symmetry

Bindings for core::scoring::symmetry namespace

class pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies

Bases: pyrosetta.rosetta.core.scoring.Energies

active_total_energies()
assign(*args, **kwargs)

Overloaded function.

  1. assign(self: pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies, rhs: pyrosetta.rosetta.core.scoring.Energies) -> pyrosetta.rosetta.core.scoring.Energies

C++: core::scoring::symmetry::SymmetricEnergies::operator=(const class core::scoring::Energies &) –> class core::scoring::Energies &

  1. assign(self: pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies, : pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies) -> pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies

C++: core::scoring::symmetry::SymmetricEnergies::operator=(const class core::scoring::symmetry::SymmetricEnergies &) –> class core::scoring::symmetry::SymmetricEnergies &

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.symmetry.SymmetricEnergies) pyrosetta.rosetta.core.scoring.Energies

C++: core::scoring::symmetry::SymmetricEnergies::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 &

derivative_graph(self: pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies) pyrosetta.rosetta.core.scoring.MinimizationGraph

C++: core::scoring::symmetry::SymmetricEnergies::derivative_graph() –> class std::shared_ptr<class core::scoring::MinimizationGraph>

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

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.symmetry.SymmetricEnergies, other: pyrosetta.rosetta.core.scoring.Energies) -> bool

  2. same_type_as_me(self: pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies, other: pyrosetta.rosetta.core.scoring.Energies, recurse: bool) -> bool

determine whether my type is the same as another Conformation’s

C++: core::scoring::symmetry::SymmetricEnergies::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_derivative_graph(self: pyrosetta.rosetta.core.scoring.symmetry.SymmetricEnergies, dg: pyrosetta.rosetta.core.scoring.MinimizationGraph) None

C++: core::scoring::symmetry::SymmetricEnergies::set_derivative_graph(class std::shared_ptr<class core::scoring::MinimizationGraph>) –> 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_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

class pyrosetta.rosetta.core.scoring.symmetry.SymmetricScoreFunction

Bases: pyrosetta.rosetta.core.scoring.ScoreFunction

This class is provided as a backward compatibility shim At this point it should be identical to the base ScoreFunction.

_add_weights_from_file(*args, **kwargs)

Overloaded function.

  1. _add_weights_from_file(self: pyrosetta.rosetta.core.scoring.ScoreFunction, filename: str) -> None

  2. _add_weights_from_file(self: pyrosetta.rosetta.core.scoring.ScoreFunction, filename: str, patch: bool) -> None

Initializes this ScoreFunction from the given <filename>

no lookup in database directory

C++: core::scoring::ScoreFunction::_add_weights_from_file(const std::string &, bool) –> void

_add_weights_from_stream(*args, **kwargs)

Overloaded function.

  1. _add_weights_from_stream(self: pyrosetta.rosetta.core.scoring.ScoreFunction, data: pyrosetta.rosetta.std.istream) -> None

  2. _add_weights_from_stream(self: pyrosetta.rosetta.core.scoring.ScoreFunction, data: pyrosetta.rosetta.std.istream, patch: bool) -> None

  3. _add_weights_from_stream(self: pyrosetta.rosetta.core.scoring.ScoreFunction, data: pyrosetta.rosetta.std.istream, patch: bool, filename: str) -> None

C++: core::scoring::ScoreFunction::_add_weights_from_stream(std::istream &, bool, const std::string &) –> void

add_extra_method(*args, **kwargs)

Overloaded function.

  1. add_extra_method(self: pyrosetta.rosetta.core.scoring.ScoreFunction, new_type: pyrosetta.rosetta.core.scoring.ScoreType, new_weight: float, new_method: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) -> None

Adds a scoring method that is not necessarily included in

the core library

C++: core::scoring::ScoreFunction::add_extra_method(const enum core::scoring::ScoreType &, const double, const class core::scoring::methods::EnergyMethod &) –> void

  1. add_extra_method(self: pyrosetta.rosetta.core.scoring.ScoreFunction, new_weights: pyrosetta.rosetta.std.map_core_scoring_ScoreType_double, new_method: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) -> None

Adds a scoring method that is not necessarily included in

the core library

C++: core::scoring::ScoreFunction::add_extra_method(const class std::map<enum core::scoring::ScoreType, double, struct std::less<enum core::scoring::ScoreType>, class std::allocator<struct std::pair<const enum core::scoring::ScoreType, double> > > &, const class core::scoring::methods::EnergyMethod &) –> void

add_to_weight(self: pyrosetta.rosetta.core.scoring.ScoreFunction, t: pyrosetta.rosetta.core.scoring.ScoreType, increment: float) None

Increments the weight for ScoreType <t> by <setting>

example(s):

scorefxn.add_to_weight(fa_sol,.5)

See also:

ScoreFunction ScoreFunction.get_weight ScoreFunction.set_weight ScoreType name_from_score_type score_type_from_name

C++: core::scoring::ScoreFunction::add_to_weight(const enum core::scoring::ScoreType &, const double &) –> void

add_weights_from_file(self: pyrosetta.rosetta.core.scoring.ScoreFunction, filename: str) None

Initializes this ScoreFunction from the given <filename>

C++: core::scoring::ScoreFunction::add_weights_from_file(const std::string &) –> void

all_methods(self: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.utility.vector1_std_shared_ptr_const_core_scoring_methods_EnergyMethod_t

C++: core::scoring::ScoreFunction::all_methods() const –> const class utility::vector1<class std::shared_ptr<const class core::scoring::methods::EnergyMethod>, class std::allocator<class std::shared_ptr<const class core::scoring::methods::EnergyMethod> > > &

any_lr_residue_pair_energy(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, res1: int, res2: int) bool

C++: core::scoring::ScoreFunction::any_lr_residue_pair_energy(const class core::pose::Pose &, unsigned long, unsigned long) const –> bool

apply_patch_from_file(self: pyrosetta.rosetta.core.scoring.ScoreFunction, filename: str) None

Applies a patch from the given <filename>

C++: core::scoring::ScoreFunction::apply_patch_from_file(const std::string &) –> void

are_they_neighbors(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, pos1: int, pos2: int) bool
Returns true if the <pose> positions <pos1> and <pos2>

are neighbors

C++: core::scoring::ScoreFunction::are_they_neighbors(const class core::pose::Pose &, const unsigned long, const unsigned long) const –> bool

assign(self: pyrosetta.rosetta.core.scoring.ScoreFunction, src: pyrosetta.rosetta.core.scoring.ScoreFunction) None
NOT FOR GENERAL USE

Copy the information about src into the current score function. There are deep interactions with subclasses, (the subclass information doesn’t necessarily get copied) so this is primarily for advanced scorefunction manipulation. Normal usage should just use clone() and replace the OP.

C++: core::scoring::ScoreFunction::assign(const class core::scoring::ScoreFunction &) –> void

bump_check_backbone(self: pyrosetta.rosetta.core.scoring.ScoreFunction, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
Scores the sidechain from <pose> Residue <rsd1> against the

backbone of Residue <rsd2>

C++: core::scoring::ScoreFunction::bump_check_backbone(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

bump_check_full(self: pyrosetta.rosetta.core.scoring.ScoreFunction, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::ScoreFunction::bump_check_full(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

cd_1b_types(self: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

convenience access to all cd 1b score types

C++: core::scoring::ScoreFunction::cd_1b_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

cd_2b_types(self: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

convenience access to all cd 2b score types

C++: core::scoring::ScoreFunction::cd_2b_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

cd_lr_2b_types(self: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

C++: core::scoring::ScoreFunction::cd_lr_2b_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

check_methods_in_right_order(self: pyrosetta.rosetta.core.scoring.ScoreFunction, score_type_in_first_method: pyrosetta.rosetta.core.scoring.ScoreType, score_type_in_second_method: pyrosetta.rosetta.core.scoring.ScoreType) bool

check order of methods

C++: core::scoring::ScoreFunction::check_methods_in_right_order(const enum core::scoring::ScoreType &, const enum core::scoring::ScoreType &) const –> bool

ci_1b_types(self: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

convenience access to all ci 1b score types

C++: core::scoring::ScoreFunction::ci_1b_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

ci_2b_types(self: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

convenience access to all ci 2b score types

C++: core::scoring::ScoreFunction::ci_2b_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

ci_lr_2b_types(self: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

C++: core::scoring::ScoreFunction::ci_lr_2b_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

clone(self: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.core.scoring.ScoreFunction
Create a copy of the scorefunction

Virtual to keep subclass information.

C++: core::scoring::ScoreFunction::clone() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

clone_as_base_class(self: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.core.scoring.ScoreFunction

If you want to discard subclass information, the following function is availible

C++: core::scoring::ScoreFunction::clone_as_base_class() const –> class std::shared_ptr<class core::scoring::ScoreFunction>

energy_method_options(self: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions
Returns the EnergyMethodOptions object contained in this

ScoreFunction (const access)

C++: core::scoring::ScoreFunction::energy_method_options() const –> const class core::scoring::methods::EnergyMethodOptions &

eval_cd_1b(self: pyrosetta.rosetta.core.scoring.ScoreFunction, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
Accumulates the unweighted one body energies of all context

dependent one body energies for <pose> Residue <rsd> into EnergyMap <emap>

: EnergyMap is an EMapVector

C++: core::scoring::ScoreFunction::eval_cd_1b(const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

eval_cd_2b(self: pyrosetta.rosetta.core.scoring.ScoreFunction, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
Accumulate the unweighted short range context dependent two body

interaction energies of <pose> between Residue <rsd1> and Residue <rsd2> into EnergyMap <emap>

: EnergyMap is an EMapVector

C++: core::scoring::ScoreFunction::eval_cd_2b(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

eval_cd_2b_bb_bb(self: pyrosetta.rosetta.core.scoring.ScoreFunction, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
Accumulates the unweighted short ranged context dependent two body

interaction energies of <pose> between the backbones of Residue <rsd1> and <rsd2> into EnergyMap <emap>

: EnergyMap is an EMapVector

C++: core::scoring::ScoreFunction::eval_cd_2b_bb_bb(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

eval_cd_2b_bb_sc(self: pyrosetta.rosetta.core.scoring.ScoreFunction, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
Accumulates the unweighted short ranged context dependent two body

interaction energies of <pose> between the backbone of Residue <rsd1> and the sidechain of Residue <rsd2> into EnergyMap <emap>

: EnergyMap is an EMapVector

C++: core::scoring::ScoreFunction::eval_cd_2b_bb_sc(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

eval_cd_2b_sc_sc(self: pyrosetta.rosetta.core.scoring.ScoreFunction, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
Accumulates the unweighted short ranged context dependent two body

interaction energies of <pose> between the sidechains of Residue <rsd1> and Residue <rsd2> into EnergyMap <emap>

: EnergyMap is an EMapVector

C++: core::scoring::ScoreFunction::eval_cd_2b_sc_sc(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

eval_cd_intrares_energy(self: pyrosetta.rosetta.core.scoring.ScoreFunction, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
Accumulates the unweighted intra-residue one body energies for all

context dependent two body terms that define intra-residue energies of <pose> Residue <rsd> into EnergyMap <emap>

: EnergyMap is an EMapVector

C++: core::scoring::ScoreFunction::eval_cd_intrares_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

eval_ci_1b(self: pyrosetta.rosetta.core.scoring.ScoreFunction, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: core::scoring::ScoreFunction::eval_ci_1b(const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

eval_ci_2b(self: pyrosetta.rosetta.core.scoring.ScoreFunction, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
Accumulates the unweighted context independent two body

interaction energies of <pose> between Residue <rsd1> and Residue <rsd2> into EnergyMap <emap>

: EnergyMap is an EMapVector

C++: core::scoring::ScoreFunction::eval_ci_2b(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

eval_ci_2b_bb_bb(self: pyrosetta.rosetta.core.scoring.ScoreFunction, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
Accumulates the unweighted context independent two body

interaction energies of <pose> between the backbones of Residue <rsd1> and Residue <rsd2> into EnergyMap <emap>

: EnergyMap is an EMapVector

C++: core::scoring::ScoreFunction::eval_ci_2b_bb_bb(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

eval_ci_2b_bb_sc(self: pyrosetta.rosetta.core.scoring.ScoreFunction, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
Accumulates the unweighted short range context independent two

body interaction energies of <pose> between the backbone of Residue <rsd1> and the sidechain of Residue <rsd2> into EnergyMap <emap>

: EnergyMap is an EMapVector

C++: core::scoring::ScoreFunction::eval_ci_2b_bb_sc(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

eval_ci_2b_sc_sc(self: pyrosetta.rosetta.core.scoring.ScoreFunction, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
Accumulates the unweighted short range context dependent two body

interaction energies of <pose> between the sidechains of Residue <rsd1> and Residue <rsd2> into Energymap <emap>

: EnergyMap is an EMapVector

C++: core::scoring::ScoreFunction::eval_ci_2b_sc_sc(const class core::conformation::Residue &, const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

eval_ci_intrares_energy(self: pyrosetta.rosetta.core.scoring.ScoreFunction, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
Accumulates the unweighted intra-residue one body energies for all

context independent two body terms that define intra-residue energies of <pose> Residue <rsd> into EnergyMap <emap>

: EnergyMap is an EMapVector

C++: core::scoring::ScoreFunction::eval_ci_intrares_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

eval_dof_derivative(self: pyrosetta.rosetta.core.scoring.ScoreFunction, dof_id: pyrosetta.rosetta.core.id.DOF_ID, torsion_id: core::id::TorsionID, pose: pyrosetta.rosetta.core.pose.Pose) float

C++: core::scoring::ScoreFunction::eval_dof_derivative(const class core::id::DOF_ID &, const class core::id::TorsionID &, const class core::pose::Pose &) const –> double

eval_intrares_energy(self: pyrosetta.rosetta.core.scoring.ScoreFunction, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, emap: pyrosetta.rosetta.core.scoring.EMapVector) None
Accumulates for rsd the unweighted intra-residue one body energies

for all context dependent and context independent two body terms that define intra-residue energies

: EnergyMap is an EMapVector

C++: core::scoring::ScoreFunction::eval_intrares_energy(const class core::conformation::Residue &, const class core::pose::Pose &, class core::scoring::EMapVector &) const –> void

eval_long_range_twobody_energies(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: core::scoring::ScoreFunction::eval_long_range_twobody_energies(class core::pose::Pose &) const –> void

eval_npd_atom_derivative(self: pyrosetta.rosetta.core.scoring.ScoreFunction, atom_id: pyrosetta.rosetta.core.id.AtomID, pose: pyrosetta.rosetta.core.pose.Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) None

C++: core::scoring::ScoreFunction::eval_npd_atom_derivative(const class core::id::AtomID &, const class core::pose::Pose &, const class ObjexxFCL::FArray1D<int> &, class numeric::xyzVector<double> &, class numeric::xyzVector<double> &) const –> void

eval_onebody_energies(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: core::scoring::ScoreFunction::eval_onebody_energies(class core::pose::Pose &) const –> void

eval_twobody_neighbor_energies(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: core::scoring::ScoreFunction::eval_twobody_neighbor_energies(class core::pose::Pose &) const –> void

evaluate_rotamer_background_energies(self: pyrosetta.rosetta.core.scoring.ScoreFunction, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, residue2: pyrosetta.rosetta.core.conformation.Residue, pose: pyrosetta.rosetta.core.pose.Pose, energy_vector: pyrosetta.rosetta.utility.vector1_float) None

C++: core::scoring::ScoreFunction::evaluate_rotamer_background_energies(const class core::conformation::RotamerSetBase &, const class core::conformation::Residue &, const class core::pose::Pose &, class utility::vector1<float, class std::allocator<float> > &) const –> void

evaluate_rotamer_intrares_energies(self: pyrosetta.rosetta.core.scoring.ScoreFunction, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: pyrosetta.rosetta.core.pose.Pose, energies: pyrosetta.rosetta.utility.vector1_float) None

C++: core::scoring::ScoreFunction::evaluate_rotamer_intrares_energies(const class core::conformation::RotamerSetBase &, const class core::pose::Pose &, class utility::vector1<float, class std::allocator<float> > &) const –> void

evaluate_rotamer_intrares_energy_maps(self: pyrosetta.rosetta.core.scoring.ScoreFunction, set: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: pyrosetta.rosetta.core.pose.Pose, emaps: pyrosetta.rosetta.utility.vector1_core_scoring_EMapVector) None

C++: core::scoring::ScoreFunction::evaluate_rotamer_intrares_energy_maps(const class core::conformation::RotamerSetBase &, const class core::pose::Pose &, class utility::vector1<class core::scoring::EMapVector, class std::allocator<class core::scoring::EMapVector> > &) const –> void

evaluate_rotamer_pair_energies(self: pyrosetta.rosetta.core.scoring.ScoreFunction, set1: pyrosetta.rosetta.core.conformation.RotamerSetBase, set2: pyrosetta.rosetta.core.conformation.RotamerSetBase, pose: pyrosetta.rosetta.core.pose.Pose, energy_table: pyrosetta.rosetta.ObjexxFCL.FArray2D_float_t) None

C++: core::scoring::ScoreFunction::evaluate_rotamer_pair_energies(const class core::conformation::RotamerSetBase &, const class core::conformation::RotamerSetBase &, const class core::pose::Pose &, class ObjexxFCL::FArray2D<float> &) const –> void

static extract_weights_from_file(*args, **kwargs)

Overloaded function.

  1. extract_weights_from_file(filename: str) -> pyrosetta.rosetta.core.scoring.EMapVector

  2. extract_weights_from_file(filename: str, patch: bool) -> pyrosetta.rosetta.core.scoring.EMapVector

C++: core::scoring::ScoreFunction::extract_weights_from_file(const std::string &, bool) –> class core::scoring::EMapVector

static extract_weights_from_stream(*args, **kwargs)

Overloaded function.

  1. extract_weights_from_stream(data: pyrosetta.rosetta.std.istream) -> pyrosetta.rosetta.core.scoring.EMapVector

  2. extract_weights_from_stream(data: pyrosetta.rosetta.std.istream, patch: bool) -> pyrosetta.rosetta.core.scoring.EMapVector

  3. extract_weights_from_stream(data: pyrosetta.rosetta.std.istream, patch: bool, filename: str) -> pyrosetta.rosetta.core.scoring.EMapVector

C++: core::scoring::ScoreFunction::extract_weights_from_stream(std::istream &, bool, const std::string &) –> class core::scoring::EMapVector

finalize_after_derivatives(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: core::scoring::ScoreFunction::finalize_after_derivatives(class core::pose::Pose &) const –> void

finalize_after_minimizing(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose) None

Called after minimization.

Vikram K. Mulligan (vmullig.edu).

C++: core::scoring::ScoreFunction::finalize_after_minimizing(class core::pose::Pose &) const –> void

get_name(self: pyrosetta.rosetta.core.scoring.ScoreFunction) str

C++: core::scoring::ScoreFunction::get_name() const –> std::string

get_nonzero_weighted_scoretypes(self: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType
Returns a list of the ScoreTypes which are non-zero with

their current weights

example(s):

scorefxn.get_nonzero_weighted_scoretypes()

See also:

ScoreFunction ScoreFunction.get_weight ScoreFunction.set_weight ScoreFunction.weights ScoreType create_score_function name_from_score_type score_type_from_name

C++: core::scoring::ScoreFunction::get_nonzero_weighted_scoretypes() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

get_self_ptr(self: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.core.scoring.ScoreFunction

C++: core::scoring::ScoreFunction::get_self_ptr() –> class std::shared_ptr<class core::scoring::ScoreFunction>

get_sub_score(*args, **kwargs)

Overloaded function.

  1. get_sub_score(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, residue_mask: pyrosetta.rosetta.utility.vector1_bool) -> float

Compute the score for subset of residues

C++: core::scoring::ScoreFunction::get_sub_score(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> double

  1. get_sub_score(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, residue_mask: pyrosetta.rosetta.utility.vector1_bool, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

Compute the score for subset of residues

C++: core::scoring::ScoreFunction::get_sub_score(const class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, class core::scoring::EMapVector &) const –> void

  1. get_sub_score(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, residue_mask: pyrosetta.rosetta.utility.vector1_bool) -> float

Compute the score for subset of residues

C++: core::scoring::ScoreFunction::get_sub_score(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> double

  1. get_sub_score(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, residue_mask: pyrosetta.rosetta.utility.vector1_bool, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

Compute the score for subset of residues

C++: core::scoring::ScoreFunction::get_sub_score(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, class core::scoring::EMapVector &) const –> void

get_sub_score_exclude_res(*args, **kwargs)

Overloaded function.

  1. get_sub_score_exclude_res(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, exclude_list: pyrosetta.rosetta.utility.vector1_unsigned_long) -> float

Compute the score for subset of residues

C++: core::scoring::ScoreFunction::get_sub_score_exclude_res(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> double

  1. get_sub_score_exclude_res(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, exclude_list: pyrosetta.rosetta.utility.vector1_unsigned_long, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

Compute the score for subset of residues

C++: core::scoring::ScoreFunction::get_sub_score_exclude_res(const class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class core::scoring::EMapVector &) const –> void

  1. get_sub_score_exclude_res(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, exclude_list: pyrosetta.rosetta.utility.vector1_unsigned_long) -> float

Compute the score for subset of residues

C++: core::scoring::ScoreFunction::get_sub_score_exclude_res(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &) const –> double

  1. get_sub_score_exclude_res(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, exclude_list: pyrosetta.rosetta.utility.vector1_unsigned_long, emap: pyrosetta.rosetta.core.scoring.EMapVector) -> None

Compute the score for subset of residues

C++: core::scoring::ScoreFunction::get_sub_score_exclude_res(class core::pose::Pose &, const class utility::vector1<unsigned long, class std::allocator<unsigned long> > &, class core::scoring::EMapVector &) const –> void

get_weight(self: pyrosetta.rosetta.core.scoring.ScoreFunction, t: pyrosetta.rosetta.core.scoring.ScoreType) float

Returns the weight for ScoreType <t>

examples(s):

scorefxn.get_weight(fa_sol)

See also:

ScoreFunction ScoreFunction.set_weight ScoreType create_score_function name_from_score_type score_type_from_name

C++: core::scoring::ScoreFunction::get_weight(const enum core::scoring::ScoreType &) const –> double

has_nonzero_weight(self: pyrosetta.rosetta.core.scoring.ScoreFunction, t: pyrosetta.rosetta.core.scoring.ScoreType) bool

Returns true if the ScoreType <t> has a non-zero weight

example(s):

scorefxn.has_nonzero_weight(fa_sol)

See also:

ScoreFunction ScoreFunction.get_weight ScoreFunction.has_zero_weight ScoreFunction.set_weight ScoreFunction.weights ScoreType create_score_function name_from_score_type score_type_from_name

C++: core::scoring::ScoreFunction::has_nonzero_weight(const enum core::scoring::ScoreType &) const –> bool

has_zero_weight(self: pyrosetta.rosetta.core.scoring.ScoreFunction, t: pyrosetta.rosetta.core.scoring.ScoreType) bool

Returns true if the ScoreType <t> has a weight of zero,

example(s):

scorefxn.has_zero_weight(fa_sol)

See also:

ScoreFunction ScoreFunction.get_weight ScoreFunction.has_nonzero_weight ScoreFunction.set_weight ScoreFunction.weights ScoreType create_score_function name_from_score_type score_type_from_name

C++: core::scoring::ScoreFunction::has_zero_weight(const enum core::scoring::ScoreType &) const –> bool

indicate_required_context_graphs(self: pyrosetta.rosetta.core.scoring.ScoreFunction, context_graphs_required: pyrosetta.rosetta.utility.vector1_bool) None

find which context graphs the energy methods require

C++: core::scoring::ScoreFunction::indicate_required_context_graphs(class utility::vector1<bool, class std::allocator<bool> > &) const –> void

info(self: pyrosetta.rosetta.core.scoring.ScoreFunction) core::scoring::ScoreFunctionInfo
return an object to describe abstractly the methods contained in this

ScoreFunction so that class Energies can ensure that the ScoreFunction is properly evaluated (ie, no obsolete cashed data is used )

C++: core::scoring::ScoreFunction::info() const –> class std::shared_ptr<class core::scoring::ScoreFunctionInfo>

initialize_from_file(self: pyrosetta.rosetta.core.scoring.ScoreFunction, filename: str) None

Resets everything before reading the <filename>

C++: core::scoring::ScoreFunction::initialize_from_file(const std::string &) –> void

static list_options_read(option_list: pyrosetta.rosetta.std.list_utility_keys_VariantKey_utility_options_OptionKey_t) None

C++: core::scoring::ScoreFunction::list_options_read(class std::list<class utility::keys::VariantKey<class utility::options::OptionKey>, class std::allocator<class utility::keys::VariantKey<class utility::options::OptionKey> > > &) –> void

max_atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.ScoreFunction) float
Returns the largest atomic interaction cutoff required by the

EnergyMethods

C++: core::scoring::ScoreFunction::max_atomic_interaction_cutoff() const –> double

merge(self: pyrosetta.rosetta.core.scoring.ScoreFunction, scorefxn_to_be_merged: pyrosetta.rosetta.core.scoring.ScoreFunction) None

Merges in the weights of another score function

example(s):

scorefxn.merge(scorefxn2)

See also:

ScoreFunction ScoreFunction.weights Energies create_score_function

C++: core::scoring::ScoreFunction::merge(const class core::scoring::ScoreFunction &) –> void

name(self: pyrosetta.rosetta.core.scoring.ScoreFunction, weights_tag: str) None
Accumulates the unweighted one body energies of all context

independent one body energies for <pose> Residue <rsd> into EnergyMap <emap>

: EnergyMap is an EMapVector

C++: core::scoring::ScoreFunction::name(const std::string &) –> void

perturb_weights(self: pyrosetta.rosetta.core.scoring.ScoreFunction) None

Randomly perturbs non-zero score function weights

C++: core::scoring::ScoreFunction::perturb_weights() –> void

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, set: pyrosetta.rosetta.core.conformation.RotamerSetBase) None
Lets the scoring functions cache anything they need to rapidly

calculate rotamer pair energies used in packing (like a trie, e.g.)

C++: core::scoring::ScoreFunction::prepare_rotamers_for_packing(const class core::pose::Pose &, class core::conformation::RotamerSetBase &) const –> void

provide_citation_info(self: pyrosetta.rosetta.core.scoring.ScoreFunction, citations: pyrosetta.rosetta.basic.citation_manager.CitationCollectionList) None
Provide citations to the passed CitationCollectionList

This allows the scorefunciton to provide citaitons for itself itself and for any modules that it invokes (particularl energy methods).

The default implementation of this provides a vector of citations from all energy methods that

C++: core::scoring::ScoreFunction::provide_citation_info(class basic::citation_manager::CitationCollectionList &) const –> void

ready_for_nonideal_scoring(self: pyrosetta.rosetta.core.scoring.ScoreFunction) bool

C++: core::scoring::ScoreFunction::ready_for_nonideal_scoring() const –> bool

reinitialize_minnode_for_residue(self: pyrosetta.rosetta.core.scoring.ScoreFunction, min_node: core::scoring::MinimizationNode, rsd: pyrosetta.rosetta.core.conformation.Residue, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, min_map: core::kinematics::MinimizerMapBase, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: core::scoring::ScoreFunction::reinitialize_minnode_for_residue(class core::scoring::MinimizationNode &, const class core::conformation::Residue &, class basic::datacache::BasicDataCache &, const class core::kinematics::MinimizerMapBase &, class core::pose::Pose &) const –> void

reset(*args, **kwargs)

Overloaded function.

  1. reset(self: pyrosetta.rosetta.core.scoring.ScoreFunction) -> None

Resets the ScoreFunction to default values, reading from the global options collection

C++: core::scoring::ScoreFunction::reset() –> void

  1. reset(self: pyrosetta.rosetta.core.scoring.ScoreFunction, options: pyrosetta.rosetta.utility.options.OptionCollection) -> None

Resets the ScoreFunction to default values, reading from a (possibly local) options collection

C++: core::scoring::ScoreFunction::reset(const class utility::options::OptionCollection &) –> void

reset_energy_methods(self: pyrosetta.rosetta.core.scoring.ScoreFunction) None

C++: core::scoring::ScoreFunction::reset_energy_methods() –> void

score(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose) float
Scores the given <pose> using this ScoreFunction. Alters the

Energies object within <pose>, but does not alter this ScoreFunction

: Synonym for () operator. Makes code look a little nicer. Doesn’t

do anything but call () operator.

C++: core::scoring::ScoreFunction::score(class core::pose::Pose &) const –> double

score_by_scoretype(*args, **kwargs)

Overloaded function.

  1. score_by_scoretype(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, t: pyrosetta.rosetta.core.scoring.ScoreType) -> float

  2. score_by_scoretype(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, t: pyrosetta.rosetta.core.scoring.ScoreType, weighted: bool) -> float

Returns the score of the ScoreType <t>

C++: core::scoring::ScoreFunction::score_by_scoretype(class core::pose::Pose &, const enum core::scoring::ScoreType, const bool) const –> double

score_types_by_method_type(self: pyrosetta.rosetta.core.scoring.ScoreFunction, t: pyrosetta.rosetta.core.scoring.methods.EnergyMethodType) pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

C++: core::scoring::ScoreFunction::score_types_by_method_type(const enum core::scoring::methods::EnergyMethodType &) const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &

serialize_weights(self: pyrosetta.rosetta.core.scoring.ScoreFunction) str
Serializes the non-zero score function term weights

Format: { term : weight, … }

C++: core::scoring::ScoreFunction::serialize_weights() const –> std::string

set_energy_method_options(self: pyrosetta.rosetta.core.scoring.ScoreFunction, energy_method_options_in: pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) None
Sets the EnergyMethodOptions object contained in this ScoreFunction.

with appropriate update of all the energy methods.

C++: core::scoring::ScoreFunction::set_energy_method_options(const class core::scoring::methods::EnergyMethodOptions &) –> void

set_etable(self: pyrosetta.rosetta.core.scoring.ScoreFunction, etable_name: str) None
Given a <filename> (represented by a std::string), set the

e_table for this ScoreFunction.

C++: core::scoring::ScoreFunction::set_etable(const std::string &) –> void

set_method_weights(self: pyrosetta.rosetta.core.scoring.ScoreFunction, t: pyrosetta.rosetta.core.scoring.ScoreType, wts: pyrosetta.rosetta.utility.vector1_double) None

C++: core::scoring::ScoreFunction::set_method_weights(const enum core::scoring::ScoreType &, const class utility::vector1<double, class std::allocator<double> > &) –> void

set_weight(self: pyrosetta.rosetta.core.scoring.ScoreFunction, t: pyrosetta.rosetta.core.scoring.ScoreType, setting: float) None

Sets the weight for ScoreType <t> to <setting>

example(s):

scorefxn.set_weight(fa_sol,.5)

See also:

ScoreFunction ScoreFunction.get_weight ScoreFunction.weights ScoreType create_score_function name_from_score_type score_type_from_name

C++: core::scoring::ScoreFunction::set_weight(const enum core::scoring::ScoreType &, const double) –> void

set_weight_if_zero(self: pyrosetta.rosetta.core.scoring.ScoreFunction, t: pyrosetta.rosetta.core.scoring.ScoreType, setting: float) None

Sets the weight for ScoreType <t> to <setting> if weight is originally zero

example(s):

scorefxn.set_weight_if_zero(fa_sol,.5)

See also:

ScoreFunction ScoreFunction.get_weight ScoreFunction.set_weight ScoreType create_score_function name_from_score_type score_type_from_name

C++: core::scoring::ScoreFunction::set_weight_if_zero(const enum core::scoring::ScoreType &, const double) –> void

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: core::scoring::ScoreFunction::setup_for_derivatives(class core::pose::Pose &) const –> void

setup_for_lr2benmeth_minimization_for_respair(*args, **kwargs)

Overloaded function.

  1. setup_for_lr2benmeth_minimization_for_respair(self: pyrosetta.rosetta.core.scoring.ScoreFunction, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, lr2benergy: pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy, g: core::scoring::MinimizationGraph, min_map: core::kinematics::MinimizerMapBase, p: pyrosetta.rosetta.core.pose.Pose, res_moving_wrt_eachother: bool, accumulate_fixed_energies: bool, rni: core::scoring::ResidueNeighborConstIterator, fixed_energies: pyrosetta.rosetta.core.scoring.EMapVector) -> None

  2. setup_for_lr2benmeth_minimization_for_respair(self: pyrosetta.rosetta.core.scoring.ScoreFunction, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, lr2benergy: pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy, g: core::scoring::MinimizationGraph, min_map: core::kinematics::MinimizerMapBase, p: pyrosetta.rosetta.core.pose.Pose, res_moving_wrt_eachother: bool, accumulate_fixed_energies: bool, rni: core::scoring::ResidueNeighborConstIterator, fixed_energies: pyrosetta.rosetta.core.scoring.EMapVector, edge_weight: float) -> None

  3. setup_for_lr2benmeth_minimization_for_respair(self: pyrosetta.rosetta.core.scoring.ScoreFunction, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, lr2benergy: pyrosetta.rosetta.core.scoring.methods.LongRangeTwoBodyEnergy, g: core::scoring::MinimizationGraph, min_map: core::kinematics::MinimizerMapBase, p: pyrosetta.rosetta.core.pose.Pose, res_moving_wrt_eachother: bool, accumulate_fixed_energies: bool, rni: core::scoring::ResidueNeighborConstIterator, fixed_energies: pyrosetta.rosetta.core.scoring.EMapVector, edge_weight: float, edge_dweight: float) -> None

Initialize an edge in the MinimizationGraph with a particular long-range two body

C++: core::scoring::ScoreFunction::setup_for_lr2benmeth_minimization_for_respair(const class core::conformation::Residue &, const class core::conformation::Residue &, class std::shared_ptr<const class core::scoring::methods::LongRangeTwoBodyEnergy>, class core::scoring::MinimizationGraph &, const class core::kinematics::MinimizerMapBase &, class core::pose::Pose &, const bool, bool, class std::shared_ptr<class core::scoring::ResidueNeighborConstIterator>, class core::scoring::EMapVector &, const double, const double) const –> void

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, min_map: core::kinematics::MinimizerMapBase) None
Initializes a MinimizationGraph and caches it in

Energies object of <pose>

: for use during minimization

C++: core::scoring::ScoreFunction::setup_for_minimizing(class core::pose::Pose &, const class core::kinematics::MinimizerMapBase &) const –> void

setup_for_minimizing_for_node(self: pyrosetta.rosetta.core.scoring.ScoreFunction, min_node: core::scoring::MinimizationNode, rsd: pyrosetta.rosetta.core.conformation.Residue, res_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache, min_map: core::kinematics::MinimizerMapBase, pose: pyrosetta.rosetta.core.pose.Pose, accumulate_fixed_energies: bool, fixed_energies: pyrosetta.rosetta.core.scoring.EMapVector) None
Initialize a single node of a MinimizationGraph with the one-body and two-body

energy methods that are held within this ScoreFunction object.

C++: core::scoring::ScoreFunction::setup_for_minimizing_for_node(class core::scoring::MinimizationNode &, const class core::conformation::Residue &, class basic::datacache::BasicDataCache &, const class core::kinematics::MinimizerMapBase &, class core::pose::Pose &, bool, class core::scoring::EMapVector &) const –> void

setup_for_minimizing_sr2b_enmeths_for_minedge(*args, **kwargs)

Overloaded function.

  1. setup_for_minimizing_sr2b_enmeths_for_minedge(self: pyrosetta.rosetta.core.scoring.ScoreFunction, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, min_edge: core::scoring::MinimizationEdge, min_map: core::kinematics::MinimizerMapBase, pose: pyrosetta.rosetta.core.pose.Pose, res_moving_wrt_eachother: bool, accumulate_fixed_energies: bool, energy_edge: core::scoring::EnergyEdge, fixed_energies: pyrosetta.rosetta.core.scoring.EMapVector) -> None

  2. setup_for_minimizing_sr2b_enmeths_for_minedge(self: pyrosetta.rosetta.core.scoring.ScoreFunction, res1: pyrosetta.rosetta.core.conformation.Residue, res2: pyrosetta.rosetta.core.conformation.Residue, min_edge: core::scoring::MinimizationEdge, min_map: core::kinematics::MinimizerMapBase, pose: pyrosetta.rosetta.core.pose.Pose, res_moving_wrt_eachother: bool, accumulate_fixed_energies: bool, energy_edge: core::scoring::EnergyEdge, fixed_energies: pyrosetta.rosetta.core.scoring.EMapVector, edge_weight: float) -> None

Initialize a single MinimizationEdge for a particular part of residues, storing

sr2b energy method pointers on the edge for those sr2b energy methods in this ScoreFunction

C++: core::scoring::ScoreFunction::setup_for_minimizing_sr2b_enmeths_for_minedge(const class core::conformation::Residue &, const class core::conformation::Residue &, class core::scoring::MinimizationEdge &, const class core::kinematics::MinimizerMapBase &, class core::pose::Pose &, const bool, bool, const class core::scoring::EnergyEdge *, class core::scoring::EMapVector &, const double) const –> void

setup_for_packing(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, residues_repacking: pyrosetta.rosetta.utility.vector1_bool, residues_designing: pyrosetta.rosetta.utility.vector1_bool) None
Lets the scoring functions cache anything they need to calculate

energies in a packing step (rotamer_trials or pack_rotamers)

: the Etable caches tries for each of the residues, the

hydrogen bond function caches backbone/backbone hydrogen bonds

C++: core::scoring::ScoreFunction::setup_for_packing(class core::pose::Pose &, const class utility::vector1<bool, class std::allocator<bool> > &, const class utility::vector1<bool, class std::allocator<bool> > &) const –> void

setup_for_packing_with_rotsets(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, rotsets: core::pack_basic::RotamerSetsBase) None
Lets the scoring functions cache anything they need to calculate

energies in a packing step (pack_rotamers) in the context of all available rotamers

The exact order of events when setting up for packing are as follows:
  1. setup_for_packing() is called for all energy methods

  2. rotamers are built

  3. setup_for_packing_with_rotsets() is called for all energy methods

  4. prepare_rotamers_for_packing() is called for all energy methods

  5. The energy methods are asked to score all rotamers and rotamer pairs

  6. Annealing begins

The pose is specifically non-const here so that energy methods can store data in it

: Used in ApproximateBuriedUnsatPenalty to pre-compute compatible rotamers

C++: core::scoring::ScoreFunction::setup_for_packing_with_rotsets(class core::pose::Pose &, const class std::shared_ptr<class core::pack_basic::RotamerSetsBase> &) const –> void

setup_for_scoring(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose) None
For external scorers: Let the energy methods prepare for

evaluating their scores on a particular structure

: invoked during scoring.

C++: core::scoring::ScoreFunction::setup_for_scoring(class core::pose::Pose &) const –> void

show(*args, **kwargs)

Overloaded function.

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

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

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

Scores <pose> and shows the raw and weighted scores for each

non-zero ScoreType

example(s):

scorefxn.show(pose)

See also:

ScoreFunction ScoreFunction.weights Energies create_score_function

C++: core::scoring::ScoreFunction::show(std::ostream &, class core::pose::Pose &) const –> void

  1. show(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose) -> None

Scores <pose> and shows the raw and weighted scores for each

non-zero ScoreType

: this function is mostly for convenience in PyRosetta

example(s):

scorefxn.show(pose)

See also:

ScoreFunction ScoreFunction.weights Energies create_score_function

C++: core::scoring::ScoreFunction::show(class core::pose::Pose &) const –> void

show_additional(*args, **kwargs)

Overloaded function.

  1. show_additional(self: pyrosetta.rosetta.core.scoring.ScoreFunction, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) -> None

  2. show_additional(self: pyrosetta.rosetta.core.scoring.ScoreFunction, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose, verbose: bool) -> None

C++: core::scoring::ScoreFunction::show_additional(std::ostream &, class core::pose::Pose &, bool) const –> void

show_line(self: pyrosetta.rosetta.core.scoring.ScoreFunction, out: pyrosetta.rosetta.std.ostream, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: core::scoring::ScoreFunction::show_line(std::ostream &, const class core::pose::Pose &) const –> void

show_line_headers(self: pyrosetta.rosetta.core.scoring.ScoreFunction, out: pyrosetta.rosetta.std.ostream) None

C++: core::scoring::ScoreFunction::show_line_headers(std::ostream &) const –> void

show_pretty(self: pyrosetta.rosetta.core.scoring.ScoreFunction, out: pyrosetta.rosetta.std.ostream) None

similar output as show( ostream, pose ) but without the pose

C++: core::scoring::ScoreFunction::show_pretty(std::ostream &) const –> void

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.ScoreFunction, pose: pyrosetta.rosetta.core.pose.Pose, resid: int) None
If inside packing, the pose changes conformation, inform the

scoring functions that any data they have cached in the Energies object is out of date. In particular, this is to update the trie(s) during rotamer trials.

C++: core::scoring::ScoreFunction::update_residue_for_packing(class core::pose::Pose &, unsigned long) const –> void

weighted_sum(self: pyrosetta.rosetta.core.scoring.ScoreFunction, unweighted: pyrosetta.rosetta.core.scoring.EMapVector) float

Returns the weighted sum of the given energy map, given the current set of weights

example(s):

scorefxn.weighted_sum(scores_emap)

See also:

ScoreFunction ScoreFunction.get_weight ScoreFunction.set_weight ScoreFunction.weights

C++: core::scoring::ScoreFunction::weighted_sum(const class core::scoring::EMapVector &) const –> double

weights(self: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.core.scoring.EMapVector

Returns an EnergyMap of the current set of weights

example(s):

scorefxn.weights()

See also:

ScoreFunction ScoreFunction.get_weight ScoreFunction.set_weight ScoreFunction.weights ScoreType create_score_function name_from_score_type score_type_from_name

C++: core::scoring::ScoreFunction::weights() const –> const class core::scoring::EMapVector &

whole_structure_types(self: pyrosetta.rosetta.core.scoring.ScoreFunction) pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

C++: core::scoring::ScoreFunction::whole_structure_types() const –> const class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> > &