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- builtins.object
-
- HSPairPotential
- NatbiasHelicesSheetPotential
- NatbiasHelixPairPotential
- NatbiasStrandPairPotential
- SSPairPotential
- rosetta.core.scoring.methods.EnergyMethodCreator(builtins.object)
-
- NatbiasSecondaryStructureEnergyCreator
- rosetta.core.scoring.methods.WholeStructureEnergy(rosetta.core.scoring.methods.EnergyMethod)
-
- NatbiasSecondaryStructureEnergy
class NatbiasHelicesSheetPotential(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential) -> NoneType
2. __init__(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, hss3set : rosetta.protocols.fldsgn.topology.HSSTripletSet) -> NoneType
3. __init__(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, hss3set : rosetta.protocols.fldsgn.topology.HSSTripletSet, hpairset : rosetta.protocols.fldsgn.topology.HelixPairingSet) -> NoneType
4. __init__(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, src : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential) -> 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.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential) -> rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential
- hpairset(...) from builtins.PyCapsule
- hpairset(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, hpairset : rosetta.protocols.fldsgn.topology.HelixPairingSet) -> NoneType
set HelixPairingSet
- hss_triplet_set(...) from builtins.PyCapsule
- hss_triplet_set(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, hss3set : rosetta.protocols.fldsgn.topology.HSSTripletSet) -> NoneType
set HSSTripletSet
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, ss_info : rosetta.protocols.fldsgn.topology.SS_Info2, hh_score : float, hs_score : float) -> NoneType
calc score
- set_angle_params_helices_on_sheet(...) from builtins.PyCapsule
- set_angle_params_helices_on_sheet(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, hh_align_angle_wts : float, hh_align_angle : float, hh_align_angle_sigma2 : float) -> NoneType
set angle parameters for helices projected onto sheet
- set_angle_params_helix_sheet(...) from builtins.PyCapsule
- set_angle_params_helix_sheet(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, hs_angle_wts : float, hs_angle : float, hs_angle_sigma2 : float) -> NoneType
set angle parameters for helix-sheet interaction
- set_atrdist_params_helix_strands(...) from builtins.PyCapsule
- set_atrdist_params_helix_strands(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, hs_dist_wts : float, hs_dist : float, hs_dist_sigma2 : float) -> NoneType
set dist parameters for helix-strands interaction
- set_hh_angle(...) from builtins.PyCapsule
- set_hh_angle(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r : float) -> NoneType
- set_hh_angle_sigma2(...) from builtins.PyCapsule
- set_hh_angle_sigma2(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r : float) -> NoneType
- set_hh_angle_wts(...) from builtins.PyCapsule
- set_hh_angle_wts(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r : float) -> NoneType
- set_hs_angle(...) from builtins.PyCapsule
- set_hs_angle(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r : float) -> NoneType
- set_hs_angle_sigma2(...) from builtins.PyCapsule
- set_hs_angle_sigma2(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r : float) -> NoneType
- set_hs_angle_wts(...) from builtins.PyCapsule
- set_hs_angle_wts(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r : float) -> NoneType
- set_hs_atr_dist(...) from builtins.PyCapsule
- set_hs_atr_dist(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r : float) -> NoneType
- set_hs_atr_dist_sigma2(...) from builtins.PyCapsule
- set_hs_atr_dist_sigma2(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r : float) -> NoneType
- set_hs_atr_dist_wts(...) from builtins.PyCapsule
- set_hs_atr_dist_wts(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r : float) -> NoneType
set dist parameters for helix-sheet interaction
- set_hsheet_repl_dist(...) from builtins.PyCapsule
- set_hsheet_repl_dist(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, r : float) -> NoneType
- set_params(...) from builtins.PyCapsule
- set_params(rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential) -> NoneType
set parameters
- set_repldist_params_helix_sheet(...) from builtins.PyCapsule
- set_repldist_params_helix_sheet(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential, hsheet_dist_repulsive : float) -> NoneType
- show_params(...) from builtins.PyCapsule
- show_params(rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential) -> NoneType
shows parameters for score calculation
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class NatbiasHelixPairPotential(builtins.object) |
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential) -> NoneType
2. __init__(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, hpairset : rosetta.protocols.fldsgn.topology.HelixPairingSet) -> NoneType
3. __init__(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, src : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential) -> 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.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential) -> rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, ss_info : rosetta.protocols.fldsgn.topology.SS_Info2, hh_score : float) -> NoneType
score secondary structure
- set_angle(...) from builtins.PyCapsule
- set_angle(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, r : float) -> NoneType
- set_angle_sigma2(...) from builtins.PyCapsule
- set_angle_sigma2(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, r : float) -> NoneType
- set_angle_wts(...) from builtins.PyCapsule
- set_angle_wts(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, r : float) -> NoneType
- set_bendangle(...) from builtins.PyCapsule
- set_bendangle(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, r : float) -> NoneType
set bend angle
- set_dist(...) from builtins.PyCapsule
- set_dist(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, r : float) -> NoneType
set distance parmeter
- set_dist_sigma2(...) from builtins.PyCapsule
- set_dist_sigma2(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, r : float) -> NoneType
- set_dist_wts(...) from builtins.PyCapsule
- set_dist_wts(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, r : float) -> NoneType
- set_hpairset(...) from builtins.PyCapsule
- set_hpairset(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, hpairset : rosetta.protocols.fldsgn.topology.HelixPairingSet) -> NoneType
- set_params(...) from builtins.PyCapsule
- set_params(rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential) -> NoneType
- set_params_angle_pot(...) from builtins.PyCapsule
- set_params_angle_pot(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, w : float, d : float, s : float) -> NoneType
set parameters for angle score of helix pair
- set_params_distance_pot(...) from builtins.PyCapsule
- set_params_distance_pot(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, w : float, d : float, s : float) -> NoneType
set parameters for distance score between mid points of helices
- show(...) from builtins.PyCapsule
- show(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential, pose : rosetta.core.pose.Pose) -> NoneType
- show_params(...) from builtins.PyCapsule
- show_params(rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential) -> NoneType
show parameters
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class NatbiasSecondaryStructureEnergy(rosetta.core.scoring.methods.WholeStructureEnergy) |
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NatbiasSecondaryStructureEnergy
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- Method resolution order:
- NatbiasSecondaryStructureEnergy
- rosetta.core.scoring.methods.WholeStructureEnergy
- rosetta.core.scoring.methods.EnergyMethod
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy) -> 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.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, : rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy) -> rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy
- atomic_interaction_cutoff(...) from builtins.PyCapsule
- atomic_interaction_cutoff(rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy) -> float
The NatbiasSecondaryStructureEnergy class requires that the EnergyGraph
span 12 Angstroms between centroids. The centroids residues build-in a
3 Angstrom radius each.
- clone(...) from builtins.PyCapsule
- clone(rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy) -> rosetta.core.scoring.methods.EnergyMethod
clone
- finalize_total_energy(...) from builtins.PyCapsule
- finalize_total_energy(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, pose : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, totals : rosetta.core.scoring.EMapVector) -> NoneType
scoring
- indicate_required_context_graphs(...) from builtins.PyCapsule
- indicate_required_context_graphs(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, context_graphs_required : rosetta.utility.vector1_bool) -> NoneType
- native_secstruct(...) from builtins.PyCapsule
- native_secstruct(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, secstruct : str) -> NoneType
set native secondary structure
- set_natbias_helices_sheet_pot(...) from builtins.PyCapsule
- set_natbias_helices_sheet_pot(*args, **kwargs)
Overloaded function.
1. set_natbias_helices_sheet_pot(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, hss3set : rosetta.protocols.fldsgn.topology.HSSTripletSet) -> NoneType
set NatbiasHelicesSheetPotential
2. set_natbias_helices_sheet_pot(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, hspot : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelicesSheetPotential) -> NoneType
set NatbiasHelicesSheetPotential
- set_natbias_hpairpot(...) from builtins.PyCapsule
- set_natbias_hpairpot(*args, **kwargs)
Overloaded function.
1. set_natbias_hpairpot(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, hpairset : rosetta.protocols.fldsgn.topology.HelixPairingSet) -> NoneType
set NatbiasHelixPairPotential
2. set_natbias_hpairpot(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, hhpot : rosetta.protocols.fldsgn.potentials.sspot.NatbiasHelixPairPotential) -> NoneType
set NatbiasHelixPairPotential
- set_natbias_spairpot(...) from builtins.PyCapsule
- set_natbias_spairpot(*args, **kwargs)
Overloaded function.
1. set_natbias_spairpot(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, spairset : rosetta.protocols.fldsgn.topology.StrandPairingSet) -> NoneType
set NatbiasStrandPairPotential
2. set_natbias_spairpot(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, sspot : protocols::fldsgn::potentials::sspot::NatbiasStrandPairPotential) -> NoneType
set native NatbiasStrandPairPotential
- setup_for_scoring(...) from builtins.PyCapsule
- setup_for_scoring(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType
scoring
- use_nobias(...) from builtins.PyCapsule
- use_nobias(self : rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy, b : bool) -> NoneType
use use original secondary structure potential
- version(...) from builtins.PyCapsule
- version(rosetta.protocols.fldsgn.potentials.sspot.NatbiasSecondaryStructureEnergy) -> int
Methods inherited from rosetta.core.scoring.methods.WholeStructureEnergy:
- method_type(...) from builtins.PyCapsule
- method_type(rosetta.core.scoring.methods.WholeStructureEnergy) -> rosetta.core.scoring.methods.EnergyMethodType
Methods inherited from rosetta.core.scoring.methods.EnergyMethod:
- defines_high_order_terms(...) from builtins.PyCapsule
- defines_high_order_terms(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose) -> bool
Should this EnergyMethod have score and derivative evaluation
evaluated both in the context of the whole Pose and in the context
of residue or residue-pairs? This covers scoring terms like env-smooth
wherein the CBeta's get derivatives for increasing the neighbor counts
for surrounding residues, and terms like constraints, which are definable
on arbitrary number of residues (e.g. more than 2); both of these terms
could be used in RTMin, and both should use the residue and residue-pair
evaluation scheme with the MinimizationGraph for the majority of the
work they do. (Now, high-order constraints (3-body or above) will not
be properly evaluated within RTMin.). The default implementation
returns "false".
- eval_atom_derivative(...) from builtins.PyCapsule
- eval_atom_derivative(self : rosetta.core.scoring.methods.EnergyMethod, id : rosetta.core.id.AtomID, pose : rosetta.core.pose.Pose, domain_map : ObjexxFCL::FArray1D<int>, sfxn : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t) -> NoneType
Evaluate the XYZ derivative for an atom in the pose.
Called during the atomtree derivative calculation, atom_tree_minimize.cc,
through the ScoreFunction::eval_atom_derivative intermediary.
F1 and F2 should not zeroed, rather, this class should accumulate its contribution
from this atom's XYZ derivative
The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984)
"Rapid Calculation of First and Second Derivatives of Conformational Energy with
Respect to Dihedral Angles for Proteins. General Recurrent Equations"
Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga,
respectively, of equations 7a & 7b in that paper.
- finalize_after_derivatives(...) from builtins.PyCapsule
- finalize_after_derivatives(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction) -> NoneType
called at the end of derivatives evaluation
- minimize_in_whole_structure_context(...) from builtins.PyCapsule
- minimize_in_whole_structure_context(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose) -> bool
Should this EnergyMethod have score and derivative evaluation
evaluated only in the context of the whole Pose, or can it be included
in a decomposed manner for a residue or a set of residue-pairs that are
not part of the Pose that's serving as their context? The default
method implemented in the base class returns true in order to grandfather
in EnergyMethods that have not had their derivatives changed to take
advantage of the new derivative-evaluation machinery. Methods that return
"true" will not have their residue-energy(-ext) / residue-pair-energy(-ext)
methods invoked by the ScoreFunction during its traversal of the
MinimizationGraph, and instead will be asked to perform all their work
during finalize_total_energies(). Similarly, they will be expected to
perform all their work during eval_atom_deriv() instead of during the
ScoreFunction's traversal of the MinimizationGraph for derivative evaluation.
IMPORTANT: Methods that return "true" cannot be included in RTMin.
- prepare_rotamers_for_packing(...) from builtins.PyCapsule
- prepare_rotamers_for_packing(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, : rosetta.core.conformation.RotamerSetBase) -> NoneType
If an energy method needs to cache data in a packing::RotamerSet object before
rotamer energies are calculated, it does so during this function. The packer
must ensure this function is called. The default behavior is to do nothing.
- score_types(...) from builtins.PyCapsule
- score_types(rosetta.core.scoring.methods.EnergyMethod) -> rosetta.utility.vector1_core_scoring_ScoreType
Returns the score types that this energy method computes.
- setup_for_derivatives(...) from builtins.PyCapsule
- setup_for_derivatives(self : rosetta.core.scoring.methods.EnergyMethod, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
Called immediately before atom- and DOF-derivatives are calculated
allowing the derived class a chance to prepare for future calls.
- setup_for_minimizing(...) from builtins.PyCapsule
- setup_for_minimizing(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, : rosetta.core.kinematics.MinimizerMapBase) -> NoneType
Called at the beginning of atom tree minimization, this method
allows the derived class the opportunity to initialize pertinent data
that will be used during minimization. During minimzation, the chemical
structure of the pose is constant, so assumptions on the number of atoms
per residue and their identities are safe so long as the pose's Energies
object's "use_nblist()" method returns true.
- setup_for_packing(...) from builtins.PyCapsule
- setup_for_packing(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, : rosetta.utility.vector1_bool, : rosetta.utility.vector1_bool) -> NoneType
if an energy method needs to cache data in the Energies object,
before packing begins, then it does so during this function. The packer
must ensure this function is called. The default behavior is to do nothing.
- update_residue_for_packing(...) from builtins.PyCapsule
- update_residue_for_packing(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, resid : int) -> NoneType
If the pose changes in the middle of a packing (as happens in rotamer trials) and if
an energy method needs to cache data in the pose that corresponds to its current state,
then the method must update that data when this function is called. The packer must
ensure this function gets called. The default behavior is to do nothing.
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class SSPairPotential(builtins.object) |
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secondary structure scoring cut from classic rosetta structure.h/structure.cc
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential) -> NoneType
2. __init__(self : rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential, : rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential) -> 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.protocols.fldsgn.potentials.sspot.SSPairPotential, : rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential) -> rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential
- score(...) from builtins.PyCapsule
- score(self : rosetta.protocols.fldsgn.potentials.sspot.SSPairPotential, pose : rosetta.core.pose.Pose, ss_info : rosetta.protocols.fldsgn.topology.SS_Info2, dimer_pairs : protocols::fldsgn::topology::DimerPairings, ss_score : float) -> NoneType
score secondary structure
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