| | |
- builtins.object
-
- ChiSet
- DunbrackRotamerSampleData
- ProbSortClass
- RotamerBuildingData
- RotamerLibraryScratchSpace
- rosetta.core.pack.rotamers.SingleResidueRotamerLibrary(builtins.object)
-
- SingleResidueDunbrackLibrary
- rosetta.core.pack.rotamers.SingleResidueRotamerLibraryCreator(builtins.object)
-
- SingleResidueDunbrackLibraryCreator
- rosetta.core.scoring.constraints.Constraint(builtins.object)
-
- DunbrackConstraint
- RotamerConstraint
- rosetta.core.scoring.constraints.ConstraintCreator(builtins.object)
-
- DunbrackConstraintCreator
- rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy(rosetta.core.scoring.methods.OneBodyEnergy)
-
- DunbrackEnergy
- rosetta.core.scoring.methods.EnergyMethodCreator(builtins.object)
-
- DunbrackEnergyCreator
- rosetta.utility.SingletonBase_core_pack_dunbrack_RotamerLibrary_t(builtins.object)
-
- RotamerLibrary
class DunbrackConstraint(rosetta.core.scoring.constraints.Constraint) |
| | |
- Method resolution order:
- DunbrackConstraint
- rosetta.core.scoring.constraints.Constraint
- builtins.object
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.core.pack.dunbrack.DunbrackConstraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(handle) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- atom(...) from builtins.PyCapsule
- atom(self : rosetta.core.pack.dunbrack.DunbrackConstraint, index : int) -> rosetta.core.id.AtomID
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.pack.dunbrack.DunbrackConstraint) -> rosetta.core.scoring.constraints.Constraint
- fill_f1_f2(...) from builtins.PyCapsule
- fill_f1_f2(self : rosetta.core.pack.dunbrack.DunbrackConstraint, atom : rosetta.core.id.AtomID, xyz : core::scoring::func::XYZ_Func, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t, weights : rosetta.core.scoring.EMapVector) -> NoneType
- natoms(...) from builtins.PyCapsule
- natoms(rosetta.core.pack.dunbrack.DunbrackConstraint) -> int
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(self : rosetta.core.pack.dunbrack.DunbrackConstraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
- score(...) from builtins.PyCapsule
- score(self : rosetta.core.pack.dunbrack.DunbrackConstraint, xyz_func : core::scoring::func::XYZ_Func, weights : rosetta.core.scoring.EMapVector, emap : rosetta.core.scoring.EMapVector) -> NoneType
- type(...) from builtins.PyCapsule
- type(rosetta.core.pack.dunbrack.DunbrackConstraint) -> str
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.
|
class DunbrackEnergy(rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy) |
| | |
- Method resolution order:
- DunbrackEnergy
- rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy
- rosetta.core.scoring.methods.OneBodyEnergy
- 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.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.pack.dunbrack.DunbrackEnergy, : rosetta.core.pack.dunbrack.DunbrackEnergy) -> rosetta.core.pack.dunbrack.DunbrackEnergy
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.pack.dunbrack.DunbrackEnergy) -> rosetta.core.scoring.methods.EnergyMethod
clone
- defines_dof_derivatives(...) from builtins.PyCapsule
- defines_dof_derivatives(self : rosetta.core.pack.dunbrack.DunbrackEnergy, p : rosetta.core.pose.Pose) -> bool
Yes. The DunbrackEnergy defines derivatives
for phi/psi and the chi dihedrals.
- eval_dof_derivative(...) from builtins.PyCapsule
- eval_dof_derivative(self : rosetta.core.pack.dunbrack.DunbrackEnergy, dof_id : rosetta.core.id.DOF_ID, tor_id : rosetta.core.id.TorsionID, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, weights : rosetta.core.scoring.EMapVector) -> float
Deprecated.
- eval_residue_dof_derivative(...) from builtins.PyCapsule
- eval_residue_dof_derivative(self : rosetta.core.pack.dunbrack.DunbrackEnergy, rsd : rosetta.core.conformation.Residue, min_data : 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 phi/psi and chi dihedral derivatives
for the input residue.
- indicate_required_context_graphs(...) from builtins.PyCapsule
- indicate_required_context_graphs(self : rosetta.core.pack.dunbrack.DunbrackEnergy, : rosetta.utility.vector1_bool) -> NoneType
DunbrackEnergy is context independent; indicates that no
context graphs are required
- minimize_in_whole_structure_context(...) from builtins.PyCapsule
- minimize_in_whole_structure_context(self : rosetta.core.pack.dunbrack.DunbrackEnergy, : rosetta.core.pose.Pose) -> bool
- residue_energy(...) from builtins.PyCapsule
- residue_energy(self : rosetta.core.pack.dunbrack.DunbrackEnergy, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType
//////////////////////////////////////////////////////////////////////////
Methods inherited from rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy:
- method_type(...) from builtins.PyCapsule
- method_type(rosetta.core.scoring.methods.ContextIndependentOneBodyEnergy) -> rosetta.core.scoring.methods.EnergyMethodType
Returns the ci_1b element of the EnergyMethodType enumeration; this
method should NOT be overridden by derived classes.
Methods inherited from rosetta.core.scoring.methods.OneBodyEnergy:
- defines_score_for_residue(...) from builtins.PyCapsule
- defines_score_for_residue(self : rosetta.core.scoring.methods.OneBodyEnergy, : rosetta.core.conformation.Residue) -> bool
During minimization, energy methods are allowed to decide that they say nothing
about a particular residue (e.g. no non-zero energy) and as a result they will not be queried for
a derivative or an energy. The default behavior is to return "true" for all residues.
- eval_residue_derivatives(...) from builtins.PyCapsule
- eval_residue_derivatives(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, min_data : core::scoring::ResSingleMinimizationData, pose : rosetta.core.pose.Pose, weights : rosetta.core.scoring.EMapVector, atom_derivs : rosetta.utility.vector1_core_scoring_DerivVectorPair) -> NoneType
Evaluate the derivatives for all atoms on this residue and increment them
into the input atom_derivs vector1. The calling function must guarantee that
setup for derivatives is called before this function is, and that the atom_derivs
vector contains at least as many entries as there are atoms in the input Residue.
This base class provides a default noop implementation of this function.
- requires_a_setup_for_derivatives_for_residue_opportunity(...) from builtins.PyCapsule
- requires_a_setup_for_derivatives_for_residue_opportunity(self : rosetta.core.scoring.methods.OneBodyEnergy, pose : rosetta.core.pose.Pose) -> bool
Does this EnergyMethod require the opportunity to examine the residue before derivative evaluation 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_opportunity(...) from builtins.PyCapsule
- requires_a_setup_for_scoring_for_residue_opportunity(self : rosetta.core.scoring.methods.OneBodyEnergy, 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.
- residue_energy_ext(...) from builtins.PyCapsule
- residue_energy_ext(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, min_data : core::scoring::ResSingleMinimizationData, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType
Evaluate the one-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
one body energies into the input EnergyMap. 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 setup_for_minimizing_for_residue before this function is
invoked. This function should not be called unless the use_extended_residue_energy_interface()
method returns "true". Default implementation provided by this base class calls
utility::exit(). The Pose merely serves as context, and the input residue is not required
to be a member of the Pose.
- setup_for_derivatives_for_residue(...) from builtins.PyCapsule
- setup_for_derivatives_for_residue(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, min_data : core::scoring::ResSingleMinimizationData) -> NoneType
Do any setup work necessary before evaluating the derivatives for this residue
- setup_for_minimizing_for_residue(...) from builtins.PyCapsule
- setup_for_minimizing_for_residue(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, : rosetta.core.pose.Pose, : rosetta.core.scoring.ScoreFunction, : rosetta.core.kinematics.MinimizerMapBase, : 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 ResSingleMinimizationData 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. The Pose merely serves as context, and the input residue is not
required to be a member of the Pose.
- setup_for_scoring_for_residue(...) from builtins.PyCapsule
- setup_for_scoring_for_residue(self : rosetta.core.scoring.methods.OneBodyEnergy, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction, min_data : 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
- use_extended_residue_energy_interface(...) from builtins.PyCapsule
- use_extended_residue_energy_interface(rosetta.core.scoring.methods.OneBodyEnergy) -> bool
Rely on the extended version of the residue_energy function during score-function
evaluation in minimization? The extended version (below) takes a ResSingleMinimizationData.
Return 'true' for the extended version. 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".
- 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
- 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.
- 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.
- version(...) from builtins.PyCapsule
- version(rosetta.core.scoring.methods.EnergyMethod) -> int
Return the version of the energy method
|
class DunbrackRotamerSampleData(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) -> NoneType
2. __init__(self : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, is_nrchi_sample : bool) -> NoneType
3. __init__(self : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign_random_chi(...) from builtins.PyCapsule
- assign_random_chi(*args, **kwargs)
Overloaded function.
1. assign_random_chi(self : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, chi_angles : rosetta.utility.vector1_double, RG : rosetta.numeric.random.RandomGenerator) -> NoneType
2. assign_random_chi(self : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, chi_angles : rosetta.utility.vector1_double, RG : rosetta.numeric.random.RandomGenerator, factor : float) -> NoneType
- chi_is_nonrotameric(...) from builtins.PyCapsule
- chi_is_nonrotameric(self : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, chi : int) -> bool
- chi_mean(...) from builtins.PyCapsule
- chi_mean(rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) -> rosetta.utility.fixedsizearray1_double_4_t
- chi_probability(...) from builtins.PyCapsule
- chi_probability(*args, **kwargs)
Overloaded function.
1. chi_probability(self : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, chi_angles : rosetta.utility.vector1_double) -> float
2. chi_probability(self : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, chi_angles : rosetta.utility.vector1_double, factor : float) -> float
- chi_sd(...) from builtins.PyCapsule
- chi_sd(rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) -> rosetta.utility.fixedsizearray1_double_4_t
- nchi(...) from builtins.PyCapsule
- nchi(rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) -> int
- nrchi_lower_boundary(...) from builtins.PyCapsule
- nrchi_lower_boundary(rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) -> float
- nrchi_probability(...) from builtins.PyCapsule
- nrchi_probability(rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) -> float
- nrchi_sample(...) from builtins.PyCapsule
- nrchi_sample(rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) -> bool
- nrchi_upper_boundary(...) from builtins.PyCapsule
- nrchi_upper_boundary(rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) -> float
- probability(...) from builtins.PyCapsule
- probability(rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) -> float
- rot_well(...) from builtins.PyCapsule
- rot_well(rosetta.core.pack.dunbrack.DunbrackRotamerSampleData) -> rosetta.utility.fixedsizearray1_unsigned_long_4_t
- set_chi_mean(...) from builtins.PyCapsule
- set_chi_mean(self : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, chi_index : int, mean : float) -> NoneType
- set_chi_sd(...) from builtins.PyCapsule
- set_chi_sd(self : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, chi_index : int, sd : float) -> NoneType
- set_nchi(...) from builtins.PyCapsule
- set_nchi(self : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, nchi : int) -> NoneType
- set_nrchi_lower_boundary(...) from builtins.PyCapsule
- set_nrchi_lower_boundary(self : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, low : float) -> NoneType
- set_nrchi_probability(...) from builtins.PyCapsule
- set_nrchi_probability(self : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, nrchi_prob : float) -> NoneType
- set_nrchi_sample(...) from builtins.PyCapsule
- set_nrchi_sample(self : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, setting : bool) -> NoneType
Setters
- set_nrchi_upper_boundary(...) from builtins.PyCapsule
- set_nrchi_upper_boundary(self : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, high : float) -> NoneType
- set_prob(...) from builtins.PyCapsule
- set_prob(self : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, probability : float) -> NoneType
- set_rotwell(...) from builtins.PyCapsule
- set_rotwell(*args, **kwargs)
Overloaded function.
1. set_rotwell(self : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, chi_index : int, rotwell : int) -> NoneType
2. set_rotwell(self : rosetta.core.pack.dunbrack.DunbrackRotamerSampleData, : rosetta.utility.vector1_unsigned_long) -> NoneType
|
class RotamerBuildingData(builtins.object) |
| |
a simple class for passing data around in virtual function
calls of the rotamer creating process. Derived classes will be simple
containers for interpolated rotameric data that 1) has to be available
to the derived class when building rotamers and 2) cannot be stored as
member data in the derived class in a thread-safe manner. Derived classes
of the RotamerBuildingData can be declared on the stack, passed into
the RotamericSingleResidueDunbrackLibrary::build_chi_sets function,
and then in the (virtual) chisamples_for_rotamer function, the derived classes
may be downcast.
|
| |
Methods defined here:
- __init__(self, /, *args, **kwargs)
- Initialize self. See help(type(self)) for accurate signature.
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.pack.dunbrack.RotamerBuildingData, : rosetta.core.pack.dunbrack.RotamerBuildingData) -> rosetta.core.pack.dunbrack.RotamerBuildingData
|
class RotamerConstraint(rosetta.core.scoring.constraints.Constraint) |
| |
This class favors a particular rotamer at a particular position by reducing its Dunbrack energy.
Specifically, the given rotamer well(s) receive a bonus equal to the
difference between their minimum energy (for the ideal rotamer in this well)
and the minimum energy of any rotamer (at the current phi,psi).
This class is used to implement the scoring component of the -unboundrot flag;
actually adding those rotamers to the library occurs in core/pack/rotamer_set/UnboundRotamersOperation.
|
| |
- Method resolution order:
- RotamerConstraint
- rosetta.core.scoring.constraints.Constraint
- builtins.object
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.core.pack.dunbrack.RotamerConstraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(handle) -> NoneType
2. __init__(handle, rosetta.core.pack.dunbrack.RotamerConstraint) -> NoneType
3. __init__(self : handle, pose : rosetta.core.pose.Pose, seqpos : int) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- add_residue(...) from builtins.PyCapsule
- add_residue(self : rosetta.core.pack.dunbrack.RotamerConstraint, rsd : rosetta.core.conformation.Residue) -> NoneType
- atom(...) from builtins.PyCapsule
- atom(self : rosetta.core.pack.dunbrack.RotamerConstraint, index : int) -> rosetta.core.id.AtomID
- clone(...) from builtins.PyCapsule
- clone(rosetta.core.pack.dunbrack.RotamerConstraint) -> rosetta.core.scoring.constraints.Constraint
- fill_f1_f2(...) from builtins.PyCapsule
- fill_f1_f2(self : rosetta.core.pack.dunbrack.RotamerConstraint, atom : rosetta.core.id.AtomID, xyz : core::scoring::func::XYZ_Func, F1 : rosetta.numeric.xyzVector_double_t, F2 : rosetta.numeric.xyzVector_double_t, weights : rosetta.core.scoring.EMapVector) -> NoneType
- natoms(...) from builtins.PyCapsule
- natoms(rosetta.core.pack.dunbrack.RotamerConstraint) -> int
- same_type_as_me(...) from builtins.PyCapsule
- same_type_as_me(self : rosetta.core.pack.dunbrack.RotamerConstraint, other : rosetta.core.scoring.constraints.Constraint) -> bool
- score(...) from builtins.PyCapsule
- score(self : rosetta.core.pack.dunbrack.RotamerConstraint, xyz_func : core::scoring::func::XYZ_Func, weights : rosetta.core.scoring.EMapVector, emap : rosetta.core.scoring.EMapVector) -> NoneType
- type(...) from builtins.PyCapsule
- type(rosetta.core.pack.dunbrack.RotamerConstraint) -> str
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.
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class RotamerLibrary(rosetta.utility.SingletonBase_core_pack_dunbrack_RotamerLibrary_t) |
| |
////////////////////////////////////////////////////////////////////////////
A class to manage the Dunbrack Rotamer Libraries
This class no longer manages arbitrary rotamer libraries.
Use core::pack::rotamers::SingleResidueRotamerLibraryFactory::get_instance()->get( restype );
to get rotamer libraries for an arbitrary ResidueType.
|
| |
- Method resolution order:
- RotamerLibrary
- rosetta.utility.SingletonBase_core_pack_dunbrack_RotamerLibrary_t
- builtins.object
Methods defined here:
- __init__(self, /, *args, **kwargs)
- Initialize self. See help(type(self)) for accurate signature.
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- best_rotamer_energy(...) from builtins.PyCapsule
- best_rotamer_energy(self : rosetta.core.pack.dunbrack.RotamerLibrary, rsd : rosetta.core.conformation.Residue, curr_rotamer_only : bool, scratch : core::pack::dunbrack::RotamerLibraryScratchSpace) -> float
- decide_read_from_binary(...) from builtins.PyCapsule
- decide_read_from_binary(rosetta.core.pack.dunbrack.RotamerLibrary) -> bool
- get_binary_name(...) from builtins.PyCapsule
- get_binary_name(rosetta.core.pack.dunbrack.RotamerLibrary) -> str
- get_library_by_aa(...) from builtins.PyCapsule
- get_library_by_aa(self : rosetta.core.pack.dunbrack.RotamerLibrary, aa : rosetta.core.chemical.AA) -> core::pack::rotamers::SingleResidueRotamerLibrary
- initialize_dun02_aa_parameters(...) from builtins.PyCapsule
- initialize_dun02_aa_parameters(*args, **kwargs)
Overloaded function.
1. initialize_dun02_aa_parameters(rotameric_amino_acids : rosetta.utility.vector1_core_chemical_AA, rotameric_n_chi : rosetta.utility.vector1_unsigned_long, rotameric_n_bb : rosetta.utility.vector1_unsigned_long) -> NoneType
2. initialize_dun02_aa_parameters(nchi_for_aa : rosetta.utility.vector1_unsigned_long, nbb_for_aa : rosetta.utility.vector1_unsigned_long, n_rotameric_aas : int) -> NoneType
- initialize_dun10_aa_parameters(...) from builtins.PyCapsule
- initialize_dun10_aa_parameters(rotameric_amino_acids : rosetta.utility.vector1_core_chemical_AA, rotameric_n_chi : rosetta.utility.vector1_unsigned_long, rotameric_n_bb : rosetta.utility.vector1_unsigned_long, sraa : rosetta.utility.vector1_core_chemical_AA, srnchi : rosetta.utility.vector1_unsigned_long, srnbb : rosetta.utility.vector1_unsigned_long, scind : rosetta.utility.vector1_bool, sampind : rosetta.utility.vector1_bool, sym : rosetta.utility.vector1_bool, astr : rosetta.utility.vector1_double) -> NoneType
- rotamer_energy(...) from builtins.PyCapsule
- rotamer_energy(self : rosetta.core.pack.dunbrack.RotamerLibrary, rsd : rosetta.core.conformation.Residue, scratch : core::pack::dunbrack::RotamerLibraryScratchSpace) -> float
- rotamer_energy_deriv(...) from builtins.PyCapsule
- rotamer_energy_deriv(self : rosetta.core.pack.dunbrack.RotamerLibrary, rsd : rosetta.core.conformation.Residue, scratch : core::pack::dunbrack::RotamerLibraryScratchSpace) -> float
to do:
- validate_dunbrack_binary(...) from builtins.PyCapsule
- validate_dunbrack_binary(rosetta.core.pack.dunbrack.RotamerLibrary) -> bool
Reload the Dunbrack Rotamer libraries from ASCII, and make sure that they match the ones loaded from binary.
Return true if the binary file is valid, false if the binary is invalid.
NOTE WELL: This is *not* a const function, as reloading from ASCII modifies internals.
It's also *VERY* thread unsafe. Never call this function from a multithreaded context.
Methods inherited from rosetta.utility.SingletonBase_core_pack_dunbrack_RotamerLibrary_t:
- get_instance(...) from builtins.PyCapsule
- get_instance() -> core::pack::dunbrack::RotamerLibrary
|
class RotamerLibraryScratchSpace(builtins.object) |
| | |
Methods defined here:
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> NoneType
2. __init__(self : rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace, : rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace, : rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace
- chidev(...) from builtins.PyCapsule
- chidev(*args, **kwargs)
Overloaded function.
1. chidev(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
2. chidev(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
- chidevpen(...) from builtins.PyCapsule
- chidevpen(*args, **kwargs)
Overloaded function.
1. chidevpen(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
2. chidevpen(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
- chimean(...) from builtins.PyCapsule
- chimean(*args, **kwargs)
Overloaded function.
1. chimean(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
2. chimean(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
- chisd(...) from builtins.PyCapsule
- chisd(*args, **kwargs)
Overloaded function.
1. chisd(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
2. chisd(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
- dE_dbb(...) from builtins.PyCapsule
- dE_dbb(*args, **kwargs)
Overloaded function.
1. dE_dbb(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_5_t
2. dE_dbb(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_5_t
- dE_dbb_dev(...) from builtins.PyCapsule
- dE_dbb_dev(*args, **kwargs)
Overloaded function.
1. dE_dbb_dev(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_5_t
2. dE_dbb_dev(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_5_t
- dE_dbb_dev_perchi(...) from builtins.PyCapsule
- dE_dbb_dev_perchi(*args, **kwargs)
Overloaded function.
1. dE_dbb_dev_perchi(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_4_5_t
2. dE_dbb_dev_perchi(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_4_5_t
- dE_dbb_rot(...) from builtins.PyCapsule
- dE_dbb_rot(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_5_t
- dE_dbb_semi(...) from builtins.PyCapsule
- dE_dbb_semi(*args, **kwargs)
Overloaded function.
1. dE_dbb_semi(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_5_t
2. dE_dbb_semi(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_5_t
- dE_dchi(...) from builtins.PyCapsule
- dE_dchi(*args, **kwargs)
Overloaded function.
1. dE_dchi(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
2. dE_dchi(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
- dE_dchi_dev(...) from builtins.PyCapsule
- dE_dchi_dev(*args, **kwargs)
Overloaded function.
1. dE_dchi_dev(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
2. dE_dchi_dev(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
- dE_dchi_semi(...) from builtins.PyCapsule
- dE_dchi_semi(*args, **kwargs)
Overloaded function.
1. dE_dchi_semi(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
2. dE_dchi_semi(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
- dchidevpen_dbb(...) from builtins.PyCapsule
- dchidevpen_dbb(*args, **kwargs)
Overloaded function.
1. dchidevpen_dbb(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_5_t
2. dchidevpen_dbb(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_5_t
- dchidevpen_dchi(...) from builtins.PyCapsule
- dchidevpen_dchi(*args, **kwargs)
Overloaded function.
1. dchidevpen_dchi(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
2. dchidevpen_dchi(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
- dchimean_dbb(...) from builtins.PyCapsule
- dchimean_dbb(*args, **kwargs)
Overloaded function.
1. dchimean_dbb(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_4_5_t
2. dchimean_dbb(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_4_5_t
- dchimean_domg(...) from builtins.PyCapsule
- dchimean_domg(*args, **kwargs)
Overloaded function.
1. dchimean_domg(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
2. dchimean_domg(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
- dchisd_dbb(...) from builtins.PyCapsule
- dchisd_dbb(*args, **kwargs)
Overloaded function.
1. dchisd_dbb(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_4_5_t
2. dchisd_dbb(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_utility_fixedsizearray1_double_4_5_t
- dchisd_domg(...) from builtins.PyCapsule
- dchisd_domg(*args, **kwargs)
Overloaded function.
1. dchisd_domg(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
2. dchisd_domg(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_4_t
- dentropy_dbb(...) from builtins.PyCapsule
- dentropy_dbb(*args, **kwargs)
Overloaded function.
1. dentropy_dbb(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_5_t
2. dentropy_dbb(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_5_t
- dneglnrotprob_dbb(...) from builtins.PyCapsule
- dneglnrotprob_dbb(*args, **kwargs)
Overloaded function.
1. dneglnrotprob_dbb(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_5_t
2. dneglnrotprob_dbb(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_5_t
- drotprob_dbb(...) from builtins.PyCapsule
- drotprob_dbb(*args, **kwargs)
Overloaded function.
1. drotprob_dbb(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_5_t
2. drotprob_dbb(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_double_5_t
- entropy(...) from builtins.PyCapsule
- entropy(*args, **kwargs)
Overloaded function.
1. entropy(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> float
2. entropy(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> float
- fa_dun_dev(...) from builtins.PyCapsule
- fa_dun_dev(*args, **kwargs)
Overloaded function.
1. fa_dun_dev(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> float
2. fa_dun_dev(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> float
- fa_dun_rot(...) from builtins.PyCapsule
- fa_dun_rot(*args, **kwargs)
Overloaded function.
1. fa_dun_rot(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> float
2. fa_dun_rot(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> float
- fa_dun_semi(...) from builtins.PyCapsule
- fa_dun_semi(*args, **kwargs)
Overloaded function.
1. fa_dun_semi(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> float
2. fa_dun_semi(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> float
- fa_dun_tot(...) from builtins.PyCapsule
- fa_dun_tot(*args, **kwargs)
Overloaded function.
1. fa_dun_tot(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> float
2. fa_dun_tot(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> float
- negln_rotprob(...) from builtins.PyCapsule
- negln_rotprob(*args, **kwargs)
Overloaded function.
1. negln_rotprob(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> float
2. negln_rotprob(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> float
- rotprob(...) from builtins.PyCapsule
- rotprob(*args, **kwargs)
Overloaded function.
1. rotprob(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> float
2. rotprob(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> float
- rotwell(...) from builtins.PyCapsule
- rotwell(*args, **kwargs)
Overloaded function.
1. rotwell(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_unsigned_long_4_t
2. rotwell(rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> rosetta.utility.fixedsizearray1_unsigned_long_4_t
|
class SingleResidueDunbrackLibrary(rosetta.core.pack.rotamers.SingleResidueRotamerLibrary) |
| | |
- Method resolution order:
- SingleResidueDunbrackLibrary
- rosetta.core.pack.rotamers.SingleResidueRotamerLibrary
- builtins.object
Methods defined here:
- __eq__(...) from builtins.PyCapsule
- __eq__(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, : rosetta.core.pack.rotamers.SingleResidueRotamerLibrary) -> bool
Comparison operator, mainly intended to use in ASCII/binary comparsion tests
Values tested should parallel those used in the read_from_binary() function.
- __init__(...) from builtins.PyCapsule
- __init__(*args, **kwargs)
Overloaded function.
1. __init__(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, aa : rosetta.core.chemical.AA, n_rotameric_chi : int, dun02 : bool) -> NoneType
2. __init__(rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary) -> NoneType
- __new__(*args, **kwargs) from builtins.type
- Create and return a new object. See help(type) for accurate signature.
- aa(...) from builtins.PyCapsule
- aa(rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary) -> rosetta.core.chemical.AA
The amino acid this library is representing
- bin_angle(...) from builtins.PyCapsule
- bin_angle(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, angle_start : float, angle_step : float, : float, nbins : int, ang : float, bin_lower : int, bin_upper : int, angle_alpha : float) -> NoneType
This is not the right place for this code, but the numeric interpolation library
uselessly indexes by 0 and the basic functions aren't inlined...
- bin_rotameric_chi(...) from builtins.PyCapsule
- bin_rotameric_chi(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, chi : float, which_chi : int) -> int
, Turns out, when non-rotameric chi are taken out of the picture,
all remaining chi are binned the same way, except proline. Valid only for
Dun10 libraries. For D-amino acids, chi must be inverted before passing
to this function.
- get_all_rotamer_samples(...) from builtins.PyCapsule
- get_all_rotamer_samples(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, bbs : rosetta.utility.fixedsizearray1_double_5_t) -> rosetta.utility.vector1_core_pack_dunbrack_DunbrackRotamerSampleData
- get_phi_from_rsd(...) from builtins.PyCapsule
- get_phi_from_rsd(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, rsd : rosetta.core.conformation.Residue) -> float
- get_probability_for_rotamer(...) from builtins.PyCapsule
- get_probability_for_rotamer(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, phi : float, psi : float, rot_ind : int) -> float
Return the probability for a particular rotamer where rotamers are
indexed in order of decreasing probability (or something very close to
decreasing probability).
- get_psi_from_rsd(...) from builtins.PyCapsule
- get_psi_from_rsd(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, rsd : rosetta.core.conformation.Residue) -> float
- get_rotamer(...) from builtins.PyCapsule
- get_rotamer(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, phi : float, psi : float, rot_ind : int) -> rosetta.core.pack.dunbrack.DunbrackRotamerSampleData
- get_rotamer_from_chi(...) from builtins.PyCapsule
- get_rotamer_from_chi(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, chi : rosetta.utility.vector1_double, rot : rosetta.utility.vector1_unsigned_long) -> NoneType
Convert a vector of chi angles (degrees) into a integer vector of rotamer wells.
Derived class should be consistent, but may be arbitrary in how wells divide angle space.
- memory_usage_in_bytes(...) from builtins.PyCapsule
- memory_usage_in_bytes(rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary) -> int
Derived classes should invoke base class function as well.
- n_rotamer_bins(...) from builtins.PyCapsule
- n_rotamer_bins(rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary) -> int
- n_rotamer_bins_for_aa(...) from builtins.PyCapsule
- n_rotamer_bins_for_aa(aa : rosetta.core.chemical.AA, rot : rosetta.utility.vector1_unsigned_long) -> NoneType
Hard coded specifics about the amino acids
- n_rotamer_bins_for_aa_02(...) from builtins.PyCapsule
- n_rotamer_bins_for_aa_02(aa : rosetta.core.chemical.AA, rot : rosetta.utility.vector1_unsigned_long) -> NoneType
Hard coded rotamer well info for the 2002 library.
- n_rotameric_bins_for_aa(...) from builtins.PyCapsule
- n_rotameric_bins_for_aa(aa : rosetta.core.chemical.AA, rot : rosetta.utility.vector1_unsigned_long, dun02 : bool) -> NoneType
Reports information about the *rotameric* chi only; no details
about the non rotameric chi.
- nbb(...) from builtins.PyCapsule
- nbb(rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary) -> int
the number of backbone dihedrals represented by the library
- nchi(...) from builtins.PyCapsule
- nchi(rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary) -> int
The number of chi represented by the library.
- packed_rotno_2_rotwell(...) from builtins.PyCapsule
- packed_rotno_2_rotwell(*args, **kwargs)
Overloaded function.
1. packed_rotno_2_rotwell(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, packed_rotno : int, rotwell : rosetta.utility.vector1_unsigned_long) -> NoneType
Convert from the packed rotamer number to the rotamer well
2. packed_rotno_2_rotwell(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, packed_rotno : int, rotwell : rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> NoneType
3. packed_rotno_2_rotwell(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, packed_rotno : int) -> rosetta.utility.vector1_unsigned_long
- prob_to_accumulate(...) from builtins.PyCapsule
- prob_to_accumulate(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, : float, : float) -> NoneType
setters for accumulation probability cutoff (to support externally-controlled option dependence)
- prob_to_accumulate_buried(...) from builtins.PyCapsule
- prob_to_accumulate_buried(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, : float) -> NoneType
- prob_to_accumulate_nonburied(...) from builtins.PyCapsule
- prob_to_accumulate_nonburied(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, : float) -> NoneType
- probability_to_accumulate_while_building_rotamers(...) from builtins.PyCapsule
- probability_to_accumulate_while_building_rotamers(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, buried : bool) -> float
When creating rotamer, what position in the CDF should one build until?
Unlikely rotamers ( < 0.5 %) are numerous, but are very infrequently useful.
- read_from_binary(...) from builtins.PyCapsule
- read_from_binary(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, in : rosetta.utility.io.izstream) -> NoneType
- read_options(...) from builtins.PyCapsule
- read_options(rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary) -> NoneType
- rotno_2_packed_rotno(...) from builtins.PyCapsule
- rotno_2_packed_rotno(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, rotno : int) -> int
Convert from the rotamer number to the compacted
"packed rotamer number". Returns 0 if rotno has no corresponding packed rotno.
- rotno_2_rotwell(...) from builtins.PyCapsule
- rotno_2_rotwell(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, rotno : int, rotwell : rosetta.utility.vector1_unsigned_long) -> NoneType
Convert from the rotamer number to the rotamer well
- rotwell_2_packed_rotno(...) from builtins.PyCapsule
- rotwell_2_packed_rotno(*args, **kwargs)
Overloaded function.
1. rotwell_2_packed_rotno(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, rotwell : rosetta.utility.vector1_unsigned_long) -> int
Convert from the rotamer bin indices for each chi to the
compacted "packed rotamer number." Returns 0 if rotwell has no corresponding packed rotno
2. rotwell_2_packed_rotno(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, rotwell : rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> int
Convert from the rotamer bin indices for each chi to the
compacted "packed rotamer number." Returns 0 if rotwell has no corresponding packed rotno
- rotwell_2_rotno(...) from builtins.PyCapsule
- rotwell_2_rotno(*args, **kwargs)
Overloaded function.
1. rotwell_2_rotno(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, rotwell : rosetta.utility.vector1_unsigned_long) -> int
Convert from the rotamer bin indices for each chi to the
(non-compact) "rotamer number"
2. rotwell_2_rotno(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, rotwell : rosetta.utility.fixedsizearray1_unsigned_long_4_t) -> int
Convert from the rotamer bin indices for each chi to the
(non-compact) "rotamer number"
- set_n_chi_bins(...) from builtins.PyCapsule
- set_n_chi_bins(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, : rosetta.utility.vector1_unsigned_long) -> NoneType
Tell the base class the number of chi bins for each rotameric
chi dimension
- write_to_binary(...) from builtins.PyCapsule
- write_to_binary(self : rosetta.core.pack.dunbrack.SingleResidueDunbrackLibrary, out : utility::io::ozstream) -> NoneType
Methods inherited from rosetta.core.pack.rotamers.SingleResidueRotamerLibrary:
- assign(...) from builtins.PyCapsule
- assign(self : rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, : rosetta.core.pack.rotamers.SingleResidueRotamerLibrary) -> rosetta.core.pack.rotamers.SingleResidueRotamerLibrary
- assign_random_rotamer_with_bias(...) from builtins.PyCapsule
- assign_random_rotamer_with_bias(self : rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, scratch : rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace, RG : rosetta.numeric.random.RandomGenerator, new_chi_angles : rosetta.utility.vector1_double, perturb_from_rotamer_center : bool) -> NoneType
Pick a rotamer for the input residue according to the rotamer probability
distribution and assign chi angles to the input rsd. If perturb_from_rotamer_center
is true, then push the rotamer off from the center; for chi angles with a normal
distribution, the perturbation is taken from a Gaussian random number with a standard
deviation matching the chi angle's standard deviation. For chi angles that are not
normally distributed, the behavior is open to the derived classe's interpretation.
- best_rotamer_energy(...) from builtins.PyCapsule
- best_rotamer_energy(self : rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rsd : rosetta.core.conformation.Residue, curr_rotamer_only : bool, scratch : rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> float
Returns the energy of the lowest-energy rotamer accessible to the given residue
(based on e.g. its current phi and psi values).
If curr_rotamer_only is true, then consider only the idealized version of the
residue's current rotamer (local optimum); otherwise, consider all rotamers (global optimum).
- bump_check(...) from builtins.PyCapsule
- bump_check(self : rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamer : rosetta.core.conformation.Residue, resid : int, sf : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, task : core::pack::task::PackerTask, packer_neighbor_graph : rosetta.core.graph.Graph) -> float
Computes the "bump energy" of a rotamer: the bump energy is the
sum of rotamer's interactions with 1) the backbone-and-side chains of
neighboring residues that are held fixed during this repacking optimization
and 2) the backbones of neighboring residues that are changable during this
repacking optimization.
- bump_filter(...) from builtins.PyCapsule
- bump_filter(self : rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers : rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid : int, sf : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose, task : core::pack::task::PackerTask, packer_neighbor_graph : rosetta.core.graph.Graph) -> NoneType
Filter a RotamerVector by "bump energy" of a rotamer:
All rotamers with bump energies over a certain threshold will be discarded
Exception: if all rotamers are over the threshold, one rotamer (with the lowest
bump energy) will be reserved.
The vector "rotamers" will be modified "in-place"
- compute_proton_chi_samplings(...) from builtins.PyCapsule
- compute_proton_chi_samplings(self : rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, concrete_residue : rosetta.core.chemical.ResidueType, rlt : core::pack::task::ResidueLevelTask, buried : bool) -> rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t
Return a vector (indexed by proton_chi number) of vectors of dihedral values
to use in proton chi sampling
- current_rotamer(...) from builtins.PyCapsule
- current_rotamer(self : rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers : rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid : int, task : core::pack::task::PackerTask, concrete_residue : rosetta.core.chemical.ResidueType, existing_residue : rosetta.core.conformation.Residue) -> int
Adds the current rotamer to rotamer vector, if the Rotlib supports it
This is in this class mainly because of historical
behavior of certain rotamer libraries not supporting current rotamers
- emergency_rotamer(...) from builtins.PyCapsule
- emergency_rotamer(self : rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers : rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid : int, pose : rosetta.core.pose.Pose, task : core::pack::task::PackerTask, concrete_residue : rosetta.core.chemical.ResidueType, existing_residue : rosetta.core.conformation.Residue) -> NoneType
Generate an "emergency rotamer" if we don't have any
This is in this class mainly because of historical
behavior of certain rotamer libraries not supporting current rotamers
- expand_proton_chis(...) from builtins.PyCapsule
- expand_proton_chis(*args, **kwargs)
Overloaded function.
1. expand_proton_chis(self : rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling : rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue : rosetta.core.chemical.ResidueType) -> rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t
Given a vector of vectors of dihedrals to sample on proton chis,
Will create the ChiSet vector combinitorially on those chi values
(Note: The ChiSets are only valid/defined over the proton chis.)
2. expand_proton_chis(self : rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, sampling : rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, concrete_residue : rosetta.core.chemical.ResidueType, max_rotamers : int) -> rosetta.utility.vector1_std_shared_ptr_core_pack_dunbrack_ChiSet_t
Given a vector of vectors of dihedrals to sample on proton chis,
Will create the ChiSet vector combinitorially on those chi values
(Note: The ChiSets are only valid/defined over the proton chis.)
- fill_rotamer_vector(...) from builtins.PyCapsule
- fill_rotamer_vector(self : rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, pose : rosetta.core.pose.Pose, scorefxn : rosetta.core.scoring.ScoreFunction, task : core::pack::task::PackerTask, packer_neighbor_graph : rosetta.core.graph.Graph, concrete_residue : rosetta.core.chemical.ResidueType, existing_residue : rosetta.core.conformation.Residue, extra_chi_steps : rosetta.utility.vector1_utility_vector1_double_std_allocator_double_t, buried : bool, rotamers : rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t) -> NoneType
- rotamer_energy(...) from builtins.PyCapsule
- rotamer_energy(self : rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rsd : rosetta.core.conformation.Residue, scratch : rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> float
- rotamer_energy_deriv(...) from builtins.PyCapsule
- rotamer_energy_deriv(self : rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rsd : rosetta.core.conformation.Residue, scratch : rosetta.core.pack.dunbrack.RotamerLibraryScratchSpace) -> float
- virtual_sidechain(...) from builtins.PyCapsule
- virtual_sidechain(self : rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, rotamers : rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t, resid : int, pose : rosetta.core.pose.Pose, task : core::pack::task::PackerTask, concrete_residue : rosetta.core.chemical.ResidueType, existing_residue : rosetta.core.conformation.Residue) -> rosetta.utility.vector1_std_shared_ptr_core_conformation_Residue_t
Add a virtualized sidechain to the rotamer vector if
settings call for it.
- write_to_file(...) from builtins.PyCapsule
- write_to_file(self : rosetta.core.pack.rotamers.SingleResidueRotamerLibrary, out : utility::io::ozstream) -> NoneType
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