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- builtins.object
-
- AACompositionEnergySetup
- AACompositionPropertiesSet
- TailFunction
- rosetta.core.scoring.constraints.Constraint(builtins.object)
-
- SequenceConstraint
-
- AACompositionConstraint
- rosetta.core.scoring.methods.EnergyMethodCreator(builtins.object)
-
- AACompositionEnergyCreator
- rosetta.core.scoring.methods.WholeStructureEnergy(rosetta.core.scoring.methods.EnergyMethod)
-
- AACompositionEnergy
class AACompositionConstraint(SequenceConstraint) |
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- Method resolution order:
- AACompositionConstraint
- SequenceConstraint
- rosetta.core.scoring.constraints.Constraint
- builtins.object
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.core.scoring.aa_composition_energy.AACompositionConstraint, : rosetta.core.scoring.constraints.Constraint) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.scoring.aa_composition_energy.AACompositionConstraint) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- aa_composition_energy_setup(...) from builtins.PyCapsule
- aa_composition_energy_setup(rosetta.core.scoring.aa_composition_energy.AACompositionConstraint) -> core::scoring::aa_composition_energy::AACompositionEnergySetup
Const access to the AACompositionEnergySetup object.
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.scoring.aa_composition_energy.AACompositionConstraint) -> rosetta.core.scoring.constraints.Constraint
Clone operator
- initialize_from_file(...) from builtins.PyCapsule
- initialize_from_file(self : rosetta.core.scoring.aa_composition_energy.AACompositionConstraint, filename : str) -> NoneType
Initialize the AACompositionEnergySetup object from a file.
- initialize_from_file_contents(...) from builtins.PyCapsule
- initialize_from_file_contents(self : rosetta.core.scoring.aa_composition_energy.AACompositionConstraint, filecontents : str) -> NoneType
Initialize the AACompositionEnergySetup object from the contents of a file.
Allows external code to initialize a constriant object without having the
object read directly from disk.
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(self : rosetta.core.scoring.aa_composition_energy.AACompositionConstraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
- selector(...) from builtins.PyCapsule
- selector(rosetta.core.scoring.aa_composition_energy.AACompositionConstraint) -> rosetta.core.select.residue_selector.ResidueSelector
Const access to the selector.
Returns a null pointer if no selector has been specified.
- set_selector(...) from builtins.PyCapsule
- set_selector(self : rosetta.core.scoring.aa_composition_energy.AACompositionConstraint, selector_in : rosetta.core.select.residue_selector.ResidueSelector) -> NoneType
Set the selector to be used by this constraint.
Clones the input.
Methods inherited from SequenceConstraint:
- atom(...) from builtins.PyCapsule
- atom(self : rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : int) -> rosetta.core.id.AtomID
Implemented because the base class requires it; not used by a sequence constraint.
Always returns AtomID(0,0).
- fill_f1_f2(...) from builtins.PyCapsule
- fill_f1_f2(self : rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : rosetta.core.id.AtomID, : core::scoring::func::XYZ_Func, : rosetta.numeric.xyzVector_double_t, : rosetta.numeric.xyzVector_double_t, : rosetta.core.scoring.EMapVector) -> NoneType
Implemented because the base class requires it; not used by a sequence constraint.
- natoms(...) from builtins.PyCapsule
- natoms(rosetta.core.scoring.aa_composition_energy.SequenceConstraint) -> int
Implemented because the base class requires it; not used by a sequence constraint.
Always returns zero.
- score(...) from builtins.PyCapsule
- score(self : rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : core::scoring::func::XYZ_Func, : rosetta.core.scoring.EMapVector, : rosetta.core.scoring.EMapVector) -> NoneType
Implemented because the base class requires it; not used by a sequence constraint.
Methods inherited from rosetta.core.scoring.constraints.Constraint:
- __ne__(...) from builtins.PyCapsule
- __ne__(self : rosetta.core.scoring.constraints.Constraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
Inequality operator to test whether two constraints are not functionally
identical.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.scoring.constraints.Constraint) -> str
- choose_effective_sequence_separation(...) from builtins.PyCapsule
- choose_effective_sequence_separation(self : rosetta.core.scoring.constraints.Constraint, sp : rosetta.core.kinematics.ShortestPathInFoldTree, : rosetta.numeric.random.RandomGenerator) -> int
- dist(...) from builtins.PyCapsule
- dist(*args, **kwargs)
Overloaded function.
1. dist(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose) -> float
return the raw "distance" before that distance is handed to the FUNC object
2. dist(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func) -> float
- effective_sequence_separation(...) from builtins.PyCapsule
- effective_sequence_separation(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.kinematics.ShortestPathInFoldTree) -> int
- get_func(...) from builtins.PyCapsule
- get_func(rosetta.core.scoring.constraints.Constraint) -> core::scoring::func::Func
Returns the func::Func object associated with this Constraint object.
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.Constraint
apply a resid remapping to this constraint, returns the remapped
constraint Does this return an owning pointer to this constraint or a
copy? Documentation would be nice.
- remapped_clone(...) from builtins.PyCapsule
- remapped_clone(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose, : rosetta.core.pose.Pose, map : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.Constraint
Copies the data from this Constraint into a new object and returns
an OP atoms are mapped to atoms with the same name in dest pose ( e.g.
for switch from centroid to fullatom ) if a sequence_mapping is present
it is used to map residue numbers .. NULL = identity mapping to the new
object. Intended to be implemented by derived classes.
- residues(...) from builtins.PyCapsule
- residues(rosetta.core.scoring.constraints.Constraint) -> rosetta.utility.vector1_unsigned_long
Returns the pose numbers of the residues involved in this constraint, in no particular order.
Used in determining one-body/two-body/multi-body status.
For historical reasons, the default uses a simple protocol based on natoms()/atom() -
feel free to reimplement more efficiently.
- score_type(...) from builtins.PyCapsule
- score_type(rosetta.core.scoring.constraints.Constraint) -> rosetta.core.scoring.ScoreType
Returns the ScoreType that this Constraint object will use.
- setup_for_derivatives(...) from builtins.PyCapsule
- setup_for_derivatives(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : rosetta.core.scoring.ScoreFunction) -> NoneType
- setup_for_scoring(...) from builtins.PyCapsule
- setup_for_scoring(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : rosetta.core.scoring.ScoreFunction) -> NoneType
- steal_def(...) from builtins.PyCapsule
- steal_def(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose) -> NoneType
take coordinates, distances, angles, etc from given pose
- to_string(...) from builtins.PyCapsule
- to_string(rosetta.core.scoring.constraints.Constraint) -> str
Convenience function, returns the results of show() as a string.
Not to be overriden by derived classes.
- type(...) from builtins.PyCapsule
- type(rosetta.core.scoring.constraints.Constraint) -> str
Returns a unique string identified for this constraint. Used in several
places, including the ConstraintIO class.
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class AACompositionEnergy(rosetta.core.scoring.methods.WholeStructureEnergy) |
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AACompositionEnergy, an energy function to penalize stretches of the same residue,
derived from base class for EnergyMethods, which are meaningful only on entire structures.
These EnergyMethods do all of their work in the "finalize_total_energy" section of score
function evaluation.
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- Method resolution order:
- AACompositionEnergy
- 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__(self : handle, options : core::scoring::methods::EnergyMethodOptions) -> NoneType
2. __init__(handle, rosetta.core.scoring.aa_composition_energy.AACompositionEnergy) -> 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.aa_composition_energy.AACompositionEnergy, : rosetta.core.scoring.aa_composition_energy.AACompositionEnergy) -> rosetta.core.scoring.aa_composition_energy.AACompositionEnergy
- calculate_energy(...) from builtins.PyCapsule
- calculate_energy(*args, **kwargs)
Overloaded function.
1. calculate_energy(self : rosetta.core.scoring.aa_composition_energy.AACompositionEnergy, resvect : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t) -> float
Calculate the total energy given a vector of const owning pointers to residues.
Called directly by the ResidueArrayAnnealingEvaluator during packer runs.
2. calculate_energy(self : rosetta.core.scoring.aa_composition_energy.AACompositionEnergy, resvect : rosetta.utility.vector1_std_shared_ptr_const_core_conformation_Residue_t, setup_helpers : rosetta.utility.vector1_std_shared_ptr_const_core_scoring_aa_composition_energy_AACompositionEnergySetup_t, masks : rosetta.utility.vector1_utility_vector1_bool_std_allocator_bool_t) -> float
Calculate the total energy given a vector of const owning pointers to residues, vectors of AACompositionEnergySetup objects, and vectors of masks.
Called by finalize_total_energy() and during packer runs. Requires
that setup_residuearrayannealablenergy_for_packing() be called first.
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.scoring.aa_composition_energy.AACompositionEnergy) -> rosetta.core.scoring.methods.EnergyMethod
Clone: create a copy of this object, and return an owning pointer
to the copy.
- finalize_total_energy(...) from builtins.PyCapsule
- finalize_total_energy(self : rosetta.core.scoring.aa_composition_energy.AACompositionEnergy, pose : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, totals : rosetta.core.scoring.EMapVector) -> NoneType
Actually calculate the total energy
Called by the scoring machinery.
- indicate_required_context_graphs(...) from builtins.PyCapsule
- indicate_required_context_graphs(self : rosetta.core.scoring.aa_composition_energy.AACompositionEnergy, context_graphs_required : rosetta.utility.vector1_bool) -> NoneType
AACompositionEnergy is context-independent and thus indicates that no context graphs need to be maintained by
class Energies.
- report(...) from builtins.PyCapsule
- report(rosetta.core.scoring.aa_composition_energy.AACompositionEnergy) -> NoneType
Get a summary of all loaded data.
- setup_residuearrayannealableenergy_for_packing(...) from builtins.PyCapsule
- setup_residuearrayannealableenergy_for_packing(self : rosetta.core.scoring.aa_composition_energy.AACompositionEnergy, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
Cache data from the pose in this EnergyMethod in anticipation of scoring.
- version(...) from builtins.PyCapsule
- version(rosetta.core.scoring.aa_composition_energy.AACompositionEnergy) -> int
AACompositionEnergy is version 1.0 right now.
Methods inherited from rosetta.core.scoring.methods.WholeStructureEnergy:
- atomic_interaction_cutoff(...) from builtins.PyCapsule
- atomic_interaction_cutoff(rosetta.core.scoring.methods.WholeStructureEnergy) -> float
how far apart must two heavy atoms be to have a zero interaction energy?
If hydrogen atoms interact at the same range as heavy atoms, then
this distance should build-in a 2 * max-bound-h-distance-cutoff buffer.
There is an improper mixing here between run-time aquired chemical knowledge
(max-bound-h-distance-cutoff) and compile time aquired scoring knowledge
(max atom cutoff); this could be resolved by adding a boolean
uses_hydrogen_interaction_distance() to the SRTBEnergy class along with
a method of the ChemicalManager max_bound_h_distance_cutoff().
This method allows the WholeStructureEnergy class to define which edges
should be included in the EnergyGraph so that during the finalize() method
the Energy class can iterate across the EnergyGraph. This iteration occurrs
in the SecondaryStructureEnergy class, where the edges must span 12 angstroms
between the centroids. Arguably, the SecondaryStructureEnergy class could use
the TwelveANeighborGraph (a context graph) and not require that the EnergyGraph
span such long distances.
- 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.
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class AACompositionEnergySetup(builtins.object) |
| |
AACompositionEnergySetup, a helper class for the AACompositionEnergy energy method
that stores all of its setup data.
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| |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) -> 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.aa_composition_energy.AACompositionEnergySetup, : rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) -> rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) -> rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup
Clone: create a copy of this object, and return an owning pointer
to the copy.
- expected_by_properties_absolute(...) from builtins.PyCapsule
- expected_by_properties_absolute(self : rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, index : int) -> int
Get the expected absolute number of residues for a given set of properties, by property set index.
Warning! For speed, there's no check that the index is in range!
- expected_by_properties_fraction(...) from builtins.PyCapsule
- expected_by_properties_fraction(self : rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, index : int) -> float
Get the expected fractional number of residues for a given set of properties, by property set index.
Warning! For speed, there's no check that the index is in range!
- fract_property_penalty(...) from builtins.PyCapsule
- fract_property_penalty(self : rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, delta_fract : float, property_set_index : int) -> float
Look up the penalty for a property set of internal index property_set_index, given a fractional content given by fract.
This version is for fractional property penalties.
The measured fractional content of amino acids matching this property set in the pose or pose subset minus the expected.
The index of this property set.
- get_tailfunction_from_name(...) from builtins.PyCapsule
- get_tailfunction_from_name(self : rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, name : str) -> rosetta.core.scoring.aa_composition_energy.TailFunction
Get tail function enum from name.
This is slow; it calls get_tailfunction_name repeatedly. Intended only for use during setup.
- get_tailfunction_name(...) from builtins.PyCapsule
- get_tailfunction_name(self : rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, tf : rosetta.core.scoring.aa_composition_energy.TailFunction) -> str
Get tail function name from enum.
- initialize_from_file(...) from builtins.PyCapsule
- initialize_from_file(self : rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, filename : str) -> NoneType
Initialize from a .comp file.
- initialize_from_file_contents(...) from builtins.PyCapsule
- initialize_from_file_contents(self : rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, filecontents : str) -> NoneType
Initialize from a string in the format of a .comp file.
Allows external code to initialize object without having it read
directly from disk.
- n_property_sets(...) from builtins.PyCapsule
- n_property_sets(rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) -> int
Get the number of sets of properties that we'll be counting.
- property_penalty(...) from builtins.PyCapsule
- property_penalty(self : rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, delta_expected : int, property_set_index : int) -> float
Look up the penalty for a property set of internal index property_set_index, given a deviation from
the desired count given by delta_expected.
- property_set_indices_matching_residue(...) from builtins.PyCapsule
- property_set_indices_matching_residue(self : rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, rsd_type : rosetta.core.chemical.ResidueType, indices_out : rosetta.utility.vector1_unsigned_long) -> NoneType
Get the indices of all of the property sets corresponding to the current residue.
Returns empty vector if none of the property sets that we're counting corresponds to the current residue.
- report(...) from builtins.PyCapsule
- report(rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) -> str
Get a summary of the data stored in this object
- reset(...) from builtins.PyCapsule
- reset(rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) -> NoneType
Reset all data in this data storage object.
- use_fract_expected_values_any(...) from builtins.PyCapsule
- use_fract_expected_values_any(rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) -> bool
Determine whether ANY of the property sets of this helper object use fractional expected values.
- use_fract_ranges(...) from builtins.PyCapsule
- use_fract_ranges(self : rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup, index : int) -> bool
Look up whether we're using absolute (return false) or fractional (return true) penalty ranges.
- use_fract_ranges_any(...) from builtins.PyCapsule
- use_fract_ranges_any(rosetta.core.scoring.aa_composition_energy.AACompositionEnergySetup) -> bool
Determine whether ANY of the property sets of this helper object use fractional ranges.
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class AACompositionPropertiesSet(builtins.object) |
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AACompositionPropertiesSet, a helper class that stores:
- names of residue types that WILL be counted (TYPE)
- names of residue types that WILL NOT be counted (NOT_TYPE)
- properties that MUST be present in order for a residue to be counted (PROPERTIES).
- properties, any of which is sufficient for a residue to be counted (OR_PROPERTIES).
- properties that MUST NOT be present in order for a residue to be counted (NOT_PROPERTIES).
The logic is as follows: a residue is counted if and only if [any TYPE matches] OR [ (no NOT_TYPE matches) AND
( {all PROPERTIES match} OR {any OR_PROPERTIES match} OR {no TYPEs defined AND no PROPERTIES defined AND no OR_PROPERTIES defined } ) AND
( no NOT_PROPERTIES match) ]
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Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(self : handle, included_type_strings : rosetta.utility.vector1_std_string, excluded_type_strings : rosetta.utility.vector1_std_string, included_properties_strings : rosetta.utility.vector1_std_string, or_properties_strings : rosetta.utility.vector1_std_string, excluded_properties_strings : rosetta.utility.vector1_std_string) -> NoneType
3. __init__(handle, rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet) -> 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.aa_composition_energy.AACompositionPropertiesSet, : rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet) -> rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet) -> rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet
Clone: create a copy of this object, and return an owning pointer
to the copy.
- one_line_report(...) from builtins.PyCapsule
- one_line_report(rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet) -> str
Generate a one-line summary of the properties stored in this AACompositionPropertySet
- parse_excluded_properites(...) from builtins.PyCapsule
- parse_excluded_properites(self : rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, proplist : rosetta.utility.vector1_std_string) -> NoneType
Take a list of excluded property strings and parse it.
Populates the excluded_properties_ vector based on the properties named in
the list.
- parse_excluded_types(...) from builtins.PyCapsule
- parse_excluded_types(self : rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, typelist : rosetta.utility.vector1_std_string) -> NoneType
Take a list of excluded type strings and add it to the list of excluded types, checking that
none of the types has already been added.
Populates the excluded_types_ vector based on the types named in the list.
- parse_included_properites(...) from builtins.PyCapsule
- parse_included_properites(self : rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, proplist : rosetta.utility.vector1_std_string) -> NoneType
Take a list of included property strings and parse it.
Populates the included_properties_ vector based on the properties named in
the list.
- parse_included_types(...) from builtins.PyCapsule
- parse_included_types(self : rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, typelist : rosetta.utility.vector1_std_string) -> NoneType
Take a list of included type strings and add it to the list of included types, checking that
none of the types has already been added.
Populates the included_types_ vector based on the types named in the list.
- parse_or_properties(...) from builtins.PyCapsule
- parse_or_properties(self : rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, proplist : rosetta.utility.vector1_std_string) -> NoneType
Take a list of included property strings and parse it.
Populates the included_properties_ vector based on the properties named in
the list.
- properties_match_this(...) from builtins.PyCapsule
- properties_match_this(self : rosetta.core.scoring.aa_composition_energy.AACompositionPropertiesSet, rsd_type : rosetta.core.chemical.ResidueType) -> bool
Check whether the properties of a residue type match those of this set.
This checks:
1. Whether the residue name matches an exlcuded name -> return false.
2. Whether the residue name matches an included name -> return true.
3. Whether the residue properties match an excluded property -> return false.
4. Whether all three of the included_types and or_properties and included_property lists are empty -> return true.
5. Whether any or_property is matched -> return true.
6. Whether there exist any proprties to match -> if not, return false.
7. Whether any properties are not matched -> return false.
Returns true
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class SequenceConstraint(rosetta.core.scoring.constraints.Constraint) |
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- Method resolution order:
- SequenceConstraint
- rosetta.core.scoring.constraints.Constraint
- builtins.object
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.core.scoring.aa_composition_energy.SequenceConstraint, t : rosetta.core.scoring.ScoreType) -> NoneType
2. __init__(rosetta.core.scoring.aa_composition_energy.SequenceConstraint, rosetta.core.scoring.aa_composition_energy.SequenceConstraint) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- atom(...) from builtins.PyCapsule
- atom(self : rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : int) -> rosetta.core.id.AtomID
Implemented because the base class requires it; not used by a sequence constraint.
Always returns AtomID(0,0).
- fill_f1_f2(...) from builtins.PyCapsule
- fill_f1_f2(self : rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : rosetta.core.id.AtomID, : core::scoring::func::XYZ_Func, : rosetta.numeric.xyzVector_double_t, : rosetta.numeric.xyzVector_double_t, : rosetta.core.scoring.EMapVector) -> NoneType
Implemented because the base class requires it; not used by a sequence constraint.
- natoms(...) from builtins.PyCapsule
- natoms(rosetta.core.scoring.aa_composition_energy.SequenceConstraint) -> int
Implemented because the base class requires it; not used by a sequence constraint.
Always returns zero.
- score(...) from builtins.PyCapsule
- score(self : rosetta.core.scoring.aa_composition_energy.SequenceConstraint, : core::scoring::func::XYZ_Func, : rosetta.core.scoring.EMapVector, : rosetta.core.scoring.EMapVector) -> NoneType
Implemented because the base class requires it; not used by a sequence constraint.
Methods inherited from rosetta.core.scoring.constraints.Constraint:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.scoring.constraints.Constraint) -> bool
Equality operator to test whether two constraints are functionally
identical.
This operator should use floating point comparison and should not
decide that two floats are identical if they are within some epsilon > 0.
This method allows developes to remove specific constraints from Poses, even
if the constraints have been cloned. Remapped constraints should not be
considered identical -- i.e., if cst1 is between residues i and j and
cst2 is between residues i+1 and j+1. All subclasses of Constraint must
implement this method.
- __ne__(...) from builtins.PyCapsule
- __ne__(self : rosetta.core.scoring.constraints.Constraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
Inequality operator to test whether two constraints are not functionally
identical.
- __str__(...) from builtins.PyCapsule
- __str__(rosetta.core.scoring.constraints.Constraint) -> str
- choose_effective_sequence_separation(...) from builtins.PyCapsule
- choose_effective_sequence_separation(self : rosetta.core.scoring.constraints.Constraint, sp : rosetta.core.kinematics.ShortestPathInFoldTree, : rosetta.numeric.random.RandomGenerator) -> int
- clone(...) from builtins.PyCapsule
- clone(*args, **kwargs)
Overloaded function.
1. clone(rosetta.core.scoring.constraints.Constraint) -> rosetta.core.scoring.constraints.Constraint
Copies the data from this %Constraint into a new object and returns
an OP to the new object. Intended to be implemented by derived classes and
used by pose.add_constraint. This function must return a *deep copy* of
itself -- meaning that if this %Constraint holds pointers to other %Constraints
that it must invoke clone on those %Constraints as well. If the %Constraint
holds a FuncOP, then the Func should also be cloned.
2. clone(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::Func) -> rosetta.core.scoring.constraints.Constraint
Clone the constraint, but where a new Func object is to be used instead.
- dist(...) from builtins.PyCapsule
- dist(*args, **kwargs)
Overloaded function.
1. dist(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose) -> float
return the raw "distance" before that distance is handed to the FUNC object
2. dist(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func) -> float
- effective_sequence_separation(...) from builtins.PyCapsule
- effective_sequence_separation(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.kinematics.ShortestPathInFoldTree) -> int
- get_func(...) from builtins.PyCapsule
- get_func(rosetta.core.scoring.constraints.Constraint) -> core::scoring::func::Func
Returns the func::Func object associated with this Constraint object.
- remap_resid(...) from builtins.PyCapsule
- remap_resid(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.Constraint
apply a resid remapping to this constraint, returns the remapped
constraint Does this return an owning pointer to this constraint or a
copy? Documentation would be nice.
- remapped_clone(...) from builtins.PyCapsule
- remapped_clone(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose, : rosetta.core.pose.Pose, map : rosetta.core.id.SequenceMapping) -> rosetta.core.scoring.constraints.Constraint
Copies the data from this Constraint into a new object and returns
an OP atoms are mapped to atoms with the same name in dest pose ( e.g.
for switch from centroid to fullatom ) if a sequence_mapping is present
it is used to map residue numbers .. NULL = identity mapping to the new
object. Intended to be implemented by derived classes.
- residues(...) from builtins.PyCapsule
- residues(rosetta.core.scoring.constraints.Constraint) -> rosetta.utility.vector1_unsigned_long
Returns the pose numbers of the residues involved in this constraint, in no particular order.
Used in determining one-body/two-body/multi-body status.
For historical reasons, the default uses a simple protocol based on natoms()/atom() -
feel free to reimplement more efficiently.
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(self : rosetta.core.scoring.constraints.Constraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
Determine if the calling class has the same type as the
input class, using dynamic casts. This is important in ensuring
that two constraints are equal: both this and other must check
that the other is the same as it. This is not an optional method
and every class should implement it, regaurdless of whether a
parent class implements it.
- score_type(...) from builtins.PyCapsule
- score_type(rosetta.core.scoring.constraints.Constraint) -> rosetta.core.scoring.ScoreType
Returns the ScoreType that this Constraint object will use.
- setup_for_derivatives(...) from builtins.PyCapsule
- setup_for_derivatives(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : rosetta.core.scoring.ScoreFunction) -> NoneType
- setup_for_scoring(...) from builtins.PyCapsule
- setup_for_scoring(self : rosetta.core.scoring.constraints.Constraint, : core::scoring::func::XYZ_Func, : rosetta.core.scoring.ScoreFunction) -> NoneType
- steal_def(...) from builtins.PyCapsule
- steal_def(self : rosetta.core.scoring.constraints.Constraint, : rosetta.core.pose.Pose) -> NoneType
take coordinates, distances, angles, etc from given pose
- to_string(...) from builtins.PyCapsule
- to_string(rosetta.core.scoring.constraints.Constraint) -> str
Convenience function, returns the results of show() as a string.
Not to be overriden by derived classes.
- type(...) from builtins.PyCapsule
- type(rosetta.core.scoring.constraints.Constraint) -> str
Returns a unique string identified for this constraint. Used in several
places, including the ConstraintIO class.
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class TailFunction(builtins.object) |
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The different types of behaviour for the penalty values past the defined range.
When values are added to this enum, they should also be added to the AACompositionEnergySetup::get_tailfunction_name() function.
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Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(rosetta.core.scoring.aa_composition_energy.TailFunction, rosetta.core.scoring.aa_composition_energy.TailFunction) -> bool
- __hash__(...) from builtins.PyCapsule
- __hash__(rosetta.core.scoring.aa_composition_energy.TailFunction) -> int
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.scoring.aa_composition_energy.TailFunction, int) -> NoneType
2. __init__(rosetta.core.scoring.aa_composition_energy.TailFunction, int) -> NoneType
- __int__(...) from builtins.PyCapsule
- __int__(rosetta.core.scoring.aa_composition_energy.TailFunction) -> int
- __ne__(...) from builtins.PyCapsule
- __ne__(rosetta.core.scoring.aa_composition_energy.TailFunction, rosetta.core.scoring.aa_composition_energy.TailFunction) -> 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.aa_composition_energy.TailFunction) -> str
Data and other attributes defined here:
- tf_constant = TailFunction.tf_constant
- tf_end_of_list = TailFunction.tf_end_of_list
- tf_linear = TailFunction.tf_linear
- tf_quadratic = TailFunction.tf_quadratic
- tf_unknown = TailFunction.tf_end_of_list
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