| | |
- builtins.object
-
- RNA_DMS_LowResolutionPotential
- RNA_DMS_Potential
- RNA_DataInfo
- RNA_Datum
- RNA_Reactivity
- RNA_ReactivityType
- rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy(rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy)
-
- RNA_DataBackboneEnergy
- rosetta.core.scoring.methods.EnergyMethodCreator(builtins.object)
-
- RNA_ChemicalMappingEnergyCreator
- RNA_DataBackboneEnergyCreator
- rosetta.core.scoring.methods.WholeStructureEnergy(rosetta.core.scoring.methods.EnergyMethod)
-
- RNA_ChemicalMappingEnergy
class RNA_ChemicalMappingEnergy(rosetta.core.scoring.methods.WholeStructureEnergy) |
| | |
- Method resolution order:
- RNA_ChemicalMappingEnergy
- rosetta.core.scoring.methods.WholeStructureEnergy
- rosetta.core.scoring.methods.EnergyMethod
- builtins.object
Methods defined here:
- __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.
- atomic_interaction_cutoff(...) from builtins.PyCapsule
- atomic_interaction_cutoff(rosetta.core.scoring.rna.data.RNA_ChemicalMappingEnergy) -> float
- calculate_energy(...) from builtins.PyCapsule
- calculate_energy(*args, **kwargs)
Overloaded function.
1. calculate_energy(self : rosetta.core.scoring.rna.data.RNA_ChemicalMappingEnergy, pose : rosetta.core.pose.Pose) -> float
//////////////////////////////////////////////////////////////////////////
2. calculate_energy(self : rosetta.core.scoring.rna.data.RNA_ChemicalMappingEnergy, pose : rosetta.core.pose.Pose, use_low_res : bool) -> float
//////////////////////////////////////////////////////////////////////////
3. calculate_energy(self : rosetta.core.scoring.rna.data.RNA_ChemicalMappingEnergy, pose : rosetta.core.pose.Pose, use_low_res : bool, rna_base_pair_computed : bool) -> float
//////////////////////////////////////////////////////////////////////////
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.scoring.rna.data.RNA_ChemicalMappingEnergy) -> rosetta.core.scoring.methods.EnergyMethod
clone
- finalize_total_energy(...) from builtins.PyCapsule
- finalize_total_energy(self : rosetta.core.scoring.rna.data.RNA_ChemicalMappingEnergy, pose : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, : rosetta.core.scoring.EMapVector) -> NoneType
- indicate_required_context_graphs(...) from builtins.PyCapsule
- indicate_required_context_graphs(self : rosetta.core.scoring.rna.data.RNA_ChemicalMappingEnergy, : rosetta.utility.vector1_bool) -> NoneType
- version(...) from builtins.PyCapsule
- version(rosetta.core.scoring.rna.data.RNA_ChemicalMappingEnergy) -> int
Methods inherited from rosetta.core.scoring.methods.WholeStructureEnergy:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.scoring.methods.WholeStructureEnergy, : rosetta.core.scoring.methods.WholeStructureEnergy) -> 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.
- setup_for_scoring(...) from builtins.PyCapsule
- setup_for_scoring(self : rosetta.core.scoring.methods.EnergyMethod, : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction) -> NoneType
if an energy method needs to cache something in the pose (e.g. in pose.energies()),
before scoring begins, it must do so in this method. All long range energy
functions must initialize their LREnergyContainers before scoring begins.
The default 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.
|
class RNA_DMS_LowResolutionPotential(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential) -> 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.rna.data.RNA_DMS_LowResolutionPotential, : rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential) -> rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential
- careful_base_pair_classifier(...) from builtins.PyCapsule
- careful_base_pair_classifier(rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential) -> bool
- evaluate(...) from builtins.PyCapsule
- evaluate(self : rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential, pose : rosetta.core.pose.Pose, rna_reactivity : rosetta.core.scoring.rna.data.RNA_Reactivity) -> float
- get_rna_base_pairing_status(...) from builtins.PyCapsule
- get_rna_base_pairing_status(*args, **kwargs)
Overloaded function.
1. get_rna_base_pairing_status(self : rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential, pose : rosetta.core.pose.Pose, wc_edge_paired : rosetta.utility.vector1_bool, hoogsteen_edge_paired : rosetta.utility.vector1_bool, sugar_edge_paired : rosetta.utility.vector1_bool, is_bulged : rosetta.utility.vector1_bool) -> NoneType
2. get_rna_base_pairing_status(self : rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential, pose : rosetta.core.pose.Pose, wc_edge_paired : rosetta.utility.vector1_bool, hoogsteen_edge_paired : rosetta.utility.vector1_bool, sugar_edge_paired : rosetta.utility.vector1_bool, is_bulged : rosetta.utility.vector1_bool, already_scored : bool) -> NoneType
- get_wc_near_o2prime(...) from builtins.PyCapsule
- get_wc_near_o2prime(self : rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential, pose : rosetta.core.pose.Pose, i : int) -> bool
- hoog_edge_paired(...) from builtins.PyCapsule
- hoog_edge_paired(rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential) -> rosetta.utility.vector1_bool
- initialize(...) from builtins.PyCapsule
- initialize(*args, **kwargs)
Overloaded function.
1. initialize(self : rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential, pose : rosetta.core.pose.Pose) -> NoneType
2. initialize(self : rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential, pose : rosetta.core.pose.Pose, rna_base_pair_computed : bool) -> NoneType
- is_bulged(...) from builtins.PyCapsule
- is_bulged(rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential) -> rosetta.utility.vector1_bool
- set_careful_base_pair_classifier(...) from builtins.PyCapsule
- set_careful_base_pair_classifier(self : rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential, setting : bool) -> NoneType
- sugar_edge_paired(...) from builtins.PyCapsule
- sugar_edge_paired(rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential) -> rosetta.utility.vector1_bool
- update_edge_paired(...) from builtins.PyCapsule
- update_edge_paired(self : rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential, i : int, k : int, wc_edge_paired : rosetta.utility.vector1_bool, hoogsteen_edge_paired : rosetta.utility.vector1_bool, sugar_edge_paired : rosetta.utility.vector1_bool) -> NoneType
- wc_edge_paired(...) from builtins.PyCapsule
- wc_edge_paired(rosetta.core.scoring.rna.data.RNA_DMS_LowResolutionPotential) -> rosetta.utility.vector1_bool
|
class RNA_DMS_Potential(builtins.object) |
| | |
Methods defined here:
- DMS_values(...) from builtins.PyCapsule
- DMS_values(rosetta.core.scoring.rna.data.RNA_DMS_Potential) -> rosetta.utility.vector1_double
- __init__(...) from builtins.PyCapsule
- __init__(rosetta.core.scoring.rna.data.RNA_DMS_Potential) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- check_chbonded(...) from builtins.PyCapsule
- check_chbonded(self : rosetta.core.scoring.rna.data.RNA_DMS_Potential, pose : rosetta.core.pose.Pose, i : int, atom_name : str) -> bool
- check_hbonded(...) from builtins.PyCapsule
- check_hbonded(self : rosetta.core.scoring.rna.data.RNA_DMS_Potential, pose : rosetta.core.pose.Pose, i : int, atom_name : str, is_acceptor : bool) -> bool
- evaluate(...) from builtins.PyCapsule
- evaluate(self : rosetta.core.scoring.rna.data.RNA_DMS_Potential, pose : rosetta.core.pose.Pose, rna_reactivity : rosetta.core.scoring.rna.data.RNA_Reactivity) -> float
- get_N1_lonepair_donor_angle(...) from builtins.PyCapsule
- get_N1_lonepair_donor_angle(self : rosetta.core.scoring.rna.data.RNA_DMS_Potential, acc_rsd : rosetta.core.conformation.Residue, don_rsd : rosetta.core.conformation.Residue, don_h_atm : int) -> float
- get_binding_energy(...) from builtins.PyCapsule
- get_binding_energy(self : rosetta.core.scoring.rna.data.RNA_DMS_Potential, i : int, probe_xyz : rosetta.numeric.xyzVector_double_t, scorefxn : rosetta.core.scoring.ScoreFunction) -> float
- get_logL_values(...) from builtins.PyCapsule
- get_logL_values(self : rosetta.core.scoring.rna.data.RNA_DMS_Potential, pose : rosetta.core.pose.Pose, i : int) -> rosetta.utility.vector1_double
- get_occupancy_densities(...) from builtins.PyCapsule
- get_occupancy_densities(self : rosetta.core.scoring.rna.data.RNA_DMS_Potential, occupancy_densities : rosetta.utility.vector1_double, pose : rosetta.core.pose.Pose, i : int, probe_xyz : rosetta.numeric.xyzVector_double_t, shells : rosetta.utility.vector1_double) -> NoneType
- get_occupancy_density(...) from builtins.PyCapsule
- get_occupancy_density(self : rosetta.core.scoring.rna.data.RNA_DMS_Potential, pose : rosetta.core.pose.Pose, i : int, probe_xyz : rosetta.numeric.xyzVector_double_t, shells : (float, float)) -> float
- get_probe_scorefxn(...) from builtins.PyCapsule
- get_probe_scorefxn(self : rosetta.core.scoring.rna.data.RNA_DMS_Potential, soft_rep : bool, just_atr_rep : bool) -> rosetta.core.scoring.ScoreFunction
- get_probe_xyz(...) from builtins.PyCapsule
- get_probe_xyz(self : rosetta.core.scoring.rna.data.RNA_DMS_Potential, rsd : rosetta.core.conformation.Residue, probe_dist : float) -> rosetta.numeric.xyzVector_double_t
- initialize(...) from builtins.PyCapsule
- initialize(self : rosetta.core.scoring.rna.data.RNA_DMS_Potential, pose : rosetta.core.pose.Pose) -> NoneType
|
class RNA_DataBackboneEnergy(rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy) |
| | |
- Method resolution order:
- RNA_DataBackboneEnergy
- rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy
- rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy
- rosetta.core.scoring.methods.TwoBodyEnergy
- rosetta.core.scoring.methods.EnergyMethod
- builtins.object
Methods defined here:
- __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.
- atomic_interaction_cutoff(...) from builtins.PyCapsule
- atomic_interaction_cutoff(rosetta.core.scoring.rna.data.RNA_DataBackboneEnergy) -> float
- check_sugar_atom(...) from builtins.PyCapsule
- check_sugar_atom(self : rosetta.core.scoring.rna.data.RNA_DataBackboneEnergy, n : int) -> bool
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.scoring.rna.data.RNA_DataBackboneEnergy) -> rosetta.core.scoring.methods.EnergyMethod
clone
- defines_intrares_energy(...) from builtins.PyCapsule
- defines_intrares_energy(self : rosetta.core.scoring.rna.data.RNA_DataBackboneEnergy, : rosetta.core.scoring.EMapVector) -> bool
- eval_atom_derivative(...) from builtins.PyCapsule
- eval_atom_derivative(self : rosetta.core.scoring.rna.data.RNA_DataBackboneEnergy, atom_id : rosetta.core.id.AtomID, pose : rosetta.core.pose.Pose, domain_map : ObjexxFCL::FArray1D<int>, scorefxn : rosetta.core.scoring.ScoreFunction, weights : rosetta.core.scoring.EMapVector, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t) -> NoneType
- eval_intrares_energy(...) from builtins.PyCapsule
- eval_intrares_energy(self : rosetta.core.scoring.rna.data.RNA_DataBackboneEnergy, : rosetta.core.conformation.Residue, : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, : rosetta.core.scoring.EMapVector) -> NoneType
- get_sugar_env_score(...) from builtins.PyCapsule
- get_sugar_env_score(self : rosetta.core.scoring.rna.data.RNA_DataBackboneEnergy, rsd_buried : rosetta.core.conformation.Residue, rsd_other : rosetta.core.conformation.Residue) -> float
- indicate_required_context_graphs(...) from builtins.PyCapsule
- indicate_required_context_graphs(self : rosetta.core.scoring.rna.data.RNA_DataBackboneEnergy, : rosetta.utility.vector1_bool) -> NoneType
- initialize_atom_numbers_sugar(...) from builtins.PyCapsule
- initialize_atom_numbers_sugar(rosetta.core.scoring.rna.data.RNA_DataBackboneEnergy) -> NoneType
- residue_pair_energy(...) from builtins.PyCapsule
- residue_pair_energy(self : rosetta.core.scoring.rna.data.RNA_DataBackboneEnergy, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector) -> NoneType
- setup_for_derivatives(...) from builtins.PyCapsule
- setup_for_derivatives(self : rosetta.core.scoring.rna.data.RNA_DataBackboneEnergy, pose : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction) -> NoneType
- setup_for_packing(...) from builtins.PyCapsule
- setup_for_packing(self : rosetta.core.scoring.rna.data.RNA_DataBackboneEnergy, pose : rosetta.core.pose.Pose, : rosetta.utility.vector1_bool, : rosetta.utility.vector1_bool) -> NoneType
- setup_for_scoring(...) from builtins.PyCapsule
- setup_for_scoring(self : rosetta.core.scoring.rna.data.RNA_DataBackboneEnergy, pose : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction) -> NoneType
//////////////////////////////////////////////////////////////////////////
Methods inherited from rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy, : rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy) -> rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy
- method_type(...) from builtins.PyCapsule
- method_type(rosetta.core.scoring.methods.ContextIndependentTwoBodyEnergy) -> rosetta.core.scoring.methods.EnergyMethodType
Methods inherited from rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy:
- divides_backbone_and_sidechain_energetics(...) from builtins.PyCapsule
- divides_backbone_and_sidechain_energetics(rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy) -> bool
A derived class should return true for this function if it implements its own
versions of the backbone_backbone_energy, backbone_sidechain_energy and
sidechain_sidechain_energy functions. The default sidechain_sidechain_energy implemented
by the TwoBodyEnergy base class calls residue_pair_energy. If the derived class implements its own
versions of these functions, then calling code may avoid calling it on pairs of residues
that are "provably distant" based on a pair of bounding spheres for a sidechains and
backbones and this method's atomic_interaction_cutoff energy method.
- evaluate_rotamer_background_energies(...) from builtins.PyCapsule
- evaluate_rotamer_background_energies(self : rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy, set : rosetta.core.conformation.RotamerSetBase, residue : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, weights : rosetta.core.scoring.EMapVector, energy_vector : rosetta.utility.vector1_float) -> NoneType
Batch computation of rotamer/background energies. Need not be overriden
in derived class -- by default, iterates over all rotamers in the set, and calls
derived class's residue_pair_energy method for each one against the background rotamer
Since short range rotamer pairs may not need calculation, the default method
looks at blocks of residue type pairs and only calls the residue_pair_energy method
if the rotamer pairs are within range
- evaluate_rotamer_background_energy_maps(...) from builtins.PyCapsule
- evaluate_rotamer_background_energy_maps(self : rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy, set : rosetta.core.conformation.RotamerSetBase, residue : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, weights : rosetta.core.scoring.EMapVector, emaps : rosetta.utility.vector1_core_scoring_EMapVector) -> NoneType
Batch computation of rotamer/background energies. Need not be overriden
in derived class -- by default, iterates over all rotamers in the set, and calls
derived class's residue_pair_energy method for each one against the background rotamer
Since short range rotamer pairs may not need calculation, the default method
looks at blocks of residue type pairs and only calls the residue_pair_energy method
if the rotamer pairs are within range
- evaluate_rotamer_pair_energies(...) from builtins.PyCapsule
- evaluate_rotamer_pair_energies(self : rosetta.core.scoring.methods.ShortRangeTwoBodyEnergy, set1 : rosetta.core.conformation.RotamerSetBase, set2 : rosetta.core.conformation.RotamerSetBase, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, weights : rosetta.core.scoring.EMapVector, energy_table : ObjexxFCL::FArray2D<float>) -> NoneType
Batch computation of rotamer pair energies. Need not be overriden in
derived class -- by default, iterates over all pairs of rotamers,
and calls derived class's residue_pair_energy method. Since short range rotamer pairs
may not need calculation, the default method looks at blocks of residue type pairs
and only calls the residue_pair_energy method if the rotamer pairs are within range
Methods inherited from rosetta.core.scoring.methods.TwoBodyEnergy:
- backbone_backbone_energy(...) from builtins.PyCapsule
- backbone_backbone_energy(self : rosetta.core.scoring.methods.TwoBodyEnergy, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector) -> NoneType
Evaluate the interaction between the backbone of rsd1 and the
backbone of rsd2 and accumulate the unweighted energies. The sum
bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must
equal the weighted result of a call to residue_pair_energy.
By default, bb_bb & bb_sc return 0 and sc_sc returns
residue pair energy.
- backbone_sidechain_energy(...) from builtins.PyCapsule
- backbone_sidechain_energy(self : rosetta.core.scoring.methods.TwoBodyEnergy, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector) -> NoneType
Evaluate the interaction between the backbone of rsd1 and the
sidechain of rsd2 and accumulate the unweighted energies. The sum
bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must
equal the unweighted result of a call to residue_pair_energy.
By default, bb_bb & bb_sc return 0 and sc_sc returns
residue pair energy.
- bump_energy_backbone(...) from builtins.PyCapsule
- bump_energy_backbone(self : rosetta.core.scoring.methods.TwoBodyEnergy, : rosetta.core.conformation.Residue, : rosetta.core.conformation.Residue, : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, : rosetta.core.scoring.EMapVector) -> NoneType
- bump_energy_full(...) from builtins.PyCapsule
- bump_energy_full(self : rosetta.core.scoring.methods.TwoBodyEnergy, : rosetta.core.conformation.Residue, : rosetta.core.conformation.Residue, : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, : rosetta.core.scoring.EMapVector) -> NoneType
- defines_intrares_dof_derivatives(...) from builtins.PyCapsule
- defines_intrares_dof_derivatives(self : rosetta.core.scoring.methods.TwoBodyEnergy, p : rosetta.core.pose.Pose) -> bool
Use the dof_derivative interface for this energy method when
calculating derivatives? It is possible to define both dof_derivatives and
atom-derivatives; they are not mutually exclusive.
- defines_intrares_energy_for_residue(...) from builtins.PyCapsule
- defines_intrares_energy_for_residue(self : rosetta.core.scoring.methods.TwoBodyEnergy, res : rosetta.core.conformation.Residue) -> bool
If a score function defines no intra-residue scores for a particular
residue, then it may opt-out of being asked during minimization to evaluate
the score for this residue.
- defines_score_for_residue_pair(...) from builtins.PyCapsule
- defines_score_for_residue_pair(self : rosetta.core.scoring.methods.TwoBodyEnergy, res1 : rosetta.core.conformation.Residue, res2 : rosetta.core.conformation.Residue, res_moving_wrt_eachother : bool) -> bool
During minimization, energy methods are allowed to decide that they say nothing
about a particular residue pair (e.g. no non-zero energy) and as a result they will not be queried for
a derivative or an energy. The default implementation returns "true" for all residue pairs.
Context-dependent two-body energies have the option of behaving as if they are context-independent
by returning "false" for residue pairs that do no move wrt each other.
- eval_intrares_derivatives(...) from builtins.PyCapsule
- eval_intrares_derivatives(self : rosetta.core.scoring.methods.TwoBodyEnergy, rsd : rosetta.core.conformation.Residue, min_data : rosetta.core.scoring.ResSingleMinimizationData, pose : rosetta.core.pose.Pose, weights : rosetta.core.scoring.EMapVector, atom_derivs : rosetta.utility.vector1_core_scoring_DerivVectorPair) -> NoneType
Evaluate the derivative for the intra-residue component of this energy method
for all the atoms in a residue in the context of a particular pose,
and increment the F1 and F2 vectors held in the atom_derivs vector1.
This base class provides a default noop implementation
of this function. The calling function must guarantee that this EnergyMethod has had the
opportunity to update the input ResSingleMinimizationData object for the given residue
in a call to prepare_for_minimization before this function is invoked.
The calling function must also guarantee that there are at least as many entries
in the atom_derivs vector1 as there are atoms in the input rsd.
- eval_intrares_energy_ext(...) from builtins.PyCapsule
- eval_intrares_energy_ext(self : rosetta.core.scoring.methods.TwoBodyEnergy, rsd : rosetta.core.conformation.Residue, data_cache : rosetta.core.scoring.ResSingleMinimizationData, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector) -> NoneType
Evaluate the intra-residue energy for a given residue using the data held within the
ResSingleMinimizationData object. This function should be invoked only on derived instances
of this class if they return "true" in a call to their use_extended_intrares_energy_interface
method. This base class provides a noop implementation for classes that do not implement this
interface, or that do not define intrares energies.
- eval_intraresidue_dof_derivative(...) from builtins.PyCapsule
- eval_intraresidue_dof_derivative(self : rosetta.core.scoring.methods.TwoBodyEnergy, rsd : rosetta.core.conformation.Residue, min_data : rosetta.core.scoring.ResSingleMinimizationData, dof_id : rosetta.core.id.DOF_ID, torsion_id : rosetta.core.id.TorsionID, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, weights : rosetta.core.scoring.EMapVector) -> float
Evaluate the DOF derivative for a particular residue. The Pose merely serves as context,
and the input residue is not required to be a member of the Pose.
- eval_residue_pair_derivatives(...) from builtins.PyCapsule
- eval_residue_pair_derivatives(self : rosetta.core.scoring.methods.TwoBodyEnergy, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, : rosetta.core.scoring.ResSingleMinimizationData, : rosetta.core.scoring.ResSingleMinimizationData, min_data : rosetta.core.scoring.ResPairMinimizationData, pose : rosetta.core.pose.Pose, weights : rosetta.core.scoring.EMapVector, r1_atom_derivs : rosetta.utility.vector1_core_scoring_DerivVectorPair, r2_atom_derivs : rosetta.utility.vector1_core_scoring_DerivVectorPair) -> NoneType
Evaluate the derivatives for all atoms on rsd1 and rsd2 with respect
to each other and increment the derivatives in atom-derivatives vector1s.
The calling function must guarantee that the r1_atom_derivs vector1 holds at
least as many entries as there are atoms in rsd1, and that the r2_atom_derivs
vector1 holds at least as many entries as there are atoms in rsd2.
- evaluate_rotamer_intrares_energies(...) from builtins.PyCapsule
- evaluate_rotamer_intrares_energies(self : rosetta.core.scoring.methods.TwoBodyEnergy, set : rosetta.core.conformation.RotamerSetBase, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, energies : rosetta.utility.vector1_float) -> NoneType
Batch computation of rotamer intrares energies. Need not be overriden in
derived class -- by default, iterates over all rotamers,
and calls derived class's intrares _energy method.
- evaluate_rotamer_intrares_energy_maps(...) from builtins.PyCapsule
- evaluate_rotamer_intrares_energy_maps(self : rosetta.core.scoring.methods.TwoBodyEnergy, set : rosetta.core.conformation.RotamerSetBase, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, emaps : rosetta.utility.vector1_core_scoring_EMapVector) -> NoneType
Batch computation of rotamer intrares energy map. Need not be overriden in
derived class -- by default, iterates over all rotamers,
and calls derived class's intrares _energy method.
- requires_a_setup_for_derivatives_for_residue_opportunity(...) from builtins.PyCapsule
- requires_a_setup_for_derivatives_for_residue_opportunity(self : rosetta.core.scoring.methods.TwoBodyEnergy, pose : rosetta.core.pose.Pose) -> bool
Does this EnergyMethod require the opportunity to examine each residue before derivative evaluation begins? Not
all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested
in doing so.
- requires_a_setup_for_derivatives_for_residue_pair_opportunity(...) from builtins.PyCapsule
- requires_a_setup_for_derivatives_for_residue_pair_opportunity(self : rosetta.core.scoring.methods.TwoBodyEnergy, pose : rosetta.core.pose.Pose) -> bool
Does this EnergyMethod require the opportunity to examine each residue pair before derivative evaluation begins? Not
all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested
in doing so.
- requires_a_setup_for_scoring_for_residue_opportunity(...) from builtins.PyCapsule
- requires_a_setup_for_scoring_for_residue_opportunity(self : rosetta.core.scoring.methods.TwoBodyEnergy, pose : rosetta.core.pose.Pose) -> bool
Does this EnergyMethod require the opportunity to examine the residue before scoring begins? Not
all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested
in doing so.
- requires_a_setup_for_scoring_for_residue_pair_opportunity(...) from builtins.PyCapsule
- requires_a_setup_for_scoring_for_residue_pair_opportunity(self : rosetta.core.scoring.methods.TwoBodyEnergy, pose : rosetta.core.pose.Pose) -> bool
Does this EnergyMethod require the opportunity to examine each residue pair before scoring begins? Not
all energy methods would. The ScoreFunction will not ask energy methods to examine residue pairs that are uninterested
in doing so.
- residue_pair_energy_ext(...) from builtins.PyCapsule
- residue_pair_energy_ext(self : rosetta.core.scoring.methods.TwoBodyEnergy, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, min_data : rosetta.core.scoring.ResPairMinimizationData, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector) -> NoneType
Evaluate the two-body energies for a particular residue, in the context of a
given Pose, and with the help of a piece of cached data for minimization, increment those
two body energies into the input EnergyMap. The calling function must guarantee that this
EnergyMethod has had the opportunity to update the input ResPairMinimizationData object
for the given residues in a call to setup_for_minimizing_for_residue_pair before this function is
invoked. This function should not be called unless the use_extended_residue_pair_energy_interface()
method returns "true". Default implementation provided by this base class calls
utility::exit().
- setup_for_derivatives_for_residue(...) from builtins.PyCapsule
- setup_for_derivatives_for_residue(self : rosetta.core.scoring.methods.TwoBodyEnergy, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, min_data : rosetta.core.scoring.ResSingleMinimizationData) -> NoneType
Do any setup work necessary before evaluating the derivatives for this residue
- setup_for_derivatives_for_residue_pair(...) from builtins.PyCapsule
- setup_for_derivatives_for_residue_pair(self : rosetta.core.scoring.methods.TwoBodyEnergy, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, minsingle_data1 : rosetta.core.scoring.ResSingleMinimizationData, minsingle_data2 : rosetta.core.scoring.ResSingleMinimizationData, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, data_cache : rosetta.core.scoring.ResPairMinimizationData) -> NoneType
Do any setup work necessary before evaluating the derivatives for this residue pair
- setup_for_minimizing_for_residue(...) from builtins.PyCapsule
- setup_for_minimizing_for_residue(self : rosetta.core.scoring.methods.TwoBodyEnergy, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, minmap : rosetta.core.kinematics.MinimizerMapBase, res_data_cache : rosetta.core.scoring.ResSingleMinimizationData) -> NoneType
Called at the beginning of minimization, allowing this energy method to cache data
pertinent for a single residue in the the ResPairMinimizationData that is used for a
particular residue in the context of a particular Pose. This base class provides a noop
implementation for this function if there is nothing that the derived class needs to perform
in this setup phase.
- setup_for_minimizing_for_residue_pair(...) from builtins.PyCapsule
- setup_for_minimizing_for_residue_pair(self : rosetta.core.scoring.methods.TwoBodyEnergy, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, minmap : rosetta.core.kinematics.MinimizerMapBase, res1_data_cache : rosetta.core.scoring.ResSingleMinimizationData, res2_data_cache : rosetta.core.scoring.ResSingleMinimizationData, data_cache : rosetta.core.scoring.ResPairMinimizationData) -> NoneType
Called at the beginning of minimization, allowing this energy method to cache data
pertinent for a single residue in the the ResPairMinimizationData that is used for a
particular residue in the context of a particular Pose. This base class provides a noop
implementation for this function if there is nothing that the derived class needs to perform
in this setup phase.
- setup_for_scoring_for_residue(...) from builtins.PyCapsule
- setup_for_scoring_for_residue(self : rosetta.core.scoring.methods.TwoBodyEnergy, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, min_data : rosetta.core.scoring.ResSingleMinimizationData) -> NoneType
Do any setup work should the coordinates of this residue (who is still guaranteed to be
of the same residue type as when setup_for_minimizing_for_residue was called) have changed so dramatically
as to possibly require some amount of setup work before scoring should proceed.
This function is used for both intra-residue setup and pre-inter-residue setup
- setup_for_scoring_for_residue_pair(...) from builtins.PyCapsule
- setup_for_scoring_for_residue_pair(self : rosetta.core.scoring.methods.TwoBodyEnergy, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, minsingle_data1 : rosetta.core.scoring.ResSingleMinimizationData, minsingle_data2 : rosetta.core.scoring.ResSingleMinimizationData, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, data_cache : rosetta.core.scoring.ResPairMinimizationData) -> NoneType
Do any setup work should the coordinates of a pair of residues, who are still guaranteed to be
of the same residue type as when setup_for_minimizing_for_residue was called, have changed so dramatically
as to possibly require some amount of setup work before scoring should proceed
- sidechain_sidechain_energy(...) from builtins.PyCapsule
- sidechain_sidechain_energy(self : rosetta.core.scoring.methods.TwoBodyEnergy, rsd1 : rosetta.core.conformation.Residue, rsd2 : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, emap : rosetta.core.scoring.EMapVector) -> NoneType
Evaluate the interaction between the sidechain of rsd1 and the
sidechain of rsd2 and accumulate the unweighted energies. The sum
bb_bb(r1,r2) + bb_sc(r1,r2) + bb_sc(r2,r1) + sc_sc( r1,r2) must
equal the unweighted result of a call to residue_pair_energy.
By default, bb_bb & bb_sc return 0 and sc_sc returns
residue pair energy.
- use_extended_intrares_energy_interface(...) from builtins.PyCapsule
- use_extended_intrares_energy_interface(rosetta.core.scoring.methods.TwoBodyEnergy) -> bool
Derived classes wishing to invoke the alternate, extended interface for eval_intrares_energy
during minimization routines should return "true" when this function is invoked on them. This
class provides a default "return false" implementation so that classes not desiring to take advantage
of this alternate interface need to do nothing.
- use_extended_residue_pair_energy_interface(...) from builtins.PyCapsule
- use_extended_residue_pair_energy_interface(rosetta.core.scoring.methods.TwoBodyEnergy) -> bool
Rely on the extended version of the residue_pair_energy function during score-function
evaluation in minimization? The extended version (below) takes a ResPairMinimizationData in which
the derived base class has (or should have) cached a piece of data that will make residue-pair
energy evaluation faster than its absense (e.g. a neighbor list). Derived energy methods should
return 'true' from this function to use the extended interface. The default method implemented
in this class returns 'false'
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".
- 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
- finalize_total_energy(...) from builtins.PyCapsule
- finalize_total_energy(self : rosetta.core.scoring.methods.EnergyMethod, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, total_energy : rosetta.core.scoring.EMapVector) -> NoneType
called by the ScoreFunction at the end of energy evaluation.
The derived class has the opportunity to accumulate a score
into the pose's total_energy EnergyMap. WholeStructure energies
operate within this method; any method using a NeighborList during
minimization would also operate within this function call.
- 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_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.
- 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.
- version(...) from builtins.PyCapsule
- version(rosetta.core.scoring.methods.EnergyMethod) -> int
Return the version of the energy method
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