solid_surface

Bindings for core::scoring::solid_surface namespace

class pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies

Bases: pyrosetta.rosetta.core.scoring.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.

  1. 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 &

  1. 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.

  1. 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

  1. 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.

  1. same_type_as_me(self: pyrosetta.rosetta.core.scoring.solid_surface.SurfaceEnergies, other: pyrosetta.rosetta.core.scoring.Energies) -> bool

  2. 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.

  1. show(self: pyrosetta.rosetta.core.scoring.Energies, out: pyrosetta.rosetta.std.ostream) -> None

C++: core::scoring::Energies::show(std::ostream &) const –> void

  1. 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

  1. show(self: pyrosetta.rosetta.core.scoring.Energies) -> None

C++: core::scoring::Energies::show() const –> void

  1. 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.

  1. 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

  1. 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