scoring

Bindings for protocols::scoring namespace

class pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck, : pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck) pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck

C++: protocols::scoring::ImplicitFastClashCheck::operator=(const class protocols::scoring::ImplicitFastClashCheck &) –> class protocols::scoring::ImplicitFastClashCheck &

clash_check(*args, **kwargs)

Overloaded function.

  1. clash_check(self: pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck, pp: pyrosetta.rosetta.numeric.xyzVector_double_t) -> bool

C++: protocols::scoring::ImplicitFastClashCheck::clash_check(const class numeric::xyzVector<double> &) const –> bool

  1. clash_check(self: pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck, pp: pyrosetta.rosetta.numeric.xyzVector_double_t, resno: int) -> bool

C++: protocols::scoring::ImplicitFastClashCheck::clash_check(const class numeric::xyzVector<double> &, unsigned long) const –> bool

clash_check_test(self: pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck, pp: pyrosetta.rosetta.numeric.xyzVector_double_t) bool

C++: protocols::scoring::ImplicitFastClashCheck::clash_check_test(const class numeric::xyzVector<double> &) const –> bool

clash_check_trimer(self: pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck, pose: pyrosetta.rosetta.core.pose.Pose, refrsd: int) bool

C++: protocols::scoring::ImplicitFastClashCheck::clash_check_trimer(const class core::pose::Pose &, unsigned long) const –> bool

clash_count(self: pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck, pp: pyrosetta.rosetta.numeric.xyzVector_double_t) int

C++: protocols::scoring::ImplicitFastClashCheck::clash_count(const class numeric::xyzVector<double> &) const –> unsigned long

dump_debug_pdb(*args, **kwargs)

Overloaded function.

  1. dump_debug_pdb(self: pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck, out: pyrosetta.rosetta.utility.io.ozstream, stub: pyrosetta.rosetta.core.kinematics.Stub) -> None

  2. dump_debug_pdb(self: pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck, out: pyrosetta.rosetta.utility.io.ozstream, stub: pyrosetta.rosetta.core.kinematics.Stub, chain: str) -> None

C++: protocols::scoring::ImplicitFastClashCheck::dump_debug_pdb(class utility::io::ozstream &, const class core::kinematics::Stub &, char) const –> void

  1. dump_debug_pdb(self: pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck, fname: str, stub: pyrosetta.rosetta.core.kinematics.Stub) -> None

  2. dump_debug_pdb(self: pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck, fname: str, stub: pyrosetta.rosetta.core.kinematics.Stub, chain: str) -> None

C++: protocols::scoring::ImplicitFastClashCheck::dump_debug_pdb(const std::string &, const class core::kinematics::Stub &, char) const –> void

init_clash_check(self: pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck, poses: pyrosetta.rosetta.utility.vector1_core_pose_Pose, neighbor_cutoff: float, ignore: pyrosetta.rosetta.utility.vector1_unsigned_long) None

C++: protocols::scoring::ImplicitFastClashCheck::init_clash_check(const class utility::vector1<class core::pose::Pose, class std::allocator<class core::pose::Pose> > &, double, class utility::vector1<unsigned long, class std::allocator<unsigned long> >) –> void

size(self: pyrosetta.rosetta.protocols.scoring.ImplicitFastClashCheck) int

C++: protocols::scoring::ImplicitFastClashCheck::size() –> unsigned long

class pyrosetta.rosetta.protocols.scoring.InterchainPotential

Bases: pyrosetta.rosetta.utility.SingletonBase_protocols_scoring_InterchainPotential_t

Singleton class to hold the interface-derived statistics for residue-pair scores at protein/protein interfaces.

This previously derived from the EnvPairPotential, which is in no way necessary because the two classes have nothing in common; rather, the InterchainPairEnergy and InterchainEnvEnergy classes can hold a pointer to both the InterchainPotential and the EnvPairPotential.

compute_interface(self: pyrosetta.rosetta.protocols.scoring.InterchainPotential, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::scoring::InterchainPotential::compute_interface(class core::pose::Pose &) const –> void

evaluate_contact_score(self: pyrosetta.rosetta.protocols.scoring.InterchainPotential, pose: pyrosetta.rosetta.core.pose.Pose, contact_score: float) None

C++: protocols::scoring::InterchainPotential::evaluate_contact_score(const class core::pose::Pose &, double &) const –> void

evaluate_env_score(self: pyrosetta.rosetta.protocols.scoring.InterchainPotential, pose: pyrosetta.rosetta.core.pose.Pose, rsd: pyrosetta.rosetta.core.conformation.Residue, env_score: float) None

C++: protocols::scoring::InterchainPotential::evaluate_env_score(const class core::pose::Pose &, const class core::conformation::Residue &, double &) const –> void

evaluate_pair_and_vdw_score(self: pyrosetta.rosetta.protocols.scoring.InterchainPotential, pose: pyrosetta.rosetta.core.pose.Pose, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue, pair_score: float, vdw_score: float) None

C++: protocols::scoring::InterchainPotential::evaluate_pair_and_vdw_score(const class core::pose::Pose &, const class core::conformation::Residue &, const class core::conformation::Residue &, double &, double &) const –> void

finalize(self: pyrosetta.rosetta.protocols.scoring.InterchainPotential, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::scoring::InterchainPotential::finalize(class core::pose::Pose &) const –> void

static get_instance() protocols::scoring::InterchainPotential

C++: utility::SingletonBase<protocols::scoring::InterchainPotential>::get_instance() –> class protocols::scoring::InterchainPotential *

interface_from_pose(self: pyrosetta.rosetta.protocols.scoring.InterchainPotential, : pyrosetta.rosetta.core.pose.Pose) protocols::scoring::InterfaceInfo

C++: protocols::scoring::InterchainPotential::interface_from_pose(const class core::pose::Pose &) const –> const class protocols::scoring::InterfaceInfo &

nonconst_interface_from_pose(self: pyrosetta.rosetta.protocols.scoring.InterchainPotential, : pyrosetta.rosetta.core.pose.Pose) protocols::scoring::InterfaceInfo

C++: protocols::scoring::InterchainPotential::nonconst_interface_from_pose(class core::pose::Pose &) const –> class protocols::scoring::InterfaceInfo &

class pyrosetta.rosetta.protocols.scoring.Interface

Bases: pybind11_builtins.pybind11_object

assign(self: pyrosetta.rosetta.protocols.scoring.Interface, : pyrosetta.rosetta.protocols.scoring.Interface) pyrosetta.rosetta.protocols.scoring.Interface

C++: protocols::scoring::Interface::operator=(const class protocols::scoring::Interface &) –> class protocols::scoring::Interface &

calculate(self: pyrosetta.rosetta.protocols.scoring.Interface, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::scoring::Interface::calculate(const class core::pose::Pose &) –> void

center(self: pyrosetta.rosetta.protocols.scoring.Interface, pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.numeric.xyzVector_double_t

C++: protocols::scoring::Interface::center(const class core::pose::Pose &) –> class numeric::xyzVector<double>

closest_interface_residue(self: pyrosetta.rosetta.protocols.scoring.Interface, pose: pyrosetta.rosetta.core.pose.Pose, src_rsd: int, distance: float) int

C++: protocols::scoring::Interface::closest_interface_residue(const class core::pose::Pose &, unsigned long, double &) –> unsigned long

contact_list(self: pyrosetta.rosetta.protocols.scoring.Interface) pyrosetta.rosetta.utility.vector1_utility_vector1_unsigned_long_std_allocator_unsigned_long_t
The contact_list is pose.size() long, each element

(contact_list_[i]) contains a list of residues from the other partner that interacts with residue i. This is calculated in protein_calculate, and used by Interface.is_pair() function as well as the interchain_vdw, interchain_env, and interchain_pair scoring components.

C++: protocols::scoring::Interface::contact_list() –> class utility::vector1<class utility::vector1<unsigned long, class std::allocator<unsigned long> >, class std::allocator<class utility::vector1<unsigned long, class std::allocator<unsigned long> > > >

distance(self: pyrosetta.rosetta.protocols.scoring.Interface, distance_in: float) None

C++: protocols::scoring::Interface::distance(const double) –> void

interface_nres(self: pyrosetta.rosetta.protocols.scoring.Interface) int
returns the total number of residues on both sides of the interface for

a given jump

C++: protocols::scoring::Interface::interface_nres() –> unsigned long

is_interface(*args, **kwargs)

Overloaded function.

  1. is_interface(self: pyrosetta.rosetta.protocols.scoring.Interface, rsd: pyrosetta.rosetta.core.conformation.Residue) -> bool

C++: protocols::scoring::Interface::is_interface(const class core::conformation::Residue &) const –> bool

  1. is_interface(self: pyrosetta.rosetta.protocols.scoring.Interface, position: int) -> bool

C++: protocols::scoring::Interface::is_interface(const unsigned long) const –> bool

is_pair(self: pyrosetta.rosetta.protocols.scoring.Interface, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) bool
returns whether the rsd1 and rsd2 are considered a contact pair

based on contact_list_ array

C++: protocols::scoring::Interface::is_pair(const class core::conformation::Residue &, const class core::conformation::Residue &) –> bool

jump(self: pyrosetta.rosetta.protocols.scoring.Interface, jump_number: int) None

C++: protocols::scoring::Interface::jump(const unsigned long) –> void

jump_id(self: pyrosetta.rosetta.protocols.scoring.Interface) int

C++: protocols::scoring::Interface::jump_id() const –> unsigned long

pair_list(self: pyrosetta.rosetta.protocols.scoring.Interface) pyrosetta.rosetta.utility.vector1_utility_vector1_int_std_allocator_int_t

Get two lists containing the residues on each side of the interface

You might expect something called pair_list() to output pairs or somehow relate to the is_pair function, but it does not. It returns a two element list.

  • The first element is a list of all residues on the lower partner of the interface.

  • The second element is a list of all the residues in the interface on the upper partner.

Both lists are sorted by residue number, so the indices of one list have no relationship to the other list.

rename this to something more logical & give it a better return type

make a function that returns a vector1<pair<core::Size,Size> > containing all interacting pairs. This would be easy to implement.

C++: protocols::scoring::Interface::pair_list() –> class utility::vector1<class utility::vector1<int, class std::allocator<int> >, class std::allocator<class utility::vector1<int, class std::allocator<int> > > >

print(self: pyrosetta.rosetta.protocols.scoring.Interface, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::scoring::Interface::print(const class core::pose::Pose &) –> void

set_pack(self: pyrosetta.rosetta.protocols.scoring.Interface, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) None

C++: protocols::scoring::Interface::set_pack(const class core::pose::Pose &, class std::shared_ptr<class core::pack::task::PackerTask>) –> void

set_symmetric_pack(self: pyrosetta.rosetta.protocols.scoring.Interface, pose: pyrosetta.rosetta.core.pose.Pose, task: pyrosetta.rosetta.core.pack.task.PackerTask) None

C++: protocols::scoring::Interface::set_symmetric_pack(const class core::pose::Pose &, class std::shared_ptr<class core::pack::task::PackerTask>) –> void

show(*args, **kwargs)

Overloaded function.

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

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

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

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

class pyrosetta.rosetta.protocols.scoring.InterfaceInfo

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

Keep track of the interface information

add_jump(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, jump_in: int) None

Adds another jump to the interface calculation, for example for multi-body docking

C++: protocols::scoring::InterfaceInfo::add_jump(unsigned long) –> void

assign(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, : pyrosetta.rosetta.protocols.scoring.InterfaceInfo) pyrosetta.rosetta.protocols.scoring.InterfaceInfo

C++: protocols::scoring::InterfaceInfo::operator=(const class protocols::scoring::InterfaceInfo &) –> class protocols::scoring::InterfaceInfo &

calculate(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, pose: pyrosetta.rosetta.core.pose.Pose) None

Calculates the interface for all jumps specified in rb_jump_

C++: protocols::scoring::InterfaceInfo::calculate(const class core::pose::Pose &) –> void

calculated(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo) bool

Returns if interface calculation is up to date

C++: protocols::scoring::InterfaceInfo::calculated() –> bool &

clear_jumps(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo) None

Removes all jumps from the interface calculation

C++: protocols::scoring::InterfaceInfo::clear_jumps() –> void

clone(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo) pyrosetta.rosetta.basic.datacache.CacheableData

C++: protocols::scoring::InterfaceInfo::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

closest_interface_residue(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, pose: pyrosetta.rosetta.core.pose.Pose, src_rsd: int, distance: float) int

C++: protocols::scoring::InterfaceInfo::closest_interface_residue(const class core::pose::Pose &, unsigned long, double &) const –> unsigned long

distance(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, distance_in: float) None

Sets the distance cutoff for interface calculations

C++: protocols::scoring::InterfaceInfo::distance(double) –> void

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

initialize(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo) None

Sets up InterfaceInfo members such as interface_list_ based on variables from construction

C++: protocols::scoring::InterfaceInfo::initialize() –> void

interface(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, interface_num: int) pyrosetta.rosetta.protocols.scoring.Interface

C++: protocols::scoring::InterfaceInfo::interface(unsigned long) const –> class std::shared_ptr<const class protocols::scoring::Interface>

interface_nres(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, jump_num: int) int

Returns the number of resides at the interface defined by jump_num

C++: protocols::scoring::InterfaceInfo::interface_nres(unsigned long) const –> unsigned long

is_interface(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, rsd: pyrosetta.rosetta.core.conformation.Residue) bool

Returns whether a residue is at any of the interfaces

C++: protocols::scoring::InterfaceInfo::is_interface(class core::conformation::Residue) const –> bool

is_pair(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo, rsd1: pyrosetta.rosetta.core.conformation.Residue, rsd2: pyrosetta.rosetta.core.conformation.Residue) bool

Returns whether the two residues are considered a residue pair at any of the interfaces

C++: protocols::scoring::InterfaceInfo::is_pair(class core::conformation::Residue, class core::conformation::Residue) const –> bool

num_jump(self: pyrosetta.rosetta.protocols.scoring.InterfaceInfo) int
Returns the number of jumps that are being used

in interface calculations

C++: protocols::scoring::InterfaceInfo::num_jump() const –> unsigned long

class pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

ResidualDipolarCouplingRigidSegmentss are mainly handled by this class

related classed: RDC — a single line in an RDC file - representing a single dipolar coupling

ResidualDipolarCouplingRigidSegmentsEnergy – an energy method which triggers computations handled by this class.

assign(self: pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments, : pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments) pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments

C++: protocols::scoring::ResidualDipolarCouplingRigidSegments::operator=(const class protocols::scoring::ResidualDipolarCouplingRigidSegments &) –> class protocols::scoring::ResidualDipolarCouplingRigidSegments &

clone(self: pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments) pyrosetta.rosetta.basic.datacache.CacheableData

C++: protocols::scoring::ResidualDipolarCouplingRigidSegments::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

compute_pairwise_score(self: pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments) float

C++: protocols::scoring::ResidualDipolarCouplingRigidSegments::compute_pairwise_score() const –> double

compute_total_score(self: pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments, pose: pyrosetta.rosetta.core.pose.Pose) float
compute dipolar score for given segment definition

alignment tensor optimization will be performed for each segment individually

C++: protocols::scoring::ResidualDipolarCouplingRigidSegments::compute_total_score(const class core::pose::Pose &) const –> double

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

show(self: pyrosetta.rosetta.protocols.scoring.ResidualDipolarCouplingRigidSegments, : pyrosetta.rosetta.std.ostream) None

C++: protocols::scoring::ResidualDipolarCouplingRigidSegments::show(std::ostream &) const –> void

class pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo

Bases: pyrosetta.rosetta.basic.datacache.CacheableData

VDW_rep_screen_info_list(self: pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo) pyrosetta.rosetta.utility.vector1_core_pose_rna_VDW_RepScreenInfo

C++: protocols::scoring::VDW_CachedRepScreenInfo::VDW_rep_screen_info_list() const –> class utility::vector1<class core::pose::rna::VDW_RepScreenInfo, class std::allocator<class core::pose::rna::VDW_RepScreenInfo> > &

VDW_screen_bin(self: pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo) pyrosetta.rosetta.core.pose.rna.VDW_Grid

C++: protocols::scoring::VDW_CachedRepScreenInfo::VDW_screen_bin() const –> class std::shared_ptr<const class core::pose::rna::VDW_Grid>

assign(self: pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo, : pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo) pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo

C++: protocols::scoring::VDW_CachedRepScreenInfo::operator=(const class protocols::scoring::VDW_CachedRepScreenInfo &) –> class protocols::scoring::VDW_CachedRepScreenInfo &

clone(self: pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo) pyrosetta.rosetta.basic.datacache.CacheableData

C++: protocols::scoring::VDW_CachedRepScreenInfo::clone() const –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) pyrosetta.rosetta.basic.datacache.CacheableData

C++: basic::datacache::CacheableData::get_self_ptr() –> class std::shared_ptr<class basic::datacache::CacheableData>

get_self_weak_ptr(self: pyrosetta.rosetta.basic.datacache.CacheableData) pyrosetta.rosetta.std.weak_ptr_basic_datacache_CacheableData_t

C++: basic::datacache::CacheableData::get_self_weak_ptr() –> class std::weak_ptr<class basic::datacache::CacheableData>

read_in_VDW_rep_screen_pose(self: pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo, VDW_rep_screen_info: pyrosetta.rosetta.core.pose.rna.VDW_RepScreenInfo) None

C++: protocols::scoring::VDW_CachedRepScreenInfo::read_in_VDW_rep_screen_pose(class core::pose::rna::VDW_RepScreenInfo &) const –> void

read_in_VDW_rep_screen_pose_from_command_line(self: pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo) None

C++: protocols::scoring::VDW_CachedRepScreenInfo::read_in_VDW_rep_screen_pose_from_command_line() const –> void

read_in_VDW_rep_screen_pose_from_options(self: pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo, options: pyrosetta.rosetta.utility.options.OptionCollection) None

C++: protocols::scoring::VDW_CachedRepScreenInfo::read_in_VDW_rep_screen_pose_from_options(const class utility::options::OptionCollection &) const –> void

class pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy

Bases: pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy

assign(self: pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy, : pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy) pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy

C++: core::scoring::methods::WholeStructureEnergy::operator=(const class core::scoring::methods::WholeStructureEnergy &) –> class core::scoring::methods::WholeStructureEnergy &

atomic_interaction_cutoff(self: pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy) float

how far apart must two heavy atoms be to have a zero interaction energy?

If hydrogen atoms interact at the same range as heavy atoms, then this distance should build-in a 2 * max-bound-h-distance-cutoff buffer. There is an improper mixing here between run-time aquired chemical knowledge (max-bound-h-distance-cutoff) and compile time aquired scoring knowledge (max atom cutoff); this could be resolved by adding a boolean uses_hydrogen_interaction_distance() to the SRTBEnergy class along with a method of the ChemicalManager max_bound_h_distance_cutoff().

This method allows the WholeStructureEnergy class to define which edges should be included in the EnergyGraph so that during the finalize() method the Energy class can iterate across the EnergyGraph. This iteration occurrs in the SecondaryStructureEnergy class, where the edges must span 12 angstroms between the centroids. Arguably, the SecondaryStructureEnergy class could use the TwelveANeighborGraph (a context graph) and not require that the EnergyGraph span such long distances.

C++: core::scoring::methods::WholeStructureEnergy::atomic_interaction_cutoff() const –> double

clone(self: pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy) pyrosetta.rosetta.core.scoring.methods.EnergyMethod

clone

C++: protocols::scoring::VDW_GridEnergy::clone() const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

defines_high_order_terms(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose) bool
Should this EnergyMethod have score and derivative evaluation

evaluated both in the context of the whole Pose and in the context of residue or residue-pairs? This covers scoring terms like env-smooth wherein the CBeta’s get derivatives for increasing the neighbor counts for surrounding residues, and terms like constraints, which are definable on arbitrary number of residues (e.g. more than 2); both of these terms could be used in RTMin, and both should use the residue and residue-pair evaluation scheme with the MinimizationGraph for the majority of the work they do. (Now, high-order constraints (3-body or above) will not be properly evaluated within RTMin.). The default implementation returns “false”.

C++: core::scoring::methods::EnergyMethod::defines_high_order_terms(const class core::pose::Pose &) const –> bool

eval_atom_derivative(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, id: pyrosetta.rosetta.core.id.AtomID, pose: core::pose::Pose, domain_map: pyrosetta.rosetta.ObjexxFCL.FArray1D_int_t, sfxn: core::scoring::ScoreFunction, emap: core::scoring::EMapVector, F1: pyrosetta.rosetta.numeric.xyzVector_double_t, F2: pyrosetta.rosetta.numeric.xyzVector_double_t) None
Evaluate the XYZ derivative for an atom in the pose.

Called during the atomtree derivative calculation, atom_tree_minimize.cc, through the ScoreFunction::eval_atom_derivative intermediary. F1 and F2 should not zeroed, rather, this class should accumulate its contribution from this atom’s XYZ derivative

The derivative scheme is based on that of Abe, Braun, Noguti and Go (1984) “Rapid Calculation of First and Second Derivatives of Conformational Energy with Respect to Dihedral Angles for Proteins. General Recurrent Equations” Computers & Chemistry 8(4) pp. 239-247. F1 and F2 correspond roughly to Fa and Ga, respectively, of equations 7a & 7b in that paper.

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

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

called at the end of derivatives evaluation

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

finalize_after_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose) None
Called after minimization, allowing a derived class to do some

teardown steps.

Base class function does nothing. Derived classes may override.

Vikram K. Mulligan (vmullig.edu).

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

finalize_total_energy(self: pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction, emap: pyrosetta.rosetta.core.scoring.EMapVector) None

C++: protocols::scoring::VDW_GridEnergy::finalize_total_energy(class core::pose::Pose &, const class core::scoring::ScoreFunction &, class core::scoring::EMapVector &) const –> void

indicate_required_context_graphs(self: pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy, : pyrosetta.rosetta.utility.vector1_bool) None
VDW_GridEnergy is context independent; indicates that no

context graphs are required

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

method_type(self: pyrosetta.rosetta.core.scoring.methods.WholeStructureEnergy) pyrosetta.rosetta.core.scoring.methods.EnergyMethodType

C++: core::scoring::methods::WholeStructureEnergy::method_type() const –> enum core::scoring::methods::EnergyMethodType

minimize_in_whole_structure_context(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose) bool
Should this EnergyMethod have score and derivative evaluation

evaluated only in the context of the whole Pose, or can it be included in a decomposed manner for a residue or a set of residue-pairs that are not part of the Pose that’s serving as their context? The default method implemented in the base class returns true in order to grandfather in EnergyMethods that have not had their derivatives changed to take advantage of the new derivative-evaluation machinery. Methods that return “true” will not have their residue-energy(-ext) / residue-pair-energy(-ext) methods invoked by the ScoreFunction during its traversal of the MinimizationGraph, and instead will be asked to perform all their work during finalize_total_energies(). Similarly, they will be expected to perform all their work during eval_atom_deriv() instead of during the ScoreFunction’s traversal of the MinimizationGraph for derivative evaluation. IMPORTANT: Methods that return “true” cannot be included in RTMin.

C++: core::scoring::methods::EnergyMethod::minimize_in_whole_structure_context(const class core::pose::Pose &) const –> bool

prepare_rotamers_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.core.conformation.RotamerSetBase) None
If an energy method needs to cache data in a packing::RotamerSet object before

rotamer energies are calculated, it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

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

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

Subclasses should add the info for themselves and any other classes they use.

The default implementation of this function does nothing. It may be overriden by energy methods wishing to provide citation information.

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

requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose) bool
Does this EnergyMethod require the opportunity to examine the residue before (regular) scoring begins? Not

all energy methods would. The ScoreFunction will not ask energy methods to examine residues that are uninterested in doing so. The default implmentation of this function returns false

C++: core::scoring::methods::EnergyMethod::requires_a_setup_for_scoring_for_residue_opportunity_during_regular_scoring(const class core::pose::Pose &) const –> bool

score_types(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod) pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType

Returns the score types that this energy method computes.

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

setup_for_derivatives(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction) None
Called immediately before atom- and DOF-derivatives are calculated

allowing the derived class a chance to prepare for future calls.

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

setup_for_minimizing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : core::scoring::ScoreFunction, : core::kinematics::MinimizerMapBase) None
Called at the beginning of atom tree minimization, this method

allows the derived class the opportunity to initialize pertinent data that will be used during minimization. During minimzation, the chemical structure of the pose is constant, so assumptions on the number of atoms per residue and their identities are safe so long as the pose’s Energies object’s “use_nblist()” method returns true.

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

setup_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, : pyrosetta.rosetta.utility.vector1_bool, : pyrosetta.rosetta.utility.vector1_bool) None
if an energy method needs to cache data in the Energies object,

before packing begins, then it does so during this function. The packer must ensure this function is called. The default behavior is to do nothing.

C++: core::scoring::methods::EnergyMethod::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.methods.EnergyMethod, pose: core::pose::Pose, rotsets: core::pack_basic::RotamerSetsBase, sfxn: core::scoring::ScoreFunction) None
if an energy method needs to cache data in the Energies object,

before packing begins and requires access to the RotamerSets object, then it does so during this function. The default behavior is to do nothing.

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

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

setup_for_scoring(self: pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy, : pyrosetta.rosetta.core.pose.Pose, : pyrosetta.rosetta.core.scoring.ScoreFunction) None

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

setup_for_scoring_for_residue(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, rsd: pyrosetta.rosetta.core.conformation.Residue, pose: core::pose::Pose, sfxn: core::scoring::ScoreFunction, residue_data_cache: pyrosetta.rosetta.basic.datacache.BasicDataCache) None
Do any setup work before scoring, caching any slow-to-compute data that will be used during

energy evaluation inside of the input Residue object’s data cache. (The Residue on the whole is given as a constant reference, but non-constant access to its data cache is granted.)

C++: core::scoring::methods::EnergyMethod::setup_for_scoring_for_residue(const class core::conformation::Residue &, const class core::pose::Pose &, const class core::scoring::ScoreFunction &, class basic::datacache::BasicDataCache &) const –> void

show_additional_info(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : pyrosetta.rosetta.std.ostream, : core::pose::Pose, : bool) None

show additional information of the energy method

C++: core::scoring::methods::EnergyMethod::show_additional_info(std::ostream &, class core::pose::Pose &, bool) const –> void

update_residue_for_packing(self: pyrosetta.rosetta.core.scoring.methods.EnergyMethod, : core::pose::Pose, resid: int) None
If the pose changes in the middle of a packing (as happens in rotamer trials) and if

an energy method needs to cache data in the pose that corresponds to its current state, then the method must update that data when this function is called. The packer must ensure this function gets called. The default behavior is to do nothing.

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

version(self: pyrosetta.rosetta.protocols.scoring.VDW_GridEnergy) int

C++: protocols::scoring::VDW_GridEnergy::version() const –> unsigned long

class pyrosetta.rosetta.protocols.scoring.VDW_GridEnergyCreator

Bases: pyrosetta.rosetta.core.scoring.methods.EnergyMethodCreator

assign(self: pyrosetta.rosetta.protocols.scoring.VDW_GridEnergyCreator, : pyrosetta.rosetta.protocols.scoring.VDW_GridEnergyCreator) pyrosetta.rosetta.protocols.scoring.VDW_GridEnergyCreator

C++: protocols::scoring::VDW_GridEnergyCreator::operator=(const class protocols::scoring::VDW_GridEnergyCreator &) –> class protocols::scoring::VDW_GridEnergyCreator &

create_energy_method(self: pyrosetta.rosetta.protocols.scoring.VDW_GridEnergyCreator, : pyrosetta.rosetta.core.scoring.methods.EnergyMethodOptions) pyrosetta.rosetta.core.scoring.methods.EnergyMethod

Instantiate a new VDW_GridEnergy

C++: protocols::scoring::VDW_GridEnergyCreator::create_energy_method(const class core::scoring::methods::EnergyMethodOptions &) const –> class std::shared_ptr<class core::scoring::methods::EnergyMethod>

score_types_for_method(self: pyrosetta.rosetta.protocols.scoring.VDW_GridEnergyCreator) pyrosetta.rosetta.utility.vector1_core_scoring_ScoreType
Return the set of score types claimed by the EnergyMethod

this EnergyMethodCreator creates in its create_energy_method() function

C++: protocols::scoring::VDW_GridEnergyCreator::score_types_for_method() const –> class utility::vector1<enum core::scoring::ScoreType, class std::allocator<enum core::scoring::ScoreType> >

pyrosetta.rosetta.protocols.scoring.const_vdw_cached_rep_screen_info_from_pose(pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo

C++: protocols::scoring::const_vdw_cached_rep_screen_info_from_pose(const class core::pose::Pose &) –> const class protocols::scoring::VDW_CachedRepScreenInfo &

pyrosetta.rosetta.protocols.scoring.fill_vdw_cached_rep_screen_info_from_command_line(pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::scoring::fill_vdw_cached_rep_screen_info_from_command_line(class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.scoring.fill_vdw_cached_rep_screen_info_from_options(pose: pyrosetta.rosetta.core.pose.Pose, options: pyrosetta.rosetta.utility.options.OptionCollection) None

C++: protocols::scoring::fill_vdw_cached_rep_screen_info_from_options(class core::pose::Pose &, const class utility::options::OptionCollection &) –> void

pyrosetta.rosetta.protocols.scoring.make_sure_vdw_cached_rep_screen_info_is_setup(pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo

C++: protocols::scoring::make_sure_vdw_cached_rep_screen_info_is_setup(class core::pose::Pose &) –> const class protocols::scoring::VDW_CachedRepScreenInfo &

pyrosetta.rosetta.protocols.scoring.nonconst_vdw_cached_rep_screen_info_from_pose(pose: pyrosetta.rosetta.core.pose.Pose) pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo

C++: protocols::scoring::nonconst_vdw_cached_rep_screen_info_from_pose(class core::pose::Pose &) –> class protocols::scoring::VDW_CachedRepScreenInfo &

pyrosetta.rosetta.protocols.scoring.option_vdw_rep_screen_info_user(options: pyrosetta.rosetta.utility.options.OptionCollection) bool

C++: protocols::scoring::option_vdw_rep_screen_info_user(const class utility::options::OptionCollection &) –> bool

pyrosetta.rosetta.protocols.scoring.retrieve_RDC_segments_from_pose(*args, **kwargs)

Overloaded function.

  1. retrieve_RDC_segments_from_pose(: pyrosetta.rosetta.core.pose.Pose) -> protocols::scoring::ResidualDipolarCouplingRigidSegments

C++: protocols::scoring::retrieve_RDC_segments_from_pose(class core::pose::Pose &) –> class std::shared_ptr<class protocols::scoring::ResidualDipolarCouplingRigidSegments>

  1. retrieve_RDC_segments_from_pose(: pyrosetta.rosetta.core.pose.Pose) -> protocols::scoring::ResidualDipolarCouplingRigidSegments

C++: protocols::scoring::retrieve_RDC_segments_from_pose(const class core::pose::Pose &) –> class std::shared_ptr<const class protocols::scoring::ResidualDipolarCouplingRigidSegments>

pyrosetta.rosetta.protocols.scoring.set_vdw_cached_rep_screen_info(pose: pyrosetta.rosetta.core.pose.Pose, vdw_cached_rep_screen_info: pyrosetta.rosetta.protocols.scoring.VDW_CachedRepScreenInfo) None

C++: protocols::scoring::set_vdw_cached_rep_screen_info(class core::pose::Pose &, class std::shared_ptr<class protocols::scoring::VDW_CachedRepScreenInfo> &) –> void

pyrosetta.rosetta.protocols.scoring.set_vdw_cached_rep_screen_info_from_pose(new_pose: pyrosetta.rosetta.core.pose.Pose, pose: pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::scoring::set_vdw_cached_rep_screen_info_from_pose(class core::pose::Pose &, const class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.scoring.store_RDC_segments_in_pose(: protocols::scoring::ResidualDipolarCouplingRigidSegments, : pyrosetta.rosetta.core.pose.Pose) None

C++: protocols::scoring::store_RDC_segments_in_pose(class std::shared_ptr<class protocols::scoring::ResidualDipolarCouplingRigidSegments>, class core::pose::Pose &) –> void

pyrosetta.rosetta.protocols.scoring.vdw_cached_rep_screen_info_is_setup(pose: pyrosetta.rosetta.core.pose.Pose) bool

C++: protocols::scoring::vdw_cached_rep_screen_info_is_setup(const class core::pose::Pose &) –> bool