Bindings for core::scoring::solid_surface namespace

Classes
		rosetta.core.scoring.Energies(builtins.object) SurfaceEnergies   class SurfaceEnergies(rosetta.core.scoring.Energies)     A derived class from class Energies for efficiently representing the interactions between a protein and a fixed surface     Method resolution order: SurfaceEnergies rosetta.core.scoring.Energies builtins.object Methods defined here: __init__(...) from builtins.PyCapsule __init__(*args, **kwargs) Overloaded function.   1. __init__(handle) -> NoneType   2. __init__(handle, rosetta.core.scoring.solid_surface.SurfaceEnergies) -> NoneType __new__(*args, **kwargs) from builtins.type Create and return a new object.  See help(type) for accurate signature. assign(...) from builtins.PyCapsule assign(*args, **kwargs) Overloaded function.   1. assign(self : rosetta.core.scoring.solid_surface.SurfaceEnergies, rhs : rosetta.core.scoring.Energies) -> rosetta.core.scoring.Energies   2. assign(self : rosetta.core.scoring.solid_surface.SurfaceEnergies,  : rosetta.core.scoring.solid_surface.SurfaceEnergies) -> rosetta.core.scoring.solid_surface.SurfaceEnergies clone(...) from builtins.PyCapsule clone(rosetta.core.scoring.solid_surface.SurfaceEnergies) -> rosetta.core.scoring.Energies reset_surface_residue_information(...) from builtins.PyCapsule reset_surface_residue_information(rosetta.core.scoring.solid_surface.SurfaceEnergies) -> NoneType   Wipe away all the information in the SurfacEnergies object describing which  residues are considered part of the surface and which residues are not part of the  surface.  (Afterwards, all residues are going to be considered part of the surface). residue_is_surface(...) from builtins.PyCapsule residue_is_surface(self : rosetta.core.scoring.solid_surface.SurfaceEnergies, seqpos : int) -> bool   Does the SurfaceEnergies object consider a particular residue to be part of the surface? same_type_as_me(...) from builtins.PyCapsule same_type_as_me(*args, **kwargs) Overloaded function.   1. same_type_as_me(self : rosetta.core.scoring.solid_surface.SurfaceEnergies, other : rosetta.core.scoring.Energies) -> bool   determine whether my type is the same as another Conformation's   2. same_type_as_me(self : rosetta.core.scoring.solid_surface.SurfaceEnergies, other : rosetta.core.scoring.Energies, recurse : bool) -> bool   determine whether my type is the same as another Conformation's set_residue_range_not_surface(...) from builtins.PyCapsule set_residue_range_not_surface(self : rosetta.core.scoring.solid_surface.SurfaceEnergies, seqpos_begin : int, seqpos_end : int) -> NoneType   Tell the SurfacEnergies that the following residues are considered not  part of the surface. set_total_residue(...) from builtins.PyCapsule set_total_residue(self : rosetta.core.scoring.solid_surface.SurfaceEnergies, total_residue : int) -> NoneType   The SurfaceEnergies object needs to know how many residues are in its pose;  it also has to be told which residues are considered part of the surface and which  residues are not part of the surface. Methods inherited from rosetta.core.scoring.Energies: __str__(...) from builtins.PyCapsule __str__(rosetta.core.scoring.Energies) -> str clear(...) from builtins.PyCapsule clear(rosetta.core.scoring.Energies) -> NoneType   kill everything (that nobody forgot about) clear_energies(...) from builtins.PyCapsule clear_energies(rosetta.core.scoring.Energies) -> NoneType   for debugging -- forget all stored energies, does not change size context_graph(...) from builtins.PyCapsule context_graph(*args, **kwargs) Overloaded function.   1. context_graph(self : rosetta.core.scoring.Energies, type : rosetta.core.scoring.ContextGraphType) -> core::scoring::ContextGraph   2. context_graph(self : rosetta.core.scoring.Energies, type : rosetta.core.scoring.ContextGraphType) -> core::scoring::ContextGraph data(...) from builtins.PyCapsule data(*args, **kwargs) Overloaded function.   1. data(rosetta.core.scoring.Energies) -> rosetta.basic.datacache.BasicDataCache   BasicDataCache indexed by enum in core/scoring/EnergiesCacheableDataType.hh   2. data(rosetta.core.scoring.Energies) -> rosetta.basic.datacache.BasicDataCache   BasicDataCache indexed by enum in core/scoring/EnergiesCacheableDataType.hh discard_conformation_domain_map(...) from builtins.PyCapsule discard_conformation_domain_map(rosetta.core.scoring.Energies) -> bool   instructs Pose whether the domain map info in the Conformation object should be discarded domain_map(...) from builtins.PyCapsule domain_map(*args, **kwargs) Overloaded function.   1. domain_map(self : rosetta.core.scoring.Energies, pos : int) -> int   Return the color assigned to a particular residue (index = pos) as held in the  domain map describing how this residue has moved with respect to the other residues in the  pose.    CAUTION new behavior: domain_map may not return 0 for residues that have undergone internal  degree of freedom changes since the last scoring.  Ask the res_moved() method for that information   2. domain_map(rosetta.core.scoring.Energies) -> ObjexxFCL::FArray1D<int>   Read access for the domain map. energies_updated(...) from builtins.PyCapsule energies_updated(rosetta.core.scoring.Energies) -> bool   Returns true if the score is up-to-date    example(s):      pose.energies().energies_updated()  See also:      Energies      Energies.residue_total_energy      Energies.residue_total_energies      Pose      ScoreFunction      ScoreFunction.show      create_score_function energy_graph(...) from builtins.PyCapsule energy_graph(*args, **kwargs) Overloaded function.   1. energy_graph(rosetta.core.scoring.Energies) -> core::scoring::EnergyGraph   Read access to the EnergyGraph.   2. energy_graph(rosetta.core.scoring.Energies) -> core::scoring::EnergyGraph   Write access to the EnergyGraph. finalized_energies(...) from builtins.PyCapsule finalized_energies(*args, **kwargs) Overloaded function.   1. finalized_energies(rosetta.core.scoring.Energies) -> rosetta.core.scoring.EMapVector   Read access to the components of the "finalized" energies;  These will include any score component calculated in the finalize  phase of score function evaluation.  These energies are copied  between Energies objects, and are not evaluated during the component-  energy update.   2. finalized_energies(rosetta.core.scoring.Energies) -> rosetta.core.scoring.EMapVector   Write access to the components of the "finalized" energies.  This access is intended only for the ScoreFunction. get_scorefxn_info(...) from builtins.PyCapsule get_scorefxn_info(rosetta.core.scoring.Energies) -> core::scoring::ScoreFunctionInfo   get scorefxn info long_range_container(...) from builtins.PyCapsule long_range_container(self : rosetta.core.scoring.Energies,  : rosetta.core.scoring.methods.LongRangeEnergyType) -> core::scoring::LREnergyContainer minimization_graph(...) from builtins.PyCapsule minimization_graph(*args, **kwargs) Overloaded function.   1. minimization_graph(rosetta.core.scoring.Energies) -> core::scoring::MinimizationGraph   2. minimization_graph(rosetta.core.scoring.Energies) -> core::scoring::MinimizationGraph nblist(...) from builtins.PyCapsule nblist(self : rosetta.core.scoring.Energies, type : rosetta.core.scoring.EnergiesCacheableDataType.Enum) -> core::scoring::NeighborList nonconst_long_range_container(...) from builtins.PyCapsule nonconst_long_range_container(self : rosetta.core.scoring.Energies,  : rosetta.core.scoring.methods.LongRangeEnergyType) -> core::scoring::LREnergyContainer onebody_energies(...) from builtins.PyCapsule onebody_energies(*args, **kwargs) Overloaded function.   1. onebody_energies(self : rosetta.core.scoring.Energies, seqpos : int) -> rosetta.core.scoring.EMapVector   Read access to the components of the one-body energies.   2. onebody_energies(self : rosetta.core.scoring.Energies, seqpos : int) -> rosetta.core.scoring.EMapVector   Write access to the components of the one-body energies.  This access is intended only for the ScoreFunction. require_context_graph(...) from builtins.PyCapsule require_context_graph(self : rosetta.core.scoring.Energies,  : rosetta.core.scoring.ContextGraphType) -> NoneType   Allows non-scorefunction components of Rosetta to impose requirements on  the context graphs that this object maintains. res_moved(...) from builtins.PyCapsule res_moved(self : rosetta.core.scoring.Energies, seqpos : int) -> bool   check if rsd has changed internal conformation, necessitating,  recomputation of 1d energies like dun,intra,prob,etc reset_nblist(...) from builtins.PyCapsule reset_nblist(rosetta.core.scoring.Energies) -> NoneType reset_res_moved(...) from builtins.PyCapsule reset_res_moved(self : rosetta.core.scoring.Energies, seqpos : int) -> NoneType residue_neighbors_updated(...) from builtins.PyCapsule residue_neighbors_updated(rosetta.core.scoring.Energies) -> bool residue_total_energies(...) from builtins.PyCapsule residue_total_energies(self : rosetta.core.scoring.Energies, seqpos : int) -> rosetta.core.scoring.EMapVector   Returns the unweighted total_energies EnergyMap for  Residue  <seqpos>     : only evaluated when requested (lazy!), inaccessible during  minimization, EnergyMap is an EMapVector    example(s):      r3 = pose.energies().residue_total_energies(3)      r3[fa_sol]  See also:      Energies      Energies.residue_total_energy      Pose      ScoreFunction      ScoreFunction.show      create_score_function      EMapVector residue_total_energy(...) from builtins.PyCapsule residue_total_energy(self : rosetta.core.scoring.Energies, seqpos : int) -> float   Returns the weighted total energy of residue  <seqpos>    example(s):      pose.energies().residue_total_energy(3)  See also:      Energies      Energies.residue_total_energies      Pose      ScoreFunction      ScoreFunction.show      create_score_function scoring(...) from builtins.PyCapsule scoring(rosetta.core.scoring.Energies) -> bool   are we in the midst of a scoring calculation? scoring_begin(...) from builtins.PyCapsule scoring_begin(self : rosetta.core.scoring.Energies, sfxn : rosetta.core.scoring.ScoreFunction, pose : rosetta.core.pose.Pose) -> NoneType   Notification of the start of a scoring calculation. scoring_end(...) from builtins.PyCapsule scoring_end(self : rosetta.core.scoring.Energies, scorefxn : rosetta.core.scoring.ScoreFunction) -> NoneType   signal from the scorefxn that scoring is over set_long_range_container(...) from builtins.PyCapsule set_long_range_container(self : rosetta.core.scoring.Energies,  : rosetta.core.scoring.methods.LongRangeEnergyType,  : core::scoring::LREnergyContainer) -> NoneType set_minimization_graph(...) from builtins.PyCapsule set_minimization_graph(self : rosetta.core.scoring.Energies,  : core::scoring::MinimizationGraph) -> NoneType set_nblist(...) from builtins.PyCapsule set_nblist(self : rosetta.core.scoring.Energies, type : rosetta.core.scoring.EnergiesCacheableDataType.Enum, nblist_in : core::scoring::NeighborList) -> NoneType set_owner(...) from builtins.PyCapsule set_owner(self : rosetta.core.scoring.Energies, owner : rosetta.core.pose.Pose) -> NoneType   Pose must claim its Energies object; this should happen once,  at the time the Pose is allocated.  Future copying of the Energies object  will not change ownership.  The purpose of ownership is to allow lazy context-graph  creation.  When context graphs are requested that have not been created, they  must be created and their edges must be updated to represent the current conformation  of the pose. set_use_nblist(...) from builtins.PyCapsule set_use_nblist(self : rosetta.core.scoring.Energies, pose : rosetta.core.pose.Pose, domain_map_in : ObjexxFCL::FArray1D<int>, use_nblist_auto_update : bool) -> NoneType show(...) from builtins.PyCapsule show(*args, **kwargs) Overloaded function.   1. show(rosetta.core.scoring.Energies) -> NoneType   2. show(self : rosetta.core.scoring.Energies, res : int) -> NoneType   Shows the energy information of residue  <seqpos>     : wrapper function of energies.show(Size) for Pyrosetta    example(s):      pose.energies().show(3)  See also:      Energies      Energies.residue_total_energies      Energies.residue_total_energy      Pose      ScoreFunction      ScoreFunction.show      create_score_function size(...) from builtins.PyCapsule size(rosetta.core.scoring.Energies) -> int   Returns the number of held residue energies    example(s):      r3 = pose.energies().residue_total_energies(3)      r3[fa_sol]  See also:      Energies      Energies.residue_total_energies      Energies.residue_total_energy      Pose      ScoreFunction      ScoreFunction.show      create_score_function structure_has_moved(...) from builtins.PyCapsule structure_has_moved(self : rosetta.core.scoring.Energies, nres : int) -> NoneType   called (eg by pose) to notify us of a change to the structure           Triggers clearing of the total energies and the twobody rsd energies         PHIL -- should also mark the neighbor links as invalid somehow...         Called by pose when someone tries to access us, if the Conformation         indicates that the structure has moved since the last score evaluation           const b/c called inside const access methods tenA_neighbor_graph(...) from builtins.PyCapsule tenA_neighbor_graph(*args, **kwargs) Overloaded function.   1. tenA_neighbor_graph(rosetta.core.scoring.Energies) -> core::scoring::TenANeighborGraph   get the graph encoding # neighbors within 10 Angstroms  If the graph has not been requested up until this point, then it will  be instantiated and filled.  If the pose has changed size since the last  score function evaluation (or if the pose has never been scored) this  function will exit.   2. tenA_neighbor_graph(rosetta.core.scoring.Energies) -> core::scoring::TenANeighborGraph   Write access to the graph encoding # neighbors within 10 Angstroms  If the graph has not been requested up until this point, then it will  be instantiated and filled.  If the pose has changed size since the last  score function evaluation (or if the pose has never been scored) this  function will exit. total_energies(...) from builtins.PyCapsule total_energies(*args, **kwargs) Overloaded function.   1. total_energies(rosetta.core.scoring.Energies) -> rosetta.core.scoring.EMapVector   Returns the total_energies EnergyMap after first computing the  component energies if they are not up-to-date   2. total_energies(rosetta.core.scoring.Energies) -> rosetta.core.scoring.EMapVector   Returns a non-const reference to the total_energies EnergyMap  so that external sources may append additional information to the Energies  object.  This is primarily useful for outputting score data with structures  when those terms are not part of the energy function.  This function will update the component energies if they are not up-to-date. total_energy(...) from builtins.PyCapsule total_energy(*args, **kwargs) Overloaded function.   1. total_energy(rosetta.core.scoring.Energies) -> float   Returns the total score    example(s):      pose.energies().total_energy()  See also:      Energies      Energies.residue_total_energy      Energies.residue_total_energies      Pose      ScoreFunction      ScoreFunction.show      create_score_function   2. total_energy(rosetta.core.scoring.Energies) -> float twelveA_neighbor_graph(...) from builtins.PyCapsule twelveA_neighbor_graph(*args, **kwargs) Overloaded function.   1. twelveA_neighbor_graph(rosetta.core.scoring.Energies) -> core::scoring::TwelveANeighborGraph   get the graph encoding # neighbors within 12 Angstroms   2. twelveA_neighbor_graph(rosetta.core.scoring.Energies) -> core::scoring::TwelveANeighborGraph update_residue_neighbors(...) from builtins.PyCapsule update_residue_neighbors(self : rosetta.core.scoring.Energies, domain_map_in : ObjexxFCL::FArray1D<int>, pose : rosetta.core.pose.Pose) -> NoneType   update the residue neighbors use_nblist(...) from builtins.PyCapsule use_nblist(rosetta.core.scoring.Energies) -> bool use_nblist_auto_update(...) from builtins.PyCapsule use_nblist_auto_update(rosetta.core.scoring.Energies) -> bool use_nblist_of_type(...) from builtins.PyCapsule use_nblist_of_type(self : rosetta.core.scoring.Energies, type : rosetta.core.scoring.EnergiesCacheableDataType.Enum) -> bool weights(...) from builtins.PyCapsule weights(*args, **kwargs) Overloaded function.   1. weights(rosetta.core.scoring.Energies) -> rosetta.core.scoring.EMapVector   Returns an EnergyMap of the ScoreFunction weights from the last  scoring    example(s):      we = pose.energies().weights()      we[fa_atr]  See also:      Energies      Energies.residue_total_energies      Energies.residue_total_energy      Pose      ScoreFunction      ScoreFunction.show      create_score_function      EMapVector   2. weights(self : rosetta.core.scoring.Energies, new_weights : rosetta.core.scoring.EMapVector) -> NoneType   Setter for the weights in this Energies object.