evaluate_rotamer_intrares_energy_maps(...) from builtins.PyCapsule evaluate_rotamer_intrares_energy_maps(self : rosetta.core.scoring.ScoreFunction, set : rosetta.core.conformation.RotamerSetBase, pose : rosetta.core.pose.Pose, emaps : rosetta.utility.vector1_core_scoring_EMapVector) -> NoneType evaluate_rotamer_pair_energies(...) from builtins.PyCapsule evaluate_rotamer_pair_energies(self : rosetta.core.scoring.ScoreFunction, set1 : rosetta.core.conformation.RotamerSetBase, set2 : rosetta.core.conformation.RotamerSetBase, pose : rosetta.core.pose.Pose, energy_table : ObjexxFCL::FArray2D<float>) -> NoneType finalize_after_derivatives(...) from builtins.PyCapsule finalize_after_derivatives(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType get_name(...) from builtins.PyCapsule get_name(rosetta.core.scoring.ScoreFunction) -> str get_nonzero_weighted_scoretypes(...) from builtins.PyCapsule get_nonzero_weighted_scoretypes(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType   Returns a list of the ScoreTypes which are non-zero with  their current weights    example(s):      scorefxn.get_nonzero_weighted_scoretypes()  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.set_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.scoring.ScoreFunction) -> rosetta.core.scoring.ScoreFunction   self pointers   2. get_self_ptr(rosetta.core.scoring.ScoreFunction) -> rosetta.core.scoring.ScoreFunction get_sub_score(...) from builtins.PyCapsule get_sub_score(*args, **kwargs) Overloaded function.   1. get_sub_score(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, residue_mask : rosetta.utility.vector1_bool) -> float   Compute the score for subset of residues   2. get_sub_score(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, residue_mask : rosetta.utility.vector1_bool, emap : rosetta.core.scoring.EMapVector) -> NoneType   Compute the score for subset of residues   3. get_sub_score(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, residue_mask : rosetta.utility.vector1_bool) -> float   Compute the score for subset of residues   4. get_sub_score(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, residue_mask : rosetta.utility.vector1_bool, emap : rosetta.core.scoring.EMapVector) -> NoneType   Compute the score for subset of residues get_sub_score_exclude_res(...) from builtins.PyCapsule get_sub_score_exclude_res(*args, **kwargs) Overloaded function.   1. get_sub_score_exclude_res(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, exclude_list : rosetta.utility.vector1_unsigned_long) -> float   Compute the score for subset of residues   2. get_sub_score_exclude_res(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, exclude_list : rosetta.utility.vector1_unsigned_long, emap : rosetta.core.scoring.EMapVector) -> NoneType   Compute the score for subset of residues   3. get_sub_score_exclude_res(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, exclude_list : rosetta.utility.vector1_unsigned_long) -> float   Compute the score for subset of residues   4. get_sub_score_exclude_res(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, exclude_list : rosetta.utility.vector1_unsigned_long, emap : rosetta.core.scoring.EMapVector) -> NoneType   Compute the score for subset of residues get_weight(...) from builtins.PyCapsule get_weight(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType) -> float   Returns the weight for ScoreType  <t>    examples(s):      scorefxn.get_weight(fa_sol)  See also:      ScoreFunction      ScoreFunction.set_weight      ScoreType      create_score_function      name_from_score_type      score_type_from_name has_nonzero_weight(...) from builtins.PyCapsule has_nonzero_weight(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType) -> bool   Returns true if the ScoreType  <t>  has a non-zero weight    example(s):      scorefxn.has_nonzero_weight(fa_sol)  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.has_zero_weight      ScoreFunction.set_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name has_zero_weight(...) from builtins.PyCapsule has_zero_weight(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType) -> bool   Returns true if the ScoreType  <t>  has a weight of zero,    example(s):      scorefxn.has_zero_weight(fa_sol)  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.has_nonzero_weight      ScoreFunction.set_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name indicate_required_context_graphs(...) from builtins.PyCapsule indicate_required_context_graphs(self : rosetta.core.scoring.ScoreFunction, context_graphs_required : rosetta.utility.vector1_bool) -> NoneType   find which context graphs the energy methods require info(...) from builtins.PyCapsule info(rosetta.core.scoring.ScoreFunction) -> core::scoring::ScoreFunctionInfo   return an object to describe abstractly the methods contained in this  ScoreFunction so that class Energies can ensure that the ScoreFunction is  properly evaluated (ie, no obsolete cashed data is used ) initialize_from_file(...) from builtins.PyCapsule initialize_from_file(self : rosetta.core.scoring.ScoreFunction, filename : str) -> NoneType   Resets everything before reading the  <filename> long_range_energies_begin(...) from builtins.PyCapsule long_range_energies_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const> > > > long_range_energies_end(...) from builtins.PyCapsule long_range_energies_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const> > > > max_atomic_interaction_cutoff(...) from builtins.PyCapsule max_atomic_interaction_cutoff(rosetta.core.scoring.ScoreFunction) -> float   Returns the largest atomic interaction cutoff required by the  EnergyMethods merge(...) from builtins.PyCapsule merge(self : rosetta.core.scoring.ScoreFunction, scorefxn_to_be_merged : rosetta.core.scoring.ScoreFunction) -> NoneType   Merges in the weights of another score function    example(s):      scorefxn.merge(scorefxn2)  See also:      ScoreFunction      ScoreFunction.weights      Energies      create_score_function name(...) from builtins.PyCapsule name(self : rosetta.core.scoring.ScoreFunction, weights_tag : str) -> NoneType   Accumulates the unweighted one body energies of all context  independent one body energies for  <pose>  Residue  <rsd>  into  EnergyMap  <emap>     : EnergyMap is an EMapVector perturb_weights(...) from builtins.PyCapsule perturb_weights(rosetta.core.scoring.ScoreFunction) -> NoneType   Randomly perturbs non-zero score function weights prepare_rotamers_for_packing(...) from builtins.PyCapsule prepare_rotamers_for_packing(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, set : rosetta.core.conformation.RotamerSetBase) -> NoneType   Lets the scoring functions cache anything they need to rapidly  calculate rotamer pair energies used in packing (like a trie, e.g.) ready_for_nonideal_scoring(...) from builtins.PyCapsule ready_for_nonideal_scoring(rosetta.core.scoring.ScoreFunction) -> bool reinitialize_minnode_for_residue(...) from builtins.PyCapsule reinitialize_minnode_for_residue(self : rosetta.core.scoring.ScoreFunction, min_node : core::scoring::MinimizationNode, rsd : rosetta.core.conformation.Residue, min_map : core::kinematics::MinimizerMapBase, pose : rosetta.core.pose.Pose) -> NoneType reset(...) from builtins.PyCapsule reset(rosetta.core.scoring.ScoreFunction) -> NoneType   Resets the ScoreFunction to default values reset_energy_methods(...) from builtins.PyCapsule reset_energy_methods(rosetta.core.scoring.ScoreFunction) -> NoneType score(...) from builtins.PyCapsule score(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> float   Scores the given  <pose>  using this ScoreFunction. Alters the  Energies object within  <pose>, but does not alter this ScoreFunction     : Synonym for () operator. Makes code look a little nicer. Doesn't  do anything but call () operator. score_by_scoretype(...) from builtins.PyCapsule score_by_scoretype(*args, **kwargs) Overloaded function.   1. score_by_scoretype(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, t : rosetta.core.scoring.ScoreType) -> float   Returns the score of the ScoreType  <t>   2. score_by_scoretype(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, t : rosetta.core.scoring.ScoreType, weighted : bool) -> float   Returns the score of the ScoreType  <t> score_types_by_method_type(...) from builtins.PyCapsule score_types_by_method_type(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.methods.EnergyMethodType) -> rosetta.utility.vector1_core_scoring_ScoreType serialize_weights(...) from builtins.PyCapsule serialize_weights(rosetta.core.scoring.ScoreFunction) -> str   Serializes the non-zero score function term weights  Format: { term : weight, ... } set_energy_method_options(...) from builtins.PyCapsule set_energy_method_options(self : rosetta.core.scoring.ScoreFunction, energy_method_options_in : core::scoring::methods::EnergyMethodOptions) -> NoneType   Sets the EnergyMethodOptions object contained in this ScoreFunction.  with appropriate update of all the energy methods. set_etable(...) from builtins.PyCapsule set_etable(self : rosetta.core.scoring.ScoreFunction, etable_name : str) -> NoneType   Given a  <filename> (represented by a std::string), set the  e_table for this ScoreFunction. set_method_weights(...) from builtins.PyCapsule set_method_weights(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType, wts : rosetta.utility.vector1_double) -> NoneType set_weight(...) from builtins.PyCapsule set_weight(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType, setting : float) -> NoneType   Sets the weight for ScoreType  <t>  to  <setting>    example(s):      scorefxn.set_weight(fa_sol,.5)  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name set_weight_if_zero(...) from builtins.PyCapsule set_weight_if_zero(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType, setting : float) -> NoneType   Sets the weight for ScoreType  <t>  to  <setting> if weight is originally zero    example(s):      scorefxn.set_weight_if_zero(fa_sol,.5)  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.set_weight      ScoreType      create_score_function      name_from_score_type      score_type_from_name setup_for_derivatives(...) from builtins.PyCapsule setup_for_derivatives(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType setup_for_lr2benmeth_minimization_for_respair(...) from builtins.PyCapsule setup_for_lr2benmeth_minimization_for_respair(*args, **kwargs) Overloaded function.   1. setup_for_lr2benmeth_minimization_for_respair(self : rosetta.core.scoring.ScoreFunction, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, lr2benergy : core::scoring::methods::LongRangeTwoBodyEnergy, g : core::scoring::MinimizationGraph, min_map : core::kinematics::MinimizerMapBase, p : rosetta.core.pose.Pose, res_moving_wrt_eachother : bool, accumulate_fixed_energies : bool, rni : core::scoring::ResidueNeighborConstIterator, fixed_energies : rosetta.core.scoring.EMapVector) -> NoneType   Initialize an edge in the MinimizationGraph with a particular long-range two body   2. setup_for_lr2benmeth_minimization_for_respair(self : rosetta.core.scoring.ScoreFunction, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, lr2benergy : core::scoring::methods::LongRangeTwoBodyEnergy, g : core::scoring::MinimizationGraph, min_map : core::kinematics::MinimizerMapBase, p : rosetta.core.pose.Pose, res_moving_wrt_eachother : bool, accumulate_fixed_energies : bool, rni : core::scoring::ResidueNeighborConstIterator, fixed_energies : rosetta.core.scoring.EMapVector, edge_weight : float) -> NoneType   Initialize an edge in the MinimizationGraph with a particular long-range two body   3. setup_for_lr2benmeth_minimization_for_respair(self : rosetta.core.scoring.ScoreFunction, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, lr2benergy : core::scoring::methods::LongRangeTwoBodyEnergy, g : core::scoring::MinimizationGraph, min_map : core::kinematics::MinimizerMapBase, p : rosetta.core.pose.Pose, res_moving_wrt_eachother : bool, accumulate_fixed_energies : bool, rni : core::scoring::ResidueNeighborConstIterator, fixed_energies : rosetta.core.scoring.EMapVector, edge_weight : float, edge_dweight : float) -> NoneType   Initialize an edge in the MinimizationGraph with a particular long-range two body setup_for_minimizing(...) from builtins.PyCapsule setup_for_minimizing(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, min_map : core::kinematics::MinimizerMapBase) -> NoneType   Initializes a MinimizationGraph and caches it in  Energies object of  <pose>     : for use during minimization setup_for_minimizing_for_node(...) from builtins.PyCapsule setup_for_minimizing_for_node(self : rosetta.core.scoring.ScoreFunction, min_node : core::scoring::MinimizationNode, rsd : rosetta.core.conformation.Residue, min_map : core::kinematics::MinimizerMapBase, pose : rosetta.core.pose.Pose, accumulate_fixed_energies : bool, fixed_energies : rosetta.core.scoring.EMapVector) -> NoneType   Initialize a single node of a MinimizationGraph with the one-body and two-body  energy methods that are held within this ScoreFunction object. setup_for_minimizing_sr2b_enmeths_for_minedge(...) from builtins.PyCapsule setup_for_minimizing_sr2b_enmeths_for_minedge(*args, **kwargs) Overloaded function.   1. setup_for_minimizing_sr2b_enmeths_for_minedge(self : rosetta.core.scoring.ScoreFunction, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, min_edge : core::scoring::MinimizationEdge, min_map : core::kinematics::MinimizerMapBase, pose : rosetta.core.pose.Pose, res_moving_wrt_eachother : bool, accumulate_fixed_energies : bool, energy_edge : core::scoring::EnergyEdge, fixed_energies : rosetta.core.scoring.EMapVector) -> NoneType   Initialize a single MinimizationEdge for a particular part of residues, storing  sr2b energy method pointers on the edge for those sr2b energy methods in this ScoreFunction   2. setup_for_minimizing_sr2b_enmeths_for_minedge(self : rosetta.core.scoring.ScoreFunction, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, min_edge : core::scoring::MinimizationEdge, min_map : core::kinematics::MinimizerMapBase, pose : rosetta.core.pose.Pose, res_moving_wrt_eachother : bool, accumulate_fixed_energies : bool, energy_edge : core::scoring::EnergyEdge, fixed_energies : rosetta.core.scoring.EMapVector, edge_weight : float) -> NoneType   Initialize a single MinimizationEdge for a particular part of residues, storing  sr2b energy method pointers on the edge for those sr2b energy methods in this ScoreFunction setup_for_packing(...) from builtins.PyCapsule setup_for_packing(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, residues_repacking : rosetta.utility.vector1_bool, residues_designing : rosetta.utility.vector1_bool) -> NoneType   Lets the scoring functions cache anything they need to calculate  energies in a packing step (rotamer_trials or pack_rotamers)     : the Etable caches tries for each of the residues, the  hydrogen bond function caches backbone/backbone hydrogen bonds setup_for_scoring(...) from builtins.PyCapsule setup_for_scoring(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType   For external scorers: Let the energy methods prepare for  evaluating their scores on a particular structure     : invoked during scoring. show(...) from builtins.PyCapsule show(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType   Scores  <pose>  and shows the raw and weighted scores for each  non-zero ScoreType     : this function is mostly for convenience in PyRosetta    example(s):      scorefxn.show(pose)  See also:      ScoreFunction      ScoreFunction.weights      Energies      create_score_function update_residue_for_packing(...) from builtins.PyCapsule update_residue_for_packing(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, resid : int) -> NoneType   If inside packing, the pose changes conformation, inform the  scoring functions that any data they have cached in the Energies object  is out of date. In particular, this is to update the trie(s) during  rotamer trials. weights(...) from builtins.PyCapsule weights(rosetta.core.scoring.ScoreFunction) -> rosetta.core.scoring.EMapVector   Returns an EnergyMap of the current set of weights    example(s):      scorefxn.weights()  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.set_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name whole_structure_types(...) from builtins.PyCapsule whole_structure_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType ws_methods_begin(...) from builtins.PyCapsule ws_methods_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::WholeStructureEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::WholeStructureEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::WholeStructureEnergy> > > > ws_methods_end(...) from builtins.PyCapsule ws_methods_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::WholeStructureEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::WholeStructureEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::WholeStructureEnergy> > > >   class MinimizationEdge(rosetta.core.graph.Edge)     Class MinimizationEdge holds ResPairMinimizationData for a certain pair of interacting residues; this data might be a neighborlist for this residue pair, for example.  The data held in this edge will be used in both scoring the residue-pair energies and evaluating atom derivatives during minimization.     Method resolution order: MinimizationEdge rosetta.core.graph.Edge builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, owner : core::scoring::MinimizationGraph, n1 : int, n2 : int) -> NoneType   2. __init__(self : handle, owner : core::scoring::MinimizationGraph, example_edge : rosetta.core.scoring.MinimizationEdge) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. active_2benmeths_begin(...) from builtins.PyCapsule active_2benmeths_begin(rosetta.core.scoring.MinimizationEdge) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > active_2benmeths_end(...) from builtins.PyCapsule active_2benmeths_end(rosetta.core.scoring.MinimizationEdge) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > active_2benmeths_ext_begin(...) from builtins.PyCapsule active_2benmeths_ext_begin(rosetta.core.scoring.MinimizationEdge) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > active_2benmeths_ext_end(...) from builtins.PyCapsule active_2benmeths_ext_end(rosetta.core.scoring.MinimizationEdge) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > active_2benmeths_std_begin(...) from builtins.PyCapsule active_2benmeths_std_begin(rosetta.core.scoring.MinimizationEdge) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > active_2benmeths_std_end(...) from builtins.PyCapsule active_2benmeths_std_end(rosetta.core.scoring.MinimizationEdge) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > add_twobody_enmeth(...) from builtins.PyCapsule add_twobody_enmeth(self : rosetta.core.scoring.MinimizationEdge, enmeth : core::scoring::methods::TwoBodyEnergy, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, residues_mwrt_eachother : bool) -> bool   Include a particular energy method as part of this edge.  It may not show up  in the active energy methods should this energy method not define an energy for the  residues. any_active_enmeths(...) from builtins.PyCapsule any_active_enmeths(rosetta.core.scoring.MinimizationEdge) -> bool   It may be possible to determine that an edge does not need to belong to the  minimization graph if there are no active two-body energy methods; this is a convenience  function that answers quickly if active_2benmths_.begin() == active_2benmeths_.end(). copy_from(...) from builtins.PyCapsule copy_from(self : rosetta.core.scoring.MinimizationEdge, source : rosetta.core.graph.Edge) -> NoneType   Copy the data held on the example edge, source.  The source edge must be castable to class MinimizationEdge. count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.scoring.MinimizationEdge) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.scoring.MinimizationEdge) -> int dweight(...) from builtins.PyCapsule dweight(*args, **kwargs) Overloaded function.   1. dweight(rosetta.core.scoring.MinimizationEdge) -> float   2. dweight(self : rosetta.core.scoring.MinimizationEdge, setting : float) -> NoneType reinitialize_active_energy_methods(...) from builtins.PyCapsule reinitialize_active_energy_methods(self : rosetta.core.scoring.MinimizationEdge, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, res_moving_wrt_eachother : bool) -> NoneType   Setup the active and inactive energy methods res_pair_min_data(...) from builtins.PyCapsule res_pair_min_data(*args, **kwargs) Overloaded function.   1. res_pair_min_data(rosetta.core.scoring.MinimizationEdge) -> rosetta.core.scoring.ResPairMinimizationData   2. res_pair_min_data(rosetta.core.scoring.MinimizationEdge) -> rosetta.core.scoring.ResPairMinimizationData setup_for_derivatives(...) from builtins.PyCapsule setup_for_derivatives(self : rosetta.core.scoring.MinimizationEdge, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType   Initialize the active energy methods for derivative evaluation setup_for_minimizing(...) from builtins.PyCapsule setup_for_minimizing(self : rosetta.core.scoring.MinimizationEdge, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, min_map : rosetta.core.kinematics.MinimizerMapBase) -> NoneType setup_for_scoring(...) from builtins.PyCapsule setup_for_scoring(self : rosetta.core.scoring.MinimizationEdge, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType   Initialize the active energy methods for score function evaluation sfd_req_2benmeths_begin(...) from builtins.PyCapsule sfd_req_2benmeths_begin(rosetta.core.scoring.MinimizationEdge) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > sfd_req_2benmeths_end(...) from builtins.PyCapsule sfd_req_2benmeths_end(rosetta.core.scoring.MinimizationEdge) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > sfs_req_2benmeths_begin(...) from builtins.PyCapsule sfs_req_2benmeths_begin(rosetta.core.scoring.MinimizationEdge) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > sfs_req_2benmeths_end(...) from builtins.PyCapsule sfs_req_2benmeths_end(rosetta.core.scoring.MinimizationEdge) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > weight(...) from builtins.PyCapsule weight(*args, **kwargs) Overloaded function.   1. weight(rosetta.core.scoring.MinimizationEdge) -> float   The minimization graph will allow the storage of edge weights, should that  prove useful for any application (e.g. symmetric minimization)   2. weight(self : rosetta.core.scoring.MinimizationEdge, setting : float) -> NoneType   Set the weight for an edge Methods inherited from rosetta.core.graph.Edge: get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.graph.Edge) -> int   returns the index of the lower node get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.graph.Edge, node_index : int) -> int   returns the index of the one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon. get_other_node(...) from builtins.PyCapsule get_other_node(*args, **kwargs) Overloaded function.   1. get_other_node(self : rosetta.core.graph.Edge, node_index : int) -> rosetta.core.graph.Node   returns a const pointer to one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon.   2. get_other_node(self : rosetta.core.graph.Edge, node_index : int) -> rosetta.core.graph.Node   returns a non-const pointer to one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon. get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.graph.Edge) -> int   returns the index of the upper node is_loop(...) from builtins.PyCapsule is_loop(rosetta.core.graph.Edge) -> bool   Is this edge a loop? In Pseudographs, loop edges are incident twice on a single vertex. same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.graph.Edge, node1 : int, node2 : int) -> bool   Is this the same edge as another edge (node1,node2)?  Note:  this graph does not work for multi-graphs.  Edges must be unique. set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.graph.Edge, edge_iterator : rosetta.core.graph.EdgeListIterator) -> NoneType   called only by class Graph, this function gives the Edge the data it needs  to later delete itself from its owner's edge list in constant time.   class MinimizationGraph(rosetta.core.graph.Graph)     Class to hold all the minimization-specific data that's required to efficiently evaluate the score function and its derivatives on a structure of fixed sequence and chemical identity.     Method resolution order: MinimizationGraph rosetta.core.graph.Graph builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : handle, num_nodes : int) -> NoneType   2. __init__(handle) -> NoneType   3. __init__(handle, rosetta.core.scoring.MinimizationGraph) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_whole_pose_context_enmeth(...) from builtins.PyCapsule add_whole_pose_context_enmeth(self : rosetta.core.scoring.MinimizationGraph, enmeth : rosetta.core.scoring.methods.EnergyMethod) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.MinimizationGraph, rhs : rosetta.core.scoring.MinimizationGraph) -> rosetta.core.scoring.MinimizationGraph delete_edge(...) from builtins.PyCapsule delete_edge(self : rosetta.core.scoring.MinimizationGraph, edge : rosetta.core.graph.Edge) -> NoneType find_minimization_edge(...) from builtins.PyCapsule find_minimization_edge(*args, **kwargs) Overloaded function.   1. find_minimization_edge(self : rosetta.core.scoring.MinimizationGraph, n1 : int, n2 : int) -> rosetta.core.scoring.MinimizationEdge   2. find_minimization_edge(self : rosetta.core.scoring.MinimizationGraph, n1 : int, n2 : int) -> rosetta.core.scoring.MinimizationEdge fixed_energies(...) from builtins.PyCapsule fixed_energies(rosetta.core.scoring.MinimizationGraph) -> rosetta.core.scoring.EMapVector get_minimization_node(...) from builtins.PyCapsule get_minimization_node(*args, **kwargs) Overloaded function.   1. get_minimization_node(self : rosetta.core.scoring.MinimizationGraph, index : int) -> rosetta.core.scoring.MinimizationNode   2. get_minimization_node(self : rosetta.core.scoring.MinimizationGraph, index : int) -> rosetta.core.scoring.MinimizationNode set_fixed_energies(...) from builtins.PyCapsule set_fixed_energies(self : rosetta.core.scoring.MinimizationGraph,  : rosetta.core.scoring.EMapVector) -> NoneType whole_pose_context_enmeths_begin(...) from builtins.PyCapsule whole_pose_context_enmeths_begin(rosetta.core.scoring.MinimizationGraph) -> std::_List_const_iterator<std::shared_ptr<core::scoring::methods::EnergyMethod const> > whole_pose_context_enmeths_end(...) from builtins.PyCapsule whole_pose_context_enmeths_end(rosetta.core.scoring.MinimizationGraph) -> std::_List_const_iterator<std::shared_ptr<core::scoring::methods::EnergyMethod const> > Methods inherited from rosetta.core.graph.Graph: add_edge(...) from builtins.PyCapsule add_edge(*args, **kwargs) Overloaded function.   1. add_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   add an edge between two vertices.  Invokes "create_edge" from the derived class.  Returns a pointer to the edge after its been added, allowing the calling function  to immediately set data for this edge.   2. add_edge(self : rosetta.core.graph.Graph, example_edge : rosetta.core.graph.Edge) -> rosetta.core.graph.Edge   add an edge to this graph copying the data from an edge in another graph.  Returns a pointer to the edge after its been added, allowing the calling function  to immediately set data for this edge. all_pairs_shortest_paths(...) from builtins.PyCapsule all_pairs_shortest_paths(rosetta.core.graph.Graph) -> ObjexxFCL::FArray2D<int>   O(V^3).  Computes all pairs shortest paths using Warshall's algorithm  and writes all the path distances to the two-dimensional table. const_edge_list_begin(...) from builtins.PyCapsule const_edge_list_begin(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex const_edge_list_end(...) from builtins.PyCapsule const_edge_list_end(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex copy_connectivity(...) from builtins.PyCapsule copy_connectivity(self : rosetta.core.graph.Graph, source : rosetta.core.graph.Graph) -> NoneType   copy the edge connectivity from a source graph with a potentially  unknown type. drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.graph.Graph) -> NoneType   delete all the edges present in the graph drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.graph.Graph, node : int) -> NoneType   delete all the edges for a single vertex in the graph edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   returns a pointer to the edge connecting nodes node1 and node2, if that edge exists  in the graph, o.w. returns 0.  Focuses the graph on this edge for fast subsequent retrieval.   2. find_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   returns a const pointer to the edge connecting nodes node1 and node2, if that edge exists  in the graph, o.w. returns 0.  Focuses the graph on this edge for fast subsequent retrieval. focused_edge(...) from builtins.PyCapsule focused_edge(*args, **kwargs) Overloaded function.   1. focused_edge(rosetta.core.graph.Graph) -> rosetta.core.graph.Edge   returns a pointer to the focused edge   2. focused_edge(rosetta.core.graph.Graph) -> rosetta.core.graph.Edge   returns a const-pointer to the focused edge getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.graph.Graph) -> int   returns a count of all the memory used by every vertex and edge in a graph  by invoking the polymorphic count_static_memory and count_dynamic_memory of each  (possibly derived) node and edge object as well as for the (possibly derived) graph  class. get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> bool   is an edge already present in the graph? O(V) worst case.  O(1) iff all vertices have O(1) edges get_node(...) from builtins.PyCapsule get_node(*args, **kwargs) Overloaded function.   1. get_node(self : rosetta.core.graph.Graph, index : int) -> rosetta.core.graph.Node   2. get_node(self : rosetta.core.graph.Graph, index : int) -> rosetta.core.graph.Node get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.graph.Graph) -> rosetta.core.graph.Graph   self pointers   2. get_self_ptr(rosetta.core.graph.Graph) -> rosetta.core.graph.Graph num_edges(...) from builtins.PyCapsule num_edges(rosetta.core.graph.Graph) -> int num_nodes(...) from builtins.PyCapsule num_nodes(rosetta.core.graph.Graph) -> int   the number of nodes in the graph print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.graph.Graph) -> NoneType   send summary information to the screen for all vertices in the graph set_num_nodes(...) from builtins.PyCapsule set_num_nodes(self : rosetta.core.graph.Graph, num_nodes : int) -> NoneType   set the number of nodes in the graph -- deletes any existing edges in the graph   class MinimizationNode(rosetta.core.graph.Node)     Class MinimizationNode holds the ResSingleMinimizationData information for a single residue in a Pose which is being minimized. The data held in this node will be used in both scoring the residue one-body energies and evaluating atom derivatives during minimization.     Method resolution order: MinimizationNode rosetta.core.graph.Node builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.graph.Graph, index : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. active_1benmeths_begin(...) from builtins.PyCapsule active_1benmeths_begin(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::OneBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> > > > active_1benmeths_end(...) from builtins.PyCapsule active_1benmeths_end(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::OneBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> > > > active_1benmeths_ext_begin(...) from builtins.PyCapsule active_1benmeths_ext_begin(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::OneBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> > > > active_1benmeths_ext_end(...) from builtins.PyCapsule active_1benmeths_ext_end(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::OneBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> > > > active_1benmeths_std_begin(...) from builtins.PyCapsule active_1benmeths_std_begin(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::OneBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> > > > active_1benmeths_std_end(...) from builtins.PyCapsule active_1benmeths_std_end(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::OneBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> > > > active_intrares2benmeths_begin(...) from builtins.PyCapsule active_intrares2benmeths_begin(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > active_intrares2benmeths_end(...) from builtins.PyCapsule active_intrares2benmeths_end(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > active_intrares2benmeths_ext_begin(...) from builtins.PyCapsule active_intrares2benmeths_ext_begin(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > active_intrares2benmeths_ext_end(...) from builtins.PyCapsule active_intrares2benmeths_ext_end(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > active_intrares2benmeths_std_begin(...) from builtins.PyCapsule active_intrares2benmeths_std_begin(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > active_intrares2benmeths_std_end(...) from builtins.PyCapsule active_intrares2benmeths_std_end(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > add_onebody_enmeth(...) from builtins.PyCapsule add_onebody_enmeth(self : rosetta.core.scoring.MinimizationNode, enmeth : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, domain_map_color : int) -> bool add_twobody_enmeth(...) from builtins.PyCapsule add_twobody_enmeth(self : rosetta.core.scoring.MinimizationNode, enmeth : core::scoring::methods::TwoBodyEnergy, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, weights : rosetta.core.scoring.EMapVector, domain_map_color : int) -> bool copy_from(...) from builtins.PyCapsule copy_from(self : rosetta.core.scoring.MinimizationNode, source : rosetta.core.graph.Node) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.scoring.MinimizationNode) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.scoring.MinimizationNode) -> int dof_deriv_1benmeths_begin(...) from builtins.PyCapsule dof_deriv_1benmeths_begin(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::OneBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> > > > dof_deriv_1benmeths_end(...) from builtins.PyCapsule dof_deriv_1benmeths_end(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::OneBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> > > > dof_deriv_2benmeths_begin(...) from builtins.PyCapsule dof_deriv_2benmeths_begin(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > dof_deriv_2benmeths_end(...) from builtins.PyCapsule dof_deriv_2benmeths_end(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > dweight(...) from builtins.PyCapsule dweight(*args, **kwargs) Overloaded function.   1. dweight(rosetta.core.scoring.MinimizationNode) -> float   2. dweight(self : rosetta.core.scoring.MinimizationNode, setting : float) -> NoneType print(...) from builtins.PyCapsule print(rosetta.core.scoring.MinimizationNode) -> NoneType res_min_data(...) from builtins.PyCapsule res_min_data(*args, **kwargs) Overloaded function.   1. res_min_data(rosetta.core.scoring.MinimizationNode) -> rosetta.core.scoring.ResSingleMinimizationData   2. res_min_data(rosetta.core.scoring.MinimizationNode) -> rosetta.core.scoring.ResSingleMinimizationData setup_for_derivatives(...) from builtins.PyCapsule setup_for_derivatives(self : rosetta.core.scoring.MinimizationNode, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType setup_for_minimizing(...) from builtins.PyCapsule setup_for_minimizing(self : rosetta.core.scoring.MinimizationNode, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, min_map : rosetta.core.kinematics.MinimizerMapBase) -> NoneType setup_for_scoring(...) from builtins.PyCapsule setup_for_scoring(self : rosetta.core.scoring.MinimizationNode, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType sfd_req_1benmeths_begin(...) from builtins.PyCapsule sfd_req_1benmeths_begin(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::OneBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> > > > sfd_req_1benmeths_end(...) from builtins.PyCapsule sfd_req_1benmeths_end(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::OneBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> > > > sfd_req_2benmeths_begin(...) from builtins.PyCapsule sfd_req_2benmeths_begin(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > sfd_req_2benmeths_end(...) from builtins.PyCapsule sfd_req_2benmeths_end(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > sfs_req_1benmeths_begin(...) from builtins.PyCapsule sfs_req_1benmeths_begin(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::OneBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> > > > sfs_req_1benmeths_end(...) from builtins.PyCapsule sfs_req_1benmeths_end(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::OneBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::OneBodyEnergy const> > > > sfs_req_2benmeths_begin(...) from builtins.PyCapsule sfs_req_2benmeths_begin(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > sfs_req_2benmeths_end(...) from builtins.PyCapsule sfs_req_2benmeths_end(rosetta.core.scoring.MinimizationNode) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy const> > > > update_active_enmeths_for_residue(...) from builtins.PyCapsule update_active_enmeths_for_residue(self : rosetta.core.scoring.MinimizationNode, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, weights : rosetta.core.scoring.EMapVector, domain_map_color : int) -> NoneType weight(...) from builtins.PyCapsule weight(*args, **kwargs) Overloaded function.   1. weight(rosetta.core.scoring.MinimizationNode) -> float   2. weight(self : rosetta.core.scoring.MinimizationNode, setting : float) -> NoneType Methods inherited from rosetta.core.graph.Node: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.graph.Node, edge_ptr : core::graph::Edge,  : rosetta.core.graph.EdgeListIterator) -> NoneType   adds edge pointer to edge list; returns an iterator to the new  list element const_edge_list_begin(...) from builtins.PyCapsule const_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its edge list const_edge_list_end(...) from builtins.PyCapsule const_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its edge list const_lower_edge_list_begin(...) from builtins.PyCapsule const_lower_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its lower-edge list const_lower_edge_list_end(...) from builtins.PyCapsule const_lower_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its lower-edge list const_upper_edge_list_begin(...) from builtins.PyCapsule const_upper_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its upper-edge list const_upper_edge_list_end(...) from builtins.PyCapsule const_upper_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its upper-edge list drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.graph.Node) -> NoneType   deletes all edges incident upon this node drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.graph.Node, edge_iterator : rosetta.core.graph.EdgeListIterator) -> NoneType   removes an edge iterator from the node's edge list.  Only called by Edge class. edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its edge list edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its edge list find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.graph.Node, other_node_index : int) -> core::graph::Edge   a "slow" (linear) search for an edge.   2. find_edge(self : rosetta.core.graph.Node, other_node_index : int) -> core::graph::Edge get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.graph.Node) -> int   the index for this node get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.graph.Node) -> int   the number of upper neighbors -- which "self" neighborness is counted if a loop edge  is present get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.graph.Node) -> int   the number of lower neighbors loop_incident(...) from builtins.PyCapsule loop_incident(rosetta.core.graph.Node) -> bool   NOTE TO SELF: remove loop support lower_edge_list_begin(...) from builtins.PyCapsule lower_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its lower-edge list lower_edge_list_end(...) from builtins.PyCapsule lower_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its lower-edge list num_edges(...) from builtins.PyCapsule num_edges(rosetta.core.graph.Node) -> int   the number of edges incident on this node, which may include a loop edge num_neighbors_counting_self(...) from builtins.PyCapsule num_neighbors_counting_self(rosetta.core.graph.Node) -> int   the number of neighbors counting "self" as a neighbor. num_neighbors_counting_self_static(...) from builtins.PyCapsule num_neighbors_counting_self_static(rosetta.core.graph.Node) -> int   the number of neighbors counting "self" as neighbor. Defaults to  num_neighbors_counting_self() but can be set to other values as well.  Useful in calculation of symmetrical structures. set_num_neighbors_counting_self_static(...) from builtins.PyCapsule set_num_neighbors_counting_self_static(self : rosetta.core.graph.Node, neighbor : int) -> NoneType   manually change the number of neighbors for a Node. Used  for symmetry scoring upper_edge_list_begin(...) from builtins.PyCapsule upper_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its upper-edge list upper_edge_list_end(...) from builtins.PyCapsule upper_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its upper-edge list   class MultipoleAxisType(builtins.object)     ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////     Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.core.scoring.MultipoleAxisType, rosetta.core.scoring.MultipoleAxisType) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.core.scoring.MultipoleAxisType) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.MultipoleAxisType, int) -> NoneType   2. __init__(rosetta.core.scoring.MultipoleAxisType, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.core.scoring.MultipoleAxisType) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.core.scoring.MultipoleAxisType, rosetta.core.scoring.MultipoleAxisType) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.core.scoring.MultipoleAxisType) -> str Data and other attributes defined here: bisector = MultipoleAxisType.bisector none = MultipoleAxisType.none three_fold = MultipoleAxisType.three_fold z_axis_only = MultipoleAxisType.z_axis_only z_then_bisector = MultipoleAxisType.z_then_bisector z_then_x = MultipoleAxisType.z_then_x   class MultipoleElecPoseInfo(rosetta.basic.datacache.CacheableData)     ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////     Method resolution order: MultipoleElecPoseInfo rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.scoring.MultipoleElecPoseInfo) -> 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.scoring.MultipoleElecPoseInfo,  : rosetta.core.scoring.MultipoleElecPoseInfo) -> rosetta.core.scoring.MultipoleElecPoseInfo being_packed(...) from builtins.PyCapsule being_packed(self : rosetta.core.scoring.MultipoleElecPoseInfo, seqpos : int) -> bool clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.MultipoleElecPoseInfo) -> rosetta.basic.datacache.CacheableData initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.scoring.MultipoleElecPoseInfo, pose : rosetta.core.pose.Pose) -> NoneType placeholder_info(...) from builtins.PyCapsule placeholder_info(self : rosetta.core.scoring.MultipoleElecPoseInfo, seqpos : int) -> rosetta.core.scoring.MultipoleElecResidueInfo placeholder_residue(...) from builtins.PyCapsule placeholder_residue(self : rosetta.core.scoring.MultipoleElecPoseInfo, seqpos : int) -> rosetta.core.conformation.Residue residue_info(...) from builtins.PyCapsule residue_info(*args, **kwargs) Overloaded function.   1. residue_info(self : rosetta.core.scoring.MultipoleElecPoseInfo, i : int) -> rosetta.core.scoring.MultipoleElecResidueInfo   2. residue_info(self : rosetta.core.scoring.MultipoleElecPoseInfo, i : int) -> rosetta.core.scoring.MultipoleElecResidueInfo set_placeholder(...) from builtins.PyCapsule set_placeholder(self : rosetta.core.scoring.MultipoleElecPoseInfo, i : int, rsd : rosetta.core.conformation.Residue, info : rosetta.core.scoring.MultipoleElecResidueInfo) -> NoneType set_repack_list(...) from builtins.PyCapsule set_repack_list(self : rosetta.core.scoring.MultipoleElecPoseInfo, repacking_residues : rosetta.utility.vector1_bool) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.scoring.MultipoleElecPoseInfo) -> int Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class MultipoleElecPotential(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.MultipoleElecPotential) -> NoneType   2. __init__(self : rosetta.core.scoring.MultipoleElecPotential,  : rosetta.core.scoring.MultipoleElecPotential) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. align_multipole_axes(...) from builtins.PyCapsule align_multipole_axes(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose) -> NoneType   called prior to scoring, eg align_residue_multipole_axes(...) from builtins.PyCapsule align_residue_multipole_axes(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose, rsd : rosetta.core.conformation.Residue, mp : rosetta.core.scoring.MultipoleElecResidueInfo) -> NoneType   called prior to scoring, eg amoeba_type_lookup(...) from builtins.PyCapsule amoeba_type_lookup(self : rosetta.core.scoring.MultipoleElecPotential, atomname : str, resname : str, variantname : str) -> int   Look up Amoeba type by resname/atomname/variant name assign_all_amoeba_types(...) from builtins.PyCapsule assign_all_amoeba_types(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose) -> NoneType   called prior to scoring, eg assign_residue_amoeba_type(...) from builtins.PyCapsule assign_residue_amoeba_type(self : rosetta.core.scoring.MultipoleElecPotential, rsd : rosetta.core.conformation.Residue, mp : rosetta.core.scoring.MultipoleElecResidueInfo) -> NoneType   called prior to scoring, eg build_frame_and_rotate(...) from builtins.PyCapsule build_frame_and_rotate(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose, mp_param : rosetta.core.scoring.MultipoleParameter, orig_atom : int, mp : rosetta.core.scoring.MultipoleElecResidueInfo, rsd : rosetta.core.conformation.Residue) -> NoneType   Build the matrix to rotate from the local frame to the  global one. calculate_and_store_all_derivs(...) from builtins.PyCapsule calculate_and_store_all_derivs(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose) -> NoneType calculate_fixed_fields_for_polarization(...) from builtins.PyCapsule calculate_fixed_fields_for_polarization(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose) -> NoneType   Get the electric field due to permanent multipoles calculate_induced_fields_for_polarization(...) from builtins.PyCapsule calculate_induced_fields_for_polarization(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose) -> NoneType   Get the electric field due to permanent multipoles calculate_res_res_fixed_fields_for_polarization(...) from builtins.PyCapsule calculate_res_res_fixed_fields_for_polarization(self : rosetta.core.scoring.MultipoleElecPotential, rsd1 : rosetta.core.conformation.Residue, mp1 : rosetta.core.scoring.MultipoleElecResidueInfo, rsd2 : rosetta.core.conformation.Residue, mp2 : rosetta.core.scoring.MultipoleElecResidueInfo) -> NoneType calculate_res_res_induced_fields_for_polarization(...) from builtins.PyCapsule calculate_res_res_induced_fields_for_polarization(self : rosetta.core.scoring.MultipoleElecPotential, rsd1 : rosetta.core.conformation.Residue, mp1 : rosetta.core.scoring.MultipoleElecResidueInfo, rsd2 : rosetta.core.conformation.Residue, mp2 : rosetta.core.scoring.MultipoleElecResidueInfo) -> NoneType clear_induced_fields(...) from builtins.PyCapsule clear_induced_fields(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose) -> NoneType   Zero out the fields due to induced dipoles determine_polarization_groups(...) from builtins.PyCapsule determine_polarization_groups(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose) -> NoneType   called prior to scoring, eg eval_residue_pair_derivatives(...) from builtins.PyCapsule eval_residue_pair_derivatives(self : rosetta.core.scoring.MultipoleElecPotential, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, mp1 : rosetta.core.scoring.MultipoleElecResidueInfo, mp2 : rosetta.core.scoring.MultipoleElecResidueInfo, pose : rosetta.core.pose.Pose, factor : float, r1_atom_derivs : rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_atom_derivs : rosetta.utility.vector1_core_scoring_DerivVectorPair) -> NoneType find_params_and_neighbors(...) from builtins.PyCapsule find_params_and_neighbors(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose, mp_param : rosetta.core.scoring.MultipoleParameter, mp : rosetta.core.scoring.MultipoleElecResidueInfo, rsd : rosetta.core.conformation.Residue, j : int, this_type : int) -> NoneType   Find the appropriate multipole params and axis atoms get_effective_radii(...) from builtins.PyCapsule get_effective_radii(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose) -> NoneType   Get the effective radii for Generalized Kirkwood get_polarization_from_fields(...) from builtins.PyCapsule get_polarization_from_fields(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose) -> NoneType   Get the electric field due to permanent multipoles get_res_res_elecE(...) from builtins.PyCapsule get_res_res_elecE(self : rosetta.core.scoring.MultipoleElecPotential, rsd1 : rosetta.core.conformation.Residue, mp1 : rosetta.core.scoring.MultipoleElecResidueInfo, rsd2 : rosetta.core.conformation.Residue, mp2 : rosetta.core.scoring.MultipoleElecResidueInfo) -> float get_rotamers_effective_radii(...) from builtins.PyCapsule get_rotamers_effective_radii(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose,  : rosetta.core.conformation.RotamerSetBase) -> NoneType   Get the effective radii for Generalized Kirkwood get_rotamers_multipole_info(...) from builtins.PyCapsule get_rotamers_multipole_info(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose,  : rosetta.core.conformation.RotamerSetBase) -> NoneType   Get the amoeba info for rotamers get_single_rotamer_effective_radii(...) from builtins.PyCapsule get_single_rotamer_effective_radii(self : rosetta.core.scoring.MultipoleElecPotential, rsd1 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, mp_info : rosetta.core.scoring.MultipoleElecPoseInfo, mp1 : rosetta.core.scoring.MultipoleElecResidueInfo) -> NoneType   Get the effective radii for Generalized Kirkwood induce_polarizable_dipoles(...) from builtins.PyCapsule induce_polarizable_dipoles(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose) -> NoneType   called prior to scoring, eg read_in_amoeba_parameters(...) from builtins.PyCapsule read_in_amoeba_parameters(rosetta.core.scoring.MultipoleElecPotential) -> NoneType   read in parameters for amoeba and mappings between  Rosetta residues/atoms and Amoeba types read_in_multipole_parameters(...) from builtins.PyCapsule read_in_multipole_parameters(rosetta.core.scoring.MultipoleElecPotential) -> NoneType   read in multipole parameters for amoeba types relax_induced_dipoles(...) from builtins.PyCapsule relax_induced_dipoles(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose, relax : float) -> float   Copies over induced dipoles to storage setup_for_packing(...) from builtins.PyCapsule setup_for_packing(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose, repacking_residues : rosetta.utility.vector1_bool) -> NoneType setup_for_scoring(...) from builtins.PyCapsule setup_for_scoring(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose) -> NoneType store_induced_dipoles(...) from builtins.PyCapsule store_induced_dipoles(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose) -> NoneType   Copies over induced dipoles to storage update_residue_for_packing(...) from builtins.PyCapsule update_residue_for_packing(self : rosetta.core.scoring.MultipoleElecPotential, pose : rosetta.core.pose.Pose, seqpos : int) -> NoneType Data descriptors defined here: Ep Ew bohr use_gen_kirkwood use_polarization   class MultipoleElecResidueInfo(rosetta.basic.datacache.CacheableData)     ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////     Method resolution order: MultipoleElecResidueInfo rosetta.basic.datacache.CacheableData builtins.object Methods defined here: Efield_fixed(...) from builtins.PyCapsule Efield_fixed(*args, **kwargs) Overloaded function.   1. Efield_fixed(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t   2. Efield_fixed(rosetta.core.scoring.MultipoleElecResidueInfo) -> rosetta.utility.vector1_numeric_xyzVector_double_t Efield_induced(...) from builtins.PyCapsule Efield_induced(*args, **kwargs) Overloaded function.   1. Efield_induced(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t   2. Efield_induced(rosetta.core.scoring.MultipoleElecResidueInfo) -> rosetta.utility.vector1_numeric_xyzVector_double_t Efield_rf_fixed(...) from builtins.PyCapsule Efield_rf_fixed(*args, **kwargs) Overloaded function.   1. Efield_rf_fixed(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t   2. Efield_rf_fixed(rosetta.core.scoring.MultipoleElecResidueInfo) -> rosetta.utility.vector1_numeric_xyzVector_double_t Efield_rf_induced(...) from builtins.PyCapsule Efield_rf_induced(*args, **kwargs) Overloaded function.   1. Efield_rf_induced(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t   2. Efield_rf_induced(rosetta.core.scoring.MultipoleElecResidueInfo) -> rosetta.utility.vector1_numeric_xyzVector_double_t __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, rsd : rosetta.core.conformation.Residue) -> NoneType   3. __init__(handle, rosetta.core.scoring.MultipoleElecResidueInfo) -> 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.scoring.MultipoleElecResidueInfo,  : rosetta.core.scoring.MultipoleElecResidueInfo) -> rosetta.core.scoring.MultipoleElecResidueInfo clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.MultipoleElecResidueInfo) -> rosetta.basic.datacache.CacheableData const_my_group(...) from builtins.PyCapsule const_my_group(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.utility.vector1_core_id_AtomID coord_frame_ref(...) from builtins.PyCapsule coord_frame_ref(*args, **kwargs) Overloaded function.   1. coord_frame_ref(rosetta.core.scoring.MultipoleElecResidueInfo) -> rosetta.utility.vector1_core_id_AtomID   2. coord_frame_ref(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.core.id.AtomID copy_clone(...) from builtins.PyCapsule copy_clone(rosetta.core.scoring.MultipoleElecResidueInfo) -> rosetta.core.scoring.MultipoleElecResidueInfo dipole(...) from builtins.PyCapsule dipole(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t induced_dipole(...) from builtins.PyCapsule induced_dipole(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t induced_rf_dipole(...) from builtins.PyCapsule induced_rf_dipole(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.scoring.MultipoleElecResidueInfo, rsd : rosetta.core.conformation.Residue) -> NoneType local_coord_matrix(...) from builtins.PyCapsule local_coord_matrix(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.numeric.xyzMatrix_double_t monopole(...) from builtins.PyCapsule monopole(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> float mp_param(...) from builtins.PyCapsule mp_param(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm1 : int) -> core::scoring::MultipoleParameter my_group(...) from builtins.PyCapsule my_group(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.utility.vector1_core_id_AtomID my_local_coord_frame(...) from builtins.PyCapsule my_local_coord_frame(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.utility.vector1_core_id_AtomID nonconst_dipole(...) from builtins.PyCapsule nonconst_dipole(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t nonconst_induced_dipole(...) from builtins.PyCapsule nonconst_induced_dipole(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t nonconst_induced_rf_dipole(...) from builtins.PyCapsule nonconst_induced_rf_dipole(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t nonconst_monopole(...) from builtins.PyCapsule nonconst_monopole(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> float nonconst_mp_param(...) from builtins.PyCapsule nonconst_mp_param(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm1 : int) -> core::scoring::MultipoleParameter nonconst_quadrupole(...) from builtins.PyCapsule nonconst_quadrupole(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.numeric.xyzMatrix_double_t nonconst_rKirkwood(...) from builtins.PyCapsule nonconst_rKirkwood(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> float nonconst_rosetta_res_type(...) from builtins.PyCapsule nonconst_rosetta_res_type(rosetta.core.scoring.MultipoleElecResidueInfo) -> str nonconst_stored_induced_dipole(...) from builtins.PyCapsule nonconst_stored_induced_dipole(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t nonconst_stored_induced_rf_dipole(...) from builtins.PyCapsule nonconst_stored_induced_rf_dipole(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t quadrupole(...) from builtins.PyCapsule quadrupole(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.numeric.xyzMatrix_double_t rKirkwood(...) from builtins.PyCapsule rKirkwood(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> float rosetta_res_type(...) from builtins.PyCapsule rosetta_res_type(rosetta.core.scoring.MultipoleElecResidueInfo) -> str set_coord_frame_ref(...) from builtins.PyCapsule set_coord_frame_ref(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int, in_val : rosetta.core.id.AtomID) -> NoneType set_type(...) from builtins.PyCapsule set_type(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int, in_val : int) -> NoneType stored_induced_dipole(...) from builtins.PyCapsule stored_induced_dipole(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t stored_induced_rf_dipole(...) from builtins.PyCapsule stored_induced_rf_dipole(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> rosetta.numeric.xyzVector_double_t type(...) from builtins.PyCapsule type(*args, **kwargs) Overloaded function.   1. type(rosetta.core.scoring.MultipoleElecResidueInfo) -> rosetta.utility.vector1_unsigned_long   2. type(self : rosetta.core.scoring.MultipoleElecResidueInfo, atm : int) -> int Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class MultipoleElecRotamerSetInfo(rosetta.basic.datacache.CacheableData)     ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////     Method resolution order: MultipoleElecRotamerSetInfo rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle, rosetta.core.scoring.MultipoleElecRotamerSetInfo) -> NoneType   2. __init__(self : handle, rotamer_set : rosetta.core.conformation.RotamerSetBase) -> 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.scoring.MultipoleElecRotamerSetInfo,  : rosetta.core.scoring.MultipoleElecRotamerSetInfo) -> rosetta.core.scoring.MultipoleElecRotamerSetInfo clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.MultipoleElecRotamerSetInfo) -> rosetta.basic.datacache.CacheableData initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.scoring.MultipoleElecRotamerSetInfo, rotamer_set : rosetta.core.conformation.RotamerSetBase) -> NoneType   dont forget to 0 the born_radii residue_info(...) from builtins.PyCapsule residue_info(*args, **kwargs) Overloaded function.   1. residue_info(self : rosetta.core.scoring.MultipoleElecRotamerSetInfo, i : int) -> rosetta.core.scoring.MultipoleElecResidueInfo   2. residue_info(self : rosetta.core.scoring.MultipoleElecRotamerSetInfo, i : int) -> rosetta.core.scoring.MultipoleElecResidueInfo size(...) from builtins.PyCapsule size(rosetta.core.scoring.MultipoleElecRotamerSetInfo) -> int Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class MultipoleParameter(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.core.scoring.MultipoleParameter, coord_type_in : rosetta.core.scoring.MultipoleAxisType, atom_type_in : rosetta.utility.vector1_unsigned_long, chirality_sign_in : float, monopole_in : float, dipole_in : rosetta.numeric.xyzVector_double_t, quadrupole_in : rosetta.numeric.xyzMatrix_double_t) -> NoneType   2. __init__(self : rosetta.core.scoring.MultipoleParameter,  : rosetta.core.scoring.MultipoleParameter) -> 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.scoring.MultipoleParameter,  : rosetta.core.scoring.MultipoleParameter) -> rosetta.core.scoring.MultipoleParameter atom_type(...) from builtins.PyCapsule atom_type(rosetta.core.scoring.MultipoleParameter) -> rosetta.utility.vector1_unsigned_long chirality_sign(...) from builtins.PyCapsule chirality_sign(rosetta.core.scoring.MultipoleParameter) -> float clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.MultipoleParameter) -> rosetta.core.scoring.MultipoleParameter coord_type(...) from builtins.PyCapsule coord_type(rosetta.core.scoring.MultipoleParameter) -> rosetta.core.scoring.MultipoleAxisType dipole(...) from builtins.PyCapsule dipole(rosetta.core.scoring.MultipoleParameter) -> rosetta.numeric.xyzVector_double_t monopole(...) from builtins.PyCapsule monopole(rosetta.core.scoring.MultipoleParameter) -> float my_group_members(...) from builtins.PyCapsule my_group_members(rosetta.core.scoring.MultipoleParameter) -> rosetta.utility.vector1_unsigned_long pdamp(...) from builtins.PyCapsule pdamp(rosetta.core.scoring.MultipoleParameter) -> float polarity(...) from builtins.PyCapsule polarity(rosetta.core.scoring.MultipoleParameter) -> float quadrupole(...) from builtins.PyCapsule quadrupole(rosetta.core.scoring.MultipoleParameter) -> rosetta.numeric.xyzMatrix_double_t thole(...) from builtins.PyCapsule thole(rosetta.core.scoring.MultipoleParameter) -> float   class NeighborList(builtins.object)     ////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.core.scoring.NeighborList, domain_map : ObjexxFCL::FArray1D<int>, XX_cutoff : float, XH_cutoff : float, HH_cutoff : float) -> NoneType   2. __init__(self : rosetta.core.scoring.NeighborList,  : rosetta.core.scoring.NeighborList) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. atom_neighbors(...) from builtins.PyCapsule atom_neighbors(*args, **kwargs) Overloaded function.   1. atom_neighbors(self : rosetta.core.scoring.NeighborList, pos : int, atomno : int) -> rosetta.utility.vector1_core_scoring_AtomNeighbor   2. atom_neighbors(self : rosetta.core.scoring.NeighborList, id : rosetta.core.id.AtomID) -> rosetta.utility.vector1_core_scoring_AtomNeighbor check_domain_map(...) from builtins.PyCapsule check_domain_map(self : rosetta.core.scoring.NeighborList, domain_map_in : ObjexxFCL::FArray1D<int>) -> NoneType clear(...) from builtins.PyCapsule clear(rosetta.core.scoring.NeighborList) -> NoneType clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.NeighborList) -> rosetta.core.scoring.NeighborList disable_auto_update(...) from builtins.PyCapsule disable_auto_update(rosetta.core.scoring.NeighborList) -> NoneType domain_map(...) from builtins.PyCapsule domain_map(rosetta.core.scoring.NeighborList) -> ObjexxFCL::FArray1D<int> intrares_upper_atom_neighbors(...) from builtins.PyCapsule intrares_upper_atom_neighbors(*args, **kwargs) Overloaded function.   1. intrares_upper_atom_neighbors(self : rosetta.core.scoring.NeighborList, pos : int, atomno : int) -> rosetta.utility.vector1_core_scoring_AtomNeighbor   2. intrares_upper_atom_neighbors(self : rosetta.core.scoring.NeighborList, id : rosetta.core.id.AtomID) -> rosetta.utility.vector1_core_scoring_AtomNeighbor set_auto_update(...) from builtins.PyCapsule set_auto_update(self : rosetta.core.scoring.NeighborList, move_tolerance : float) -> NoneType upper_atom_neighbors(...) from builtins.PyCapsule upper_atom_neighbors(*args, **kwargs) Overloaded function.   1. upper_atom_neighbors(self : rosetta.core.scoring.NeighborList, pos : int, atomno : int) -> rosetta.utility.vector1_core_scoring_AtomNeighbor   2. upper_atom_neighbors(self : rosetta.core.scoring.NeighborList, id : rosetta.core.id.AtomID) -> rosetta.utility.vector1_core_scoring_AtomNeighbor   class OmegaTether(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.OmegaTether) -> 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.scoring.OmegaTether,  : rosetta.core.scoring.OmegaTether) -> rosetta.core.scoring.OmegaTether eval_omega_score_all(...) from builtins.PyCapsule eval_omega_score_all(self : rosetta.core.scoring.OmegaTether, pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType eval_omega_score_residue(...) from builtins.PyCapsule eval_omega_score_residue(*args, **kwargs) Overloaded function.   1. eval_omega_score_residue(self : rosetta.core.scoring.OmegaTether, res_aa : rosetta.core.chemical.AA, omega : float, phi : float, psi : float) -> float   2. eval_omega_score_residue(self : rosetta.core.scoring.OmegaTether, res : rosetta.core.conformation.Residue, energy : float, denergy_domega : float, denergy_dphi : float, denergy_dpsi : float) -> NoneType   3. eval_omega_score_residue(self : rosetta.core.scoring.OmegaTether, res_aa : rosetta.core.chemical.AA, omega : float, phi : float, psi : float, energy : float, denergy_domega : float, denergy_dphi : float, denergy_dpsi : float) -> NoneType omega_index(...) from builtins.PyCapsule omega_index(self : rosetta.core.scoring.OmegaTether, rsd : rosetta.core.conformation.Residue) -> int   Returns the mainchain torsion index corresponding to "omega".      Should be 3 for alpha amino acids, 4 for beta amino acids.      Vikram K. Mulligan (vmullig.edu) phi_index(...) from builtins.PyCapsule phi_index(self : rosetta.core.scoring.OmegaTether, rsd : rosetta.core.conformation.Residue) -> int   Returns the mainchain torsion index corresponding to "phi".      Generally 1.  Set to 2 for beta-amino acids so that derivatives are calculated  for the dihedral two spaces before the peptide bond.      Vikram K. Mulligan (vmullig.edu) psi_index(...) from builtins.PyCapsule psi_index(self : rosetta.core.scoring.OmegaTether, rsd : rosetta.core.conformation.Residue) -> int   Returns the mainchain torsion index corresponding to "psi".      Generally 2 (alpha-amino acids) or 3 (beta-amino acids).      Vikram K. Mulligan (vmullig.edu)   class OneToAllEnergyContainer(LREnergyContainer)     ////////////////////////////////////////////////////////////////////////     Method resolution order: OneToAllEnergyContainer LREnergyContainer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, fixed_res_idx : int, size_in : int, score_type_in : rosetta.core.scoring.ScoreType) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. any_neighbors_for_residue(...) from builtins.PyCapsule any_neighbors_for_residue(self : rosetta.core.scoring.OneToAllEnergyContainer,  : int) -> bool any_upper_neighbors_for_residue(...) from builtins.PyCapsule any_upper_neighbors_for_residue(self : rosetta.core.scoring.OneToAllEnergyContainer, resid : int) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.OneToAllEnergyContainer,  : rosetta.core.scoring.OneToAllEnergyContainer) -> rosetta.core.scoring.OneToAllEnergyContainer clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.OneToAllEnergyContainer) -> rosetta.core.scoring.LREnergyContainer const_neighbor_iterator_begin(...) from builtins.PyCapsule const_neighbor_iterator_begin(self : rosetta.core.scoring.OneToAllEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborConstIterator   ///////////////// const versions const_neighbor_iterator_end(...) from builtins.PyCapsule const_neighbor_iterator_end(self : rosetta.core.scoring.OneToAllEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborConstIterator const_upper_neighbor_iterator_begin(...) from builtins.PyCapsule const_upper_neighbor_iterator_begin(self : rosetta.core.scoring.OneToAllEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborConstIterator const_upper_neighbor_iterator_end(...) from builtins.PyCapsule const_upper_neighbor_iterator_end(self : rosetta.core.scoring.OneToAllEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborConstIterator empty(...) from builtins.PyCapsule empty(rosetta.core.scoring.OneToAllEnergyContainer) -> bool fixed(...) from builtins.PyCapsule fixed(rosetta.core.scoring.OneToAllEnergyContainer) -> int neighbor_iterator_begin(...) from builtins.PyCapsule neighbor_iterator_begin(self : rosetta.core.scoring.OneToAllEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborIterator   ///////////////// non-const versions neighbor_iterator_end(...) from builtins.PyCapsule neighbor_iterator_end(self : rosetta.core.scoring.OneToAllEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborIterator set_num_nodes(...) from builtins.PyCapsule set_num_nodes(self : rosetta.core.scoring.OneToAllEnergyContainer, size_in : int) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.scoring.OneToAllEnergyContainer) -> int upper_neighbor_iterator_begin(...) from builtins.PyCapsule upper_neighbor_iterator_begin(self : rosetta.core.scoring.OneToAllEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborIterator upper_neighbor_iterator_end(...) from builtins.PyCapsule upper_neighbor_iterator_end(self : rosetta.core.scoring.OneToAllEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborIterator   class OneToAllNeighborConstIterator(ResidueNeighborConstIterator)     ////////////////////////////////////////////////////     Method resolution order: OneToAllNeighborConstIterator ResidueNeighborConstIterator builtins.object Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.scoring.OneToAllNeighborConstIterator, other : rosetta.core.scoring.ResidueNeighborConstIterator) -> bool __init__(...) from builtins.PyCapsule __init__(self : handle, pos1_in : int, pos2_in : int, operating_on_pos1_in : bool, st : rosetta.core.scoring.ScoreType, table_in : rosetta.utility.vector1_double, computed_in : rosetta.utility.vector1_bool) -> NoneType __ne__(...) from builtins.PyCapsule __ne__(self : rosetta.core.scoring.OneToAllNeighborConstIterator, other : rosetta.core.scoring.ResidueNeighborConstIterator) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. accumulate_energy(...) from builtins.PyCapsule accumulate_energy(self : rosetta.core.scoring.OneToAllNeighborConstIterator, emap : rosetta.core.scoring.EMapVector) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.OneToAllNeighborConstIterator, src : rosetta.core.scoring.ResidueNeighborConstIterator) -> rosetta.core.scoring.ResidueNeighborConstIterator energy_computed(...) from builtins.PyCapsule energy_computed(rosetta.core.scoring.OneToAllNeighborConstIterator) -> bool lower_neighbor_id(...) from builtins.PyCapsule lower_neighbor_id(rosetta.core.scoring.OneToAllNeighborConstIterator) -> int neighbor_id(...) from builtins.PyCapsule neighbor_id(rosetta.core.scoring.OneToAllNeighborConstIterator) -> int plus_plus(...) from builtins.PyCapsule plus_plus(rosetta.core.scoring.OneToAllNeighborConstIterator) -> rosetta.core.scoring.ResidueNeighborConstIterator residue_iterated_on(...) from builtins.PyCapsule residue_iterated_on(rosetta.core.scoring.OneToAllNeighborConstIterator) -> int retrieve_energy(...) from builtins.PyCapsule retrieve_energy(self : rosetta.core.scoring.OneToAllNeighborConstIterator, emap : rosetta.core.scoring.EMapVector) -> NoneType upper_neighbor_id(...) from builtins.PyCapsule upper_neighbor_id(rosetta.core.scoring.OneToAllNeighborConstIterator) -> int   class OneToAllNeighborIterator(ResidueNeighborIterator)     ////////////////////////////////////////////////////     Method resolution order: OneToAllNeighborIterator ResidueNeighborIterator builtins.object Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.scoring.OneToAllNeighborIterator, other : rosetta.core.scoring.ResidueNeighborIterator) -> bool __init__(...) from builtins.PyCapsule __init__(self : handle, pos1_in : int, pos2_in : int, operating_on_pos1_in : bool, st : rosetta.core.scoring.ScoreType, table_in : rosetta.utility.vector1_double, computed_in : rosetta.utility.vector1_bool) -> NoneType __ne__(...) from builtins.PyCapsule __ne__(self : rosetta.core.scoring.OneToAllNeighborIterator, other : rosetta.core.scoring.ResidueNeighborIterator) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. accumulate_energy(...) from builtins.PyCapsule accumulate_energy(self : rosetta.core.scoring.OneToAllNeighborIterator, emap : rosetta.core.scoring.EMapVector) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.OneToAllNeighborIterator, src : rosetta.core.scoring.ResidueNeighborIterator) -> rosetta.core.scoring.ResidueNeighborIterator energy_computed(...) from builtins.PyCapsule energy_computed(rosetta.core.scoring.OneToAllNeighborIterator) -> bool lower_neighbor_id(...) from builtins.PyCapsule lower_neighbor_id(rosetta.core.scoring.OneToAllNeighborIterator) -> int mark_energy_computed(...) from builtins.PyCapsule mark_energy_computed(rosetta.core.scoring.OneToAllNeighborIterator) -> NoneType mark_energy_uncomputed(...) from builtins.PyCapsule mark_energy_uncomputed(rosetta.core.scoring.OneToAllNeighborIterator) -> NoneType neighbor_id(...) from builtins.PyCapsule neighbor_id(rosetta.core.scoring.OneToAllNeighborIterator) -> int plus_plus(...) from builtins.PyCapsule plus_plus(rosetta.core.scoring.OneToAllNeighborIterator) -> rosetta.core.scoring.ResidueNeighborIterator residue_iterated_on(...) from builtins.PyCapsule residue_iterated_on(rosetta.core.scoring.OneToAllNeighborIterator) -> int retrieve_energy(...) from builtins.PyCapsule retrieve_energy(self : rosetta.core.scoring.OneToAllNeighborIterator, emap : rosetta.core.scoring.EMapVector) -> NoneType save_energy(...) from builtins.PyCapsule save_energy(self : rosetta.core.scoring.OneToAllNeighborIterator, emap : rosetta.core.scoring.EMapVector) -> NoneType upper_neighbor_id(...) from builtins.PyCapsule upper_neighbor_id(rosetta.core.scoring.OneToAllNeighborIterator) -> int   class PDatom(builtins.object)     ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.PDatom) -> 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.scoring.PDatom,  : rosetta.core.scoring.PDatom) -> rosetta.core.scoring.PDatom atom(...) from builtins.PyCapsule atom(rosetta.core.scoring.PDatom) -> int nonconst_atom(...) from builtins.PyCapsule nonconst_atom(rosetta.core.scoring.PDatom) -> int nonconst_rad(...) from builtins.PyCapsule nonconst_rad(rosetta.core.scoring.PDatom) -> float nonconst_rad2(...) from builtins.PyCapsule nonconst_rad2(rosetta.core.scoring.PDatom) -> float nonconst_res(...) from builtins.PyCapsule nonconst_res(rosetta.core.scoring.PDatom) -> int nonconst_xyz(...) from builtins.PyCapsule nonconst_xyz(rosetta.core.scoring.PDatom) -> rosetta.numeric.xyzVector_double_t rad(...) from builtins.PyCapsule rad(rosetta.core.scoring.PDatom) -> float rad2(...) from builtins.PyCapsule rad2(rosetta.core.scoring.PDatom) -> float res(...) from builtins.PyCapsule res(rosetta.core.scoring.PDatom) -> int vertices(...) from builtins.PyCapsule vertices(rosetta.core.scoring.PDatom) -> rosetta.std.list_std_shared_ptr_core_scoring_PDvertex_std_allocator_std_shared_ptr_core_scoring_PDvertex_t xyz(...) from builtins.PyCapsule xyz(rosetta.core.scoring.PDatom) -> rosetta.numeric.xyzVector_double_t   class PDinter(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.scoring.PDinter, xyz : rosetta.numeric.xyzVector_double_t, v1 : rosetta.core.scoring.PDvertex, v2 : rosetta.core.scoring.PDvertex) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_atom(...) from builtins.PyCapsule add_atom(self : rosetta.core.scoring.PDinter, pa : rosetta.core.scoring.PDatom) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.PDinter,  : rosetta.core.scoring.PDinter) -> rosetta.core.scoring.PDinter atoms(...) from builtins.PyCapsule atoms(rosetta.core.scoring.PDinter) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_PDatom_t circle(...) from builtins.PyCapsule circle(rosetta.core.scoring.PDinter) -> bool vrt1(...) from builtins.PyCapsule vrt1(rosetta.core.scoring.PDinter) -> rosetta.core.scoring.PDvertex vrt2(...) from builtins.PyCapsule vrt2(rosetta.core.scoring.PDinter) -> rosetta.core.scoring.PDvertex xyz(...) from builtins.PyCapsule xyz(rosetta.core.scoring.PDinter) -> rosetta.numeric.xyzVector_double_t   class PDvertex(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.PDvertex) -> 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.scoring.PDvertex,  : rosetta.core.scoring.PDvertex) -> rosetta.core.scoring.PDvertex direction(...) from builtins.PyCapsule direction(rosetta.core.scoring.PDvertex) -> rosetta.numeric.xyzVector_double_t finite(...) from builtins.PyCapsule finite(rosetta.core.scoring.PDvertex) -> bool generators(...) from builtins.PyCapsule generators(rosetta.core.scoring.PDvertex) -> rosetta.utility.vector1_std_shared_ptr_core_scoring_PDatom_t id(...) from builtins.PyCapsule id(rosetta.core.scoring.PDvertex) -> int live(...) from builtins.PyCapsule live(rosetta.core.scoring.PDvertex) -> bool nonconst_direction(...) from builtins.PyCapsule nonconst_direction(rosetta.core.scoring.PDvertex) -> rosetta.numeric.xyzVector_double_t nonconst_generators(...) from builtins.PyCapsule nonconst_generators(rosetta.core.scoring.PDvertex) -> rosetta.utility.vector1_std_shared_ptr_core_scoring_PDatom_t nonconst_id(...) from builtins.PyCapsule nonconst_id(rosetta.core.scoring.PDvertex) -> int nonconst_partners(...) from builtins.PyCapsule nonconst_partners(rosetta.core.scoring.PDvertex) -> rosetta.utility.vector1_std_shared_ptr_core_scoring_PDvertex_t nonconst_power(...) from builtins.PyCapsule nonconst_power(rosetta.core.scoring.PDvertex) -> float nonconst_xyz(...) from builtins.PyCapsule nonconst_xyz(rosetta.core.scoring.PDvertex) -> rosetta.numeric.xyzVector_double_t partners(...) from builtins.PyCapsule partners(rosetta.core.scoring.PDvertex) -> rosetta.utility.vector1_std_shared_ptr_core_scoring_PDvertex_t power(...) from builtins.PyCapsule power(rosetta.core.scoring.PDvertex) -> float set_finite(...) from builtins.PyCapsule set_finite(self : rosetta.core.scoring.PDvertex, in_val : bool) -> NoneType set_live(...) from builtins.PyCapsule set_live(self : rosetta.core.scoring.PDvertex, in_val : bool) -> NoneType xyz(...) from builtins.PyCapsule xyz(rosetta.core.scoring.PDvertex) -> rosetta.numeric.xyzVector_double_t   class PQR(builtins.object)     ------------------------------------------------------------------------------------- PQR     Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.scoring.PQR, pose : rosetta.core.pose.Pose, natoms : int, charged_residues : rosetta.std.map_std_string_bool) -> 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.scoring.PQR,  : rosetta.core.scoring.PQR) -> rosetta.core.scoring.PQR get_natoms(...) from builtins.PyCapsule get_natoms(rosetta.core.scoring.PQR) -> int Data descriptors defined here: charge natoms_ radius x y z   class P_AA(builtins.object)       Methods defined here: P_AA_energy(...) from builtins.PyCapsule P_AA_energy(self : rosetta.core.scoring.P_AA,  : rosetta.core.conformation.Residue) -> float   Probability energies for P(aa) P_AA_pp_energy(...) from builtins.PyCapsule P_AA_pp_energy(*args, **kwargs) Overloaded function.   1. P_AA_pp_energy(self : rosetta.core.scoring.P_AA,  : rosetta.core.conformation.Residue) -> float   2. P_AA_pp_energy(self : rosetta.core.scoring.P_AA, aa : rosetta.core.chemical.AA, phi : float, psi : float) -> float __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.P_AA) -> 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.scoring.P_AA,  : rosetta.core.scoring.P_AA) -> rosetta.core.scoring.P_AA get_Paa_pp_deriv(...) from builtins.PyCapsule get_Paa_pp_deriv(self : rosetta.core.scoring.P_AA, res : rosetta.core.conformation.Residue, tor_id : rosetta.core.id.TorsionID) -> float   class P_AA_ss(builtins.object)       Methods defined here: P_AA_ss_energy(...) from builtins.PyCapsule P_AA_ss_energy(self : rosetta.core.scoring.P_AA_ss, aa : rosetta.core.chemical.AA, ss : str) -> float   Probability energies from P(aa|ss) __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.P_AA_ss) -> 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.scoring.P_AA_ss,  : rosetta.core.scoring.P_AA_ss) -> rosetta.core.scoring.P_AA_ss read_P_AA_ss(...) from builtins.PyCapsule read_P_AA_ss(rosetta.core.scoring.P_AA_ss) -> NoneType   Read the ss-dep amino acid probability file into P_AA_ss   class PairEPotential(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.PairEPotential) -> NoneType   2. __init__(self : rosetta.core.scoring.PairEPotential,  : rosetta.core.scoring.PairEPotential) -> 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.scoring.PairEPotential,  : rosetta.core.scoring.PairEPotential) -> rosetta.core.scoring.PairEPotential pair_term_energy(...) from builtins.PyCapsule pair_term_energy(self : rosetta.core.scoring.PairEPotential, res1 : rosetta.core.conformation.Residue, res1_num_10A_neighbors : int, res2 : rosetta.core.conformation.Residue, res2_num_10A_neighbors : int) -> float pair_term_energy_and_deriv(...) from builtins.PyCapsule pair_term_energy_and_deriv(self : rosetta.core.scoring.PairEPotential, res1 : rosetta.core.conformation.Residue, res1_num_10A_neighbors : int, res2 : rosetta.core.conformation.Residue, res2_num_10A_neighbors : int, dpairE_dr : float) -> float pair_term_energy_exists(...) from builtins.PyCapsule pair_term_energy_exists(self : rosetta.core.scoring.PairEPotential, rsd : rosetta.core.conformation.Residue) -> bool range(...) from builtins.PyCapsule range(rosetta.core.scoring.PairEPotential) -> float   class PoissonBoltzmannPotential(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.PoissonBoltzmannPotential) -> NoneType   2. __init__(self : rosetta.core.scoring.PoissonBoltzmannPotential,  : rosetta.core.scoring.PoissonBoltzmannPotential) -> 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.scoring.PoissonBoltzmannPotential,  : rosetta.core.scoring.PoissonBoltzmannPotential) -> rosetta.core.scoring.PoissonBoltzmannPotential cart2idx(...) from builtins.PyCapsule cart2idx(self : rosetta.core.scoring.PoissonBoltzmannPotential, cartX : rosetta.numeric.xyzVector_double_t, idxX : rosetta.numeric.xyzVector_double_t) -> NoneType   /////////////////////////////// /////////////////////////////// eval_PB_energy_residue(...) from builtins.PyCapsule eval_PB_energy_residue(self : rosetta.core.scoring.PoissonBoltzmannPotential, rsd : rosetta.core.conformation.Residue, PB_energy_residue : float, PB_energy_backbone : float, PB_energy_sidechain : float, PB_burial_weight : float) -> NoneType get_potential(...) from builtins.PyCapsule get_potential(self : rosetta.core.scoring.PoissonBoltzmannPotential, potential : ObjexxFCL::FArray3D<double>, cartX : rosetta.numeric.xyzVector_double_t) -> float lower_bound(...) from builtins.PyCapsule lower_bound(rosetta.core.scoring.PoissonBoltzmannPotential) -> rosetta.numeric.xyzVector_double_t out_of_bounds(...) from builtins.PyCapsule out_of_bounds(self : rosetta.core.scoring.PoissonBoltzmannPotential, cartX : rosetta.numeric.xyzVector_double_t) -> bool solve_pb(...) from builtins.PyCapsule solve_pb(self : rosetta.core.scoring.PoissonBoltzmannPotential, pose : rosetta.core.pose.Pose, state_tag : str, is_residue_charged_by_name : rosetta.std.map_std_string_bool) -> NoneType   Execute ABPS to freshly compute the electrotatic field.       The pose      Arbitrary string for generating APBS files.  e.g. The current energy state.      Which residues are charged?  The key is the residue name. upper_bound(...) from builtins.PyCapsule upper_bound(rosetta.core.scoring.PoissonBoltzmannPotential) -> rosetta.numeric.xyzVector_double_t   class PolymerBondedEnergyContainer(LREnergyContainer)     ////////////////////////////////////////////////////////////////////////     Method resolution order: PolymerBondedEnergyContainer LREnergyContainer builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, pose : rosetta.core.pose.Pose, score_type_in : rosetta.utility.vector1_core_scoring_ScoreType) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. any_neighbors_for_residue(...) from builtins.PyCapsule any_neighbors_for_residue(self : rosetta.core.scoring.PolymerBondedEnergyContainer,  : int) -> bool any_upper_neighbors_for_residue(...) from builtins.PyCapsule any_upper_neighbors_for_residue(self : rosetta.core.scoring.PolymerBondedEnergyContainer,  : int) -> bool assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.PolymerBondedEnergyContainer,  : rosetta.core.scoring.PolymerBondedEnergyContainer) -> rosetta.core.scoring.PolymerBondedEnergyContainer clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.PolymerBondedEnergyContainer) -> rosetta.core.scoring.LREnergyContainer const_neighbor_iterator_begin(...) from builtins.PyCapsule const_neighbor_iterator_begin(self : rosetta.core.scoring.PolymerBondedEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborConstIterator const_neighbor_iterator_end(...) from builtins.PyCapsule const_neighbor_iterator_end(self : rosetta.core.scoring.PolymerBondedEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborConstIterator const_upper_neighbor_iterator_begin(...) from builtins.PyCapsule const_upper_neighbor_iterator_begin(self : rosetta.core.scoring.PolymerBondedEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborConstIterator const_upper_neighbor_iterator_end(...) from builtins.PyCapsule const_upper_neighbor_iterator_end(self : rosetta.core.scoring.PolymerBondedEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborConstIterator empty(...) from builtins.PyCapsule empty(rosetta.core.scoring.PolymerBondedEnergyContainer) -> bool get_computed(...) from builtins.PyCapsule get_computed(self : rosetta.core.scoring.PolymerBondedEnergyContainer, resnum : int) -> bool get_energy(...) from builtins.PyCapsule get_energy(self : rosetta.core.scoring.PolymerBondedEnergyContainer, resnum : int, scoreterm : int) -> float is_valid(...) from builtins.PyCapsule is_valid(self : rosetta.core.scoring.PolymerBondedEnergyContainer, pose : rosetta.core.pose.Pose) -> bool   Is this PolymerBondedEnergyContainer properly set up for the pose?      Vikram K. Mulligan (vmullig.edu). neighbor_iterator_begin(...) from builtins.PyCapsule neighbor_iterator_begin(self : rosetta.core.scoring.PolymerBondedEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborIterator   ///////////////// non-const versions neighbor_iterator_end(...) from builtins.PyCapsule neighbor_iterator_end(self : rosetta.core.scoring.PolymerBondedEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborIterator score_types(...) from builtins.PyCapsule score_types(rosetta.core.scoring.PolymerBondedEnergyContainer) -> rosetta.utility.vector1_core_scoring_ScoreType set_computed(...) from builtins.PyCapsule set_computed(self : rosetta.core.scoring.PolymerBondedEnergyContainer, resnum : int, val : bool) -> NoneType set_energy(...) from builtins.PyCapsule set_energy(self : rosetta.core.scoring.PolymerBondedEnergyContainer, resnum : int, scoreterm : int, E : float) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.scoring.PolymerBondedEnergyContainer) -> int upper_neighbor_iterator_begin(...) from builtins.PyCapsule upper_neighbor_iterator_begin(self : rosetta.core.scoring.PolymerBondedEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborIterator upper_neighbor_iterator_end(...) from builtins.PyCapsule upper_neighbor_iterator_end(self : rosetta.core.scoring.PolymerBondedEnergyContainer, resid : int) -> rosetta.core.scoring.ResidueNeighborIterator Methods inherited from LREnergyContainer: set_num_nodes(...) from builtins.PyCapsule set_num_nodes(self : rosetta.core.scoring.LREnergyContainer,  : int) -> NoneType   class PolymerBondedNeighborConstIterator(ResidueNeighborConstIterator)     ////////////////////////////////////////////////////     Method resolution order: PolymerBondedNeighborConstIterator ResidueNeighborConstIterator builtins.object Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.scoring.PolymerBondedNeighborConstIterator, other : rosetta.core.scoring.ResidueNeighborConstIterator) -> bool __init__(...) from builtins.PyCapsule __init__(self : handle, base_in : int, positions_in : rosetta.utility.vector1_unsigned_long, parent : core::scoring::PolymerBondedEnergyContainer) -> NoneType __ne__(...) from builtins.PyCapsule __ne__(self : rosetta.core.scoring.PolymerBondedNeighborConstIterator, other : rosetta.core.scoring.ResidueNeighborConstIterator) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. accumulate_energy(...) from builtins.PyCapsule accumulate_energy(self : rosetta.core.scoring.PolymerBondedNeighborConstIterator, emap : rosetta.core.scoring.EMapVector) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.PolymerBondedNeighborConstIterator, src : rosetta.core.scoring.ResidueNeighborConstIterator) -> rosetta.core.scoring.ResidueNeighborConstIterator energy_computed(...) from builtins.PyCapsule energy_computed(rosetta.core.scoring.PolymerBondedNeighborConstIterator) -> bool lower_neighbor_id(...) from builtins.PyCapsule lower_neighbor_id(rosetta.core.scoring.PolymerBondedNeighborConstIterator) -> int neighbor_id(...) from builtins.PyCapsule neighbor_id(rosetta.core.scoring.PolymerBondedNeighborConstIterator) -> int plus_plus(...) from builtins.PyCapsule plus_plus(rosetta.core.scoring.PolymerBondedNeighborConstIterator) -> rosetta.core.scoring.ResidueNeighborConstIterator residue_iterated_on(...) from builtins.PyCapsule residue_iterated_on(rosetta.core.scoring.PolymerBondedNeighborConstIterator) -> int retrieve_energy(...) from builtins.PyCapsule retrieve_energy(self : rosetta.core.scoring.PolymerBondedNeighborConstIterator, emap : rosetta.core.scoring.EMapVector) -> NoneType upper_neighbor_id(...) from builtins.PyCapsule upper_neighbor_id(rosetta.core.scoring.PolymerBondedNeighborConstIterator) -> int   class PolymerBondedNeighborIterator(ResidueNeighborIterator)     ////////////////////////////////////////////////////     Method resolution order: PolymerBondedNeighborIterator ResidueNeighborIterator builtins.object Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.scoring.PolymerBondedNeighborIterator, other : rosetta.core.scoring.ResidueNeighborIterator) -> bool __init__(...) from builtins.PyCapsule __init__(self : handle, base_in : int, positions_in : rosetta.utility.vector1_unsigned_long, parent : core::scoring::PolymerBondedEnergyContainer) -> NoneType __ne__(...) from builtins.PyCapsule __ne__(self : rosetta.core.scoring.PolymerBondedNeighborIterator, other : rosetta.core.scoring.ResidueNeighborIterator) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. accumulate_energy(...) from builtins.PyCapsule accumulate_energy(self : rosetta.core.scoring.PolymerBondedNeighborIterator, emap : rosetta.core.scoring.EMapVector) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.PolymerBondedNeighborIterator, src : rosetta.core.scoring.ResidueNeighborIterator) -> rosetta.core.scoring.ResidueNeighborIterator energy_computed(...) from builtins.PyCapsule energy_computed(rosetta.core.scoring.PolymerBondedNeighborIterator) -> bool lower_neighbor_id(...) from builtins.PyCapsule lower_neighbor_id(rosetta.core.scoring.PolymerBondedNeighborIterator) -> int mark_energy_computed(...) from builtins.PyCapsule mark_energy_computed(rosetta.core.scoring.PolymerBondedNeighborIterator) -> NoneType mark_energy_uncomputed(...) from builtins.PyCapsule mark_energy_uncomputed(rosetta.core.scoring.PolymerBondedNeighborIterator) -> NoneType neighbor_id(...) from builtins.PyCapsule neighbor_id(rosetta.core.scoring.PolymerBondedNeighborIterator) -> int plus_plus(...) from builtins.PyCapsule plus_plus(rosetta.core.scoring.PolymerBondedNeighborIterator) -> rosetta.core.scoring.ResidueNeighborIterator residue_iterated_on(...) from builtins.PyCapsule residue_iterated_on(rosetta.core.scoring.PolymerBondedNeighborIterator) -> int retrieve_energy(...) from builtins.PyCapsule retrieve_energy(self : rosetta.core.scoring.PolymerBondedNeighborIterator, emap : rosetta.core.scoring.EMapVector) -> NoneType save_energy(...) from builtins.PyCapsule save_energy(self : rosetta.core.scoring.PolymerBondedNeighborIterator, emap : rosetta.core.scoring.EMapVector) -> NoneType upper_neighbor_id(...) from builtins.PyCapsule upper_neighbor_id(rosetta.core.scoring.PolymerBondedNeighborIterator) -> int   class Predicate(builtins.object)     //////////////////////////////////////////     Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.core.scoring.Predicate, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, resno : int, atomno : int) -> bool __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.Predicate) -> NoneType   2. __init__(rosetta.core.scoring.Predicate, rosetta.core.scoring.Predicate) -> 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.scoring.Predicate,  : rosetta.core.scoring.Predicate) -> rosetta.core.scoring.Predicate   class ProQPotential(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.ProQPotential) -> NoneType   2. __init__(self : rosetta.core.scoring.ProQPotential,  : rosetta.core.scoring.ProQPotential) -> 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.scoring.ProQPotential,  : rosetta.core.scoring.ProQPotential) -> rosetta.core.scoring.ProQPotential num_features_proq2(...) from builtins.PyCapsule num_features_proq2(rosetta.core.scoring.ProQPotential) -> int num_features_proqm(...) from builtins.PyCapsule num_features_proqm(rosetta.core.scoring.ProQPotential) -> int score(...) from builtins.PyCapsule score(*args, **kwargs) Overloaded function.   1. score(self : rosetta.core.scoring.ProQPotential, pose : rosetta.core.pose.Pose, feature_vector : ObjexxFCL::FArray2D<double>, score : ObjexxFCL::FArray1D<double>) -> NoneType   2. score(self : rosetta.core.scoring.ProQPotential, pose : rosetta.core.pose.Pose, feature_vector : ObjexxFCL::FArray2D<double>, score : ObjexxFCL::FArray1D<double>, ProQ2 : bool) -> NoneType setup_for_scoring(...) from builtins.PyCapsule setup_for_scoring(self : rosetta.core.scoring.ProQPotential, pose : rosetta.core.pose.Pose) -> NoneType   class ProteinTorsion(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.core.scoring.ProteinTorsion, rosetta.core.scoring.ProteinTorsion) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.core.scoring.ProteinTorsion) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.ProteinTorsion, int) -> NoneType   2. __init__(rosetta.core.scoring.ProteinTorsion, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.core.scoring.ProteinTorsion) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.core.scoring.ProteinTorsion, rosetta.core.scoring.ProteinTorsion) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.core.scoring.ProteinTorsion) -> str Data and other attributes defined here: CHI1 = ProteinTorsion.CHI1 CHI2 = ProteinTorsion.CHI2 CHI3 = ProteinTorsion.CHI3 CHI4 = ProteinTorsion.CHI4 OMEGA = ProteinTorsion.OMEGA PHI = ProteinTorsion.PHI PSI = ProteinTorsion.PSI protein_torsion_end = ProteinTorsion.protein_torsion_end   class RDC(builtins.object)     //////////////////////////////////////////////     Methods defined here: Dconst(...) from builtins.PyCapsule Dconst(rosetta.core.scoring.RDC) -> float Jcomputed(...) from builtins.PyCapsule Jcomputed(*args, **kwargs) Overloaded function.   1. Jcomputed(rosetta.core.scoring.RDC) -> float   2. Jcomputed(rosetta.core.scoring.RDC) -> float Jdipolar(...) from builtins.PyCapsule Jdipolar(rosetta.core.scoring.RDC) -> float Reduced_Jdipolar(...) from builtins.PyCapsule Reduced_Jdipolar(rosetta.core.scoring.RDC) -> float __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.RDC) -> NoneType   2. __init__(rosetta.core.scoring.RDC, int, str, int, str, float) -> NoneType   doc   3. __init__(rosetta.core.scoring.RDC, int, str, int, str, float, float) -> NoneType   doc   4. __init__(self : rosetta.core.scoring.RDC, res1 : int, atom1 : str, res2 : int, atom2 : str, Jdipolar : float, weight : float, expid : int) -> NoneType   5. __init__(self : rosetta.core.scoring.RDC,  : rosetta.core.scoring.RDC) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.scoring.RDC) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.RDC,  : rosetta.core.scoring.RDC) -> rosetta.core.scoring.RDC atom1(...) from builtins.PyCapsule atom1(rosetta.core.scoring.RDC) -> str atom2(...) from builtins.PyCapsule atom2(rosetta.core.scoring.RDC) -> str expid(...) from builtins.PyCapsule expid(rosetta.core.scoring.RDC) -> int fij(...) from builtins.PyCapsule fij(rosetta.core.scoring.RDC) -> rosetta.numeric.xyzVector_double_t fixed_dist(...) from builtins.PyCapsule fixed_dist(rosetta.core.scoring.RDC) -> float get_RDC_data_type(...) from builtins.PyCapsule get_RDC_data_type(self : rosetta.core.scoring.RDC, atom1 : str, atom2 : str) -> rosetta.core.scoring.RDC_TYPE   which type of RDC pairing are we dealing with ? res1(...) from builtins.PyCapsule res1(rosetta.core.scoring.RDC) -> int res2(...) from builtins.PyCapsule res2(rosetta.core.scoring.RDC) -> int type(...) from builtins.PyCapsule type(rosetta.core.scoring.RDC) -> rosetta.core.scoring.RDC_TYPE weight(...) from builtins.PyCapsule weight(*args, **kwargs) Overloaded function.   1. weight(rosetta.core.scoring.RDC) -> float   2. weight(self : rosetta.core.scoring.RDC, w_in : float) -> NoneType Data descriptors defined here: Jdipolar_computed_ fij_ Data and other attributes defined here: RDC_TYPE = <class 'rosetta.core.scoring.RDC.RDC_TYPE'> RDC_TYPE_CC = RDC_TYPE.RDC_TYPE_CC RDC_TYPE_CH = RDC_TYPE.RDC_TYPE_CH RDC_TYPE_CHN = RDC_TYPE.RDC_TYPE_CHN RDC_TYPE_NC = RDC_TYPE.RDC_TYPE_NC RDC_TYPE_NCA = RDC_TYPE.RDC_TYPE_NCA RDC_TYPE_NH = RDC_TYPE.RDC_TYPE_NH   class RDC_Rohl(builtins.object)     //////////////////////////////////////////////     Methods defined here: Jdipolar(...) from builtins.PyCapsule Jdipolar(rosetta.core.scoring.RDC_Rohl) -> float Reduced_Jdipolar(...) from builtins.PyCapsule Reduced_Jdipolar(rosetta.core.scoring.RDC_Rohl) -> float __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.RDC_Rohl) -> NoneType   2. __init__(rosetta.core.scoring.RDC_Rohl, int, int, float) -> NoneType   doc   3. __init__(self : rosetta.core.scoring.RDC_Rohl, type : int, res : int, Jdipolar : float, weight : float) -> NoneType   4. __init__(self : rosetta.core.scoring.RDC_Rohl,  : rosetta.core.scoring.RDC_Rohl) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. fixed_dist(...) from builtins.PyCapsule fixed_dist(rosetta.core.scoring.RDC_Rohl) -> float invDcnst(...) from builtins.PyCapsule invDcnst(rosetta.core.scoring.RDC_Rohl) -> float res(...) from builtins.PyCapsule res(rosetta.core.scoring.RDC_Rohl) -> int type(...) from builtins.PyCapsule type(rosetta.core.scoring.RDC_Rohl) -> int weight(...) from builtins.PyCapsule weight(*args, **kwargs) Overloaded function.   1. weight(rosetta.core.scoring.RDC_Rohl) -> float   2. weight(self : rosetta.core.scoring.RDC_Rohl, w_in : float) -> NoneType   class RamaPrePro(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.RamaPrePro) -> 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.scoring.RamaPrePro,  : rosetta.core.scoring.RamaPrePro) -> rosetta.core.scoring.RamaPrePro eval_rpp_rama_score(...) from builtins.PyCapsule eval_rpp_rama_score(self : rosetta.core.scoring.RamaPrePro, res_aa1 : rosetta.core.chemical.AA, res_aa2 : rosetta.core.chemical.AA, phi : float, psi : float, score_rama : float, denergy_dphi : float, denergy_dpsi : float) -> NoneType   class Rama_Table_Type(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.core.scoring.Rama_Table_Type, rosetta.core.scoring.Rama_Table_Type) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.core.scoring.Rama_Table_Type) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.Rama_Table_Type, int) -> NoneType   2. __init__(rosetta.core.scoring.Rama_Table_Type, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.core.scoring.Rama_Table_Type) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.core.scoring.Rama_Table_Type, rosetta.core.scoring.Rama_Table_Type) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.core.scoring.Rama_Table_Type) -> str Data and other attributes defined here: end_of_ramatable_type_list = Rama_Table_Type.end_of_ramatable_type_list flat_d_aa_ramatable = Rama_Table_Type.flat_d_aa_ramatable flat_d_aa_ramatable_stringent = Rama_Table_Type.flat_d_aa_ramatable_stringent flat_l_aa_ramatable = Rama_Table_Type.flat_l_aa_ramatable flat_l_aa_ramatable_stringent = Rama_Table_Type.flat_l_aa_ramatable_stringent flat_symm_dl_aa_ramatable = Rama_Table_Type.flat_symm_dl_aa_ramatable flat_symm_dl_aa_ramatable_stringent = Rama_Table_Type.flat_symm_dl_aa_ramatable_stringent flat_symm_gly_ramatable = Rama_Table_Type.flat_symm_gly_ramatable flat_symm_gly_ramatable_stringent = Rama_Table_Type.flat_symm_gly_ramatable_stringent flat_symm_pro_ramatable = Rama_Table_Type.flat_symm_pro_ramatable flat_symm_pro_ramatable_stringent = Rama_Table_Type.flat_symm_pro_ramatable_stringent unknown_ramatable_type = Rama_Table_Type.end_of_ramatable_type_list   class Ramachandran(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.Ramachandran) -> NoneType   2. __init__(self : rosetta.core.scoring.Ramachandran, rama_map_filename : str, use_bicubic_interpolation : bool) -> NoneType   3. __init__(self : rosetta.core.scoring.Ramachandran,  : rosetta.core.scoring.Ramachandran) -> 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.scoring.Ramachandran,  : rosetta.core.scoring.Ramachandran) -> rosetta.core.scoring.Ramachandran cdf_for_aa(...) from builtins.PyCapsule cdf_for_aa(self : rosetta.core.scoring.Ramachandran, aa : rosetta.core.chemical.AA) -> rosetta.utility.vector1_double cdf_for_aa_for_torsion_bin(...) from builtins.PyCapsule cdf_for_aa_for_torsion_bin(self : rosetta.core.scoring.Ramachandran, aa : rosetta.core.chemical.AA,  : rosetta.core.conformation.ppo_torsion_bin) -> rosetta.utility.vector1_double draw_random_phi_psi_from_extra_cdf(...) from builtins.PyCapsule draw_random_phi_psi_from_extra_cdf(self : rosetta.core.scoring.Ramachandran, type : rosetta.core.scoring.Rama_Table_Type, phi : float, psi : float) -> NoneType   Pick a random phi, psi value from a custom Rama table.      The custom Rama table is lazily loaded, so this function  is necessarily non-const.  By default, only the 20 canonical Rama  tables are loaded.      The type of custom rama table (an enum value).      Randomly-drawn phi value, biased by the custom rama  table.      Randomly-drawn psi value, biased by the custom rama  table.      Vikram K. Mulligan (vmullig.edu). eval_rama_score_all(...) from builtins.PyCapsule eval_rama_score_all(self : rosetta.core.scoring.Ramachandran, pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   //////////////////////////// eval_rama_score_residue(...) from builtins.PyCapsule eval_rama_score_residue(*args, **kwargs) Overloaded function.   1. eval_rama_score_residue(self : rosetta.core.scoring.Ramachandran, res : rosetta.core.conformation.Residue) -> float   2. eval_rama_score_residue(self : rosetta.core.scoring.Ramachandran, res_aa : rosetta.core.chemical.AA, phi : float, psi : float) -> float   3. eval_rama_score_residue(self : rosetta.core.scoring.Ramachandran, res : rosetta.core.conformation.Residue, rama : float, drama_dphi : float, drama_dpsi : float) -> NoneType   4. eval_rama_score_residue(self : rosetta.core.scoring.Ramachandran, res_aa : rosetta.core.chemical.AA, phi : float, psi : float, rama : float, drama_dphi : float, drama_dpsi : float) -> NoneType   5. eval_rama_score_residue(self : rosetta.core.scoring.Ramachandran, use_bicubic_interpolation : bool, rama_not_squared : bool, res_aa : rosetta.core.chemical.AA, phi : float, psi : float, rama : float, drama_dphi : float, drama_dpsi : float) -> NoneType eval_rama_score_residue_nonstandard_connection(...) from builtins.PyCapsule eval_rama_score_residue_nonstandard_connection(self : rosetta.core.scoring.Ramachandran, mypose : rosetta.core.pose.Pose, res : rosetta.core.conformation.Residue, rama : float, drama_dphi : float, drama_dpsi : float) -> NoneType   Function to evaluate the rama score for residues whose connection partners are not necessarily adjacent  in linear sequence (e.g. for backbone-cyclized peptides).  Note that this assumes that rama is being used only  for scoring alpha-amino acids (L- or D-).      Vikram K. Mulligan get_custom_rama_table_filename(...) from builtins.PyCapsule get_custom_rama_table_filename(self : rosetta.core.scoring.Ramachandran, type : rosetta.core.scoring.Rama_Table_Type) -> str   Given a custom Rama table type, get the filename of the database file containing  the data.      Accesses the options system for this information.      Vikram K. Mulligan (vmullig.edu) get_l_equivalent(...) from builtins.PyCapsule get_l_equivalent(self : rosetta.core.scoring.Ramachandran, d_aa : rosetta.core.chemical.AA) -> rosetta.core.chemical.AA get_ramatable_name_by_type(...) from builtins.PyCapsule get_ramatable_name_by_type(self : rosetta.core.scoring.Ramachandran, type : rosetta.core.scoring.Rama_Table_Type) -> str   Given a Rama_Table_Type, return the name.      Vikram K. Mulligan (vmullig.edu) get_ramatable_type_by_name(...) from builtins.PyCapsule get_ramatable_type_by_name(self : rosetta.core.scoring.Ramachandran, name : str) -> rosetta.core.scoring.Rama_Table_Type   Given a Rama_Table_Type name, return the type.      Calls get_rama_table_name_by_type().      Vikram K. Mulligan (vmullig.edu) is_canonical_d_aminoacid(...) from builtins.PyCapsule is_canonical_d_aminoacid(self : rosetta.core.scoring.Ramachandran, res_aa : rosetta.core.chemical.AA) -> bool is_normally_connected(...) from builtins.PyCapsule is_normally_connected(self : rosetta.core.scoring.Ramachandran, res : rosetta.core.conformation.Residue) -> bool   Function to do a quick check that the upper connection is seqpos+1 and the lower connection is seqpos-1.  Returns true if this is so, false otherwise.      Vikram K. Mulligan minimum_sampling_probability(...) from builtins.PyCapsule minimum_sampling_probability(rosetta.core.scoring.Ramachandran) -> float n_phi_bins(...) from builtins.PyCapsule n_phi_bins(rosetta.core.scoring.Ramachandran) -> int n_psi_bins(...) from builtins.PyCapsule n_psi_bins(rosetta.core.scoring.Ramachandran) -> int phipsi_in_allowed_rama(...) from builtins.PyCapsule phipsi_in_allowed_rama(self : rosetta.core.scoring.Ramachandran, res_aa : rosetta.core.chemical.AA, phi : float, psi : float) -> bool   Return true if the given phi/psi pair is in the allowed space  sampled by uniform_phipsi_from_allowed_rama. phipsi_in_forbidden_rama(...) from builtins.PyCapsule phipsi_in_forbidden_rama(self : rosetta.core.scoring.Ramachandran, res_aa : rosetta.core.chemical.AA, phi : float, psi : float) -> bool   Return false if the given phi/psi pair is in the allowed space  sampled by uniform_phipsi_from_allowed_rama. rama_power(...) from builtins.PyCapsule rama_power(rosetta.core.scoring.Ramachandran) -> float   Get rama_power value.      If used, rama values over 0 are raised to the Nth power.  Unused by default.      Vikram K. Mulligan (vmullig.edu) and Brian Koepnick. rama_probability(...) from builtins.PyCapsule rama_probability(self : rosetta.core.scoring.Ramachandran, aa : rosetta.core.chemical.AA, phi : float, psi : float) -> float random_phipsi_from_rama(...) from builtins.PyCapsule random_phipsi_from_rama(self : rosetta.core.scoring.Ramachandran, res_aa : rosetta.core.chemical.AA, phi : float, psi : float) -> NoneType   Generate random values for phi and psi, biased by the Ramachandran plot of a particular amino acid.      The amino acid in question.      Output phi value.      Output psi value. random_phipsi_from_rama_by_torsion_bin(...) from builtins.PyCapsule random_phipsi_from_rama_by_torsion_bin(self : rosetta.core.scoring.Ramachandran, res_aa : rosetta.core.chemical.AA, phi : float, psi : float, torsion_bin : rosetta.core.conformation.ppo_torsion_bin) -> NoneType   functions for torsion-bin specific but otherwise random phi/psi angles      Amelie Stein set_rama_power(...) from builtins.PyCapsule set_rama_power(self : rosetta.core.scoring.Ramachandran, setting : float) -> NoneType   Set rama_power value.      If used, rama values over 0 are raised to the Nth power.  Unused by default.      Vikram K. Mulligan (vmullig.edu) and Brian Koepnick. set_use_rama_power(...) from builtins.PyCapsule set_use_rama_power(self : rosetta.core.scoring.Ramachandran, setting : bool) -> NoneType   Set whether we're using the rama_power option, which scales rama values over 0.      Vikram K. Mulligan (vmullig.edu) and Brian Koepnick. uniform_phipsi_from_allowed_rama(...) from builtins.PyCapsule uniform_phipsi_from_allowed_rama(self : rosetta.core.scoring.Ramachandran, res_aa : rosetta.core.chemical.AA, phi : float, psi : float) -> NoneType   Return a phi/psi pair picked uniformly from the regions of rama  space with nonzero weight.  Sampling with this method will not give a  rama distribution; it will give a flat distribution in only the allowed  regions of rama space. use_rama_power(...) from builtins.PyCapsule use_rama_power(rosetta.core.scoring.Ramachandran) -> bool   Get whether we're using the rama_power option, which scales rama values over 0.      Vikram K. Mulligan (vmullig.edu) and Brian Koepnick. write_rama_score_all(...) from builtins.PyCapsule write_rama_score_all(self : rosetta.core.scoring.Ramachandran, pose : rosetta.core.pose.Pose) -> NoneType   class Ramachandran2B(builtins.object)       Methods defined here: IdealizeRamaEnergy(...) from builtins.PyCapsule IdealizeRamaEnergy(self : rosetta.core.scoring.Ramachandran2B, phi : float, psi : float, rama : float, drama_dphi : float, drama_dpsi : float, entropy : float, rama_for_res : ObjexxFCL::FArray2A<double>) -> NoneType RamaE(...) from builtins.PyCapsule RamaE(*args, **kwargs) Overloaded function.   1. RamaE(self : rosetta.core.scoring.Ramachandran2B, rsd : rosetta.core.conformation.Residue) -> float   2. RamaE(self : rosetta.core.scoring.Ramachandran2B, rsd : rosetta.core.conformation.Residue, drama_dphi : float, drama_dpsi : float) -> float   3. RamaE(self : rosetta.core.scoring.Ramachandran2B, phi : float, psi : float, rsd : rosetta.core.chemical.AA, drama_dphi : float, drama_dpsi : float) -> float RamaE_Lower(...) from builtins.PyCapsule RamaE_Lower(*args, **kwargs) Overloaded function.   1. RamaE_Lower(self : rosetta.core.scoring.Ramachandran2B, rsd : rosetta.core.conformation.Residue, neighbor : rosetta.core.chemical.AA) -> float   2. RamaE_Lower(self : rosetta.core.scoring.Ramachandran2B, rsd : rosetta.core.conformation.Residue, neighbor : rosetta.core.chemical.AA, drama_dphi : float, drama_dpsi : float) -> float   3. RamaE_Lower(self : rosetta.core.scoring.Ramachandran2B, phi : float, psi : float, rsd : rosetta.core.chemical.AA, neighbor : rosetta.core.chemical.AA) -> float   4. RamaE_Lower(self : rosetta.core.scoring.Ramachandran2B, phi : float, psi : float, rsd : rosetta.core.chemical.AA, neighbor : rosetta.core.chemical.AA, drama_dphi : float, drama_dpsi : float) -> float RamaE_Upper(...) from builtins.PyCapsule RamaE_Upper(*args, **kwargs) Overloaded function.   1. RamaE_Upper(self : rosetta.core.scoring.Ramachandran2B, rsd : rosetta.core.conformation.Residue, neighbor : rosetta.core.chemical.AA) -> float   2. RamaE_Upper(self : rosetta.core.scoring.Ramachandran2B, rsd : rosetta.core.conformation.Residue, neighbor : rosetta.core.chemical.AA, drama_dphi : float, drama_dpsi : float) -> float   3. RamaE_Upper(self : rosetta.core.scoring.Ramachandran2B, phi : float, psi : float, rsd : rosetta.core.chemical.AA, neighbor : rosetta.core.chemical.AA) -> float   4. RamaE_Upper(self : rosetta.core.scoring.Ramachandran2B, phi : float, psi : float, rsd : rosetta.core.chemical.AA, neighbor : rosetta.core.chemical.AA, drama_dphi : float, drama_dpsi : float) -> float __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.Ramachandran2B) -> NoneType   2. __init__(self : rosetta.core.scoring.Ramachandran2B,  : rosetta.core.scoring.Ramachandran2B) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. eval_rama_score_all(...) from builtins.PyCapsule eval_rama_score_all(self : rosetta.core.scoring.Ramachandran2B, pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   //////////////////////////// eval_rama_score_residue(...) from builtins.PyCapsule eval_rama_score_residue(*args, **kwargs) Overloaded function.   1. eval_rama_score_residue(self : rosetta.core.scoring.Ramachandran2B, res_aa : rosetta.core.chemical.AA, phi : float, psi : float) -> float   2. eval_rama_score_residue(self : rosetta.core.scoring.Ramachandran2B, res : rosetta.core.conformation.Residue, left_aa : rosetta.core.chemical.AA, right_aa : rosetta.core.chemical.AA, rama : float, drama_dphi : float, drama_dpsi : float) -> NoneType   3. eval_rama_score_residue(self : rosetta.core.scoring.Ramachandran2B, phi : float, psi : float, res : rosetta.core.chemical.AA, left_aa : rosetta.core.chemical.AA, right_aa : rosetta.core.chemical.AA) -> float   4. eval_rama_score_residue(self : rosetta.core.scoring.Ramachandran2B, phi : float, psi : float, res : rosetta.core.chemical.AA, left_aa : rosetta.core.chemical.AA, right_aa : rosetta.core.chemical.AA, drama_dphi : float, drama_dpsi : float) -> float   5. eval_rama_score_residue(self : rosetta.core.scoring.Ramachandran2B, res : rosetta.core.conformation.Residue, rama : float, drama_dphi : float, drama_dpsi : float) -> NoneType   6. eval_rama_score_residue(self : rosetta.core.scoring.Ramachandran2B, res_aa : rosetta.core.chemical.AA, phi : float, psi : float, rama : float, drama_dphi : float, drama_dpsi : float) -> NoneType left_cdf(...) from builtins.PyCapsule left_cdf(self : rosetta.core.scoring.Ramachandran2B, aa_left : rosetta.core.chemical.AA, aa_center : rosetta.core.chemical.AA) -> rosetta.utility.vector1_double left_cdf_for_torsion_bin(...) from builtins.PyCapsule left_cdf_for_torsion_bin(self : rosetta.core.scoring.Ramachandran2B, aa_left : rosetta.core.chemical.AA, aa_center : rosetta.core.chemical.AA,  : rosetta.core.conformation.ppo_torsion_bin) -> rosetta.utility.vector1_double minimum_sampling_probability(...) from builtins.PyCapsule minimum_sampling_probability(rosetta.core.scoring.Ramachandran2B) -> float n_phi_bins(...) from builtins.PyCapsule n_phi_bins(rosetta.core.scoring.Ramachandran2B) -> int n_psi_bins(...) from builtins.PyCapsule n_psi_bins(rosetta.core.scoring.Ramachandran2B) -> int rama_bin_probability_left(...) from builtins.PyCapsule rama_bin_probability_left(self : rosetta.core.scoring.Ramachandran2B, aa_left : rosetta.core.chemical.AA, aa_center : rosetta.core.chemical.AA, phi : float, psi : float) -> float rama_bin_probability_right(...) from builtins.PyCapsule rama_bin_probability_right(self : rosetta.core.scoring.Ramachandran2B, aa_center : rosetta.core.chemical.AA, aa_right : rosetta.core.chemical.AA, phi : float, psi : float) -> float random_phipsi_from_rama_by_torsion_bin_left(...) from builtins.PyCapsule random_phipsi_from_rama_by_torsion_bin_left(self : rosetta.core.scoring.Ramachandran2B, left_aa : rosetta.core.chemical.AA, pos_aa : rosetta.core.chemical.AA, phi : float, psi : float, torsion_bin : rosetta.core.conformation.ppo_torsion_bin) -> NoneType   function for torsion-bin specific but otherwise random phi/psi angles      Amelie Stein random_phipsi_from_rama_by_torsion_bin_right(...) from builtins.PyCapsule random_phipsi_from_rama_by_torsion_bin_right(self : rosetta.core.scoring.Ramachandran2B, pos_aa : rosetta.core.chemical.AA, right_aa : rosetta.core.chemical.AA, phi : float, psi : float, torsion_bin : rosetta.core.conformation.ppo_torsion_bin) -> NoneType random_phipsi_from_rama_left(...) from builtins.PyCapsule random_phipsi_from_rama_left(self : rosetta.core.scoring.Ramachandran2B, left_aa : rosetta.core.chemical.AA, pos_aa : rosetta.core.chemical.AA, phi : float, psi : float) -> NoneType   pick a phi/psi pair chosen from the rama2b distribution so that the most  commonly observed phi/psi pairs are chosen at higher probability than the least  commonly observed pairs; use the phi/psi distribution for the central aa (the pos aa)  based on its "left" (n-terminal) neighbor's amino acid type. random_phipsi_from_rama_right(...) from builtins.PyCapsule random_phipsi_from_rama_right(self : rosetta.core.scoring.Ramachandran2B, pos_aa : rosetta.core.chemical.AA, right_aa : rosetta.core.chemical.AA, phi : float, psi : float) -> NoneType   pick a phi/psi pair chosen from the rama2b distribution so that the most  commonly observed phi/psi pairs are chosen at higher probability than the least  commonly observed pairs; use the phi/psi distribution for the central aa (the pos aa)  based on its "right" (c-terminal) neighbor's amino acid type. right_cdf(...) from builtins.PyCapsule right_cdf(self : rosetta.core.scoring.Ramachandran2B, aa_center : rosetta.core.chemical.AA, aa_right : rosetta.core.chemical.AA) -> rosetta.utility.vector1_double right_cdf_for_torsion_bin(...) from builtins.PyCapsule right_cdf_for_torsion_bin(self : rosetta.core.scoring.Ramachandran2B, aa_center : rosetta.core.chemical.AA, aa_right : rosetta.core.chemical.AA,  : rosetta.core.conformation.ppo_torsion_bin) -> rosetta.utility.vector1_double write_rama_score_all(...) from builtins.PyCapsule write_rama_score_all(self : rosetta.core.scoring.Ramachandran2B, pose : rosetta.core.pose.Pose) -> NoneType   class ResPairMinimizationData(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.ResPairMinimizationData) -> NoneType   2. __init__(self : rosetta.core.scoring.ResPairMinimizationData,  : rosetta.core.scoring.ResPairMinimizationData) -> 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.scoring.ResPairMinimizationData,  : rosetta.core.scoring.ResPairMinimizationData) -> rosetta.core.scoring.ResPairMinimizationData get_data(...) from builtins.PyCapsule get_data(*args, **kwargs) Overloaded function.   1. get_data(self : rosetta.core.scoring.ResPairMinimizationData, index : rosetta.core.scoring.min_pair_data) -> rosetta.basic.datacache.CacheableData   2. get_data(self : rosetta.core.scoring.ResPairMinimizationData, index : rosetta.core.scoring.min_pair_data) -> rosetta.basic.datacache.CacheableData get_data_ref(...) from builtins.PyCapsule get_data_ref(*args, **kwargs) Overloaded function.   1. get_data_ref(self : rosetta.core.scoring.ResPairMinimizationData, index : rosetta.core.scoring.min_pair_data) -> rosetta.basic.datacache.CacheableData   2. get_data_ref(self : rosetta.core.scoring.ResPairMinimizationData, index : rosetta.core.scoring.min_pair_data) -> rosetta.basic.datacache.CacheableData set_data(...) from builtins.PyCapsule set_data(self : rosetta.core.scoring.ResPairMinimizationData, index : rosetta.core.scoring.min_pair_data,  : rosetta.basic.datacache.CacheableData) -> NoneType   class ResRangePredicate(Predicate)     ///////////////////     Method resolution order: ResRangePredicate Predicate builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.core.scoring.ResRangePredicate, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, resno : int, atomno : int) -> bool __init__(...) from builtins.PyCapsule __init__(self : handle, start : int, end : int, predicate : rosetta.core.scoring.Predicate) -> 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.scoring.ResRangePredicate,  : rosetta.core.scoring.ResRangePredicate) -> rosetta.core.scoring.ResRangePredicate   class ResSingleMinimizationData(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.ResSingleMinimizationData) -> NoneType   2. __init__(self : rosetta.core.scoring.ResSingleMinimizationData,  : rosetta.core.scoring.ResSingleMinimizationData) -> 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.scoring.ResSingleMinimizationData,  : rosetta.core.scoring.ResSingleMinimizationData) -> rosetta.core.scoring.ResSingleMinimizationData get_data(...) from builtins.PyCapsule get_data(*args, **kwargs) Overloaded function.   1. get_data(self : rosetta.core.scoring.ResSingleMinimizationData, index : rosetta.core.scoring.min_single_data) -> rosetta.basic.datacache.CacheableData   2. get_data(self : rosetta.core.scoring.ResSingleMinimizationData, index : rosetta.core.scoring.min_single_data) -> rosetta.basic.datacache.CacheableData get_data_ref(...) from builtins.PyCapsule get_data_ref(*args, **kwargs) Overloaded function.   1. get_data_ref(self : rosetta.core.scoring.ResSingleMinimizationData, index : rosetta.core.scoring.min_single_data) -> rosetta.basic.datacache.CacheableData   2. get_data_ref(self : rosetta.core.scoring.ResSingleMinimizationData, index : rosetta.core.scoring.min_single_data) -> rosetta.basic.datacache.CacheableData set_data(...) from builtins.PyCapsule set_data(self : rosetta.core.scoring.ResSingleMinimizationData, index : rosetta.core.scoring.min_single_data, data : rosetta.basic.datacache.CacheableData) -> NoneType   class ResidualDipolarCoupling(rosetta.basic.datacache.CacheableData)     ResidualDipolarCouplings are mainly handled by this class     related classed: RDC --- a single line in an RDC file - representing a single dipolar coupling                         ResidualDipolarCouplingEnergy -- an energy method which triggers computations handled by this class.     Method resolution order: ResidualDipolarCoupling rosetta.basic.datacache.CacheableData builtins.object Methods defined here: Q(...) from builtins.PyCapsule Q(rosetta.core.scoring.ResidualDipolarCoupling) -> float   return the Q value ( cornilescu )  --- only valid after compute_dipscore R(...) from builtins.PyCapsule R(rosetta.core.scoring.ResidualDipolarCoupling) -> float   return the R value ( M Clore )  --- only valid after compute_dipscore __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   doc   2. __init__(self : handle, filename : str) -> NoneType   3. __init__(self : handle, data_in : rosetta.utility.vector1_core_scoring_RDC) -> NoneType   4. __init__(handle, rosetta.core.scoring.ResidualDipolarCoupling) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.scoring.ResidualDipolarCoupling) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.ResidualDipolarCoupling, other : rosetta.core.scoring.ResidualDipolarCoupling) -> rosetta.core.scoring.ResidualDipolarCoupling clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.ResidualDipolarCoupling) -> rosetta.basic.datacache.CacheableData compute_dipscore(...) from builtins.PyCapsule compute_dipscore(self : rosetta.core.scoring.ResidualDipolarCoupling, pose : rosetta.core.pose.Pose) -> float   compute dipolar score for given pose  will set alignment tensor and force-fields in RDC compute_dipscore_nls(...) from builtins.PyCapsule compute_dipscore_nls(*args, **kwargs) Overloaded function.   1. compute_dipscore_nls(self : rosetta.core.scoring.ResidualDipolarCoupling, pose : rosetta.core.pose.Pose) -> float   fit rdc using RDC data   2. compute_dipscore_nls(self : rosetta.core.scoring.ResidualDipolarCoupling, pose : rosetta.core.pose.Pose, tensorDa : rosetta.utility.vector1_double, tensorR : rosetta.utility.vector1_double) -> float compute_dipscore_nlsDa(...) from builtins.PyCapsule compute_dipscore_nlsDa(self : rosetta.core.scoring.ResidualDipolarCoupling, pose : rosetta.core.pose.Pose, tensorDa : rosetta.utility.vector1_double) -> float compute_dipscore_nlsDaR(...) from builtins.PyCapsule compute_dipscore_nlsDaR(self : rosetta.core.scoring.ResidualDipolarCoupling, pose : rosetta.core.pose.Pose, tensorDa : rosetta.utility.vector1_double, tensorR : rosetta.utility.vector1_double) -> float compute_dipscore_nlsR(...) from builtins.PyCapsule compute_dipscore_nlsR(self : rosetta.core.scoring.ResidualDipolarCoupling, pose : rosetta.core.pose.Pose, tensorR : rosetta.utility.vector1_double) -> float compute_tensor_stats(...) from builtins.PyCapsule compute_tensor_stats(rosetta.core.scoring.ResidualDipolarCoupling) -> NoneType do_correct_NH(...) from builtins.PyCapsule do_correct_NH(self : rosetta.core.scoring.ResidualDipolarCoupling, it : __gnu_cxx::__normal_iterator<core::scoring::RDC const*, std::vector<core::scoring::RDC, std::allocator<core::scoring::RDC> > >, r : rosetta.numeric.xyzVector_double_t, r2 : float, invr : float) -> NoneType get_RDC_data(...) from builtins.PyCapsule get_RDC_data(rosetta.core.scoring.ResidualDipolarCoupling) -> rosetta.utility.vector1_core_scoring_RDC   get the raw RDC data get_al_tensor_max_z(...) from builtins.PyCapsule get_al_tensor_max_z(self : rosetta.core.scoring.ResidualDipolarCoupling, ex : int) -> float get_al_tensor_trace(...) from builtins.PyCapsule get_al_tensor_trace(self : rosetta.core.scoring.ResidualDipolarCoupling, ex : int) -> float get_n_alignments(...) from builtins.PyCapsule get_n_alignments(rosetta.core.scoring.ResidualDipolarCoupling) -> int iterate_tensor_weights(...) from builtins.PyCapsule iterate_tensor_weights(self : rosetta.core.scoring.ResidualDipolarCoupling, pose : rosetta.core.pose.Pose, sigma2 : float, tolerance : float, reset : bool) -> float preprocess_data(...) from builtins.PyCapsule preprocess_data(rosetta.core.scoring.ResidualDipolarCoupling) -> NoneType   fill internal buffers... call always when RDC lines change. read_RDC_file(...) from builtins.PyCapsule read_RDC_file(rosetta.core.scoring.ResidualDipolarCoupling) -> NoneType   read RDC data from file release_buffers(...) from builtins.PyCapsule release_buffers(rosetta.core.scoring.ResidualDipolarCoupling) -> NoneType   free memory of buffers reserve_buffers(...) from builtins.PyCapsule reserve_buffers(rosetta.core.scoring.ResidualDipolarCoupling) -> NoneType   get memory for buffers tensor(...) from builtins.PyCapsule tensor(rosetta.core.scoring.ResidualDipolarCoupling) -> rosetta.utility.vector0_utility_fixedsizearray0_utility_fixedsizearray0_double_3_3_t   return tensor of certain experiment... exp_id starts at 1 Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class ResidualDipolarCoupling_Rohl(rosetta.basic.datacache.CacheableData)       Method resolution order: ResidualDipolarCoupling_Rohl rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, data_in : rosetta.utility.vector1_core_scoring_RDC_Rohl) -> NoneType   3. __init__(handle, rosetta.core.scoring.ResidualDipolarCoupling_Rohl) -> 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.scoring.ResidualDipolarCoupling_Rohl,  : rosetta.core.scoring.ResidualDipolarCoupling_Rohl) -> rosetta.core.scoring.ResidualDipolarCoupling_Rohl clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.ResidualDipolarCoupling_Rohl) -> rosetta.basic.datacache.CacheableData get_RDC_data(...) from builtins.PyCapsule get_RDC_data(rosetta.core.scoring.ResidualDipolarCoupling_Rohl) -> rosetta.utility.vector1_core_scoring_RDC_Rohl get_RDC_data_type(...) from builtins.PyCapsule get_RDC_data_type(self : rosetta.core.scoring.ResidualDipolarCoupling_Rohl, atom1 : str, atom2 : str) -> int read_RDC_file(...) from builtins.PyCapsule read_RDC_file(rosetta.core.scoring.ResidualDipolarCoupling_Rohl) -> NoneType Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class ResidueNblistData(rosetta.basic.datacache.CacheableData)       Method resolution order: ResidueNblistData rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.scoring.ResidueNblistData) -> 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.scoring.ResidueNblistData,  : rosetta.core.scoring.ResidueNblistData) -> rosetta.core.scoring.ResidueNblistData atom_neighbors(...) from builtins.PyCapsule atom_neighbors(rosetta.core.scoring.ResidueNblistData) -> rosetta.utility.vector1_core_scoring_SmallAtNb clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.ResidueNblistData) -> rosetta.basic.datacache.CacheableData initialize(...) from builtins.PyCapsule initialize(*args, **kwargs) Overloaded function.   1. initialize(self : rosetta.core.scoring.ResidueNblistData, res : rosetta.core.conformation.Residue, cpfxn : rosetta.core.scoring.etable.count_pair.CountPairFunction) -> NoneType   Initialize the residue-nblist; if there are no intra-residue interactions, then provide a null-pointing  count-pair function.   2. initialize(self : rosetta.core.scoring.ResidueNblistData, res : rosetta.core.conformation.Residue, cpfxn : rosetta.core.scoring.etable.count_pair.CountPairFunction, heavy_heavy_dist_cutoff : float) -> NoneType   Initialize the residue-nblist; if there are no intra-residue interactions, then provide a null-pointing  count-pair function.   3. initialize(self : rosetta.core.scoring.ResidueNblistData, res : rosetta.core.conformation.Residue, cpfxn : rosetta.core.scoring.etable.count_pair.CountPairFunction, heavy_heavy_dist_cutoff : float, heavy_hydrogen_dist_cutoff : float) -> NoneType   Initialize the residue-nblist; if there are no intra-residue interactions, then provide a null-pointing  count-pair function.   4. initialize(self : rosetta.core.scoring.ResidueNblistData, res : rosetta.core.conformation.Residue, cpfxn : rosetta.core.scoring.etable.count_pair.CountPairFunction, heavy_heavy_dist_cutoff : float, heavy_hydrogen_dist_cutoff : float, hydrogen_hydrogen_dist_cutoff : float) -> NoneType   Initialize the residue-nblist; if there are no intra-residue interactions, then provide a null-pointing  count-pair function. Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class ResidueNeighborConstIterator(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.scoring.ResidueNeighborConstIterator,  : rosetta.core.scoring.ResidueNeighborConstIterator) -> bool __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.ResidueNeighborConstIterator) -> NoneType __ne__(...) from builtins.PyCapsule __ne__(self : rosetta.core.scoring.ResidueNeighborConstIterator,  : rosetta.core.scoring.ResidueNeighborConstIterator) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. accumulate_energy(...) from builtins.PyCapsule accumulate_energy(self : rosetta.core.scoring.ResidueNeighborConstIterator,  : rosetta.core.scoring.EMapVector) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.ResidueNeighborConstIterator,  : rosetta.core.scoring.ResidueNeighborConstIterator) -> rosetta.core.scoring.ResidueNeighborConstIterator energy_computed(...) from builtins.PyCapsule energy_computed(rosetta.core.scoring.ResidueNeighborConstIterator) -> bool lower_neighbor_id(...) from builtins.PyCapsule lower_neighbor_id(rosetta.core.scoring.ResidueNeighborConstIterator) -> int neighbor_id(...) from builtins.PyCapsule neighbor_id(rosetta.core.scoring.ResidueNeighborConstIterator) -> int plus_plus(...) from builtins.PyCapsule plus_plus(rosetta.core.scoring.ResidueNeighborConstIterator) -> rosetta.core.scoring.ResidueNeighborConstIterator residue_iterated_on(...) from builtins.PyCapsule residue_iterated_on(rosetta.core.scoring.ResidueNeighborConstIterator) -> int retrieve_energy(...) from builtins.PyCapsule retrieve_energy(self : rosetta.core.scoring.ResidueNeighborConstIterator,  : rosetta.core.scoring.EMapVector) -> NoneType upper_neighbor_id(...) from builtins.PyCapsule upper_neighbor_id(rosetta.core.scoring.ResidueNeighborConstIterator) -> int   class ResidueNeighborIterator(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(self : rosetta.core.scoring.ResidueNeighborIterator,  : rosetta.core.scoring.ResidueNeighborIterator) -> bool __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.ResidueNeighborIterator) -> NoneType __ne__(...) from builtins.PyCapsule __ne__(self : rosetta.core.scoring.ResidueNeighborIterator,  : rosetta.core.scoring.ResidueNeighborIterator) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. accumulate_energy(...) from builtins.PyCapsule accumulate_energy(self : rosetta.core.scoring.ResidueNeighborIterator,  : rosetta.core.scoring.EMapVector) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.ResidueNeighborIterator,  : rosetta.core.scoring.ResidueNeighborIterator) -> rosetta.core.scoring.ResidueNeighborIterator energy_computed(...) from builtins.PyCapsule energy_computed(rosetta.core.scoring.ResidueNeighborIterator) -> bool lower_neighbor_id(...) from builtins.PyCapsule lower_neighbor_id(rosetta.core.scoring.ResidueNeighborIterator) -> int mark_energy_computed(...) from builtins.PyCapsule mark_energy_computed(rosetta.core.scoring.ResidueNeighborIterator) -> NoneType mark_energy_uncomputed(...) from builtins.PyCapsule mark_energy_uncomputed(rosetta.core.scoring.ResidueNeighborIterator) -> NoneType neighbor_id(...) from builtins.PyCapsule neighbor_id(rosetta.core.scoring.ResidueNeighborIterator) -> int plus_plus(...) from builtins.PyCapsule plus_plus(rosetta.core.scoring.ResidueNeighborIterator) -> rosetta.core.scoring.ResidueNeighborIterator residue_iterated_on(...) from builtins.PyCapsule residue_iterated_on(rosetta.core.scoring.ResidueNeighborIterator) -> int retrieve_energy(...) from builtins.PyCapsule retrieve_energy(self : rosetta.core.scoring.ResidueNeighborIterator,  : rosetta.core.scoring.EMapVector) -> NoneType save_energy(...) from builtins.PyCapsule save_energy(self : rosetta.core.scoring.ResidueNeighborIterator,  : rosetta.core.scoring.EMapVector) -> NoneType upper_neighbor_id(...) from builtins.PyCapsule upper_neighbor_id(rosetta.core.scoring.ResidueNeighborIterator) -> int   class ResiduePairNeighborList(rosetta.basic.datacache.CacheableData)       Method resolution order: ResiduePairNeighborList rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.scoring.ResiduePairNeighborList) -> 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.scoring.ResiduePairNeighborList,  : rosetta.core.scoring.ResiduePairNeighborList) -> rosetta.core.scoring.ResiduePairNeighborList atom_neighbors(...) from builtins.PyCapsule atom_neighbors(rosetta.core.scoring.ResiduePairNeighborList) -> rosetta.utility.vector1_core_scoring_SmallAtNb clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.ResiduePairNeighborList) -> rosetta.basic.datacache.CacheableData initialize_from_residues(...) from builtins.PyCapsule initialize_from_residues(*args, **kwargs) Overloaded function.   1. initialize_from_residues(self : rosetta.core.scoring.ResiduePairNeighborList, vvd2 : float, hvd2 : float, hhd2 : float, r1 : rosetta.core.conformation.Residue, r2 : rosetta.core.conformation.Residue, cpfxn : rosetta.core.scoring.etable.count_pair.CountPairFunction) -> NoneType   2. initialize_from_residues(self : rosetta.core.scoring.ResiduePairNeighborList, vvd2 : float, hvd2 : float, hhd2 : float, r1 : rosetta.core.conformation.Residue, r2 : rosetta.core.conformation.Residue, cpfxn : rosetta.core.scoring.etable.count_pair.CountPairFunction, r1_map : rosetta.std.map_unsigned_long_unsigned_long, r2_map : rosetta.std.map_unsigned_long_unsigned_long) -> NoneType Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class SASAPotential(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.SASAPotential) -> 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.scoring.SASAPotential,  : rosetta.core.scoring.SASAPotential) -> rosetta.core.scoring.SASAPotential eval_residue_pair_derivatives(...) from builtins.PyCapsule eval_residue_pair_derivatives(self : rosetta.core.scoring.SASAPotential, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, factor : float, r1_atom_derivs : rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_atom_derivs : rosetta.utility.vector1_core_scoring_DerivVectorPair) -> NoneType get_res_res_sasa(...) from builtins.PyCapsule get_res_res_sasa(self : rosetta.core.scoring.SASAPotential, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue) -> float setup_for_scoring(...) from builtins.PyCapsule setup_for_scoring(self : rosetta.core.scoring.SASAPotential, pose : rosetta.core.pose.Pose) -> NoneType vertex_count(...) from builtins.PyCapsule vertex_count(rosetta.core.scoring.SASAPotential) -> int   class SAnode(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.core.scoring.SAnode, inter : rosetta.core.scoring.PDinter, other_atom : rosetta.core.scoring.PDatom, ct : float, phi : float) -> NoneType   2. __init__(self : rosetta.core.scoring.SAnode, inter : rosetta.core.scoring.PDinter, other_atom : rosetta.core.scoring.PDatom) -> 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.scoring.SAnode,  : rosetta.core.scoring.SAnode) -> rosetta.core.scoring.SAnode cos_theta(...) from builtins.PyCapsule cos_theta(rosetta.core.scoring.SAnode) -> float inter(...) from builtins.PyCapsule inter(rosetta.core.scoring.SAnode) -> rosetta.core.scoring.PDinter other_atom(...) from builtins.PyCapsule other_atom(rosetta.core.scoring.SAnode) -> rosetta.core.scoring.PDatom phi(...) from builtins.PyCapsule phi(rosetta.core.scoring.SAnode) -> float set_cos_theta(...) from builtins.PyCapsule set_cos_theta(self : rosetta.core.scoring.SAnode, ct : float) -> NoneType set_phi(...) from builtins.PyCapsule set_phi(self : rosetta.core.scoring.SAnode, p : float) -> NoneType xyz(...) from builtins.PyCapsule xyz(rosetta.core.scoring.SAnode) -> rosetta.numeric.xyzVector_double_t   class SS_Info(rosetta.basic.datacache.CacheableData)     ///////////////////////////////////////////////////////////////////////////////////////////////////     Method resolution order: SS_Info rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle, rosetta.core.scoring.SS_Info) -> NoneType   2. __init__(handle) -> 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.scoring.SS_Info,  : rosetta.core.scoring.SS_Info) -> rosetta.core.scoring.SS_Info bb_pos(...) from builtins.PyCapsule bb_pos(*args, **kwargs) Overloaded function.   1. bb_pos(rosetta.core.scoring.SS_Info) -> rosetta.core.scoring.BB_Pos   2. bb_pos(rosetta.core.scoring.SS_Info) -> rosetta.core.scoring.BB_Pos clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.SS_Info) -> rosetta.basic.datacache.CacheableData helices(...) from builtins.PyCapsule helices(*args, **kwargs) Overloaded function.   1. helices(rosetta.core.scoring.SS_Info) -> rosetta.core.scoring.Helices   2. helices(rosetta.core.scoring.SS_Info) -> rosetta.core.scoring.Helices resize(...) from builtins.PyCapsule resize(self : rosetta.core.scoring.SS_Info, nres : int) -> NoneType strands(...) from builtins.PyCapsule strands(*args, **kwargs) Overloaded function.   1. strands(rosetta.core.scoring.SS_Info) -> rosetta.core.scoring.Strands   2. strands(rosetta.core.scoring.SS_Info) -> rosetta.core.scoring.Strands Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class SS_Killhairpins_Info(rosetta.basic.datacache.CacheableData)     ///////////////////////////////////////////////////////////////////////////////////////////////////     Method resolution order: SS_Killhairpins_Info rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.scoring.SS_Killhairpins_Info) -> 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.scoring.SS_Killhairpins_Info,  : rosetta.core.scoring.SS_Killhairpins_Info) -> rosetta.core.scoring.SS_Killhairpins_Info check_hairpin(...) from builtins.PyCapsule check_hairpin(self : rosetta.core.scoring.SS_Killhairpins_Info, strand1_res : int, strand2_res : int) -> bool clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.SS_Killhairpins_Info) -> rosetta.basic.datacache.CacheableData hairpins(...) from builtins.PyCapsule hairpins(*args, **kwargs) Overloaded function.   1. hairpins(rosetta.core.scoring.SS_Killhairpins_Info) -> rosetta.core.scoring.Hairpins   2. hairpins(rosetta.core.scoring.SS_Killhairpins_Info) -> rosetta.core.scoring.Hairpins kill_antiparallel(...) from builtins.PyCapsule kill_antiparallel(rosetta.core.scoring.SS_Killhairpins_Info) -> bool kill_parallel(...) from builtins.PyCapsule kill_parallel(rosetta.core.scoring.SS_Killhairpins_Info) -> bool setup_from_kill_hairpins_file(...) from builtins.PyCapsule setup_from_kill_hairpins_file(self : rosetta.core.scoring.SS_Killhairpins_Info, input_file : rosetta.utility.io.izstream) -> NoneType setup_from_psipred(...) from builtins.PyCapsule setup_from_psipred(self : rosetta.core.scoring.SS_Killhairpins_Info, input_file : rosetta.utility.io.izstream) -> NoneType setup_killhairpins(...) from builtins.PyCapsule setup_killhairpins(rosetta.core.scoring.SS_Killhairpins_Info) -> NoneType Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class ScoreFunction(builtins.object)     This object defines a ScoreFunction, it contains methods for calculating the various scoring components (called ScoreType's) used in Rosetta. It also contains weights that are applied to each of those components. Only scoring components with non-zero weights are calculated.     Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> float   //////////////////////////////////////////////////////////////////////////      Scores the given  <pose>  using this ScoreFunction. Alters the  Energies object within  <pose>, but does not alter this ScoreFunction __getitem__(...) from builtins.PyCapsule __getitem__(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType) -> float   Returns the weight of the ScoreType  <t>    example(s):      scorefxn[fa_sol]  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.set_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name __init__(...) from builtins.PyCapsule __init__(handle) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.scoring.ScoreFunction) -> str add_extra_method(...) from builtins.PyCapsule add_extra_method(*args, **kwargs) Overloaded function.   1. add_extra_method(self : rosetta.core.scoring.ScoreFunction, new_type : rosetta.core.scoring.ScoreType, new_weight : float, new_method : core::scoring::methods::EnergyMethod) -> NoneType   Adds a scoring method that is not necessarily included in  the core library   2. add_extra_method(self : rosetta.core.scoring.ScoreFunction, new_weights : rosetta.std.map_core_scoring_ScoreType_double, new_method : core::scoring::methods::EnergyMethod) -> NoneType   Adds a scoring method that is not necessarily included in  the core library add_weights_from_file(...) from builtins.PyCapsule add_weights_from_file(self : rosetta.core.scoring.ScoreFunction, filename : str) -> NoneType   Initializes this ScoreFunction from the given  <filename> all_energies_begin(...) from builtins.PyCapsule all_energies_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::EnergyMethod const> const*, std::vector<std::shared_ptr<core::scoring::methods::EnergyMethod const>, std::allocator<std::shared_ptr<core::scoring::methods::EnergyMethod const> > > > all_energies_end(...) from builtins.PyCapsule all_energies_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::EnergyMethod const> const*, std::vector<std::shared_ptr<core::scoring::methods::EnergyMethod const>, std::allocator<std::shared_ptr<core::scoring::methods::EnergyMethod const> > > > all_methods(...) from builtins.PyCapsule all_methods(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t any_lr_residue_pair_energy(...) from builtins.PyCapsule any_lr_residue_pair_energy(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, res1 : int, res2 : int) -> bool apply_patch_from_file(...) from builtins.PyCapsule apply_patch_from_file(self : rosetta.core.scoring.ScoreFunction, filename : str) -> NoneType   Applies a patch from the given  <filename> are_they_neighbors(...) from builtins.PyCapsule are_they_neighbors(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, pos1 : int, pos2 : int) -> bool   Returns true if the  <pose>  positions  <pos1>  and  <pos2>  are neighbors assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.ScoreFunction, src : rosetta.core.scoring.ScoreFunction) -> NoneType   NOT FOR GENERAL USE  Copy the information about src into the current score function.  There are deep interactions with subclasses,  (the subclass information doesn't necessarily get copied)  so this is primarily for advanced scorefunction manipulation.  Normal usage should just use clone() and replace the OP. bump_check_backbone(...) from builtins.PyCapsule bump_check_backbone(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Scores the sidechain from  <pose>  Residue  <rsd1>  against the  backbone of Residue  <rsd2> bump_check_full(...) from builtins.PyCapsule bump_check_full(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType cd_1b_types(...) from builtins.PyCapsule cd_1b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType   convenience access to all cd 1b score types cd_2b_begin(...) from builtins.PyCapsule cd_2b_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy> > > > cd_2b_end(...) from builtins.PyCapsule cd_2b_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextDependentTwoBodyEnergy> > > > cd_2b_intrares_begin(...) from builtins.PyCapsule cd_2b_intrares_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> > > > cd_2b_intrares_end(...) from builtins.PyCapsule cd_2b_intrares_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> > > > cd_2b_types(...) from builtins.PyCapsule cd_2b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType   convenience access to all cd 2b score types cd_lr_2b_methods_begin(...) from builtins.PyCapsule cd_lr_2b_methods_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy> > > > cd_lr_2b_methods_end(...) from builtins.PyCapsule cd_lr_2b_methods_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextDependentLRTwoBodyEnergy> > > > cd_lr_2b_types(...) from builtins.PyCapsule cd_lr_2b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType check_methods_in_right_order(...) from builtins.PyCapsule check_methods_in_right_order(self : rosetta.core.scoring.ScoreFunction, score_type_in_first_method : rosetta.core.scoring.ScoreType, score_type_in_second_method : rosetta.core.scoring.ScoreType) -> bool   check order of methods ci_1b_types(...) from builtins.PyCapsule ci_1b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType   convenience access to all ci 1b score types ci_2b_begin(...) from builtins.PyCapsule ci_2b_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy> > > > ci_2b_end(...) from builtins.PyCapsule ci_2b_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextIndependentTwoBodyEnergy> > > > ci_2b_intrares_begin(...) from builtins.PyCapsule ci_2b_intrares_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> > > > ci_2b_intrares_end(...) from builtins.PyCapsule ci_2b_intrares_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::TwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::TwoBodyEnergy> > > > ci_2b_types(...) from builtins.PyCapsule ci_2b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType   convenience access to all ci 2b score types ci_lr_2b_methods_begin(...) from builtins.PyCapsule ci_lr_2b_methods_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy> > > > ci_lr_2b_methods_end(...) from builtins.PyCapsule ci_lr_2b_methods_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::ContextIndependentLRTwoBodyEnergy> > > > ci_lr_2b_types(...) from builtins.PyCapsule ci_lr_2b_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.ScoreFunction) -> rosetta.core.scoring.ScoreFunction   Create a copy of the scorefunction  Virtual to keep subclass information. clone_as_base_class(...) from builtins.PyCapsule clone_as_base_class(rosetta.core.scoring.ScoreFunction) -> rosetta.core.scoring.ScoreFunction   If you *want* to discard subclass information, the following function is availible energy_method_options(...) from builtins.PyCapsule energy_method_options(rosetta.core.scoring.ScoreFunction) -> core::scoring::methods::EnergyMethodOptions   Returns the EnergyMethodOptions object contained in this  ScoreFunction (const access) eval_cd_1b(...) from builtins.PyCapsule eval_cd_1b(self : rosetta.core.scoring.ScoreFunction, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted one body energies of all context  dependent one body energies for  <pose>  Residue  <rsd>  into  EnergyMap  <emap>     : EnergyMap is an EMapVector eval_cd_2b(...) from builtins.PyCapsule eval_cd_2b(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulate the unweighted short range context dependent two body  interaction energies of  <pose>  between Residue  <rsd1>  and Residue  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_cd_2b_bb_bb(...) from builtins.PyCapsule eval_cd_2b_bb_bb(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted short ranged context dependent two body  interaction energies of  <pose>  between the backbones of Residue  <rsd1>  and  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_cd_2b_bb_sc(...) from builtins.PyCapsule eval_cd_2b_bb_sc(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted short ranged context dependent two body  interaction energies of  <pose>  between the backbone of Residue  <rsd1>  and the sidechain of Residue  <rsd2>  into EnergyMap <emap>     : EnergyMap is an EMapVector eval_cd_2b_sc_sc(...) from builtins.PyCapsule eval_cd_2b_sc_sc(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted short ranged context dependent two body  interaction energies of  <pose>  between the sidechains of Residue  <rsd1>  and Residue  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_cd_intrares_energy(...) from builtins.PyCapsule eval_cd_intrares_energy(self : rosetta.core.scoring.ScoreFunction, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted intra-residue one body energies for all  context dependent two body terms that define intra-residue energies of  <pose>  Residue  <rsd>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_ci_1b(...) from builtins.PyCapsule eval_ci_1b(self : rosetta.core.scoring.ScoreFunction, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType eval_ci_2b(...) from builtins.PyCapsule eval_ci_2b(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted context independent two body  interaction energies of  <pose>  between Residue  <rsd1>  and Residue  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_ci_2b_bb_bb(...) from builtins.PyCapsule eval_ci_2b_bb_bb(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted context independent two body  interaction energies of  <pose>  between the backbones of Residue  <rsd1>  and Residue  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_ci_2b_bb_sc(...) from builtins.PyCapsule eval_ci_2b_bb_sc(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted short range context independent two  body interaction energies of  <pose>  between the backbone of Residue  <rsd1>  and the sidechain of Residue  <rsd2>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_ci_2b_sc_sc(...) from builtins.PyCapsule eval_ci_2b_sc_sc(self : rosetta.core.scoring.ScoreFunction, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted short range context dependent two body  interaction energies of  <pose>  between the sidechains of Residue  <rsd1>  and Residue  <rsd2>  into Energymap  <emap>     : EnergyMap is an EMapVector eval_ci_intrares_energy(...) from builtins.PyCapsule eval_ci_intrares_energy(self : rosetta.core.scoring.ScoreFunction, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates the unweighted intra-residue one body energies for all  context independent two body terms that define intra-residue energies of  <pose>  Residue  <rsd>  into EnergyMap  <emap>     : EnergyMap is an EMapVector eval_dof_derivative(...) from builtins.PyCapsule eval_dof_derivative(self : rosetta.core.scoring.ScoreFunction, dof_id : rosetta.core.id.DOF_ID, torsion_id : core::id::TorsionID, pose : rosetta.core.pose.Pose) -> float eval_intrares_energy(...) from builtins.PyCapsule eval_intrares_energy(self : rosetta.core.scoring.ScoreFunction, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType   Accumulates for rsd the unweighted intra-residue one body energies  for all context dependent and context independent two body terms that  define intra-residue energies     : EnergyMap is an EMapVector eval_long_range_twobody_energies(...) from builtins.PyCapsule eval_long_range_twobody_energies(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType eval_npd_atom_derivative(...) from builtins.PyCapsule eval_npd_atom_derivative(self : rosetta.core.scoring.ScoreFunction, atom_id : rosetta.core.id.AtomID, pose : rosetta.core.pose.Pose, domain_map : ObjexxFCL::FArray1D<int>, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t) -> NoneType eval_onebody_energies(...) from builtins.PyCapsule eval_onebody_energies(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType eval_twobody_neighbor_energies(...) from builtins.PyCapsule eval_twobody_neighbor_energies(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType evaluate_rotamer_background_energies(...) from builtins.PyCapsule evaluate_rotamer_background_energies(self : rosetta.core.scoring.ScoreFunction, set1 : rosetta.core.conformation.RotamerSetBase, residue2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, energy_vector : rosetta.utility.vector1_float) -> NoneType evaluate_rotamer_intrares_energies(...) from builtins.PyCapsule evaluate_rotamer_intrares_energies(self : rosetta.core.scoring.ScoreFunction, set : rosetta.core.conformation.RotamerSetBase, pose : rosetta.core.pose.Pose, energies : rosetta.utility.vector1_float) -> NoneType evaluate_rotamer_intrares_energy_maps(...) from builtins.PyCapsule evaluate_rotamer_intrares_energy_maps(self : rosetta.core.scoring.ScoreFunction, set : rosetta.core.conformation.RotamerSetBase, pose : rosetta.core.pose.Pose, emaps : rosetta.utility.vector1_core_scoring_EMapVector) -> NoneType evaluate_rotamer_pair_energies(...) from builtins.PyCapsule evaluate_rotamer_pair_energies(self : rosetta.core.scoring.ScoreFunction, set1 : rosetta.core.conformation.RotamerSetBase, set2 : rosetta.core.conformation.RotamerSetBase, pose : rosetta.core.pose.Pose, energy_table : ObjexxFCL::FArray2D<float>) -> NoneType finalize_after_derivatives(...) from builtins.PyCapsule finalize_after_derivatives(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType get_name(...) from builtins.PyCapsule get_name(rosetta.core.scoring.ScoreFunction) -> str get_nonzero_weighted_scoretypes(...) from builtins.PyCapsule get_nonzero_weighted_scoretypes(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType   Returns a list of the ScoreTypes which are non-zero with  their current weights    example(s):      scorefxn.get_nonzero_weighted_scoretypes()  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.set_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.scoring.ScoreFunction) -> rosetta.core.scoring.ScoreFunction   self pointers   2. get_self_ptr(rosetta.core.scoring.ScoreFunction) -> rosetta.core.scoring.ScoreFunction get_sub_score(...) from builtins.PyCapsule get_sub_score(*args, **kwargs) Overloaded function.   1. get_sub_score(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, residue_mask : rosetta.utility.vector1_bool) -> float   Compute the score for subset of residues   2. get_sub_score(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, residue_mask : rosetta.utility.vector1_bool, emap : rosetta.core.scoring.EMapVector) -> NoneType   Compute the score for subset of residues   3. get_sub_score(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, residue_mask : rosetta.utility.vector1_bool) -> float   Compute the score for subset of residues   4. get_sub_score(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, residue_mask : rosetta.utility.vector1_bool, emap : rosetta.core.scoring.EMapVector) -> NoneType   Compute the score for subset of residues get_sub_score_exclude_res(...) from builtins.PyCapsule get_sub_score_exclude_res(*args, **kwargs) Overloaded function.   1. get_sub_score_exclude_res(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, exclude_list : rosetta.utility.vector1_unsigned_long) -> float   Compute the score for subset of residues   2. get_sub_score_exclude_res(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, exclude_list : rosetta.utility.vector1_unsigned_long, emap : rosetta.core.scoring.EMapVector) -> NoneType   Compute the score for subset of residues   3. get_sub_score_exclude_res(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, exclude_list : rosetta.utility.vector1_unsigned_long) -> float   Compute the score for subset of residues   4. get_sub_score_exclude_res(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, exclude_list : rosetta.utility.vector1_unsigned_long, emap : rosetta.core.scoring.EMapVector) -> NoneType   Compute the score for subset of residues get_weight(...) from builtins.PyCapsule get_weight(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType) -> float   Returns the weight for ScoreType  <t>    examples(s):      scorefxn.get_weight(fa_sol)  See also:      ScoreFunction      ScoreFunction.set_weight      ScoreType      create_score_function      name_from_score_type      score_type_from_name has_nonzero_weight(...) from builtins.PyCapsule has_nonzero_weight(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType) -> bool   Returns true if the ScoreType  <t>  has a non-zero weight    example(s):      scorefxn.has_nonzero_weight(fa_sol)  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.has_zero_weight      ScoreFunction.set_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name has_zero_weight(...) from builtins.PyCapsule has_zero_weight(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType) -> bool   Returns true if the ScoreType  <t>  has a weight of zero,    example(s):      scorefxn.has_zero_weight(fa_sol)  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.has_nonzero_weight      ScoreFunction.set_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name indicate_required_context_graphs(...) from builtins.PyCapsule indicate_required_context_graphs(self : rosetta.core.scoring.ScoreFunction, context_graphs_required : rosetta.utility.vector1_bool) -> NoneType   find which context graphs the energy methods require info(...) from builtins.PyCapsule info(rosetta.core.scoring.ScoreFunction) -> core::scoring::ScoreFunctionInfo   return an object to describe abstractly the methods contained in this  ScoreFunction so that class Energies can ensure that the ScoreFunction is  properly evaluated (ie, no obsolete cashed data is used ) initialize_from_file(...) from builtins.PyCapsule initialize_from_file(self : rosetta.core.scoring.ScoreFunction, filename : str) -> NoneType   Resets everything before reading the  <filename> long_range_energies_begin(...) from builtins.PyCapsule long_range_energies_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const> > > > long_range_energies_end(...) from builtins.PyCapsule long_range_energies_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const> const*, std::vector<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const>, std::allocator<std::shared_ptr<core::scoring::methods::LongRangeTwoBodyEnergy const> > > > max_atomic_interaction_cutoff(...) from builtins.PyCapsule max_atomic_interaction_cutoff(rosetta.core.scoring.ScoreFunction) -> float   Returns the largest atomic interaction cutoff required by the  EnergyMethods merge(...) from builtins.PyCapsule merge(self : rosetta.core.scoring.ScoreFunction, scorefxn_to_be_merged : rosetta.core.scoring.ScoreFunction) -> NoneType   Merges in the weights of another score function    example(s):      scorefxn.merge(scorefxn2)  See also:      ScoreFunction      ScoreFunction.weights      Energies      create_score_function name(...) from builtins.PyCapsule name(self : rosetta.core.scoring.ScoreFunction, weights_tag : str) -> NoneType   Accumulates the unweighted one body energies of all context  independent one body energies for  <pose>  Residue  <rsd>  into  EnergyMap  <emap>     : EnergyMap is an EMapVector perturb_weights(...) from builtins.PyCapsule perturb_weights(rosetta.core.scoring.ScoreFunction) -> NoneType   Randomly perturbs non-zero score function weights prepare_rotamers_for_packing(...) from builtins.PyCapsule prepare_rotamers_for_packing(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, set : rosetta.core.conformation.RotamerSetBase) -> NoneType   Lets the scoring functions cache anything they need to rapidly  calculate rotamer pair energies used in packing (like a trie, e.g.) ready_for_nonideal_scoring(...) from builtins.PyCapsule ready_for_nonideal_scoring(rosetta.core.scoring.ScoreFunction) -> bool reinitialize_minnode_for_residue(...) from builtins.PyCapsule reinitialize_minnode_for_residue(self : rosetta.core.scoring.ScoreFunction, min_node : core::scoring::MinimizationNode, rsd : rosetta.core.conformation.Residue, min_map : core::kinematics::MinimizerMapBase, pose : rosetta.core.pose.Pose) -> NoneType reset(...) from builtins.PyCapsule reset(rosetta.core.scoring.ScoreFunction) -> NoneType   Resets the ScoreFunction to default values reset_energy_methods(...) from builtins.PyCapsule reset_energy_methods(rosetta.core.scoring.ScoreFunction) -> NoneType score(...) from builtins.PyCapsule score(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> float   Scores the given  <pose>  using this ScoreFunction. Alters the  Energies object within  <pose>, but does not alter this ScoreFunction     : Synonym for () operator. Makes code look a little nicer. Doesn't  do anything but call () operator. score_by_scoretype(...) from builtins.PyCapsule score_by_scoretype(*args, **kwargs) Overloaded function.   1. score_by_scoretype(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, t : rosetta.core.scoring.ScoreType) -> float   Returns the score of the ScoreType  <t>   2. score_by_scoretype(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, t : rosetta.core.scoring.ScoreType, weighted : bool) -> float   Returns the score of the ScoreType  <t> score_types_by_method_type(...) from builtins.PyCapsule score_types_by_method_type(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.methods.EnergyMethodType) -> rosetta.utility.vector1_core_scoring_ScoreType serialize_weights(...) from builtins.PyCapsule serialize_weights(rosetta.core.scoring.ScoreFunction) -> str   Serializes the non-zero score function term weights  Format: { term : weight, ... } set_energy_method_options(...) from builtins.PyCapsule set_energy_method_options(self : rosetta.core.scoring.ScoreFunction, energy_method_options_in : core::scoring::methods::EnergyMethodOptions) -> NoneType   Sets the EnergyMethodOptions object contained in this ScoreFunction.  with appropriate update of all the energy methods. set_etable(...) from builtins.PyCapsule set_etable(self : rosetta.core.scoring.ScoreFunction, etable_name : str) -> NoneType   Given a  <filename> (represented by a std::string), set the  e_table for this ScoreFunction. set_method_weights(...) from builtins.PyCapsule set_method_weights(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType, wts : rosetta.utility.vector1_double) -> NoneType set_weight(...) from builtins.PyCapsule set_weight(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType, setting : float) -> NoneType   Sets the weight for ScoreType  <t>  to  <setting>    example(s):      scorefxn.set_weight(fa_sol,.5)  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name set_weight_if_zero(...) from builtins.PyCapsule set_weight_if_zero(self : rosetta.core.scoring.ScoreFunction, t : rosetta.core.scoring.ScoreType, setting : float) -> NoneType   Sets the weight for ScoreType  <t>  to  <setting> if weight is originally zero    example(s):      scorefxn.set_weight_if_zero(fa_sol,.5)  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.set_weight      ScoreType      create_score_function      name_from_score_type      score_type_from_name setup_for_derivatives(...) from builtins.PyCapsule setup_for_derivatives(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType setup_for_lr2benmeth_minimization_for_respair(...) from builtins.PyCapsule setup_for_lr2benmeth_minimization_for_respair(*args, **kwargs) Overloaded function.   1. setup_for_lr2benmeth_minimization_for_respair(self : rosetta.core.scoring.ScoreFunction, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, lr2benergy : core::scoring::methods::LongRangeTwoBodyEnergy, g : core::scoring::MinimizationGraph, min_map : core::kinematics::MinimizerMapBase, p : rosetta.core.pose.Pose, res_moving_wrt_eachother : bool, accumulate_fixed_energies : bool, rni : core::scoring::ResidueNeighborConstIterator, fixed_energies : rosetta.core.scoring.EMapVector) -> NoneType   Initialize an edge in the MinimizationGraph with a particular long-range two body   2. setup_for_lr2benmeth_minimization_for_respair(self : rosetta.core.scoring.ScoreFunction, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, lr2benergy : core::scoring::methods::LongRangeTwoBodyEnergy, g : core::scoring::MinimizationGraph, min_map : core::kinematics::MinimizerMapBase, p : rosetta.core.pose.Pose, res_moving_wrt_eachother : bool, accumulate_fixed_energies : bool, rni : core::scoring::ResidueNeighborConstIterator, fixed_energies : rosetta.core.scoring.EMapVector, edge_weight : float) -> NoneType   Initialize an edge in the MinimizationGraph with a particular long-range two body   3. setup_for_lr2benmeth_minimization_for_respair(self : rosetta.core.scoring.ScoreFunction, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, lr2benergy : core::scoring::methods::LongRangeTwoBodyEnergy, g : core::scoring::MinimizationGraph, min_map : core::kinematics::MinimizerMapBase, p : rosetta.core.pose.Pose, res_moving_wrt_eachother : bool, accumulate_fixed_energies : bool, rni : core::scoring::ResidueNeighborConstIterator, fixed_energies : rosetta.core.scoring.EMapVector, edge_weight : float, edge_dweight : float) -> NoneType   Initialize an edge in the MinimizationGraph with a particular long-range two body setup_for_minimizing(...) from builtins.PyCapsule setup_for_minimizing(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, min_map : core::kinematics::MinimizerMapBase) -> NoneType   Initializes a MinimizationGraph and caches it in  Energies object of  <pose>     : for use during minimization setup_for_minimizing_for_node(...) from builtins.PyCapsule setup_for_minimizing_for_node(self : rosetta.core.scoring.ScoreFunction, min_node : core::scoring::MinimizationNode, rsd : rosetta.core.conformation.Residue, min_map : core::kinematics::MinimizerMapBase, pose : rosetta.core.pose.Pose, accumulate_fixed_energies : bool, fixed_energies : rosetta.core.scoring.EMapVector) -> NoneType   Initialize a single node of a MinimizationGraph with the one-body and two-body  energy methods that are held within this ScoreFunction object. setup_for_minimizing_sr2b_enmeths_for_minedge(...) from builtins.PyCapsule setup_for_minimizing_sr2b_enmeths_for_minedge(*args, **kwargs) Overloaded function.   1. setup_for_minimizing_sr2b_enmeths_for_minedge(self : rosetta.core.scoring.ScoreFunction, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, min_edge : core::scoring::MinimizationEdge, min_map : core::kinematics::MinimizerMapBase, pose : rosetta.core.pose.Pose, res_moving_wrt_eachother : bool, accumulate_fixed_energies : bool, energy_edge : core::scoring::EnergyEdge, fixed_energies : rosetta.core.scoring.EMapVector) -> NoneType   Initialize a single MinimizationEdge for a particular part of residues, storing  sr2b energy method pointers on the edge for those sr2b energy methods in this ScoreFunction   2. setup_for_minimizing_sr2b_enmeths_for_minedge(self : rosetta.core.scoring.ScoreFunction, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, min_edge : core::scoring::MinimizationEdge, min_map : core::kinematics::MinimizerMapBase, pose : rosetta.core.pose.Pose, res_moving_wrt_eachother : bool, accumulate_fixed_energies : bool, energy_edge : core::scoring::EnergyEdge, fixed_energies : rosetta.core.scoring.EMapVector, edge_weight : float) -> NoneType   Initialize a single MinimizationEdge for a particular part of residues, storing  sr2b energy method pointers on the edge for those sr2b energy methods in this ScoreFunction setup_for_packing(...) from builtins.PyCapsule setup_for_packing(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, residues_repacking : rosetta.utility.vector1_bool, residues_designing : rosetta.utility.vector1_bool) -> NoneType   Lets the scoring functions cache anything they need to calculate  energies in a packing step (rotamer_trials or pack_rotamers)     : the Etable caches tries for each of the residues, the  hydrogen bond function caches backbone/backbone hydrogen bonds setup_for_scoring(...) from builtins.PyCapsule setup_for_scoring(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType   For external scorers: Let the energy methods prepare for  evaluating their scores on a particular structure     : invoked during scoring. show(...) from builtins.PyCapsule show(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType   Scores  <pose>  and shows the raw and weighted scores for each  non-zero ScoreType     : this function is mostly for convenience in PyRosetta    example(s):      scorefxn.show(pose)  See also:      ScoreFunction      ScoreFunction.weights      Energies      create_score_function update_residue_for_packing(...) from builtins.PyCapsule update_residue_for_packing(self : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, resid : int) -> NoneType   If inside packing, the pose changes conformation, inform the  scoring functions that any data they have cached in the Energies object  is out of date. In particular, this is to update the trie(s) during  rotamer trials. weights(...) from builtins.PyCapsule weights(rosetta.core.scoring.ScoreFunction) -> rosetta.core.scoring.EMapVector   Returns an EnergyMap of the current set of weights    example(s):      scorefxn.weights()  See also:      ScoreFunction      ScoreFunction.get_weight      ScoreFunction.set_weight      ScoreFunction.weights      ScoreType      create_score_function      name_from_score_type      score_type_from_name whole_structure_types(...) from builtins.PyCapsule whole_structure_types(rosetta.core.scoring.ScoreFunction) -> rosetta.utility.vector1_core_scoring_ScoreType ws_methods_begin(...) from builtins.PyCapsule ws_methods_begin(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::WholeStructureEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::WholeStructureEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::WholeStructureEnergy> > > > ws_methods_end(...) from builtins.PyCapsule ws_methods_end(rosetta.core.scoring.ScoreFunction) -> __gnu_cxx::__normal_iterator<std::shared_ptr<core::scoring::methods::WholeStructureEnergy> const*, std::vector<std::shared_ptr<core::scoring::methods::WholeStructureEnergy>, std::allocator<std::shared_ptr<core::scoring::methods::WholeStructureEnergy> > > >   class ScoreFunctionFactory(builtins.object)     A collection of functions for making a single score_function     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.ScoreFunctionFactory) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. create_score_function(...) from builtins.PyCapsule create_score_function(*args, **kwargs) Overloaded function.   1. create_score_function(weights_tag : str) -> rosetta.core.scoring.ScoreFunction   Returns a ScoreFunction from the database weights file  <weights_tag>    example(s):      scorefxn = create_score_function('standard')  See also:      ScoreFunction      ScoreFunction.show      ScoreFunction.weights      ScoreType   2. create_score_function(options : rosetta.utility.options.OptionCollection, weights_tag : str) -> rosetta.core.scoring.ScoreFunction   3. create_score_function(weights_tag : str, patch_tag : str) -> rosetta.core.scoring.ScoreFunction   Returns a ScoreFunction from the database weights file  <weights_tag>  with the patch <patch_tag>    example(s):  See also:      ScoreFunction      ScoreFunction.show      ScoreFunction.weights      ScoreType   4. create_score_function(options : rosetta.utility.options.OptionCollection, weights_tag : str, patch_tag : str) -> rosetta.core.scoring.ScoreFunction   5. create_score_function(weights_tag : str, patch_tags : rosetta.utility.vector1_std_string) -> rosetta.core.scoring.ScoreFunction   Returns a ScoreFunction from the database weights file  <weights_tag>  with patches in <patch_tags>   6. create_score_function(options : rosetta.utility.options.OptionCollection, weights_tag : str, patch_tags : rosetta.utility.vector1_std_string) -> rosetta.core.scoring.ScoreFunction list_read_options(...) from builtins.PyCapsule list_read_options(opts : rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_std_allocator_utility_keys_VariantKey_utility_options_OptionKey_t) -> NoneType   A documentation function which reports the set of options read by the create_score_function variants   class ScoreFunctionInfo(builtins.object)     This object is handed to the pose's Energies object and stored along with the cached energies. It is used in the next scoring evaluation to decide whether it's safe to reuse cached energies.   It must describe the kinds of context that the Energies object provides to the scoring function.  If any scoring function requires a tenA neighbor graph, then that information is stored here.  If a scoring function requires a different kind of neighborness graph (think centroid mode), then this class will indicate the kind of storage.   Finally, it must describe the maximum atom-to-atom distance cutoff that characterizes the energy function.   So all we need is a constructor and an operator==     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.ScoreFunctionInfo) -> NoneType   2. __init__(self : rosetta.core.scoring.ScoreFunctionInfo, src : rosetta.core.scoring.ScoreFunctionInfo) -> NoneType   3. __init__(self : rosetta.core.scoring.ScoreFunctionInfo, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. initialize_from(...) from builtins.PyCapsule initialize_from(self : rosetta.core.scoring.ScoreFunctionInfo, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType max_atomic_interaction_distance(...) from builtins.PyCapsule max_atomic_interaction_distance(rosetta.core.scoring.ScoreFunctionInfo) -> float max_context_neighbor_cutoff(...) from builtins.PyCapsule max_context_neighbor_cutoff(rosetta.core.scoring.ScoreFunctionInfo) -> float requires_context_graph(...) from builtins.PyCapsule requires_context_graph(self : rosetta.core.scoring.ScoreFunctionInfo, cgt : rosetta.core.scoring.ContextGraphType) -> bool scores_present(...) from builtins.PyCapsule scores_present(rosetta.core.scoring.ScoreFunctionInfo) -> rosetta.core.scoring.EMapVector   class ScoreType(builtins.object)     Type for looking up cached energies     I guess we could get rid of the fa_ prefix, except maybe for fa_pair, to distinguish from std::pair and the centroid pair score...     Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.core.scoring.ScoreType, rosetta.core.scoring.ScoreType) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.core.scoring.ScoreType) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.ScoreType, int) -> NoneType   2. __init__(rosetta.core.scoring.ScoreType, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.core.scoring.ScoreType) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.core.scoring.ScoreType, rosetta.core.scoring.ScoreType) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.core.scoring.ScoreType) -> str Data and other attributes defined here: DFIRE = ScoreType.DFIRE FaMPEnv = ScoreType.FaMPEnv FaMPEnvSmooth = ScoreType.FaMPEnvSmooth FaMPSolv = ScoreType.FaMPSolv Hpol_bond_geometry = ScoreType.Hpol_bond_geometry MPCbeta = ScoreType.MPCbeta MPEnv = ScoreType.MPEnv MPLipo = ScoreType.MPLipo MPNonHelix = ScoreType.MPNonHelix MPPair = ScoreType.MPPair MPTMProj = ScoreType.MPTMProj MPTermini = ScoreType.MPTermini Mcbeta = ScoreType.Mcbeta Menv = ScoreType.Menv Menv_non_helix = ScoreType.Menv_non_helix Menv_smooth = ScoreType.Menv_smooth Menv_termini = ScoreType.Menv_termini Menv_tm_proj = ScoreType.Menv_tm_proj Mlipo = ScoreType.Mlipo Mpair = ScoreType.Mpair PB_elec = ScoreType.PB_elec ProQ = ScoreType.ProQ ProQM = ScoreType.ProQM PyRosettaEnergy_first = ScoreType.PyRosettaEnergy_first PyRosettaEnergy_last = ScoreType.PyRosettaEnergy_last PyRosettaTwoBodyContextDependentEnergy_first = ScoreType.PyRosettaTwoBodyContextDependentEnergy_first PyRosettaTwoBodyContextDependentEnergy_last = ScoreType.PyRosettaTwoBodyContextDependentEnergy_last PyRosettaTwoBodyContextIndepenedentEnergy_first = ScoreType.PyRosettaTwoBodyContextIndepenedentEnergy_first PyRosettaTwoBodyContextIndepenedentEnergy_last = ScoreType.PyRosettaTwoBodyContextIndepenedentEnergy_last aa_cmp = ScoreType.aa_cmp aa_composition = ScoreType.aa_composition aa_repeat = ScoreType.aa_repeat abego = ScoreType.abego angle_constraint = ScoreType.angle_constraint atom_pair_constraint = ScoreType.atom_pair_constraint backbone_stub_constraint = ScoreType.backbone_stub_constraint backbone_stub_linear_constraint = ScoreType.backbone_stub_linear_constraint base_pair_constraint = ScoreType.base_pair_constraint big_bin_constraint = ScoreType.big_bin_constraint bond_geometry = ScoreType.bond_geometry burial = ScoreType.burial cart_bonded = ScoreType.cart_bonded cart_bonded_angle = ScoreType.cart_bonded_angle cart_bonded_length = ScoreType.cart_bonded_length cart_bonded_torsion = ScoreType.cart_bonded_torsion cbeta = ScoreType.cbeta cbeta_smooth = ScoreType.cbeta_smooth cen_env_smooth = ScoreType.cen_env_smooth cen_hb = ScoreType.cen_hb cen_pair_motif_degree = ScoreType.cen_pair_motif_degree cen_pair_motifs = ScoreType.cen_pair_motifs cen_pair_smooth = ScoreType.cen_pair_smooth cen_rot_cbeta = ScoreType.cen_rot_cbeta cen_rot_dun = ScoreType.cen_rot_dun cen_rot_env = ScoreType.cen_rot_env cen_rot_pair = ScoreType.cen_rot_pair cen_rot_pair_ang = ScoreType.cen_rot_pair_ang cen_rot_pair_dih = ScoreType.cen_rot_pair_dih cenpack = ScoreType.cenpack cenpack_smooth = ScoreType.cenpack_smooth ch_bond = ScoreType.ch_bond ch_bond_bb_bb = ScoreType.ch_bond_bb_bb ch_bond_bb_sc = ScoreType.ch_bond_bb_sc ch_bond_sc_sc = ScoreType.ch_bond_sc_sc chainbreak = ScoreType.chainbreak co = ScoreType.co coarse_beadlj = ScoreType.coarse_beadlj coarse_chainbreak_constraint = ScoreType.coarse_chainbreak_constraint coarse_fa_atr = ScoreType.coarse_fa_atr coarse_fa_rep = ScoreType.coarse_fa_rep coarse_fa_sol = ScoreType.coarse_fa_sol constant_constraint = ScoreType.constant_constraint coordinate_constraint = ScoreType.coordinate_constraint csa = ScoreType.csa custom_atom_pair = ScoreType.custom_atom_pair d2h_sa = ScoreType.d2h_sa dab_sasa = ScoreType.dab_sasa dab_sev = ScoreType.dab_sev dc = ScoreType.dc dihedral_constraint = ScoreType.dihedral_constraint distance_chainbreak = ScoreType.distance_chainbreak dna_base_distance = ScoreType.dna_base_distance dna_bb_torsion = ScoreType.dna_bb_torsion dna_bp = ScoreType.dna_bp dna_bs = ScoreType.dna_bs dna_chi = ScoreType.dna_chi dna_dihedral_bb = ScoreType.dna_dihedral_bb dna_dihedral_chi = ScoreType.dna_dihedral_chi dna_dihedral_sugar = ScoreType.dna_dihedral_sugar dna_dr = ScoreType.dna_dr dna_env = ScoreType.dna_env dna_pair = ScoreType.dna_pair dna_ref = ScoreType.dna_ref dna_sugar_close = ScoreType.dna_sugar_close dock_ens_conf = ScoreType.dock_ens_conf dof_constraint = ScoreType.dof_constraint dslf_ca_dih = ScoreType.dslf_ca_dih dslf_cbs_ds = ScoreType.dslf_cbs_ds dslf_cs_ang = ScoreType.dslf_cs_ang dslf_fa13 = ScoreType.dslf_fa13 dslf_fa13_ref = ScoreType.dslf_fa13_ref dslf_ss_dih = ScoreType.dslf_ss_dih dslf_ss_dst = ScoreType.dslf_ss_dst dslfc_RT = ScoreType.dslfc_RT dslfc_ang = ScoreType.dslfc_ang dslfc_bb_dih = ScoreType.dslfc_bb_dih dslfc_cb_dih = ScoreType.dslfc_cb_dih dslfc_cb_dst = ScoreType.dslfc_cb_dst dslfc_cen_dst = ScoreType.dslfc_cen_dst dslfc_rot = ScoreType.dslfc_rot dslfc_trans = ScoreType.dslfc_trans dummy_score_type = ScoreType.end_of_score_type_enumeration dunbrack_constraint = ScoreType.dunbrack_constraint e_pH = ScoreType.e_pH elec_dens_atomwise = ScoreType.elec_dens_atomwise elec_dens_fast = ScoreType.elec_dens_fast elec_dens_whole_structure_allatom = ScoreType.elec_dens_whole_structure_allatom elec_dens_whole_structure_ca = ScoreType.elec_dens_whole_structure_ca elec_dens_window = ScoreType.elec_dens_window end_of_score_type_enumeration = ScoreType.end_of_score_type_enumeration env = ScoreType.env envsmooth = ScoreType.envsmooth fa_atr = ScoreType.fa_atr fa_atr_dummy = ScoreType.fa_atr_dummy fa_atr_ref = ScoreType.fa_atr_ref fa_cust_pair_dist = ScoreType.fa_cust_pair_dist fa_dun = ScoreType.fa_dun fa_dun_dev = ScoreType.fa_dun_dev fa_dun_dev_ref = ScoreType.fa_dun_dev_ref fa_dun_ref = ScoreType.fa_dun_ref fa_dun_rot = ScoreType.fa_dun_rot fa_dun_rot_ref = ScoreType.fa_dun_rot_ref fa_dun_semi = ScoreType.fa_dun_semi fa_dun_semi_ref = ScoreType.fa_dun_semi_ref fa_elec = ScoreType.fa_elec fa_elec_aro_all = ScoreType.fa_elec_aro_all fa_elec_aro_aro = ScoreType.fa_elec_aro_aro fa_elec_bb_bb = ScoreType.fa_elec_bb_bb fa_elec_bb_sc = ScoreType.fa_elec_bb_sc fa_elec_ref = ScoreType.fa_elec_ref fa_elec_rna_base_base = ScoreType.fa_elec_rna_base_base fa_elec_rna_base_base_fast = ScoreType.fa_elec_rna_base_base_fast fa_elec_rna_phos_base = ScoreType.fa_elec_rna_phos_base fa_elec_rna_phos_base_fast = ScoreType.fa_elec_rna_phos_base_fast fa_elec_rna_phos_phos = ScoreType.fa_elec_rna_phos_phos fa_elec_rna_phos_phos_fast = ScoreType.fa_elec_rna_phos_phos_fast fa_elec_rna_phos_sugr = ScoreType.fa_elec_rna_phos_sugr fa_elec_rna_phos_sugr_fast = ScoreType.fa_elec_rna_phos_sugr_fast fa_elec_rna_sugr_base = ScoreType.fa_elec_rna_sugr_base fa_elec_rna_sugr_base_fast = ScoreType.fa_elec_rna_sugr_base_fast fa_elec_rna_sugr_sugr = ScoreType.fa_elec_rna_sugr_sugr fa_elec_rna_sugr_sugr_fast = ScoreType.fa_elec_rna_sugr_sugr_fast fa_elec_sc_sc = ScoreType.fa_elec_sc_sc fa_grpelec = ScoreType.fa_grpelec fa_intra_RNA_base_phos_atr = ScoreType.fa_intra_RNA_base_phos_atr fa_intra_RNA_base_phos_rep = ScoreType.fa_intra_RNA_base_phos_rep fa_intra_RNA_base_phos_sol = ScoreType.fa_intra_RNA_base_phos_sol fa_intra_atr = ScoreType.fa_intra_atr fa_intra_atr_ref = ScoreType.fa_intra_atr_ref fa_intra_atr_xover4 = ScoreType.fa_intra_atr_xover4 fa_intra_rep = ScoreType.fa_intra_rep fa_intra_rep_ref = ScoreType.fa_intra_rep_ref fa_intra_rep_xover4 = ScoreType.fa_intra_rep_xover4 fa_intra_sol = ScoreType.fa_intra_sol fa_intra_sol_ref = ScoreType.fa_intra_sol_ref fa_intra_sol_xover4 = ScoreType.fa_intra_sol_xover4 fa_mbenv = ScoreType.fa_mbenv fa_mbsolv = ScoreType.fa_mbsolv fa_pair = ScoreType.fa_pair fa_pair_aro_aro = ScoreType.fa_pair_aro_aro fa_pair_aro_pol = ScoreType.fa_pair_aro_pol fa_pair_pol_pol = ScoreType.fa_pair_pol_pol fa_plane = ScoreType.fa_plane fa_rep = ScoreType.fa_rep fa_rep_dummy = ScoreType.fa_rep_dummy fa_rep_ref = ScoreType.fa_rep_ref fa_sasa = ScoreType.fa_sasa fa_sol = ScoreType.fa_sol fa_sol_dummy = ScoreType.fa_sol_dummy fa_sol_ref = ScoreType.fa_sol_ref fa_stack = ScoreType.fa_stack fa_stack_aro = ScoreType.fa_stack_aro fa_stack_ext = ScoreType.fa_stack_ext fa_stack_lower = ScoreType.fa_stack_lower fa_stack_lr = ScoreType.fa_stack_lr fa_stack_sol = ScoreType.fa_stack_sol fa_stack_upper = ScoreType.fa_stack_upper fa_vdw_tinker = ScoreType.fa_vdw_tinker facts_elec = ScoreType.facts_elec facts_sasa = ScoreType.facts_sasa facts_solv = ScoreType.facts_solv fastsaxs = ScoreType.fastsaxs fiberdiffraction = ScoreType.fiberdiffraction fiberdiffractiondens = ScoreType.fiberdiffractiondens free_2HOprime = ScoreType.free_2HOprime free_base = ScoreType.free_base free_dof = ScoreType.free_dof free_res = ScoreType.free_res free_side_chain = ScoreType.free_side_chain free_suite = ScoreType.free_suite gauss = ScoreType.gauss gb_elec = ScoreType.gb_elec geom_sol = ScoreType.geom_sol geom_sol_fast = ScoreType.geom_sol_fast geom_sol_fast_intra_RNA = ScoreType.geom_sol_fast_intra_RNA geom_sol_intra_RNA = ScoreType.geom_sol_intra_RNA goap = ScoreType.goap goap_angle = ScoreType.goap_angle goap_dist = ScoreType.goap_dist grid_vdw = ScoreType.grid_vdw h2o_hbond = ScoreType.h2o_hbond h2o_intra = ScoreType.h2o_intra hack_aro = ScoreType.hack_aro hbond = ScoreType.hbond hbond_bb_sc = ScoreType.hbond_bb_sc hbond_intra = ScoreType.hbond_intra hbond_lr_bb = ScoreType.hbond_lr_bb hbond_lr_bb_sc = ScoreType.hbond_lr_bb_sc hbond_ref = ScoreType.hbond_ref hbond_sc = ScoreType.hbond_sc hbond_sr_bb = ScoreType.hbond_sr_bb hbond_sr_bb_sc = ScoreType.hbond_sr_bb_sc hoh_ref = ScoreType.hoh_ref holes = ScoreType.holes holes_decoy = ScoreType.holes_decoy holes_min = ScoreType.holes_min holes_min_mean = ScoreType.holes_min_mean holes_resl = ScoreType.holes_resl hpatch = ScoreType.hpatch hs_pair = ScoreType.hs_pair hybrid_vdw = ScoreType.hybrid_vdw interchain_contact = ScoreType.interchain_contact interchain_env = ScoreType.interchain_env interchain_pair = ScoreType.interchain_pair interchain_vdw = ScoreType.n_shortranged_2b_score_types interface_dd_pair = ScoreType.interface_dd_pair intermol = ScoreType.intermol linear_chainbreak = ScoreType.linear_chainbreak lk_ball = ScoreType.lk_ball lk_ball_iso = ScoreType.lk_ball_iso lk_ball_wtd = ScoreType.lk_ball_wtd lk_costheta = ScoreType.lk_costheta lk_hack = ScoreType.lk_hack lk_nonpolar = ScoreType.lk_nonpolar lk_nonpolar_intra_RNA = ScoreType.lk_nonpolar_intra_RNA lk_polar = ScoreType.lk_polar lk_polar_intra_RNA = ScoreType.lk_polar_intra_RNA loop_close = ScoreType.loop_close metalbinding_constraint = ScoreType.metalbinding_constraint metalhash_constraint = ScoreType.metalhash_constraint mg = ScoreType.mg mg_lig = ScoreType.mg_lig mg_ref = ScoreType.mg_ref mg_sol = ScoreType.mg_sol missing_res = ScoreType.missing_res mm_bend = ScoreType.mm_bend mm_lj_inter_atr = ScoreType.mm_lj_inter_atr mm_lj_inter_rep = ScoreType.mm_lj_inter_rep mm_lj_intra_atr = ScoreType.mm_lj_intra_atr mm_lj_intra_atr_ref = ScoreType.mm_lj_intra_atr_ref mm_lj_intra_rep = ScoreType.mm_lj_intra_rep mm_lj_intra_rep_ref = ScoreType.mm_lj_intra_rep_ref mm_stretch = ScoreType.mm_stretch mm_twist = ScoreType.mm_twist mm_twist_ref = ScoreType.mm_twist_ref multipole_elec = ScoreType.multipole_elec n_ci_2b_score_types = ScoreType.n_ci_2b_score_types n_score_types = ScoreType.end_of_score_type_enumeration n_shortranged_2b_score_types = ScoreType.n_shortranged_2b_score_types natbias_hh = ScoreType.natbias_hh natbias_hs = ScoreType.natbias_hs natbias_ss = ScoreType.natbias_ss natbias_stwist = ScoreType.natbias_stwist neigh_count = ScoreType.neigh_count neigh_vect = ScoreType.neigh_vect neigh_vect_raw = ScoreType.neigh_vect_raw nmer_pssm = ScoreType.nmer_pssm nmer_ref = ScoreType.nmer_ref nmer_svm = ScoreType.nmer_svm occ_sol_exact = ScoreType.occ_sol_exact occ_sol_fitted = ScoreType.occ_sol_fitted occ_sol_fitted_onebody = ScoreType.occ_sol_fitted_onebody omega = ScoreType.omega omega_ref = ScoreType.omega_ref orbitals_hpol_bb = ScoreType.orbitals_hpol_bb other_pose = ScoreType.other_pose overlap_chainbreak = ScoreType.overlap_chainbreak p_aa = ScoreType.p_aa p_aa_pp = ScoreType.p_aa_pp p_aa_pp_ref = ScoreType.p_aa_pp_ref p_aa_ss = ScoreType.p_aa_ss pack_stat = ScoreType.pack_stat pair = ScoreType.pair pci_cation_pi = ScoreType.pci_cation_pi pci_hbond = ScoreType.pci_hbond pci_pi_pi = ScoreType.pci_pi_pi pci_salt_bridge = ScoreType.pci_salt_bridge pcs = ScoreType.pcs pcs2 = ScoreType.pcs2 pcsTs1 = ScoreType.pcsTs1 pcsTs2 = ScoreType.pcsTs2 pcsTs3 = ScoreType.pcsTs3 pcsTs4 = ScoreType.pcsTs4 pddf_score = ScoreType.pddf_score peptide_bond = ScoreType.peptide_bond pocket_constraint = ScoreType.pocket_constraint pro_close = ScoreType.pro_close pro_close_ref = ScoreType.pro_close_ref python = ScoreType.n_ci_2b_score_types rama = ScoreType.rama rama2b = ScoreType.rama2b rama_prepro = ScoreType.rama_prepro rama_ref = ScoreType.rama_ref rdc = ScoreType.rdc rdc_rohl = ScoreType.rdc_rohl rdc_segments = ScoreType.rdc_segments ref = ScoreType.ref ref_nc = ScoreType.ref_nc res_type_constraint = ScoreType.res_type_constraint res_type_linking_constraint = ScoreType.res_type_linking_constraint rg = ScoreType.rg rg_local = ScoreType.rg_local ring_close = ScoreType.ring_close rms = ScoreType.rms rna_backbone_backbone = ScoreType.rna_backbone_backbone rna_base_axis = ScoreType.rna_base_axis rna_base_axis_pairwise = ScoreType.rna_base_axis_pairwise rna_base_backbone = ScoreType.rna_base_backbone rna_base_pair = ScoreType.rna_base_pair rna_base_pair_pairwise = ScoreType.rna_base_pair_pairwise rna_base_stack = ScoreType.rna_base_stack rna_base_stack_axis = ScoreType.rna_base_stack_axis rna_base_stack_axis_pairwise = ScoreType.rna_base_stack_axis_pairwise rna_base_stack_pairwise = ScoreType.rna_base_stack_pairwise rna_base_stagger = ScoreType.rna_base_stagger rna_base_stagger_pairwise = ScoreType.rna_base_stagger_pairwise rna_bond_geometry = ScoreType.rna_bond_geometry rna_bulge = ScoreType.rna_bulge rna_chem_map = ScoreType.rna_chem_map rna_chem_map_lores = ScoreType.rna_chem_map_lores rna_chem_shift = ScoreType.rna_chem_shift rna_data_backbone = ScoreType.rna_data_backbone rna_data_base = ScoreType.rna_data_base rna_fa_atr_base = ScoreType.rna_fa_atr_base rna_fa_rep_base = ScoreType.rna_fa_rep_base rna_jr_suite = ScoreType.rna_jr_suite rna_mg_point = ScoreType.rna_mg_point rna_mg_point_indirect = ScoreType.rna_mg_point_indirect rna_repulsive = ScoreType.rna_repulsive rna_rg = ScoreType.rna_rg rna_sugar_close = ScoreType.rna_sugar_close rna_suite = ScoreType.rna_suite rna_torsion = ScoreType.rna_torsion rna_torsion_sc = ScoreType.rna_torsion_sc rna_vdw = ScoreType.rna_vdw rsigma = ScoreType.rsigma sa = ScoreType.sa saxs_cen_score = ScoreType.saxs_cen_score saxs_fa_score = ScoreType.saxs_fa_score saxs_score = ScoreType.saxs_score seqdep_ref = ScoreType.seqdep_ref sheet = ScoreType.sheet sidechain_neighbors = ScoreType.sidechain_neighbors site_constraint = ScoreType.site_constraint special_rot = ScoreType.special_rot split_unfolded_two_body = ScoreType.split_unfolded_two_body ss_contact_worst = ScoreType.ss_contact_worst ss_pair = ScoreType.ss_pair stack_elec = ScoreType.stack_elec stack_elec_base_base = ScoreType.stack_elec_base_base stack_elec_base_bb = ScoreType.stack_elec_base_bb suck = ScoreType.suck sugar_bb = ScoreType.sugar_bb suiteness_bonus = ScoreType.suiteness_bonus surface = ScoreType.surface symE_bonus = ScoreType.symE_bonus sym_lig = ScoreType.sym_lig total_score = ScoreType.total_score unfolded = ScoreType.unfolded vdw = ScoreType.vdw xtal_ml = ScoreType.xtal_ml xtal_rfree = ScoreType.xtal_rfree xtal_rwork = ScoreType.xtal_rwork yhh_planarity = ScoreType.yhh_planarity   class ScoreTypeManager(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.ScoreTypeManager) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. is_score_type(...) from builtins.PyCapsule is_score_type(name : str) -> bool name_from_score_type(...) from builtins.PyCapsule name_from_score_type(score_type : rosetta.core.scoring.ScoreType) -> str score_type_from_name(...) from builtins.PyCapsule score_type_from_name(name : str) -> rosetta.core.scoring.ScoreType   class ScoringManager(rosetta.utility.SingletonBase_core_scoring_ScoringManager_t)       Method resolution order: ScoringManager rosetta.utility.SingletonBase_core_scoring_ScoringManager_t builtins.object Methods defined here: __init__(self, /, *args, **kwargs) Initialize self.  See help(type(self)) for accurate signature. __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_memb_etable(...) from builtins.PyCapsule add_memb_etable(self : rosetta.core.scoring.ScoringManager, name : str, etable : core::scoring::etable::MembEtable) -> NoneType   pba energy_method(...) from builtins.PyCapsule energy_method(self : rosetta.core.scoring.ScoringManager, t : rosetta.core.scoring.ScoreType, options : core::scoring::methods::EnergyMethodOptions) -> rosetta.core.scoring.methods.EnergyMethod etable(...) from builtins.PyCapsule etable(*args, **kwargs) Overloaded function.   1. etable(self : rosetta.core.scoring.ScoringManager, options_in : core::scoring::methods::EnergyMethodOptions) -> rosetta.std.weak_ptr_const_core_scoring_etable_Etable_t   Request an etable specifying an EnergyMethodOptions object; internally  this will retrieve the EtableOptions object, and invoke the EtableOptions  version of this function.   2. etable(self : rosetta.core.scoring.ScoringManager, options_in : rosetta.core.scoring.etable.EtableOptions) -> rosetta.std.weak_ptr_const_core_scoring_etable_Etable_t   Request an etable specifying an EtableOptions; internally this will  query the ScoringManager's map from EtableOptions to Etables for the desired  Etable, and construct a new one if needed.   3. etable(self : rosetta.core.scoring.ScoringManager, etable_id : str) -> rosetta.std.weak_ptr_const_core_scoring_etable_Etable_t   Create and return an etable specified only by the etable_type of the  etable::EtableOptions class.  This, internally, will create an EtableOptions object,  initialized from the command line, set the etable_type of this object, and then  invoke the etable( EtableOptions ) method. factory_register(...) from builtins.PyCapsule factory_register(self : rosetta.core.scoring.ScoringManager, creator : rosetta.core.scoring.methods.EnergyMethodCreator) -> NoneType get_AtomVDW(...) from builtins.PyCapsule get_AtomVDW(self : rosetta.core.scoring.ScoringManager, atom_type_set_name : str) -> rosetta.core.scoring.AtomVDW get_CHIEnergyFunction(...) from builtins.PyCapsule get_CHIEnergyFunction(*args, **kwargs) Overloaded function.   1. get_CHIEnergyFunction(rosetta.core.scoring.ScoringManager) -> core::scoring::carbohydrates::CHIEnergyFunction   2. get_CHIEnergyFunction(self : rosetta.core.scoring.ScoringManager, setup_sampling_data : bool) -> core::scoring::carbohydrates::CHIEnergyFunction   3. get_CHIEnergyFunction(self : rosetta.core.scoring.ScoringManager, setup_sampling_data : bool, sampling_step_size : float) -> core::scoring::carbohydrates::CHIEnergyFunction get_CarbonHBondPotential(...) from builtins.PyCapsule get_CarbonHBondPotential(rosetta.core.scoring.ScoringManager) -> core::scoring::carbon_hbonds::CarbonHBondPotential get_CenHBPotential(...) from builtins.PyCapsule get_CenHBPotential(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.CenHBPotential get_CenRotEnvPairPotential(...) from builtins.PyCapsule get_CenRotEnvPairPotential(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.CenRotEnvPairPotential get_CentroidDisulfidePotential(...) from builtins.PyCapsule get_CentroidDisulfidePotential(rosetta.core.scoring.ScoringManager) -> core::scoring::disulfides::CentroidDisulfidePotential get_DDPLookupTable(...) from builtins.PyCapsule get_DDPLookupTable(rosetta.core.scoring.ScoringManager) -> core::scoring::interface_::DDPlookup get_DNABFormPotential(...) from builtins.PyCapsule get_DNABFormPotential(rosetta.core.scoring.ScoringManager) -> core::scoring::dna::DNABFormPotential get_DNATorsionPotential(...) from builtins.PyCapsule get_DNATorsionPotential(rosetta.core.scoring.ScoringManager) -> core::scoring::dna::DNATorsionPotential get_DNA_BasePotential(...) from builtins.PyCapsule get_DNA_BasePotential(rosetta.core.scoring.ScoringManager) -> core::scoring::dna::DNA_BasePotential get_DNA_DihedralPotential(...) from builtins.PyCapsule get_DNA_DihedralPotential(rosetta.core.scoring.ScoringManager) -> core::scoring::dna::DNA_DihedralPotential get_DNA_EnvPairPotential(...) from builtins.PyCapsule get_DNA_EnvPairPotential(rosetta.core.scoring.ScoringManager) -> core::scoring::dna::DNA_EnvPairPotential get_DatabaseOccSolEne(...) from builtins.PyCapsule get_DatabaseOccSolEne(self : rosetta.core.scoring.ScoringManager, atom_type_set_name : str, min_occ_energy : float) -> core::scoring::geometric_solvation::DatabaseOccSolEne get_DirectReadoutPotential(...) from builtins.PyCapsule get_DirectReadoutPotential(rosetta.core.scoring.ScoringManager) -> core::scoring::dna::DirectReadoutPotential get_DisulfideMatchingPotential(...) from builtins.PyCapsule get_DisulfideMatchingPotential(rosetta.core.scoring.ScoringManager) -> core::scoring::disulfides::DisulfideMatchingPotential get_EnvPairPotential(...) from builtins.PyCapsule get_EnvPairPotential(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.EnvPairPotential get_FACTSPotential(...) from builtins.PyCapsule get_FACTSPotential(rosetta.core.scoring.ScoringManager) -> core::scoring::FACTSPotential get_FullatomDisulfidePotential(...) from builtins.PyCapsule get_FullatomDisulfidePotential(rosetta.core.scoring.ScoringManager) -> core::scoring::disulfides::FullatomDisulfidePotential get_GenBornPotential(...) from builtins.PyCapsule get_GenBornPotential(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.GenBornPotential get_MMBondAngleLibrary(...) from builtins.PyCapsule get_MMBondAngleLibrary(rosetta.core.scoring.ScoringManager) -> core::scoring::mm::MMBondAngleLibrary get_MMBondLengthLibrary(...) from builtins.PyCapsule get_MMBondLengthLibrary(rosetta.core.scoring.ScoringManager) -> core::scoring::mm::MMBondLengthLibrary get_MMLJEnergyTable(...) from builtins.PyCapsule get_MMLJEnergyTable(rosetta.core.scoring.ScoringManager) -> core::scoring::mm::MMLJEnergyTable get_MMLJLibrary(...) from builtins.PyCapsule get_MMLJLibrary(rosetta.core.scoring.ScoringManager) -> core::scoring::mm::MMLJLibrary get_MMTorsionLibrary(...) from builtins.PyCapsule get_MMTorsionLibrary(rosetta.core.scoring.ScoringManager) -> core::scoring::mm::MMTorsionLibrary get_MembraneData(...) from builtins.PyCapsule get_MembraneData(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.membrane.MembraneData get_MembranePotential(...) from builtins.PyCapsule get_MembranePotential(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.MembranePotential get_Membrane_FAPotential(...) from builtins.PyCapsule get_Membrane_FAPotential(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.Membrane_FAPotential get_MultipoleElecPotential(...) from builtins.PyCapsule get_MultipoleElecPotential(self : rosetta.core.scoring.ScoringManager, options : core::scoring::methods::EnergyMethodOptions) -> rosetta.core.scoring.MultipoleElecPotential get_NVLookupTable(...) from builtins.PyCapsule get_NVLookupTable(rosetta.core.scoring.ScoringManager) -> core::scoring::nv::NVlookup get_OmegaTether(...) from builtins.PyCapsule get_OmegaTether(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.OmegaTether get_OrbitalsLookupTable(...) from builtins.PyCapsule get_OrbitalsLookupTable(rosetta.core.scoring.ScoringManager) -> core::scoring::orbitals::OrbitalsLookup get_P_AA(...) from builtins.PyCapsule get_P_AA(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.P_AA get_P_AA_ss(...) from builtins.PyCapsule get_P_AA_ss(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.P_AA_ss get_PairEPotential(...) from builtins.PyCapsule get_PairEPotential(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.PairEPotential get_PoissonBoltzmannPotential(...) from builtins.PyCapsule get_PoissonBoltzmannPotential(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.PoissonBoltzmannPotential get_ProQPotential(...) from builtins.PyCapsule get_ProQPotential(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.ProQPotential get_RNA_AtomVDW(...) from builtins.PyCapsule get_RNA_AtomVDW(rosetta.core.scoring.ScoringManager) -> core::scoring::rna::RNA_AtomVDW get_RNA_ChemicalShiftPotential(...) from builtins.PyCapsule get_RNA_ChemicalShiftPotential(rosetta.core.scoring.ScoringManager) -> core::scoring::rna::chemical_shift::RNA_ChemicalShiftPotential get_RNA_DMS_LowResolutionPotential(...) from builtins.PyCapsule get_RNA_DMS_LowResolutionPotential(rosetta.core.scoring.ScoringManager) -> core::scoring::rna::data::RNA_DMS_LowResolutionPotential get_RNA_DMS_Potential(...) from builtins.PyCapsule get_RNA_DMS_Potential(rosetta.core.scoring.ScoringManager) -> core::scoring::rna::data::RNA_DMS_Potential get_RNA_LowResolutionPotential(...) from builtins.PyCapsule get_RNA_LowResolutionPotential(rosetta.core.scoring.ScoringManager) -> core::scoring::rna::RNA_LowResolutionPotential get_RamaPrePro(...) from builtins.PyCapsule get_RamaPrePro(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.RamaPrePro   RotamerLibrary & get_RotamerLibrary() const; get_Ramachandran(...) from builtins.PyCapsule get_Ramachandran(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.Ramachandran get_Ramachandran2B(...) from builtins.PyCapsule get_Ramachandran2B(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.Ramachandran2B get_Ramachandran2B_ptr(...) from builtins.PyCapsule get_Ramachandran2B_ptr(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.Ramachandran2B get_Ramachandran_nonconst(...) from builtins.PyCapsule get_Ramachandran_nonconst(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.Ramachandran   Get a non-const reference to the Ramachandran object.      Warning!  Probably not threadsafe!  Needed, though, for  lazy loading. get_Ramachandran_ptr(...) from builtins.PyCapsule get_Ramachandran_ptr(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.Ramachandran get_Ramachandran_ptr_nonconst(...) from builtins.PyCapsule get_Ramachandran_ptr_nonconst(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.Ramachandran   Get a non-const owning pointer to the Ramachandran object.      Warning!  Probably not threadsafe!  Needed, though, for  lazy loading. get_SASAPotential(...) from builtins.PyCapsule get_SASAPotential(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.SASAPotential get_SecondaryStructurePotential(...) from builtins.PyCapsule get_SecondaryStructurePotential(rosetta.core.scoring.ScoringManager) -> core::scoring::SecondaryStructurePotential get_SmoothEnvPairPotential(...) from builtins.PyCapsule get_SmoothEnvPairPotential(rosetta.core.scoring.ScoringManager) -> rosetta.core.scoring.SmoothEnvPairPotential get_SplitUnfoldedTwoBodyPotential(...) from builtins.PyCapsule get_SplitUnfoldedTwoBodyPotential(self : rosetta.core.scoring.ScoringManager, label_type : str, value_type : str, score_func_type : str) -> core::scoring::SplitUnfoldedTwoBodyPotential get_UnfoldedStatePotential(...) from builtins.PyCapsule get_UnfoldedStatePotential(self : rosetta.core.scoring.ScoringManager, type : str) -> core::scoring::UnfoldedStatePotential get_VdWTinkerPotential(...) from builtins.PyCapsule get_VdWTinkerPotential(rosetta.core.scoring.ScoringManager) -> core::scoring::VdWTinkerPotential get_WaterAdductHBondPotential(...) from builtins.PyCapsule get_WaterAdductHBondPotential(rosetta.core.scoring.ScoringManager) -> core::scoring::WaterAdductHBondPotential get_cloned_aa_comp_setup_helpers(...) from builtins.PyCapsule get_cloned_aa_comp_setup_helpers(self : rosetta.core.scoring.ScoringManager, options : core::scoring::methods::EnergyMethodOptions) -> rosetta.utility.vector1_std_shared_ptr_core_scoring_aa_composition_energy_AACompositionEnergySetup_t   Get a vector of owning pointers to data used by the AACompositionEnergy score term.      If this vector has not yet been populated, this loads the data from disk (lazy loading).  NOT THREADSAFE.      Vikram K. Mulligan (vmullig.edu). get_cp_rep_map_byname(...) from builtins.PyCapsule get_cp_rep_map_byname(rosetta.core.scoring.ScoringManager) -> rosetta.std.map_std_string_std_map_std_string_std_string_std_less_std_string_std_allocator_std_pair_const_std_string_std_string_t   Get an owning pointer to data used by the FA_ElecEnergy in beta_nov15 mode.      If the data have not been loaded, this loads the data (lazy loading).  NOT THREADSAFE.      Vikram K. Mulligan (vmullig.edu). has_energy_method(...) from builtins.PyCapsule has_energy_method(self : rosetta.core.scoring.ScoringManager, t : rosetta.core.scoring.ScoreType) -> bool make_partially_soft_etable(...) from builtins.PyCapsule make_partially_soft_etable(self : rosetta.core.scoring.ScoringManager, name : str, etable_options : rosetta.core.scoring.etable.EtableOptions) -> core::scoring::etable::Etable   make etable for extra partially softies memb_etable(...) from builtins.PyCapsule memb_etable(self : rosetta.core.scoring.ScoringManager, table_id : str) -> rosetta.std.weak_ptr_const_core_scoring_etable_MembEtable_t   pba Methods inherited from rosetta.utility.SingletonBase_core_scoring_ScoringManager_t: get_instance(...) from builtins.PyCapsule get_instance() -> core::scoring::ScoringManager   class SecondaryStructurePotential(builtins.object)     secondary structure scoring cut from classic rosetta structure.h/structure.cc     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.SecondaryStructurePotential) -> NoneType   2. __init__(self : rosetta.core.scoring.SecondaryStructurePotential,  : rosetta.core.scoring.SecondaryStructurePotential) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. rsigma_dot_initializer(...) from builtins.PyCapsule rsigma_dot_initializer(rsigma_dot : ObjexxFCL::FArray4D<double>) -> NoneType score(...) from builtins.PyCapsule score(self : rosetta.core.scoring.SecondaryStructurePotential, pose : rosetta.core.pose.Pose, weights : rosetta.core.scoring.SecondaryStructureWeights, hs_score : float, ss_score : float, rsigma_score : float, sheet_score : float) -> NoneType   score secondary structure setup_for_scoring(...) from builtins.PyCapsule setup_for_scoring(self : rosetta.core.scoring.SecondaryStructurePotential, pose : rosetta.core.pose.Pose) -> NoneType   class SecondaryStructureWeights(builtins.object)     Holds weights and flags for configuring a SecondaryStructureEnergy evaluation     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.SecondaryStructureWeights) -> NoneType   2. __init__(self : rosetta.core.scoring.SecondaryStructureWeights, s : rosetta.core.scoring.SecondaryStructureWeights) -> 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.scoring.SecondaryStructureWeights, s : rosetta.core.scoring.SecondaryStructureWeights) -> rosetta.core.scoring.SecondaryStructureWeights   copy assignment get_antiparallel_weight(...) from builtins.PyCapsule get_antiparallel_weight(rosetta.core.scoring.SecondaryStructureWeights) -> float   antiparallel strand weight get_handedness_score_flag(...) from builtins.PyCapsule get_handedness_score_flag(rosetta.core.scoring.SecondaryStructureWeights) -> bool   using handedness score? get_localstrandpair_penalty(...) from builtins.PyCapsule get_localstrandpair_penalty(rosetta.core.scoring.SecondaryStructureWeights) -> float   local strand pair penalty get_max_strand_dist_cutoff(...) from builtins.PyCapsule get_max_strand_dist_cutoff(rosetta.core.scoring.SecondaryStructureWeights) -> float   max strand distance cutoff get_parallel_weight(...) from builtins.PyCapsule get_parallel_weight(rosetta.core.scoring.SecondaryStructureWeights) -> float   parallel strand weight get_seq_sep_scale(...) from builtins.PyCapsule get_seq_sep_scale(rosetta.core.scoring.SecondaryStructureWeights) -> float   sequence separation scale get_ss_cutoff(...) from builtins.PyCapsule get_ss_cutoff(rosetta.core.scoring.SecondaryStructureWeights) -> int get_ss_lowstrand(...) from builtins.PyCapsule get_ss_lowstrand(rosetta.core.scoring.SecondaryStructureWeights) -> int get_strand_dist_cutoff(...) from builtins.PyCapsule get_strand_dist_cutoff(rosetta.core.scoring.SecondaryStructureWeights) -> float   strand distance cutoff get_stretch_strand_dist_cutoff(...) from builtins.PyCapsule get_stretch_strand_dist_cutoff(rosetta.core.scoring.SecondaryStructureWeights) -> bool   stretching the strand distance cutoff? set_antiparallel_weight(...) from builtins.PyCapsule set_antiparallel_weight(self : rosetta.core.scoring.SecondaryStructureWeights, weight : float) -> NoneType   set antiparallel strand weight set_handedness_score_flag(...) from builtins.PyCapsule set_handedness_score_flag(self : rosetta.core.scoring.SecondaryStructureWeights, flag : bool) -> NoneType   use the handedness score set_localstrandpair_penalty(...) from builtins.PyCapsule set_localstrandpair_penalty(self : rosetta.core.scoring.SecondaryStructureWeights, penalty : float) -> NoneType   set local strand pair penalty set_max_strand_dist_cutoff(...) from builtins.PyCapsule set_max_strand_dist_cutoff(self : rosetta.core.scoring.SecondaryStructureWeights, cutoff : float) -> NoneType   set max strand distance cutoff set_parallel_weight(...) from builtins.PyCapsule set_parallel_weight(self : rosetta.core.scoring.SecondaryStructureWeights, weight : float) -> NoneType   set parallel strand weight set_seq_sep_scale(...) from builtins.PyCapsule set_seq_sep_scale(self : rosetta.core.scoring.SecondaryStructureWeights, scale : float) -> NoneType   set sequence separation scale set_ss_cutoff(...) from builtins.PyCapsule set_ss_cutoff(self : rosetta.core.scoring.SecondaryStructureWeights, setting : int) -> NoneType set_ss_lowstrand(...) from builtins.PyCapsule set_ss_lowstrand(self : rosetta.core.scoring.SecondaryStructureWeights, setting : int) -> NoneType set_strand_dist_cutoff(...) from builtins.PyCapsule set_strand_dist_cutoff(self : rosetta.core.scoring.SecondaryStructureWeights, cutoff : float) -> NoneType   set strand distance cutoff set_stretch_strand_dist_cutoff(...) from builtins.PyCapsule set_stretch_strand_dist_cutoff(self : rosetta.core.scoring.SecondaryStructureWeights, flag : bool) -> NoneType   stretch the strand distance cutoff setup_parallel_antiparallel_weights(...) from builtins.PyCapsule setup_parallel_antiparallel_weights(*args, **kwargs) Overloaded function.   1. setup_parallel_antiparallel_weights(rosetta.core.scoring.SecondaryStructureWeights) -> NoneType   setup parallel/antiparallel weights according to scheme   2. setup_parallel_antiparallel_weights(self : rosetta.core.scoring.SecondaryStructureWeights, randomize_weights : bool) -> NoneType   setup parallel/antiparallel weights according to scheme   class SelectedResPredicate(Predicate)       Method resolution order: SelectedResPredicate Predicate builtins.object Methods defined here: __call__(...) from builtins.PyCapsule __call__(self : rosetta.core.scoring.SelectedResPredicate, pose1 : rosetta.core.pose.Pose, pose2 : rosetta.core.pose.Pose, resno : int, atomno : int) -> bool __init__(...) from builtins.PyCapsule __init__(self : handle, selected : rosetta.std.list_unsigned_long_std_allocator_unsigned_long_t, predicate : rosetta.core.scoring.Predicate) -> 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.scoring.SelectedResPredicate,  : rosetta.core.scoring.SelectedResPredicate) -> rosetta.core.scoring.SelectedResPredicate   class SmallAtNb(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.scoring.SmallAtNb, at1 : int, at2 : int, path_dist : int, weight : float) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. atomno1(...) from builtins.PyCapsule atomno1(rosetta.core.scoring.SmallAtNb) -> int atomno2(...) from builtins.PyCapsule atomno2(rosetta.core.scoring.SmallAtNb) -> int path_dist(...) from builtins.PyCapsule path_dist(rosetta.core.scoring.SmallAtNb) -> int weight(...) from builtins.PyCapsule weight(rosetta.core.scoring.SmallAtNb) -> float   class SmoothEnvPairPotential(builtins.object)     ///////////////////// /////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.SmoothEnvPairPotential) -> 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.scoring.SmoothEnvPairPotential,  : rosetta.core.scoring.SmoothEnvPairPotential) -> rosetta.core.scoring.SmoothEnvPairPotential compute_centroid_environment(...) from builtins.PyCapsule compute_centroid_environment(self : rosetta.core.scoring.SmoothEnvPairPotential, pose : rosetta.core.pose.Pose) -> NoneType compute_dcentroid_environment(...) from builtins.PyCapsule compute_dcentroid_environment(self : rosetta.core.scoring.SmoothEnvPairPotential, pose : rosetta.core.pose.Pose) -> NoneType evaluate_env_and_cbeta_deriv(...) from builtins.PyCapsule evaluate_env_and_cbeta_deriv(self : rosetta.core.scoring.SmoothEnvPairPotential, pose : rosetta.core.pose.Pose, rsd : rosetta.core.conformation.Residue, d_env_score : rosetta.numeric.xyzVector_double_t, d_cb_score6 : rosetta.numeric.xyzVector_double_t, d_cb_score12 : rosetta.numeric.xyzVector_double_t) -> NoneType evaluate_env_and_cbeta_scores(...) from builtins.PyCapsule evaluate_env_and_cbeta_scores(self : rosetta.core.scoring.SmoothEnvPairPotential, pose : rosetta.core.pose.Pose, rsd : rosetta.core.conformation.Residue, env_score : float, cb_score6 : float, cb_score12 : float) -> NoneType evaluate_pair_and_cenpack_deriv(...) from builtins.PyCapsule evaluate_pair_and_cenpack_deriv(self : rosetta.core.scoring.SmoothEnvPairPotential, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, cendist : float, d_pair : float, d_cenpack : float) -> NoneType evaluate_pair_and_cenpack_score(...) from builtins.PyCapsule evaluate_pair_and_cenpack_score(self : rosetta.core.scoring.SmoothEnvPairPotential, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, cendist : float, pair_contribution : float, cenpack_contribution : float) -> NoneType finalize(...) from builtins.PyCapsule finalize(self : rosetta.core.scoring.SmoothEnvPairPotential, pose : rosetta.core.pose.Pose) -> NoneType   class SmoothScoreTermCoeffs(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.SmoothScoreTermCoeffs) -> NoneType   2. __init__(self : rosetta.core.scoring.SmoothScoreTermCoeffs,  : rosetta.core.scoring.SmoothScoreTermCoeffs) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_gaussian(...) from builtins.PyCapsule add_gaussian(self : rosetta.core.scoring.SmoothScoreTermCoeffs, g_in : rosetta.numeric.xyzVector_double_t) -> NoneType add_sigmoid(...) from builtins.PyCapsule add_sigmoid(self : rosetta.core.scoring.SmoothScoreTermCoeffs, s_in : rosetta.numeric.xyzVector_double_t) -> NoneType assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.SmoothScoreTermCoeffs,  : rosetta.core.scoring.SmoothScoreTermCoeffs) -> rosetta.core.scoring.SmoothScoreTermCoeffs clear(...) from builtins.PyCapsule clear(rosetta.core.scoring.SmoothScoreTermCoeffs) -> NoneType dfunc(...) from builtins.PyCapsule dfunc(self : rosetta.core.scoring.SmoothScoreTermCoeffs, x : float) -> float func(...) from builtins.PyCapsule func(self : rosetta.core.scoring.SmoothScoreTermCoeffs, x : float) -> float gaussian(...) from builtins.PyCapsule gaussian(self : rosetta.core.scoring.SmoothScoreTermCoeffs, i : int) -> rosetta.numeric.xyzVector_double_t ngaussians(...) from builtins.PyCapsule ngaussians(rosetta.core.scoring.SmoothScoreTermCoeffs) -> int nsigmoids(...) from builtins.PyCapsule nsigmoids(rosetta.core.scoring.SmoothScoreTermCoeffs) -> int shift(...) from builtins.PyCapsule shift(*args, **kwargs) Overloaded function.   1. shift(self : rosetta.core.scoring.SmoothScoreTermCoeffs, s_in : float) -> NoneType   2. shift(rosetta.core.scoring.SmoothScoreTermCoeffs) -> float sigmoid(...) from builtins.PyCapsule sigmoid(self : rosetta.core.scoring.SmoothScoreTermCoeffs, i : int) -> rosetta.numeric.xyzVector_double_t   class SplitUnfoldedTwoBodyPotential(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(self : rosetta.core.scoring.SplitUnfoldedTwoBodyPotential, filename : str) -> NoneType   2. __init__(self : rosetta.core.scoring.SplitUnfoldedTwoBodyPotential, filename : str, atom_type_label_name : str) -> NoneType   3. __init__(self : rosetta.core.scoring.SplitUnfoldedTwoBodyPotential,  : rosetta.core.scoring.SplitUnfoldedTwoBodyPotential) -> 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.scoring.SplitUnfoldedTwoBodyPotential,  : rosetta.core.scoring.SplitUnfoldedTwoBodyPotential) -> rosetta.core.scoring.SplitUnfoldedTwoBodyPotential get_restype_emap(...) from builtins.PyCapsule get_restype_emap(self : rosetta.core.scoring.SplitUnfoldedTwoBodyPotential, restype : rosetta.core.chemical.ResidueType, emap : rosetta.core.scoring.EMapVector) -> NoneType get_weights(...) from builtins.PyCapsule get_weights(rosetta.core.scoring.SplitUnfoldedTwoBodyPotential) -> rosetta.core.scoring.EMapVector   class Strands(builtins.object)     ///////////////////////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.Strands) -> NoneType   2. __init__(self : rosetta.core.scoring.Strands, total_residue : int) -> NoneType   3. __init__(self : rosetta.core.scoring.Strands, s : rosetta.core.scoring.Strands) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __str__(...) from builtins.PyCapsule __str__(rosetta.core.scoring.Strands) -> str assign(...) from builtins.PyCapsule assign(self : rosetta.core.scoring.Strands, s : rosetta.core.scoring.Strands) -> rosetta.core.scoring.Strands   copy assignment clear(...) from builtins.PyCapsule clear(rosetta.core.scoring.Strands) -> NoneType resize(...) from builtins.PyCapsule resize(self : rosetta.core.scoring.Strands, nres : int) -> NoneType Data descriptors defined here: SS_dimer SS_resnum SS_strand SS_strand_end dimer_neighbor total_SS_dimer total_strands   class TMscore(builtins.object)       Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.scoring.TMscore, p1 : ObjexxFCL::FArray2D<double>) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. apply(...) from builtins.PyCapsule apply(*args, **kwargs) Overloaded function.   1. apply(self : rosetta.core.scoring.TMscore, p2 : ObjexxFCL::FArray2D<double>) -> NoneType   2. apply(self : rosetta.core.scoring.TMscore, p2 : ObjexxFCL::FArray2D<double>, u : rosetta.utility.vector0_numeric_xyzVector_double_t, t : rosetta.numeric.xyzVector_double_t, get_ut : bool) -> NoneType get_GDTHA(...) from builtins.PyCapsule get_GDTHA(rosetta.core.scoring.TMscore) -> float get_GDTTS(...) from builtins.PyCapsule get_GDTTS(rosetta.core.scoring.TMscore) -> float get_TMscore(...) from builtins.PyCapsule get_TMscore(rosetta.core.scoring.TMscore) -> float   class TMscoreStore(builtins.object)     /////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.TMscoreStore) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_residue_dis(...) from builtins.PyCapsule add_residue_dis(self : rosetta.core.scoring.TMscoreStore, d0 : float, dis : float) -> NoneType apply(...) from builtins.PyCapsule apply(rosetta.core.scoring.TMscoreStore) -> NoneType clear(...) from builtins.PyCapsule clear(rosetta.core.scoring.TMscoreStore) -> NoneType set_nseq(...) from builtins.PyCapsule set_nseq(self : rosetta.core.scoring.TMscoreStore, nseq : int) -> NoneType update(...) from builtins.PyCapsule update(rosetta.core.scoring.TMscoreStore) -> NoneType Data descriptors defined here: GDTHA GDTTS TM TM10 TM10_max TM_max TM_sum TM_sum10 maxsub maxsub_max maxsub_sum n_GDT05 n_GDT05_max n_GDT1 n_GDT1_max n_GDT2 n_GDT2_max n_GDT4 n_GDT4_max n_GDT8 n_GDT8_max n_cut nseq_ nseq_ref_   class TenANeighborEdge(rosetta.core.graph.Edge)       Method resolution order: TenANeighborEdge rosetta.core.graph.Edge builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.graph.Graph, first_node_ind : int, second_node_ind : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. copy_from(...) from builtins.PyCapsule copy_from(self : rosetta.core.scoring.TenANeighborEdge, source : rosetta.core.graph.Edge) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.scoring.TenANeighborEdge) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.scoring.TenANeighborEdge) -> int Methods inherited from rosetta.core.graph.Edge: get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.graph.Edge) -> int   returns the index of the lower node get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.graph.Edge, node_index : int) -> int   returns the index of the one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon. get_other_node(...) from builtins.PyCapsule get_other_node(*args, **kwargs) Overloaded function.   1. get_other_node(self : rosetta.core.graph.Edge, node_index : int) -> rosetta.core.graph.Node   returns a const pointer to one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon.   2. get_other_node(self : rosetta.core.graph.Edge, node_index : int) -> rosetta.core.graph.Node   returns a non-const pointer to one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon. get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.graph.Edge) -> int   returns the index of the upper node is_loop(...) from builtins.PyCapsule is_loop(rosetta.core.graph.Edge) -> bool   Is this edge a loop? In Pseudographs, loop edges are incident twice on a single vertex. same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.graph.Edge, node1 : int, node2 : int) -> bool   Is this the same edge as another edge (node1,node2)?  Note:  this graph does not work for multi-graphs.  Edges must be unique. set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.graph.Edge, edge_iterator : rosetta.core.graph.EdgeListIterator) -> NoneType   called only by class Graph, this function gives the Edge the data it needs  to later delete itself from its owner's edge list in constant time.   class TenANeighborGraph(ContextGraph)       Method resolution order: TenANeighborGraph ContextGraph rosetta.core.graph.Graph builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, num_nodes : int) -> NoneType   3. __init__(handle, rosetta.core.scoring.TenANeighborGraph) -> 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.scoring.TenANeighborGraph, source : rosetta.core.scoring.TenANeighborGraph) -> rosetta.core.scoring.TenANeighborGraph clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.TenANeighborGraph) -> rosetta.core.scoring.ContextGraph conditionally_add_edge(...) from builtins.PyCapsule conditionally_add_edge(self : rosetta.core.scoring.TenANeighborGraph, lower_node_id : int, upper_node_id : int, dsq : float) -> NoneType delete_edge(...) from builtins.PyCapsule delete_edge(self : rosetta.core.scoring.TenANeighborGraph, edge : rosetta.core.graph.Edge) -> NoneType neighbor_cutoff(...) from builtins.PyCapsule neighbor_cutoff(rosetta.core.scoring.TenANeighborGraph) -> float update_from_pose(...) from builtins.PyCapsule update_from_pose(self : rosetta.core.scoring.TenANeighborGraph, pose : rosetta.core.pose.Pose) -> NoneType Methods inherited from rosetta.core.graph.Graph: add_edge(...) from builtins.PyCapsule add_edge(*args, **kwargs) Overloaded function.   1. add_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   add an edge between two vertices.  Invokes "create_edge" from the derived class.  Returns a pointer to the edge after its been added, allowing the calling function  to immediately set data for this edge.   2. add_edge(self : rosetta.core.graph.Graph, example_edge : rosetta.core.graph.Edge) -> rosetta.core.graph.Edge   add an edge to this graph copying the data from an edge in another graph.  Returns a pointer to the edge after its been added, allowing the calling function  to immediately set data for this edge. all_pairs_shortest_paths(...) from builtins.PyCapsule all_pairs_shortest_paths(rosetta.core.graph.Graph) -> ObjexxFCL::FArray2D<int>   O(V^3).  Computes all pairs shortest paths using Warshall's algorithm  and writes all the path distances to the two-dimensional table. const_edge_list_begin(...) from builtins.PyCapsule const_edge_list_begin(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex const_edge_list_end(...) from builtins.PyCapsule const_edge_list_end(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex copy_connectivity(...) from builtins.PyCapsule copy_connectivity(self : rosetta.core.graph.Graph, source : rosetta.core.graph.Graph) -> NoneType   copy the edge connectivity from a source graph with a potentially  unknown type. drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.graph.Graph) -> NoneType   delete all the edges present in the graph drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.graph.Graph, node : int) -> NoneType   delete all the edges for a single vertex in the graph edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   returns a pointer to the edge connecting nodes node1 and node2, if that edge exists  in the graph, o.w. returns 0.  Focuses the graph on this edge for fast subsequent retrieval.   2. find_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   returns a const pointer to the edge connecting nodes node1 and node2, if that edge exists  in the graph, o.w. returns 0.  Focuses the graph on this edge for fast subsequent retrieval. focused_edge(...) from builtins.PyCapsule focused_edge(*args, **kwargs) Overloaded function.   1. focused_edge(rosetta.core.graph.Graph) -> rosetta.core.graph.Edge   returns a pointer to the focused edge   2. focused_edge(rosetta.core.graph.Graph) -> rosetta.core.graph.Edge   returns a const-pointer to the focused edge getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.graph.Graph) -> int   returns a count of all the memory used by every vertex and edge in a graph  by invoking the polymorphic count_static_memory and count_dynamic_memory of each  (possibly derived) node and edge object as well as for the (possibly derived) graph  class. get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> bool   is an edge already present in the graph? O(V) worst case.  O(1) iff all vertices have O(1) edges get_node(...) from builtins.PyCapsule get_node(*args, **kwargs) Overloaded function.   1. get_node(self : rosetta.core.graph.Graph, index : int) -> rosetta.core.graph.Node   2. get_node(self : rosetta.core.graph.Graph, index : int) -> rosetta.core.graph.Node get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.graph.Graph) -> rosetta.core.graph.Graph   self pointers   2. get_self_ptr(rosetta.core.graph.Graph) -> rosetta.core.graph.Graph num_edges(...) from builtins.PyCapsule num_edges(rosetta.core.graph.Graph) -> int num_nodes(...) from builtins.PyCapsule num_nodes(rosetta.core.graph.Graph) -> int   the number of nodes in the graph print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.graph.Graph) -> NoneType   send summary information to the screen for all vertices in the graph set_num_nodes(...) from builtins.PyCapsule set_num_nodes(self : rosetta.core.graph.Graph, num_nodes : int) -> NoneType   set the number of nodes in the graph -- deletes any existing edges in the graph   class TenANeighborNode(rosetta.core.graph.Node)       Method resolution order: TenANeighborNode rosetta.core.graph.Node builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle,  : rosetta.core.graph.Graph, node_id : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. add_neighbors_mass(...) from builtins.PyCapsule add_neighbors_mass(self : rosetta.core.scoring.TenANeighborNode, neighbors_mass : float) -> NoneType   To be called by TenANeighborEdge only  called at the time of edge addition copy_from(...) from builtins.PyCapsule copy_from(self : rosetta.core.scoring.TenANeighborNode, source : rosetta.core.graph.Node) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.scoring.TenANeighborNode) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.scoring.TenANeighborNode) -> int neighbor_mass(...) from builtins.PyCapsule neighbor_mass(*args, **kwargs) Overloaded function.   1. neighbor_mass(self : rosetta.core.scoring.TenANeighborNode, mass : float) -> NoneType   set the neighbor mass for a vertex   2. neighbor_mass(rosetta.core.scoring.TenANeighborNode) -> float   return the neighbor mass for a vertex subtract_neighbors_mass(...) from builtins.PyCapsule subtract_neighbors_mass(self : rosetta.core.scoring.TenANeighborNode, neighbors_mass : float) -> NoneType   To be called by TenANeighborEdge only  called at the time of edge deletion sum_of_neighbors_masses(...) from builtins.PyCapsule sum_of_neighbors_masses(rosetta.core.scoring.TenANeighborNode) -> float Methods inherited from rosetta.core.graph.Node: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.graph.Node, edge_ptr : core::graph::Edge,  : rosetta.core.graph.EdgeListIterator) -> NoneType   adds edge pointer to edge list; returns an iterator to the new  list element const_edge_list_begin(...) from builtins.PyCapsule const_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its edge list const_edge_list_end(...) from builtins.PyCapsule const_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its edge list const_lower_edge_list_begin(...) from builtins.PyCapsule const_lower_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its lower-edge list const_lower_edge_list_end(...) from builtins.PyCapsule const_lower_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its lower-edge list const_upper_edge_list_begin(...) from builtins.PyCapsule const_upper_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its upper-edge list const_upper_edge_list_end(...) from builtins.PyCapsule const_upper_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its upper-edge list drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.graph.Node) -> NoneType   deletes all edges incident upon this node drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.graph.Node, edge_iterator : rosetta.core.graph.EdgeListIterator) -> NoneType   removes an edge iterator from the node's edge list.  Only called by Edge class. edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its edge list edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its edge list find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.graph.Node, other_node_index : int) -> core::graph::Edge   a "slow" (linear) search for an edge.   2. find_edge(self : rosetta.core.graph.Node, other_node_index : int) -> core::graph::Edge get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.graph.Node) -> int   the index for this node get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.graph.Node) -> int   the number of upper neighbors -- which "self" neighborness is counted if a loop edge  is present get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.graph.Node) -> int   the number of lower neighbors loop_incident(...) from builtins.PyCapsule loop_incident(rosetta.core.graph.Node) -> bool   NOTE TO SELF: remove loop support lower_edge_list_begin(...) from builtins.PyCapsule lower_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its lower-edge list lower_edge_list_end(...) from builtins.PyCapsule lower_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its lower-edge list num_edges(...) from builtins.PyCapsule num_edges(rosetta.core.graph.Node) -> int   the number of edges incident on this node, which may include a loop edge num_neighbors_counting_self(...) from builtins.PyCapsule num_neighbors_counting_self(rosetta.core.graph.Node) -> int   the number of neighbors counting "self" as a neighbor. num_neighbors_counting_self_static(...) from builtins.PyCapsule num_neighbors_counting_self_static(rosetta.core.graph.Node) -> int   the number of neighbors counting "self" as neighbor. Defaults to  num_neighbors_counting_self() but can be set to other values as well.  Useful in calculation of symmetrical structures. print(...) from builtins.PyCapsule print(rosetta.core.graph.Node) -> NoneType   send summaray data about this node to the screen set_num_neighbors_counting_self_static(...) from builtins.PyCapsule set_num_neighbors_counting_self_static(self : rosetta.core.graph.Node, neighbor : int) -> NoneType   manually change the number of neighbors for a Node. Used  for symmetry scoring upper_edge_list_begin(...) from builtins.PyCapsule upper_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its upper-edge list upper_edge_list_end(...) from builtins.PyCapsule upper_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its upper-edge list   class TwelveANeighborEdge(rosetta.core.graph.Edge)       Method resolution order: TwelveANeighborEdge rosetta.core.graph.Edge builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle, owner : rosetta.core.graph.Graph, first_node_ind : int, second_node_ind : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. copy_from(...) from builtins.PyCapsule copy_from(self : rosetta.core.scoring.TwelveANeighborEdge, source : rosetta.core.graph.Edge) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.scoring.TwelveANeighborEdge) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.scoring.TwelveANeighborEdge) -> int Methods inherited from rosetta.core.graph.Edge: get_first_node_ind(...) from builtins.PyCapsule get_first_node_ind(rosetta.core.graph.Edge) -> int   returns the index of the lower node get_other_ind(...) from builtins.PyCapsule get_other_ind(self : rosetta.core.graph.Edge, node_index : int) -> int   returns the index of the one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon. get_other_node(...) from builtins.PyCapsule get_other_node(*args, **kwargs) Overloaded function.   1. get_other_node(self : rosetta.core.graph.Edge, node_index : int) -> rosetta.core.graph.Node   returns a const pointer to one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon.   2. get_other_node(self : rosetta.core.graph.Edge, node_index : int) -> rosetta.core.graph.Node   returns a non-const pointer to one node given the index of the other.  node_index must be one of the two nodes that this edge is incident upon. get_second_node_ind(...) from builtins.PyCapsule get_second_node_ind(rosetta.core.graph.Edge) -> int   returns the index of the upper node is_loop(...) from builtins.PyCapsule is_loop(rosetta.core.graph.Edge) -> bool   Is this edge a loop? In Pseudographs, loop edges are incident twice on a single vertex. same_edge(...) from builtins.PyCapsule same_edge(self : rosetta.core.graph.Edge, node1 : int, node2 : int) -> bool   Is this the same edge as another edge (node1,node2)?  Note:  this graph does not work for multi-graphs.  Edges must be unique. set_pos_in_owners_list(...) from builtins.PyCapsule set_pos_in_owners_list(self : rosetta.core.graph.Edge, edge_iterator : rosetta.core.graph.EdgeListIterator) -> NoneType   called only by class Graph, this function gives the Edge the data it needs  to later delete itself from its owner's edge list in constant time.   class TwelveANeighborGraph(ContextGraph)       Method resolution order: TwelveANeighborGraph ContextGraph rosetta.core.graph.Graph builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, num_nodes : int) -> NoneType   3. __init__(handle, rosetta.core.scoring.TwelveANeighborGraph) -> 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.scoring.TwelveANeighborGraph, source : rosetta.core.scoring.TwelveANeighborGraph) -> rosetta.core.scoring.TwelveANeighborGraph clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.TwelveANeighborGraph) -> rosetta.core.scoring.ContextGraph conditionally_add_edge(...) from builtins.PyCapsule conditionally_add_edge(self : rosetta.core.scoring.TwelveANeighborGraph, lower_node_id : int, upper_node_id : int, dsq : float) -> NoneType delete_edge(...) from builtins.PyCapsule delete_edge(self : rosetta.core.scoring.TwelveANeighborGraph, edge : rosetta.core.graph.Edge) -> NoneType neighbor_cutoff(...) from builtins.PyCapsule neighbor_cutoff(rosetta.core.scoring.TwelveANeighborGraph) -> float update_from_pose(...) from builtins.PyCapsule update_from_pose(self : rosetta.core.scoring.TwelveANeighborGraph, pose : rosetta.core.pose.Pose) -> NoneType Methods inherited from rosetta.core.graph.Graph: add_edge(...) from builtins.PyCapsule add_edge(*args, **kwargs) Overloaded function.   1. add_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   add an edge between two vertices.  Invokes "create_edge" from the derived class.  Returns a pointer to the edge after its been added, allowing the calling function  to immediately set data for this edge.   2. add_edge(self : rosetta.core.graph.Graph, example_edge : rosetta.core.graph.Edge) -> rosetta.core.graph.Edge   add an edge to this graph copying the data from an edge in another graph.  Returns a pointer to the edge after its been added, allowing the calling function  to immediately set data for this edge. all_pairs_shortest_paths(...) from builtins.PyCapsule all_pairs_shortest_paths(rosetta.core.graph.Graph) -> ObjexxFCL::FArray2D<int>   O(V^3).  Computes all pairs shortest paths using Warshall's algorithm  and writes all the path distances to the two-dimensional table. const_edge_list_begin(...) from builtins.PyCapsule const_edge_list_begin(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex const_edge_list_end(...) from builtins.PyCapsule const_edge_list_end(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex copy_connectivity(...) from builtins.PyCapsule copy_connectivity(self : rosetta.core.graph.Graph, source : rosetta.core.graph.Graph) -> NoneType   copy the edge connectivity from a source graph with a potentially  unknown type. drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.graph.Graph) -> NoneType   delete all the edges present in the graph drop_all_edges_for_node(...) from builtins.PyCapsule drop_all_edges_for_node(self : rosetta.core.graph.Graph, node : int) -> NoneType   delete all the edges for a single vertex in the graph edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.graph.Graph) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of the (unordered) edge list for the graph.  this edge list contains all the edges in the graph, not simply those for a particular vertex find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   returns a pointer to the edge connecting nodes node1 and node2, if that edge exists  in the graph, o.w. returns 0.  Focuses the graph on this edge for fast subsequent retrieval.   2. find_edge(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> rosetta.core.graph.Edge   returns a const pointer to the edge connecting nodes node1 and node2, if that edge exists  in the graph, o.w. returns 0.  Focuses the graph on this edge for fast subsequent retrieval. focused_edge(...) from builtins.PyCapsule focused_edge(*args, **kwargs) Overloaded function.   1. focused_edge(rosetta.core.graph.Graph) -> rosetta.core.graph.Edge   returns a pointer to the focused edge   2. focused_edge(rosetta.core.graph.Graph) -> rosetta.core.graph.Edge   returns a const-pointer to the focused edge getTotalMemoryUsage(...) from builtins.PyCapsule getTotalMemoryUsage(rosetta.core.graph.Graph) -> int   returns a count of all the memory used by every vertex and edge in a graph  by invoking the polymorphic count_static_memory and count_dynamic_memory of each  (possibly derived) node and edge object as well as for the (possibly derived) graph  class. get_edge_exists(...) from builtins.PyCapsule get_edge_exists(self : rosetta.core.graph.Graph, node1 : int, node2 : int) -> bool   is an edge already present in the graph? O(V) worst case.  O(1) iff all vertices have O(1) edges get_node(...) from builtins.PyCapsule get_node(*args, **kwargs) Overloaded function.   1. get_node(self : rosetta.core.graph.Graph, index : int) -> rosetta.core.graph.Node   2. get_node(self : rosetta.core.graph.Graph, index : int) -> rosetta.core.graph.Node get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.core.graph.Graph) -> rosetta.core.graph.Graph   self pointers   2. get_self_ptr(rosetta.core.graph.Graph) -> rosetta.core.graph.Graph num_edges(...) from builtins.PyCapsule num_edges(rosetta.core.graph.Graph) -> int num_nodes(...) from builtins.PyCapsule num_nodes(rosetta.core.graph.Graph) -> int   the number of nodes in the graph print_vertices(...) from builtins.PyCapsule print_vertices(rosetta.core.graph.Graph) -> NoneType   send summary information to the screen for all vertices in the graph set_num_nodes(...) from builtins.PyCapsule set_num_nodes(self : rosetta.core.graph.Graph, num_nodes : int) -> NoneType   set the number of nodes in the graph -- deletes any existing edges in the graph   class TwelveANeighborNode(rosetta.core.graph.Node)       Method resolution order: TwelveANeighborNode rosetta.core.graph.Node builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : handle,  : rosetta.core.graph.Graph, node_id : int) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. copy_from(...) from builtins.PyCapsule copy_from(self : rosetta.core.scoring.TwelveANeighborNode, source : rosetta.core.graph.Node) -> NoneType count_dynamic_memory(...) from builtins.PyCapsule count_dynamic_memory(rosetta.core.scoring.TwelveANeighborNode) -> int count_static_memory(...) from builtins.PyCapsule count_static_memory(rosetta.core.scoring.TwelveANeighborNode) -> int Methods inherited from rosetta.core.graph.Node: add_edge(...) from builtins.PyCapsule add_edge(self : rosetta.core.graph.Node, edge_ptr : core::graph::Edge,  : rosetta.core.graph.EdgeListIterator) -> NoneType   adds edge pointer to edge list; returns an iterator to the new  list element const_edge_list_begin(...) from builtins.PyCapsule const_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its edge list const_edge_list_end(...) from builtins.PyCapsule const_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its edge list const_lower_edge_list_begin(...) from builtins.PyCapsule const_lower_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its lower-edge list const_lower_edge_list_end(...) from builtins.PyCapsule const_lower_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its lower-edge list const_upper_edge_list_begin(...) from builtins.PyCapsule const_upper_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the beginning of its upper-edge list const_upper_edge_list_end(...) from builtins.PyCapsule const_upper_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListConstIterator   returns a const iterator to the end of its upper-edge list drop_all_edges(...) from builtins.PyCapsule drop_all_edges(rosetta.core.graph.Node) -> NoneType   deletes all edges incident upon this node drop_edge(...) from builtins.PyCapsule drop_edge(self : rosetta.core.graph.Node, edge_iterator : rosetta.core.graph.EdgeListIterator) -> NoneType   removes an edge iterator from the node's edge list.  Only called by Edge class. edge_list_begin(...) from builtins.PyCapsule edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its edge list edge_list_end(...) from builtins.PyCapsule edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its edge list find_edge(...) from builtins.PyCapsule find_edge(*args, **kwargs) Overloaded function.   1. find_edge(self : rosetta.core.graph.Node, other_node_index : int) -> core::graph::Edge   a "slow" (linear) search for an edge.   2. find_edge(self : rosetta.core.graph.Node, other_node_index : int) -> core::graph::Edge get_node_index(...) from builtins.PyCapsule get_node_index(rosetta.core.graph.Node) -> int   the index for this node get_num_edges_to_larger_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_larger_indexed_nodes(rosetta.core.graph.Node) -> int   the number of upper neighbors -- which "self" neighborness is counted if a loop edge  is present get_num_edges_to_smaller_indexed_nodes(...) from builtins.PyCapsule get_num_edges_to_smaller_indexed_nodes(rosetta.core.graph.Node) -> int   the number of lower neighbors loop_incident(...) from builtins.PyCapsule loop_incident(rosetta.core.graph.Node) -> bool   NOTE TO SELF: remove loop support lower_edge_list_begin(...) from builtins.PyCapsule lower_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its lower-edge list lower_edge_list_end(...) from builtins.PyCapsule lower_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its lower-edge list num_edges(...) from builtins.PyCapsule num_edges(rosetta.core.graph.Node) -> int   the number of edges incident on this node, which may include a loop edge num_neighbors_counting_self(...) from builtins.PyCapsule num_neighbors_counting_self(rosetta.core.graph.Node) -> int   the number of neighbors counting "self" as a neighbor. num_neighbors_counting_self_static(...) from builtins.PyCapsule num_neighbors_counting_self_static(rosetta.core.graph.Node) -> int   the number of neighbors counting "self" as neighbor. Defaults to  num_neighbors_counting_self() but can be set to other values as well.  Useful in calculation of symmetrical structures. print(...) from builtins.PyCapsule print(rosetta.core.graph.Node) -> NoneType   send summaray data about this node to the screen set_num_neighbors_counting_self_static(...) from builtins.PyCapsule set_num_neighbors_counting_self_static(self : rosetta.core.graph.Node, neighbor : int) -> NoneType   manually change the number of neighbors for a Node. Used  for symmetry scoring upper_edge_list_begin(...) from builtins.PyCapsule upper_edge_list_begin(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the beginning of its upper-edge list upper_edge_list_end(...) from builtins.PyCapsule upper_edge_list_end(rosetta.core.graph.Node) -> rosetta.core.graph.EdgeListIterator   returns a non-const iterator to the end of its upper-edge list   class UnfoldedStatePotential(builtins.object)     making this a separate class because it relies on a database file. rather than putting the code to read the database file in the energy method class, it seems like the design we're following is to have a class like this one that reads the file and provides the lookup into the data structure holding the database information and a separate class for the energy method implementation.     Methods defined here: __init__(...) from builtins.PyCapsule __init__(self : rosetta.core.scoring.UnfoldedStatePotential, filename : str) -> 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.scoring.UnfoldedStatePotential,  : rosetta.core.scoring.UnfoldedStatePotential) -> rosetta.core.scoring.UnfoldedStatePotential get_unfoled_potential_file_weights(...) from builtins.PyCapsule get_unfoled_potential_file_weights(rosetta.core.scoring.UnfoldedStatePotential) -> rosetta.core.scoring.EMapVector   returns an emap of the energy method weights specfied in the unfolded energy file pose_raw_unfolded_state_energymap(...) from builtins.PyCapsule pose_raw_unfolded_state_energymap(self : rosetta.core.scoring.UnfoldedStatePotential, pose : rosetta.core.pose.Pose, e : rosetta.core.scoring.EMapVector) -> NoneType   returns the unweighted unfolded state energy for the whole pose as an emap (i.e. broken up by score type) raw_unfolded_state_energymap(...) from builtins.PyCapsule raw_unfolded_state_energymap(self : rosetta.core.scoring.UnfoldedStatePotential, aa_name3 : str, e : rosetta.core.scoring.EMapVector) -> NoneType   returns the database values for an aa in the unfolded state - these are unweighted values!   class VdWTinkerPoseInfo(rosetta.basic.datacache.CacheableData)     ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////     Method resolution order: VdWTinkerPoseInfo rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.scoring.VdWTinkerPoseInfo) -> 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.scoring.VdWTinkerPoseInfo,  : rosetta.core.scoring.VdWTinkerPoseInfo) -> rosetta.core.scoring.VdWTinkerPoseInfo being_packed(...) from builtins.PyCapsule being_packed(self : rosetta.core.scoring.VdWTinkerPoseInfo, seqpos : int) -> bool clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.VdWTinkerPoseInfo) -> rosetta.basic.datacache.CacheableData initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.scoring.VdWTinkerPoseInfo, pose : rosetta.core.pose.Pose) -> NoneType placeholder_info(...) from builtins.PyCapsule placeholder_info(self : rosetta.core.scoring.VdWTinkerPoseInfo, seqpos : int) -> rosetta.core.scoring.VdWTinkerResidueInfo placeholder_residue(...) from builtins.PyCapsule placeholder_residue(self : rosetta.core.scoring.VdWTinkerPoseInfo, seqpos : int) -> rosetta.core.conformation.Residue residue_info(...) from builtins.PyCapsule residue_info(*args, **kwargs) Overloaded function.   1. residue_info(self : rosetta.core.scoring.VdWTinkerPoseInfo, i : int) -> rosetta.core.scoring.VdWTinkerResidueInfo   2. residue_info(self : rosetta.core.scoring.VdWTinkerPoseInfo, i : int) -> rosetta.core.scoring.VdWTinkerResidueInfo set_placeholder(...) from builtins.PyCapsule set_placeholder(self : rosetta.core.scoring.VdWTinkerPoseInfo, i : int, rsd : rosetta.core.conformation.Residue, info : rosetta.core.scoring.VdWTinkerResidueInfo) -> NoneType set_repack_list(...) from builtins.PyCapsule set_repack_list(self : rosetta.core.scoring.VdWTinkerPoseInfo, repacking_residues : rosetta.utility.vector1_bool) -> NoneType size(...) from builtins.PyCapsule size(rosetta.core.scoring.VdWTinkerPoseInfo) -> int Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class VdWTinkerPotential(builtins.object)     ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.VdWTinkerPotential) -> NoneType   2. __init__(self : rosetta.core.scoring.VdWTinkerPotential,  : rosetta.core.scoring.VdWTinkerPotential) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. amoeba_type_lookup(...) from builtins.PyCapsule amoeba_type_lookup(self : rosetta.core.scoring.VdWTinkerPotential, atomname : str, resname : str, variantname : str) -> int   Look up Amoeba type by resname/atomname/variant name assign_all_amoeba_types(...) from builtins.PyCapsule assign_all_amoeba_types(self : rosetta.core.scoring.VdWTinkerPotential, pose : rosetta.core.pose.Pose) -> NoneType   called prior to scoring, eg assign_residue_amoeba_type(...) from builtins.PyCapsule assign_residue_amoeba_type(self : rosetta.core.scoring.VdWTinkerPotential, rsd : rosetta.core.conformation.Residue, mp : rosetta.core.scoring.VdWTinkerResidueInfo) -> NoneType   called prior to scoring, eg eval_residue_pair_derivatives(...) from builtins.PyCapsule eval_residue_pair_derivatives(self : rosetta.core.scoring.VdWTinkerPotential, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, mp1 : rosetta.core.scoring.VdWTinkerResidueInfo, mp2 : rosetta.core.scoring.VdWTinkerResidueInfo, pose : rosetta.core.pose.Pose, factor : float, r1_atom_derivs : rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_atom_derivs : rosetta.utility.vector1_core_scoring_DerivVectorPair) -> NoneType get_res_res_vdw(...) from builtins.PyCapsule get_res_res_vdw(self : rosetta.core.scoring.VdWTinkerPotential, rsd1 : rosetta.core.conformation.Residue, mp1 : rosetta.core.scoring.VdWTinkerResidueInfo, rsd2 : rosetta.core.conformation.Residue, mp2 : rosetta.core.scoring.VdWTinkerResidueInfo) -> float get_rotamers_vdw_info(...) from builtins.PyCapsule get_rotamers_vdw_info(self : rosetta.core.scoring.VdWTinkerPotential, pose : rosetta.core.pose.Pose,  : rosetta.core.conformation.RotamerSetBase) -> NoneType   Get the amoeba info for rotamers read_in_amoeba_parameters(...) from builtins.PyCapsule read_in_amoeba_parameters(rosetta.core.scoring.VdWTinkerPotential) -> NoneType   read in parameters for amoeba and mappings between  Rosetta residues/atoms and Amoeba types read_in_vdw_tinker_parameters(...) from builtins.PyCapsule read_in_vdw_tinker_parameters(rosetta.core.scoring.VdWTinkerPotential) -> NoneType   read in vdw parameters for amoeba types setup_for_packing(...) from builtins.PyCapsule setup_for_packing(self : rosetta.core.scoring.VdWTinkerPotential, pose : rosetta.core.pose.Pose, repacking_residues : rosetta.utility.vector1_bool) -> NoneType setup_for_scoring(...) from builtins.PyCapsule setup_for_scoring(self : rosetta.core.scoring.VdWTinkerPotential, pose : rosetta.core.pose.Pose) -> NoneType update_residue_for_packing(...) from builtins.PyCapsule update_residue_for_packing(self : rosetta.core.scoring.VdWTinkerPotential, pose : rosetta.core.pose.Pose, seqpos : int) -> NoneType   class VdWTinkerResidueInfo(rosetta.basic.datacache.CacheableData)     ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////     Method resolution order: VdWTinkerResidueInfo rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(self : handle, rsd : rosetta.core.conformation.Residue) -> NoneType   3. __init__(handle, rosetta.core.scoring.VdWTinkerResidueInfo) -> 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.scoring.VdWTinkerResidueInfo,  : rosetta.core.scoring.VdWTinkerResidueInfo) -> rosetta.core.scoring.VdWTinkerResidueInfo clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.VdWTinkerResidueInfo) -> rosetta.basic.datacache.CacheableData copy_clone(...) from builtins.PyCapsule copy_clone(rosetta.core.scoring.VdWTinkerResidueInfo) -> rosetta.core.scoring.VdWTinkerResidueInfo initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.scoring.VdWTinkerResidueInfo, rsd : rosetta.core.conformation.Residue) -> NoneType nonconst_vdw_type(...) from builtins.PyCapsule nonconst_vdw_type(self : rosetta.core.scoring.VdWTinkerResidueInfo, atm : int) -> int vdw_type(...) from builtins.PyCapsule vdw_type(self : rosetta.core.scoring.VdWTinkerResidueInfo, atm : int) -> int Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class VdWTinkerRotamerSetInfo(rosetta.basic.datacache.CacheableData)     ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////     Method resolution order: VdWTinkerRotamerSetInfo rosetta.basic.datacache.CacheableData builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle, rosetta.core.scoring.VdWTinkerRotamerSetInfo) -> NoneType   2. __init__(self : handle, rotamer_set : rosetta.core.conformation.RotamerSetBase) -> 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.scoring.VdWTinkerRotamerSetInfo,  : rosetta.core.scoring.VdWTinkerRotamerSetInfo) -> rosetta.core.scoring.VdWTinkerRotamerSetInfo clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.VdWTinkerRotamerSetInfo) -> rosetta.basic.datacache.CacheableData initialize(...) from builtins.PyCapsule initialize(self : rosetta.core.scoring.VdWTinkerRotamerSetInfo, rotamer_set : rosetta.core.conformation.RotamerSetBase) -> NoneType   dont forget to 0 the born_radii residue_info(...) from builtins.PyCapsule residue_info(*args, **kwargs) Overloaded function.   1. residue_info(self : rosetta.core.scoring.VdWTinkerRotamerSetInfo, i : int) -> rosetta.core.scoring.VdWTinkerResidueInfo   2. residue_info(self : rosetta.core.scoring.VdWTinkerRotamerSetInfo, i : int) -> rosetta.core.scoring.VdWTinkerResidueInfo size(...) from builtins.PyCapsule size(rosetta.core.scoring.VdWTinkerRotamerSetInfo) -> int Methods inherited from rosetta.basic.datacache.CacheableData: get_self_ptr(...) from builtins.PyCapsule get_self_ptr(*args, **kwargs) Overloaded function.   1. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData   self pointers   2. get_self_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.basic.datacache.CacheableData get_self_weak_ptr(...) from builtins.PyCapsule get_self_weak_ptr(*args, **kwargs) Overloaded function.   1. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_const_basic_datacache_CacheableData_t   2. get_self_weak_ptr(rosetta.basic.datacache.CacheableData) -> rosetta.std.weak_ptr_basic_datacache_CacheableData_t   class WaterAdductHBondPotential(builtins.object)     ///////////////////////////////////////////////////////////////////////////////////////////////// ///////////////////////////////////////////////////////////////////////////////////////////////// /////////////////////////////////////////////////////////////////////////////////////////////////     Methods defined here: __init__(...) from builtins.PyCapsule __init__(rosetta.core.scoring.WaterAdductHBondPotential) -> 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.scoring.WaterAdductHBondPotential,  : rosetta.core.scoring.WaterAdductHBondPotential) -> rosetta.core.scoring.WaterAdductHBondPotential fill_h2o_hbond_set(...) from builtins.PyCapsule fill_h2o_hbond_set(self : rosetta.core.scoring.WaterAdductHBondPotential, pose : rosetta.core.pose.Pose, hbond_set : core::scoring::hbonds::HBondSet) -> NoneType   Fills the hbond set with hydrogen bonds to water; clears the original hbonds in the set  and also resets the hbond_options in the input hbond set. get_residue_residue_h2o_hbonds_1way(...) from builtins.PyCapsule get_residue_residue_h2o_hbonds_1way(self : rosetta.core.scoring.WaterAdductHBondPotential, don_rsd : rosetta.core.conformation.Residue, acc_rsd : rosetta.core.conformation.Residue, don_nb : int, acc_nb : int, hbond_set : core::scoring::hbonds::HBondSet) -> NoneType h2o_hbond_score_1way(...) from builtins.PyCapsule h2o_hbond_score_1way(self : rosetta.core.scoring.WaterAdductHBondPotential, h2o_rsd : rosetta.core.conformation.Residue, other_rsd : rosetta.core.conformation.Residue) -> float water_adduct_hbond_score(...) from builtins.PyCapsule water_adduct_hbond_score(self : rosetta.core.scoring.WaterAdductHBondPotential, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue) -> float   class min_pair_data(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.core.scoring.min_pair_data, rosetta.core.scoring.min_pair_data) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.core.scoring.min_pair_data) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.min_pair_data, int) -> NoneType   2. __init__(rosetta.core.scoring.min_pair_data, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.core.scoring.min_pair_data) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.core.scoring.min_pair_data, rosetta.core.scoring.min_pair_data) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.core.scoring.min_pair_data) -> str Data and other attributes defined here: cst_respair_data = min_pair_data.cst_respair_data elec_pair_nblist = min_pair_data.elec_pair_nblist etab_classic_intrares_pair_nblist = min_pair_data.etab_classic_intrares_pair_nblist etab_pair_nblist = min_pair_data.etab_pair_nblist fa_custom_pair_dist_data = min_pair_data.fa_custom_pair_dist_data fa_dslf_respair_data = min_pair_data.fa_dslf_respair_data geom_solv_pair_nblist = min_pair_data.geom_solv_pair_nblist hbond_respair_data = min_pair_data.n_min_pair_data lk_PolarNonPolar_pair_nblist = min_pair_data.lk_PolarNonPolar_pair_nblist lkb_respair_data = min_pair_data.lkb_respair_data mg_pair_nblist = min_pair_data.mg_pair_nblist mp_respair_data = min_pair_data.mp_respair_data n_min_pair_data = min_pair_data.n_min_pair_data vdw_respair_data = min_pair_data.vdw_respair_data   class min_single_data(builtins.object)       Methods defined here: __eq__(...) from builtins.PyCapsule __eq__(rosetta.core.scoring.min_single_data, rosetta.core.scoring.min_single_data) -> bool __hash__(...) from builtins.PyCapsule __hash__(rosetta.core.scoring.min_single_data) -> int __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(rosetta.core.scoring.min_single_data, int) -> NoneType   2. __init__(rosetta.core.scoring.min_single_data, int) -> NoneType __int__(...) from builtins.PyCapsule __int__(rosetta.core.scoring.min_single_data) -> int __ne__(...) from builtins.PyCapsule __ne__(rosetta.core.scoring.min_single_data, rosetta.core.scoring.min_single_data) -> bool __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. __repr__(...) from builtins.PyCapsule __repr__(rosetta.core.scoring.min_single_data) -> str Data and other attributes defined here: cst_res_data = min_single_data.cst_res_data etab_classic_intrares_single_nblist = min_single_data.etab_classic_intrares_single_nblist etab_single_nblist = min_single_data.etab_single_nblist hbond_res_data = min_single_data.n_min_single_data lkb_res_data = min_single_data.lkb_res_data mm_lj_intra_nblist = min_single_data.mm_lj_intra_nblist mp_res_data = min_single_data.mp_res_data n_min_single_data = min_single_data.n_min_single_data vdw_res_data = min_single_data.vdw_res_data