solid_surface¶
Bindings for core::scoring::solid_surface namespace
- class pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies¶
Bases:
Energies
A derived class from class Energies for efficiently representing the interactions between a protein and a fixed surface
- active_total_energies()¶
- assign(*args, **kwargs)¶
Overloaded function.
assign(self: pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies, rhs: pyrosetta.rosetta.core.scoring.Energies) -> pyrosetta.rosetta.core.scoring.Energies
C++: core::scoring::solid_surface::SurfaceEnergies::operator=(const class core::scoring::Energies &) –> class core::scoring::Energies &
assign(self: pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies, : pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies) -> pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies
C++: core::scoring::solid_surface::SurfaceEnergies::operator=(const class core::scoring::solid_surface::SurfaceEnergies &) –> class core::scoring::solid_surface::SurfaceEnergies &
- clear(self: pyrosetta.rosetta.core.scoring.Energies) None ¶
kill everything (that nobody forgot about)
C++: core::scoring::Energies::clear() –> void
- clear_energies(self: pyrosetta.rosetta.core.scoring.Energies) None ¶
for debugging – forget all stored energies, does not change size
C++: core::scoring::Energies::clear_energies() –> void
- clone(self: pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies) pyrosetta.rosetta.core.scoring.Energies ¶
C++: core::scoring::solid_surface::SurfaceEnergies::clone() const –> class std::shared_ptr<class core::scoring::Energies>
- context_graph(self: pyrosetta.rosetta.core.scoring.Energies, type: pyrosetta.rosetta.core.scoring.ContextGraphType) pyrosetta.rosetta.core.scoring.ContextGraph ¶
C++: core::scoring::Energies::context_graph(enum core::scoring::ContextGraphType) –> class std::shared_ptr<class core::scoring::ContextGraph>
- data(self: pyrosetta.rosetta.core.scoring.Energies) pyrosetta.rosetta.basic.datacache.BasicDataCache ¶
BasicDataCache indexed by enum in core/scoring/EnergiesCacheableDataType.hh
C++: core::scoring::Energies::data() –> class basic::datacache::BasicDataCache &
- discard_conformation_domain_map(self: pyrosetta.rosetta.core.scoring.Energies) bool ¶
instructs Pose whether the domain map info in the Conformation object should be discarded
C++: core::scoring::Energies::discard_conformation_domain_map() const –> bool
- domain_map(*args, **kwargs)¶
Overloaded function.
domain_map(self: pyrosetta.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
C++: core::scoring::Energies::domain_map(const int) const –> int
domain_map(self: pyrosetta.rosetta.core.scoring.Energies) -> pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t
Read access for the domain map.
C++: core::scoring::Energies::domain_map() const –> const class ObjexxFCL::FArray1D<int> &
- energies_updated(self: pyrosetta.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
C++: core::scoring::Energies::energies_updated() const –> bool
- energy_graph(self: pyrosetta.rosetta.core.scoring.Energies) core::scoring::EnergyGraph ¶
Write access to the EnergyGraph.
C++: core::scoring::Energies::energy_graph() –> class core::scoring::EnergyGraph &
- finalized_energies(self: pyrosetta.rosetta.core.scoring.Energies) pyrosetta.rosetta.core.scoring.EMapVector ¶
- Write access to the components of the “finalized” energies.
This access is intended only for the ScoreFunction.
C++: core::scoring::Energies::finalized_energies() –> class core::scoring::EMapVector &
- get_scorefxn_info(self: pyrosetta.rosetta.core.scoring.Energies) core::scoring::ScoreFunctionInfo ¶
get scorefxn info
C++: core::scoring::Energies::get_scorefxn_info() const –> const class core::scoring::ScoreFunctionInfo &
- long_range_container(self: pyrosetta.rosetta.core.scoring.Energies, : pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType) core::scoring::LREnergyContainer ¶
C++: core::scoring::Energies::long_range_container(enum core::scoring::methods::LongRangeEnergyType) const –> class std::shared_ptr<const class core::scoring::LREnergyContainer>
- minimization_graph(self: pyrosetta.rosetta.core.scoring.Energies) core::scoring::MinimizationGraph ¶
C++: core::scoring::Energies::minimization_graph() –> class std::shared_ptr<class core::scoring::MinimizationGraph>
- nblist(self: pyrosetta.rosetta.core.scoring.Energies, type: pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum) core::scoring::NeighborList ¶
C++: core::scoring::Energies::nblist(const enum core::scoring::EnergiesCacheableDataType::Enum &) const –> const class core::scoring::NeighborList &
- nonconst_long_range_container(self: pyrosetta.rosetta.core.scoring.Energies, : pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType) core::scoring::LREnergyContainer ¶
C++: core::scoring::Energies::nonconst_long_range_container(enum core::scoring::methods::LongRangeEnergyType) –> class std::shared_ptr<class core::scoring::LREnergyContainer>
- nonzero_weights(out=None)¶
Gets energy terms weights in the given energies object. returns:
{ score_term : score_weight }
- onebody_energies(self: pyrosetta.rosetta.core.scoring.Energies, seqpos: int) pyrosetta.rosetta.core.scoring.EMapVector ¶
- Write access to the components of the one-body energies.
This access is intended only for the ScoreFunction.
C++: core::scoring::Energies::onebody_energies(const int) –> class core::scoring::EMapVector &
- require_context_graph(self: pyrosetta.rosetta.core.scoring.Energies, : pyrosetta.rosetta.core.scoring.ContextGraphType) None ¶
- Allows non-scorefunction components of Rosetta to impose requirements on
the context graphs that this object maintains.
C++: core::scoring::Energies::require_context_graph(enum core::scoring::ContextGraphType) const –> void
- res_moved(self: pyrosetta.rosetta.core.scoring.Energies, seqpos: int) bool ¶
check if rsd has changed internal conformation, necessitating, recomputation of 1d energies like dun,intra,prob,etc
C++: core::scoring::Energies::res_moved(const int) const –> bool
- reset_nblist(self: pyrosetta.rosetta.core.scoring.Energies) None ¶
C++: core::scoring::Energies::reset_nblist() –> void
- reset_res_moved(self: pyrosetta.rosetta.core.scoring.Energies, seqpos: int) None ¶
C++: core::scoring::Energies::reset_res_moved(const int) –> void
- reset_surface_residue_information(self: pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies) None ¶
- 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).
C++: core::scoring::solid_surface::SurfaceEnergies::reset_surface_residue_information() –> void
- residue_is_surface(self: pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies, seqpos: int) bool ¶
Does the SurfaceEnergies object consider a particular residue to be part of the surface?
C++: core::scoring::solid_surface::SurfaceEnergies::residue_is_surface(unsigned long) const –> bool
- residue_neighbors_updated(self: pyrosetta.rosetta.core.scoring.Energies) bool ¶
C++: core::scoring::Energies::residue_neighbors_updated() const –> bool
- residue_onebody_energies_array(residue_selection=None, out=None)¶
Gets table of energy terms with non-zero weight on a per-residue basis. returns:
structure_array of shape n_residue, with per-score-term entries
- residue_pair_energies_array(from_residue_selection=None, to_residue_selection=None)¶
Generate pair energy table from the given energies object. returns: energy_table - 2d energy type structured array.
shape - (energies.size, energies.size) dtype - [(<type>, float)] for every nonzero weight energy type.
- residue_total_energies(self: pyrosetta.rosetta.core.scoring.Energies, seqpos: int) pyrosetta.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
C++: core::scoring::Energies::residue_total_energies(const int) const –> const class core::scoring::EMapVector &
- residue_total_energies_array(residue_selection=None, out=None)¶
Gets table of energy terms with non-zero weight on a per-residue basis. returns:
structure_array of shape n_residue, with per-score-term entries
- residue_total_energy(self: pyrosetta.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
C++: core::scoring::Energies::residue_total_energy(const int) const –> double
- same_type_as_me(*args, **kwargs)¶
Overloaded function.
same_type_as_me(self: pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies, other: pyrosetta.rosetta.core.scoring.Energies) -> bool
same_type_as_me(self: pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies, other: pyrosetta.rosetta.core.scoring.Energies, recurse: bool) -> bool
determine whether my type is the same as another Conformation’s
C++: core::scoring::solid_surface::SurfaceEnergies::same_type_as_me(const class core::scoring::Energies &, bool) const –> bool
- scoring(self: pyrosetta.rosetta.core.scoring.Energies) bool ¶
are we in the midst of a scoring calculation?
C++: core::scoring::Energies::scoring() const –> bool
- scoring_begin(self: pyrosetta.rosetta.core.scoring.Energies, sfxn: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
Notification of the start of a scoring calculation.
C++: core::scoring::Energies::scoring_begin(const class core::scoring::ScoreFunction &, const class core::pose::Pose &) –> void
- scoring_end(self: pyrosetta.rosetta.core.scoring.Energies, scorefxn: pyrosetta.rosetta.core.scoring.ScoreFunction) None ¶
signal from the scorefxn that scoring is over
C++: core::scoring::Energies::scoring_end(const class core::scoring::ScoreFunction &) –> void
- set_long_range_container(self: pyrosetta.rosetta.core.scoring.Energies, : pyrosetta.rosetta.core.scoring.methods.LongRangeEnergyType, : core::scoring::LREnergyContainer) None ¶
C++: core::scoring::Energies::set_long_range_container(enum core::scoring::methods::LongRangeEnergyType, class std::shared_ptr<class core::scoring::LREnergyContainer>) –> void
- set_minimization_graph(self: pyrosetta.rosetta.core.scoring.Energies, : core::scoring::MinimizationGraph) None ¶
C++: core::scoring::Energies::set_minimization_graph(class std::shared_ptr<class core::scoring::MinimizationGraph>) –> void
- set_nblist(self: pyrosetta.rosetta.core.scoring.Energies, type: pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum, nblist_in: core::scoring::NeighborList) None ¶
C++: core::scoring::Energies::set_nblist(const enum core::scoring::EnergiesCacheableDataType::Enum &, class std::shared_ptr<class core::scoring::NeighborList>) –> void
- set_owner(self: pyrosetta.rosetta.core.scoring.Energies, owner: pyrosetta.rosetta.core.pose.Pose) None ¶
- 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.
C++: core::scoring::Energies::set_owner(class core::pose::Pose *) –> void
- set_residue_range_not_surface(self: pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies, seqpos_begin: int, seqpos_end: int) None ¶
- Tell the SurfacEnergies that the following residues are considered not
part of the surface.
C++: core::scoring::solid_surface::SurfaceEnergies::set_residue_range_not_surface(unsigned long, unsigned long) –> void
- set_total_residue(self: pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies, total_residue: int) None ¶
- 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.
C++: core::scoring::solid_surface::SurfaceEnergies::set_total_residue(unsigned long) –> void
- set_use_nblist(self: pyrosetta.rosetta.core.scoring.Energies, pose: pyrosetta.rosetta.core.pose.Pose, domain_map_in: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, use_nblist_auto_update: bool) None ¶
C++: core::scoring::Energies::set_use_nblist(const class core::pose::Pose &, const class ObjexxFCL::FArray1D<int> &, const bool) –> void
- show(*args, **kwargs)¶
Overloaded function.
show(self: pyrosetta.rosetta.core.scoring.Energies, out: pyrosetta.rosetta.std.ostream) -> None
C++: core::scoring::Energies::show(std::ostream &) const –> void
show(self: pyrosetta.rosetta.core.scoring.Energies, out: pyrosetta.rosetta.std.ostream, res: int) -> None
C++: core::scoring::Energies::show(std::ostream &, unsigned long) const –> void
show(self: pyrosetta.rosetta.core.scoring.Energies) -> None
C++: core::scoring::Energies::show() const –> void
show(self: pyrosetta.rosetta.core.scoring.Energies, res: int) -> None
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
C++: core::scoring::Energies::show(unsigned long) const –> void
- show_total_headers(self: pyrosetta.rosetta.core.scoring.Energies, out: pyrosetta.rosetta.std.ostream) None ¶
C++: core::scoring::Energies::show_total_headers(std::ostream &) const –> void
- show_totals(self: pyrosetta.rosetta.core.scoring.Energies, out: pyrosetta.rosetta.std.ostream) None ¶
C++: core::scoring::Energies::show_totals(std::ostream &) const –> void
- size(self: pyrosetta.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
C++: core::scoring::Energies::size() const –> unsigned long
- structure_has_moved(self: pyrosetta.rosetta.core.scoring.Energies, nres: int) None ¶
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
C++: core::scoring::Energies::structure_has_moved(const unsigned long) const –> void
- tenA_neighbor_graph(self: pyrosetta.rosetta.core.scoring.Energies) pyrosetta.rosetta.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.
C++: core::scoring::Energies::tenA_neighbor_graph() –> class core::scoring::TenANeighborGraph &
- total_energies(self: pyrosetta.rosetta.core.scoring.Energies) pyrosetta.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.
C++: core::scoring::Energies::total_energies() –> class core::scoring::EMapVector &
- total_energies_array(out=None)¶
Get total structured dtype with non-zero energies.
- total_energies_weighted(self: pyrosetta.rosetta.core.scoring.Energies) pyrosetta.rosetta.core.scoring.EMapVector ¶
Returns the weighted total energies.
C++: core::scoring::Energies::total_energies_weighted() const –> class core::scoring::EMapVector
- total_energy(self: pyrosetta.rosetta.core.scoring.Energies) float ¶
C++: core::scoring::Energies::total_energy() –> double &
- twelveA_neighbor_graph(self: pyrosetta.rosetta.core.scoring.Energies) core::scoring::TwelveANeighborGraph ¶
C++: core::scoring::Energies::twelveA_neighbor_graph() –> class core::scoring::TwelveANeighborGraph &
- update_residue_neighbors(self: pyrosetta.rosetta.core.scoring.Energies, domain_map_in: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, pose: pyrosetta.rosetta.core.pose.Pose) None ¶
update the residue neighbors
C++: core::scoring::Energies::update_residue_neighbors(const class ObjexxFCL::FArray1D<int> &, const class core::pose::Pose &) –> void
- use_nblist(self: pyrosetta.rosetta.core.scoring.Energies) bool ¶
C++: core::scoring::Energies::use_nblist() const –> bool
- use_nblist_auto_update(self: pyrosetta.rosetta.core.scoring.Energies) bool ¶
C++: core::scoring::Energies::use_nblist_auto_update() const –> bool
- use_nblist_of_type(self: pyrosetta.rosetta.core.scoring.Energies, type: pyrosetta.rosetta.core.scoring.EnergiesCacheableDataType.Enum) bool ¶
C++: core::scoring::Energies::use_nblist_of_type(const enum core::scoring::EnergiesCacheableDataType::Enum &) const –> bool
- weights(*args, **kwargs)¶
Overloaded function.
weights(self: pyrosetta.rosetta.core.scoring.Energies) -> pyrosetta.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
C++: core::scoring::Energies::weights() const –> class core::scoring::EMapVector
weights(self: pyrosetta.rosetta.core.scoring.Energies, new_weights: pyrosetta.rosetta.core.scoring.EMapVector) -> None
Setter for the weights in this Energies object.
C++: core::scoring::Energies::weights(class core::scoring::EMapVector) –> void