rosetta.protocols.fldsgn.potentials
index
(built-in)

Bindings for protocols::fldsgn::potentials namespace

 
Modules
       
rosetta.protocols.fldsgn.potentials.sspot

 
Classes
       
rosetta.core.scoring.methods.ContextDependentOneBodyEnergy(rosetta.core.scoring.methods.OneBodyEnergy)
AACompositionEnergy
rosetta.core.scoring.methods.EnergyMethodCreator(builtins.object)
AACompositionEnergyCreator
rosetta.protocols.moves.Mover(builtins.object)
SetAACompositionPotential
SetSecStructEnergies
rosetta.protocols.moves.MoverCreator(builtins.object)
SetAACompositionPotentialCreator
SetSecStructEnergiesCreator

 
class AACompositionEnergy(rosetta.core.scoring.methods.ContextDependentOneBodyEnergy)
    AACompositionEnergy
 
 
Method resolution order:
AACompositionEnergy
rosetta.core.scoring.methods.ContextDependentOneBodyEnergy
rosetta.core.scoring.methods.OneBodyEnergy
rosetta.core.scoring.methods.EnergyMethod
builtins.object

Methods defined here:
__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs)
Overloaded function.
 
1. __init__(handle) -> NoneType
 
2. __init__(self : handle, comp_constraint_aas : rosetta.std.map_core_chemical_AA_std_pair_double_double_t) -> NoneType
 
3. __init__(handle, rosetta.protocols.fldsgn.potentials.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.protocols.fldsgn.potentials.AACompositionEnergy,  : rosetta.protocols.fldsgn.potentials.AACompositionEnergy) -> rosetta.protocols.fldsgn.potentials.AACompositionEnergy
clone(...) from builtins.PyCapsule
clone(rosetta.protocols.fldsgn.potentials.AACompositionEnergy) -> rosetta.core.scoring.methods.EnergyMethod
 
clone
indicate_required_context_graphs(...) from builtins.PyCapsule
indicate_required_context_graphs(self : rosetta.protocols.fldsgn.potentials.AACompositionEnergy,  : rosetta.utility.vector1_bool) -> NoneType
 
DunbrackEnergy is context independent; indicates that no
 context graphs are required
residue_energy(...) from builtins.PyCapsule
residue_energy(self : rosetta.protocols.fldsgn.potentials.AACompositionEnergy, rsd : rosetta.core.conformation.Residue, pose : rosetta.core.pose.Pose, emap : rosetta.core.scoring.EMapVector) -> NoneType
 
//////////////////////////////////////////////////////////////////////////
set_comp_constraint_aa(...) from builtins.PyCapsule
set_comp_constraint_aa(self : rosetta.protocols.fldsgn.potentials.AACompositionEnergy, comp_constraint_aas : rosetta.std.map_core_chemical_AA_std_pair_double_double_t) -> NoneType
version(...) from builtins.PyCapsule
version(rosetta.protocols.fldsgn.potentials.AACompositionEnergy) -> int

Methods inherited from rosetta.core.scoring.methods.ContextDependentOneBodyEnergy:
method_type(...) from builtins.PyCapsule
method_type(rosetta.core.scoring.methods.ContextDependentOneBodyEnergy) -> rosetta.core.scoring.methods.EnergyMethodType
 
Returns the cd_1b element of the EnergyMethodType enumeration; this method
 should NOT be overridden by derived classes.

Methods inherited from rosetta.core.scoring.methods.OneBodyEnergy:
defines_dof_derivatives(...) from builtins.PyCapsule
defines_dof_derivatives(self : rosetta.core.scoring.methods.OneBodyEnergy, p : rosetta.core.pose.Pose) -> bool
 
Use the dof_derivative interface for this energy method when
 calculating derivatives?  It is possible to define both dof_derivatives and
 atom-derivatives; they are not mutually exclusive.
defines_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.
eval_residue_dof_derivative(...) from builtins.PyCapsule
eval_residue_dof_derivative(self : rosetta.core.scoring.methods.OneBodyEnergy, 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 DOF derivative for a particular residue.  The Pose merely serves as context,
 and the input residue is not required to be a member of the Pose.
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.
minimize_in_whole_structure_context(...) from builtins.PyCapsule
minimize_in_whole_structure_context(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose) -> bool
 
Should this EnergyMethod have score and derivative evaluation
 evaluated only in the context of the whole Pose, or can it be included
 in a decomposed manner for a residue or a set of residue-pairs that are
 not part of the Pose that's serving as their context?  The default
 method implemented in the base class returns true in order to grandfather
 in EnergyMethods that have not had their derivatives changed to take
 advantage of the new derivative-evaluation machinery.  Methods that return
 "true" will not have their residue-energy(-ext) / residue-pair-energy(-ext)
 methods invoked by the ScoreFunction during its traversal of the
 MinimizationGraph, and instead will be asked to perform all their work
 during finalize_total_energies().  Similarly, they will be expected to
 perform all their work during eval_atom_deriv() instead of during the
 ScoreFunction's traversal of the MinimizationGraph for derivative evaluation.
 IMPORTANT: Methods that return "true" cannot be included in RTMin.
prepare_rotamers_for_packing(...) from builtins.PyCapsule
prepare_rotamers_for_packing(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose,  : rosetta.core.conformation.RotamerSetBase) -> NoneType
 
If an energy method needs to cache data in a packing::RotamerSet object before
 rotamer energies are calculated, it does so during this function. The packer
 must ensure this function is called. The default behavior is to do nothing.
score_types(...) from builtins.PyCapsule
score_types(rosetta.core.scoring.methods.EnergyMethod) -> rosetta.utility.vector1_core_scoring_ScoreType
 
Returns the score types that this energy method computes.
setup_for_derivatives(...) from builtins.PyCapsule
setup_for_derivatives(self : rosetta.core.scoring.methods.EnergyMethod, pose : rosetta.core.pose.Pose, sfxn : rosetta.core.scoring.ScoreFunction) -> NoneType
 
Called immediately before atom- and DOF-derivatives are calculated
 allowing the derived class a chance to prepare for future calls.
setup_for_minimizing(...) from builtins.PyCapsule
setup_for_minimizing(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose,  : rosetta.core.scoring.ScoreFunction,  : rosetta.core.kinematics.MinimizerMapBase) -> NoneType
 
Called at the beginning of atom tree minimization, this method
 allows the derived class the opportunity to initialize pertinent data
 that will be used during minimization.  During minimzation, the chemical
 structure of the pose is constant, so assumptions on the number of atoms
 per residue and their identities are safe so long as the pose's Energies
 object's "use_nblist()" method returns true.
setup_for_packing(...) from builtins.PyCapsule
setup_for_packing(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose,  : rosetta.utility.vector1_bool,  : rosetta.utility.vector1_bool) -> NoneType
 
if an energy method needs to cache data in the Energies object,
 before packing begins, then it does so during this function. The packer
 must ensure this function is called. The default behavior is to do nothing.
setup_for_scoring(...) from builtins.PyCapsule
setup_for_scoring(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose,  : rosetta.core.scoring.ScoreFunction) -> NoneType
 
if an energy method needs to cache something in the pose (e.g. in pose.energies()),
 before scoring begins, it must do so in this method.  All long range energy
 functions must initialize their LREnergyContainers before scoring begins.
 The default is to do nothing.
update_residue_for_packing(...) from builtins.PyCapsule
update_residue_for_packing(self : rosetta.core.scoring.methods.EnergyMethod,  : rosetta.core.pose.Pose, resid : int) -> NoneType
 
If the pose changes in the middle of a packing (as happens in rotamer trials) and if
 an energy method needs to cache data in the pose that corresponds to its current state,
 then the method must update that data when this function is called.  The packer must
 ensure this function gets called.  The default behavior is to do nothing.

 
class AACompositionEnergyCreator(rosetta.core.scoring.methods.EnergyMethodCreator)
    
Method resolution order:
AACompositionEnergyCreator
rosetta.core.scoring.methods.EnergyMethodCreator
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.protocols.fldsgn.potentials.AACompositionEnergyCreator,  : rosetta.protocols.fldsgn.potentials.AACompositionEnergyCreator) -> rosetta.protocols.fldsgn.potentials.AACompositionEnergyCreator
create_energy_method(...) from builtins.PyCapsule
create_energy_method(self : rosetta.protocols.fldsgn.potentials.AACompositionEnergyCreator,  : rosetta.core.scoring.methods.EnergyMethodOptions) -> rosetta.core.scoring.methods.EnergyMethod
 
Instantiate a new AACompositionEnergy
score_types_for_method(...) from builtins.PyCapsule
score_types_for_method(rosetta.protocols.fldsgn.potentials.AACompositionEnergyCreator) -> rosetta.utility.vector1_core_scoring_ScoreType
 
Return the set of score types claimed by the EnergyMethod
 this EnergyMethodCreator creates in its create_energy_method() function

 
class SetAACompositionPotential(rosetta.protocols.moves.Mover)
    
Method resolution order:
SetAACompositionPotential
rosetta.protocols.moves.Mover
builtins.object

Methods defined here:
__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs)
Overloaded function.
 
1. __init__(handle) -> NoneType
 
2. __init__(handle, rosetta.protocols.fldsgn.potentials.SetAACompositionPotential) -> NoneType
__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.
apply(...) from builtins.PyCapsule
apply(self : rosetta.protocols.fldsgn.potentials.SetAACompositionPotential,  : rosetta.core.pose.Pose) -> NoneType
 
apply defined moves to given Pose
clone(...) from builtins.PyCapsule
clone(rosetta.protocols.fldsgn.potentials.SetAACompositionPotential) -> rosetta.protocols.moves.Mover
 
clone this object
fresh_instance(...) from builtins.PyCapsule
fresh_instance(rosetta.protocols.fldsgn.potentials.SetAACompositionPotential) -> rosetta.protocols.moves.Mover
 
create this type of object
get_name(...) from builtins.PyCapsule
get_name(rosetta.protocols.fldsgn.potentials.SetAACompositionPotential) -> str

Methods inherited from rosetta.protocols.moves.Mover:
assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.moves.Mover, other : rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
clear_info(...) from builtins.PyCapsule
clear_info(rosetta.protocols.moves.Mover) -> NoneType
 
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
 
 
 clear_info is called by jd2 before calling apply
create(...) from builtins.PyCapsule
create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
get_additional_output(...) from builtins.PyCapsule
get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
 
fpd
 
 
 Mechanism by which a mover may return multiple output poses from a single input pose.
get_current_job(...) from builtins.PyCapsule
get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
get_current_tag(...) from builtins.PyCapsule
get_current_tag(rosetta.protocols.moves.Mover) -> str
 
A tag is a unique identifier used to identify structures produced
 by this Moverget_current_tag() returns the tag, and set_current_tag( std::string tag )
 sets the tag.  This functionality is not intended for use with the 2008 job distributor.
get_input_pose(...) from builtins.PyCapsule
get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
get_last_move_status(...) from builtins.PyCapsule
get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
 
returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
get_native_pose(...) from builtins.PyCapsule
get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
get_self_ptr(...) from builtins.PyCapsule
get_self_ptr(*args, **kwargs)
Overloaded function.
 
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
 
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
get_self_weak_ptr(...) from builtins.PyCapsule
get_self_weak_ptr(*args, **kwargs)
Overloaded function.
 
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
 
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
get_type(...) from builtins.PyCapsule
get_type(rosetta.protocols.moves.Mover) -> str
info(...) from builtins.PyCapsule
info(*args, **kwargs)
Overloaded function.
 
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
 
non-const accessor
 
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
 
const accessor
last_proposal_density_ratio(...) from builtins.PyCapsule
last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
name(...) from builtins.PyCapsule
name() -> str
register_options(...) from builtins.PyCapsule
register_options(*args, **kwargs)
Overloaded function.
 
1. register_options() -> NoneType
 
Overload this static method if you access options within the mover.
 
 
 These options will end up in -help of your application if users of this mover call register_options.
 Do this recursively!
 If you use movers within your mover, call their register_options in your register_options() method.
 
2. register_options() -> NoneType
 
3. register_options() -> NoneType
 
4. register_options() -> NoneType
 
5. register_options() -> NoneType
 
6. register_options() -> NoneType
 
7. register_options() -> NoneType
 
8. register_options() -> NoneType
 
9. register_options() -> NoneType
 
Associates relevant options with the AntibodyModeler class
 
10. register_options() -> NoneType
 
Associates relevant options with the AntibodyModeler class
 
11. register_options() -> NoneType
 
Associates relevant options with the SnugDock class
 
12. register_options() -> NoneType
 
Associates relevant options with the SnugDockProtocol class
 
13. register_options() -> NoneType
 
Register the options used by this mover with the global options
 system.
 
14. register_options() -> NoneType
 
15. register_options() -> NoneType
 
Associate relevant options with the TemperedDocking class.
 
16. register_options() -> NoneType
 
17. register_options() -> NoneType
 
18. register_options() -> NoneType
 
Associates relevant options with the TemperedDocking class.
 
19. register_options() -> NoneType
 
20. register_options() -> NoneType
 
Associates relevant options with the ConstraintSetMover class
 
21. register_options() -> NoneType
 
22. register_options() -> NoneType
 
Associates relevant options with the DockingInitialPerturbation class
 
23. register_options() -> NoneType
 
Associates relevant options with the DockingProtocol class
 
24. register_options() -> NoneType
 
Associates relevant options with the TemperedDocking class
 
25. register_options() -> NoneType
 
26. register_options() -> NoneType
 
27. register_options() -> NoneType
 
28. register_options() -> NoneType
 
register options
 
29. register_options() -> NoneType
 
30. register_options() -> NoneType
 
Registers applicable options
 
31. register_options() -> NoneType
 
Register options with the option system.
 
32. register_options() -> NoneType
 
33. register_options() -> NoneType
 
34. register_options() -> NoneType
 
Associates relevant options with the LoopRefineInnerCycle class
 
35. register_options() -> NoneType
 
Associates relevant options with the LoopRefineInnerCycleContainer class
 
36. register_options() -> NoneType
 
Associates relevant options with the LoopRefineInnerCycle class
 
37. register_options() -> NoneType
 
Associates relevant options with the LoopRefineInnerCycle class
 
38. register_options() -> NoneType
 
39. register_options() -> NoneType
 
Register options with the option system.
 
40. register_options() -> NoneType
reinitialize_for_each_job(...) from builtins.PyCapsule
reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
 
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
 each use.
reinitialize_for_new_input(...) from builtins.PyCapsule
reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
 
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
 pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
 that one input pose).
reset_status(...) from builtins.PyCapsule
reset_status(rosetta.protocols.moves.Mover) -> NoneType
 
resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
set_current_job(...) from builtins.PyCapsule
set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
 
////////////////////////////end Job Distributor interface////////////////////////////////////////
set_current_tag(...) from builtins.PyCapsule
set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
set_input_pose(...) from builtins.PyCapsule
set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
 
setter for poses contained for rms
set_native_pose(...) from builtins.PyCapsule
set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
 
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
set_type(...) from builtins.PyCapsule
set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
test_move(...) from builtins.PyCapsule
test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
 
: Unit test support function.  Apply one move to a given pose.
      Allows extra test specific functions to be called before applying
type(...) from builtins.PyCapsule
type(*args, **kwargs)
Overloaded function.
 
1. type(rosetta.protocols.moves.Mover) -> str
 
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType

 
class SetAACompositionPotentialCreator(rosetta.protocols.moves.MoverCreator)
    
Method resolution order:
SetAACompositionPotentialCreator
rosetta.protocols.moves.MoverCreator
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.protocols.fldsgn.potentials.SetAACompositionPotentialCreator,  : rosetta.protocols.fldsgn.potentials.SetAACompositionPotentialCreator) -> rosetta.protocols.fldsgn.potentials.SetAACompositionPotentialCreator
create_mover(...) from builtins.PyCapsule
create_mover(rosetta.protocols.fldsgn.potentials.SetAACompositionPotentialCreator) -> rosetta.protocols.moves.Mover
keyname(...) from builtins.PyCapsule
keyname(rosetta.protocols.fldsgn.potentials.SetAACompositionPotentialCreator) -> str
mover_name(...) from builtins.PyCapsule
mover_name() -> str

 
class SetSecStructEnergies(rosetta.protocols.moves.Mover)
    
Method resolution order:
SetSecStructEnergies
rosetta.protocols.moves.Mover
builtins.object

Methods defined here:
__init__(...) from builtins.PyCapsule
__init__(*args, **kwargs)
Overloaded function.
 
1. __init__(handle) -> NoneType
 
2. __init__(handle, rosetta.core.scoring.ScoreFunction, str) -> NoneType
 
doc
 
3. __init__(self : handle, sfx : rosetta.core.scoring.ScoreFunction, filename : str, ss_from_blueprint : bool) -> NoneType
 
4. __init__(handle, rosetta.core.scoring.ScoreFunction, protocols::jd2::parser::BluePrint) -> NoneType
 
doc
 
5. __init__(self : handle, sfx : rosetta.core.scoring.ScoreFunction, blueprintOP : protocols::jd2::parser::BluePrint, ss_from_blueprint : bool) -> NoneType
 
6. __init__(handle, rosetta.protocols.fldsgn.potentials.SetSecStructEnergies) -> NoneType
__new__(*args, **kwargs) from builtins.type
Create and return a new object.  See help(type) for accurate signature.
apply(...) from builtins.PyCapsule
apply(self : rosetta.protocols.fldsgn.potentials.SetSecStructEnergies, pose : rosetta.core.pose.Pose) -> NoneType
 
apply defined moves to given Pose
clone(...) from builtins.PyCapsule
clone(rosetta.protocols.fldsgn.potentials.SetSecStructEnergies) -> rosetta.protocols.moves.Mover
 
clone this object
fresh_instance(...) from builtins.PyCapsule
fresh_instance(rosetta.protocols.fldsgn.potentials.SetSecStructEnergies) -> rosetta.protocols.moves.Mover
 
create this type of object
get_name(...) from builtins.PyCapsule
get_name(rosetta.protocols.fldsgn.potentials.SetSecStructEnergies) -> str
scorefunction(...) from builtins.PyCapsule
scorefunction(*args, **kwargs)
Overloaded function.
 
1. scorefunction(self : rosetta.protocols.fldsgn.potentials.SetSecStructEnergies, sfx : rosetta.core.scoring.ScoreFunction) -> NoneType
 
set the centroid level score function
 
2. scorefunction(self : rosetta.protocols.fldsgn.potentials.SetSecStructEnergies, sfx : rosetta.core.scoring.ScoreFunction) -> NoneType
 
set the centroid level score function
set_blueprint(...) from builtins.PyCapsule
set_blueprint(*args, **kwargs)
Overloaded function.
 
1. set_blueprint(self : rosetta.protocols.fldsgn.potentials.SetSecStructEnergies, filename : str) -> NoneType
 
set blueprint file by filename
 
2. set_blueprint(self : rosetta.protocols.fldsgn.potentials.SetSecStructEnergies, blp : protocols::jd2::parser::BluePrint) -> NoneType
 
set blueprint file
ss_from_blueprint(...) from builtins.PyCapsule
ss_from_blueprint(self : rosetta.protocols.fldsgn.potentials.SetSecStructEnergies, flag : bool) -> NoneType
 
define secondary structrue by blueprint

Methods inherited from rosetta.protocols.moves.Mover:
assign(...) from builtins.PyCapsule
assign(self : rosetta.protocols.moves.Mover, other : rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
clear_info(...) from builtins.PyCapsule
clear_info(rosetta.protocols.moves.Mover) -> NoneType
 
Strings container can be used to return miscellaneous info (as std::string) from a mover, such as notes about the results of apply(). The job distributor (Apr 09 vintage) will check this function to see if your protocol wants to add string info to the Job that ran this mover. One way this can be useful is that later, a JobOutputter may include/append this info to an output file.
 
 
 clear_info is called by jd2 before calling apply
create(...) from builtins.PyCapsule
create(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
get_additional_output(...) from builtins.PyCapsule
get_additional_output(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
 
fpd
 
 
 Mechanism by which a mover may return multiple output poses from a single input pose.
get_current_job(...) from builtins.PyCapsule
get_current_job(rosetta.protocols.moves.Mover) -> protocols::jobdist::BasicJob
get_current_tag(...) from builtins.PyCapsule
get_current_tag(rosetta.protocols.moves.Mover) -> str
 
A tag is a unique identifier used to identify structures produced
 by this Moverget_current_tag() returns the tag, and set_current_tag( std::string tag )
 sets the tag.  This functionality is not intended for use with the 2008 job distributor.
get_input_pose(...) from builtins.PyCapsule
get_input_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
get_last_move_status(...) from builtins.PyCapsule
get_last_move_status(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.MoverStatus
 
returns status after an apply().  The job distributor (august 08 vintage) will check this function to see if your protocol wants to filter its results - if your protocol wants to say "that run was no good, skip it" then use the protected last_move_status(MoverStatus) to change the value that this function will return.
get_native_pose(...) from builtins.PyCapsule
get_native_pose(rosetta.protocols.moves.Mover) -> rosetta.core.pose.Pose
get_self_ptr(...) from builtins.PyCapsule
get_self_ptr(*args, **kwargs)
Overloaded function.
 
1. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
 
2. get_self_ptr(rosetta.protocols.moves.Mover) -> rosetta.protocols.moves.Mover
get_self_weak_ptr(...) from builtins.PyCapsule
get_self_weak_ptr(*args, **kwargs)
Overloaded function.
 
1. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_const_protocols_moves_Mover_t
 
2. get_self_weak_ptr(rosetta.protocols.moves.Mover) -> rosetta.std.weak_ptr_protocols_moves_Mover_t
get_type(...) from builtins.PyCapsule
get_type(rosetta.protocols.moves.Mover) -> str
info(...) from builtins.PyCapsule
info(*args, **kwargs)
Overloaded function.
 
1. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
 
non-const accessor
 
2. info(rosetta.protocols.moves.Mover) -> rosetta.std.list_std_string_std_allocator_std_string_t
 
const accessor
last_proposal_density_ratio(...) from builtins.PyCapsule
last_proposal_density_ratio(rosetta.protocols.moves.Mover) -> float
name(...) from builtins.PyCapsule
name() -> str
register_options(...) from builtins.PyCapsule
register_options(*args, **kwargs)
Overloaded function.
 
1. register_options() -> NoneType
 
Overload this static method if you access options within the mover.
 
 
 These options will end up in -help of your application if users of this mover call register_options.
 Do this recursively!
 If you use movers within your mover, call their register_options in your register_options() method.
 
2. register_options() -> NoneType
 
3. register_options() -> NoneType
 
4. register_options() -> NoneType
 
5. register_options() -> NoneType
 
6. register_options() -> NoneType
 
7. register_options() -> NoneType
 
8. register_options() -> NoneType
 
9. register_options() -> NoneType
 
Associates relevant options with the AntibodyModeler class
 
10. register_options() -> NoneType
 
Associates relevant options with the AntibodyModeler class
 
11. register_options() -> NoneType
 
Associates relevant options with the SnugDock class
 
12. register_options() -> NoneType
 
Associates relevant options with the SnugDockProtocol class
 
13. register_options() -> NoneType
 
Register the options used by this mover with the global options
 system.
 
14. register_options() -> NoneType
 
15. register_options() -> NoneType
 
Associate relevant options with the TemperedDocking class.
 
16. register_options() -> NoneType
 
17. register_options() -> NoneType
 
18. register_options() -> NoneType
 
Associates relevant options with the TemperedDocking class.
 
19. register_options() -> NoneType
 
20. register_options() -> NoneType
 
Associates relevant options with the ConstraintSetMover class
 
21. register_options() -> NoneType
 
22. register_options() -> NoneType
 
Associates relevant options with the DockingInitialPerturbation class
 
23. register_options() -> NoneType
 
Associates relevant options with the DockingProtocol class
 
24. register_options() -> NoneType
 
Associates relevant options with the TemperedDocking class
 
25. register_options() -> NoneType
 
26. register_options() -> NoneType
 
27. register_options() -> NoneType
 
28. register_options() -> NoneType
 
register options
 
29. register_options() -> NoneType
 
30. register_options() -> NoneType
 
Registers applicable options
 
31. register_options() -> NoneType
 
Register options with the option system.
 
32. register_options() -> NoneType
 
33. register_options() -> NoneType
 
34. register_options() -> NoneType
 
Associates relevant options with the LoopRefineInnerCycle class
 
35. register_options() -> NoneType
 
Associates relevant options with the LoopRefineInnerCycleContainer class
 
36. register_options() -> NoneType
 
Associates relevant options with the LoopRefineInnerCycle class
 
37. register_options() -> NoneType
 
Associates relevant options with the LoopRefineInnerCycle class
 
38. register_options() -> NoneType
 
39. register_options() -> NoneType
 
Register options with the option system.
 
40. register_options() -> NoneType
reinitialize_for_each_job(...) from builtins.PyCapsule
reinitialize_for_each_job(rosetta.protocols.moves.Mover) -> bool
 
Inform the Job Distributor (August '08 vintage) whether this object needs to be freshly regenerated on
 each use.
reinitialize_for_new_input(...) from builtins.PyCapsule
reinitialize_for_new_input(rosetta.protocols.moves.Mover) -> bool
 
Inform the Job Distributor (August '08 vintage) whether this object needs to be regenerated when the input
 pose is about to change, (for example, if the Mover has special code on the first apply() that is only valid for
 that one input pose).
reset_status(...) from builtins.PyCapsule
reset_status(rosetta.protocols.moves.Mover) -> NoneType
 
resets status to SUCCESS, meant to be used before an apply().  The job distributor (august 08 vintage) uses this to ensure non-accumulation of status across apply()s.
set_current_job(...) from builtins.PyCapsule
set_current_job(self : rosetta.protocols.moves.Mover, job : protocols::jobdist::BasicJob) -> NoneType
 
////////////////////////////end Job Distributor interface////////////////////////////////////////
set_current_tag(...) from builtins.PyCapsule
set_current_tag(self : rosetta.protocols.moves.Mover, new_tag : str) -> NoneType
set_input_pose(...) from builtins.PyCapsule
set_input_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
 
setter for poses contained for rms
set_native_pose(...) from builtins.PyCapsule
set_native_pose(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
 
setter for native poses contained for rms ---- we should get rid of this method? it is widely used, but a bit unsafe
set_type(...) from builtins.PyCapsule
set_type(self : rosetta.protocols.moves.Mover, setting : str) -> NoneType
test_move(...) from builtins.PyCapsule
test_move(self : rosetta.protocols.moves.Mover, pose : rosetta.core.pose.Pose) -> NoneType
 
: Unit test support function.  Apply one move to a given pose.
      Allows extra test specific functions to be called before applying
type(...) from builtins.PyCapsule
type(*args, **kwargs)
Overloaded function.
 
1. type(rosetta.protocols.moves.Mover) -> str
 
2. type(self : rosetta.protocols.moves.Mover, type_in : str) -> NoneType

 
class SetSecStructEnergiesCreator(rosetta.protocols.moves.MoverCreator)
    
Method resolution order:
SetSecStructEnergiesCreator
rosetta.protocols.moves.MoverCreator
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.protocols.fldsgn.potentials.SetSecStructEnergiesCreator,  : rosetta.protocols.fldsgn.potentials.SetSecStructEnergiesCreator) -> rosetta.protocols.fldsgn.potentials.SetSecStructEnergiesCreator
create_mover(...) from builtins.PyCapsule
create_mover(rosetta.protocols.fldsgn.potentials.SetSecStructEnergiesCreator) -> rosetta.protocols.moves.Mover
keyname(...) from builtins.PyCapsule
keyname(rosetta.protocols.fldsgn.potentials.SetSecStructEnergiesCreator) -> str
mover_name(...) from builtins.PyCapsule
mover_name() -> str